Clostridium difficile infection: epidemiology, diagnosis and understanding transmission.

PubMed

Martin, Jessica S H; Monaghan, Tanya M; Wilcox, Mark H

2016-04-01

Clostridium difficile infection (CDI) continues to affect patients in hospitals and communities worldwide. The spectrum of clinical disease ranges from mild diarrhoea to toxic megacolon, colonic perforation and death. However, this bacterium might also be carried asymptomatically in the gut, potentially leading to 'silent' onward transmission. Modern technologies, such as whole-genome sequencing and multi-locus variable-number tandem-repeat analysis, are helping to track C. difficile transmission across health-care facilities, countries and continents, offering the potential to illuminate previously under-recognized sources of infection. These typing strategies have also demonstrated heterogeneity in terms of CDI incidence and strain types reflecting different stages of epidemic spread. However, comparison of CDI epidemiology, particularly between countries, is challenging due to wide-ranging approaches to sampling and testing. Diagnostic strategies for C. difficile are complicated both by the wide range of bacterial targets and tests available and the need to differentiate between toxin-producing and non-toxigenic strains. Multistep diagnostic algorithms have been recommended to improve sensitivity and specificity. In this Review, we describe the latest advances in the understanding of C. difficile epidemiology, transmission and diagnosis, and discuss the effect of these developments on the clinical management of CDI.

Evolution and molecular epidemiology of classical swine fever virus during a multi-annual outbreak amongst European wild boar.

PubMed

Goller, Katja V; Gabriel, Claudia; Dimna, Mireille Le; Le Potier, Marie-Frédérique; Rossi, Sophie; Staubach, Christoph; Merboth, Matthias; Beer, Martin; Blome, Sandra

2016-03-01

Classical swine fever is a viral disease of pigs that carries tremendous socio-economic impact. In outbreak situations, genetic typing is carried out for the purpose of molecular epidemiology in both domestic pigs and wild boar. These analyses are usually based on harmonized partial sequences. However, for high-resolution analyses towards the understanding of genetic variability and virus evolution, full-genome sequences are more appropriate. In this study, a unique set of representative virus strains was investigated that was collected during an outbreak in French free-ranging wild boar in the Vosges-du-Nord mountains between 2003 and 2007. Comparative sequence and evolutionary analyses of the nearly full-length sequences showed only slow evolution of classical swine fever virus strains over the years and no impact of vaccination on mutation rates. However, substitution rates varied amongst protein genes; furthermore, a spatial and temporal pattern could be observed whereby two separate clusters were formed that coincided with physical barriers.

Spatial evolutionary epidemiology of spreading epidemics

PubMed Central

2016-01-01

Most spatial models of host–parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. PMID:27798295

Spatial evolutionary epidemiology of spreading epidemics.

PubMed

Lion, S; Gandon, S

2016-10-26

Most spatial models of host-parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. © 2016 The Author(s).

Acute Kidney Injury: Definition, Pathophysiology and Clinical Phenotypes

PubMed Central

Makris, Konstantinos; Spanou, Loukia

2016-01-01

Acute kidney injury (AKI) is a clinical syndrome that complicates the course and worsens the outcome in a significant number of hospitalised patients. Recent advances in clinical and basic research will help with a more accurate definition of this syndrome and in the elucidation of its pathogenesis. With this knowledge we will be able to conduct more accurate epidemiologic studies in an effort to gain a better understanding of the impact of this syndrome. AKI is a syndrome that rarely has a sole and distinct pathophysiology. Recent evidence, in both basic science and clinical research, is beginning to change our view for AKI from a single organ failure syndrome to a syndrome where the kidney plays an active role in the progress of multi-organ dysfunction. Accurate and prompt recognition of AKI and better understanding of the pathophysiologic mechanisms underlying the various clinical phenotypes are of great importance to research for effective therapeutic interventions. In this review we provide the most recent updates in the definition, epidemiology and pathophysiology of AKI. PMID:28303073

Acute Kidney Injury: Definition, Pathophysiology and Clinical Phenotypes.

PubMed

Makris, Konstantinos; Spanou, Loukia

2016-05-01

Acute kidney injury (AKI) is a clinical syndrome that complicates the course and worsens the outcome in a significant number of hospitalised patients. Recent advances in clinical and basic research will help with a more accurate definition of this syndrome and in the elucidation of its pathogenesis. With this knowledge we will be able to conduct more accurate epidemiologic studies in an effort to gain a better understanding of the impact of this syndrome. AKI is a syndrome that rarely has a sole and distinct pathophysiology. Recent evidence, in both basic science and clinical research, is beginning to change our view for AKI from a single organ failure syndrome to a syndrome where the kidney plays an active role in the progress of multi-organ dysfunction. Accurate and prompt recognition of AKI and better understanding of the pathophysiologic mechanisms underlying the various clinical phenotypes are of great importance to research for effective therapeutic interventions. In this review we provide the most recent updates in the definition, epidemiology and pathophysiology of AKI.

Population Structure of the Bacterial Pathogen Xylella fastidiosa among Street Trees in Washington D.C.

PubMed Central

Harris, Jordan Lee; Balci, Yilmaz

2015-01-01

Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship. PMID:25815838

Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

PubMed

Harris, Jordan Lee; Balci, Yilmaz

2015-01-01

Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship.

Multi-locus variable-number tandem repeat analysis of Chinese Brucella strains isolated from 1953 to 2013.

PubMed

Tian, Guo-Zhong; Cui, Bu-Yun; Piao, Dong-Ri; Zhao, Hong-Yan; Li, Lan-Yu; Liu, Xi; Xiao, Pei; Zhao, Zhong-Zhi; Xu, Li-Qing; Jiang, Hai; Li, Zhen-Jun

2017-05-02

Brucellosis was a common human and livestock disease caused by Brucella strains, the category B priority pathogens by the US Center for Disease Control (CDC). Identified as a priority disease in human and livestock populations, the increasing incidence in recent years in China needs urgent control measures for this disease but the molecular background important for monitoring the epidemiology of Brucella strains at the national level is still lacking. A total of 600 Brucella isolates collected during 60 years (from 1953 to 2013) in China were genotyped by multiple locus variable-number tandem repeat analysis (MLVA) and the variation degree of MLVA11 loci was calculated by the Hunter Gaston Diversity Index (HGDI) values. The charts and map were processed by Excel 2013, and cluster analysis and epidemiological distribution was performed using BioNumerics (version 5.1). The 600 representative Brucella isolates fell into 104 genotypes with 58 singleton genotypes by the MLVA11 assay, including B. melitensis biovars 2 and 3 (five main genotypes), B. abortus biovars 1 and 3 (two main genotypes), B. suis biovars 1 and 3 (three main genotypes), and B. canis (two main genotypes) respectively. While most B. suis biovar 1 and biovar 3 were respectively found in northern provinces and southern provinces, B. melitensis and B. abortus strains were dominant in China. Canine Brucellosis was only found in animals without any human cases reported. Eight Brucellosis epidemic peaks emerged during the 60 years between 1953 and 2013: 1955 - 1959, 1962 - 1969, 1971 - 1975, 1977 - 1983, 1985 - 1989, 1992 - 1997, 2000 - 2008 and 2010 - 2013 in China. Brucellosis has its unique molecular epidemiological patterns with specific spatial and temporal distribution according to MLVA. IDOP-D-16-00101.

Surveillance of Diarrheagenic Escherichia coli Strains Isolated from Diarrhea Cases from Children, Adults and Elderly at Northwest of Mexico

PubMed Central

Canizalez-Roman, Adrian; Flores-Villaseñor, Héctor M.; Gonzalez-Nuñez, Edgar; Velazquez-Roman, Jorge; Vidal, Jorge E.; Muro-Amador, Secundino; Alapizco-Castro, Gerardo; Díaz-Quiñonez, J. Alberto; León-Sicairos, Nidia

2016-01-01

Diarrheagenic Escherichia coli (DEC) strains are a main cause of gastrointestinal disease in developing countries. In this study we report the epidemiologic surveillance in a 4-year period (January 2011 to December 2014) of DEC strains causing acute diarrhea throughout the Sinaloa State, Mexico. DEC strains were isolated from outpatients of all ages with acute diarrhea (N = 1,037). Specific DEC pathotypes were identified by PCR-amplification of genes encoding virulence factors. The adhesion phenotype and antibiotic resistance were also investigated. DEC strains were detected in 23.3% (242/1037) of cases. The most frequently DEC strain isolated was EAEC [(12.2%), 126/242] followed by EPEC [(5.1%), 53/242], ETEC [(4.3%), 43/242] DAEC [(1.4%), 15/242], STEC [(0.3%), 3/242], and EIEC [(0.2%), 2/242]. EHEC strains were not detected. Overall DEC strains were more prevalent in children ≤2 years of age with EPEC strains the most common of DEC pathotypes. While ∼65% of EAEC strains were classified as typical variant based on the aggregative adherence to in vitro cultures of HEp-2 cells, a high proportion of EPEC strains was classified as atypical strains. EAEC, EPEC, ETEC, and DAEC strains were distributed in the north, central and south regions of Sinaloa state. Among all DEC strains, >90% were resistant to at least one commonly prescribed antibiotic. Strains were commonly resistant to first-line antibiotics such as tetracycline, ampicillin, and sulfamethoxazole-trimethoprim. Furthermore, more than 80% of DEC isolates were multi-drug resistant and EPEC and DAEC were the categories with major proportion of this feature. In conclusion, in nearly one out of four cases of acute diarrhea in Northwestern Mexico a multi-drug resistant DEC strain was isolated, in these cases EAEC was the most prevalent (52%) pathotype. PMID:27965648

A Bayesian inferential approach to quantify the transmission intensity of disease outbreak.

PubMed

Kadi, Adiveppa S; Avaradi, Shivakumari R

2015-01-01

Emergence of infectious diseases like influenza pandemic (H1N1) 2009 has become great concern, which posed new challenges to the health authorities worldwide. To control these diseases various studies have been developed in the field of mathematical modelling, which is useful tool for understanding the epidemiological dynamics and their dependence on social mixing patterns. We have used Bayesian approach to quantify the disease outbreak through key epidemiological parameter basic reproduction number (R0), using effective contacts, defined as sum of the product of incidence cases and probability of generation time distribution. We have estimated R0 from daily case incidence data for pandemic influenza A/H1N1 2009 in India, for the initial phase. The estimated R0 with 95% credible interval is consistent with several other studies on the same strain. Through sensitivity analysis our study indicates that infectiousness affects the estimate of R0. Basic reproduction number R0 provides the useful information to the public health system to do some effort in controlling the disease by using mitigation strategies like vaccination, quarantine, and so forth.

Neonatal infections due to multi-resistant strains: Epidemiology, current treatment, emerging therapeutic approaches and prevention.

PubMed

Tzialla, Chryssoula; Borghesi, Alessandro; Pozzi, Margherita; Stronati, Mauro

2015-12-07

Severe infections represent the main cause of neonatal mortality accounting for more than one million neonatal deaths worldwide every year. Antibiotics are the most commonly prescribed medications in neonatal intensive care units. The benefits of antibiotic therapy when indicated are clearly enormous, but the continued and widespread use of antibiotics has generated over the years a strong selective pressure on microorganisms, favoring the emergence of resistant strains. Health agencies worldwide are galvanizing attention toward antibiotic resistance in gram-positive and gram-negative bacteria. Infections in neonatal units due to multidrug and extensively multidrug resistant bacteria are rising and are already seriously challenging antibiotic treatment options. While there is a growing choice of agents against multi-resistant gram-positive bacteria, new options for multi-resistant gram-negative bacteria in the clinical practice have decreased significantly in the last 20 years making the treatment of infections caused by multidrug-resistant pathogens challenging mostly in neonates. Treatment options are currently limited and will be some years before any new treatment for neonates become available for clinical use, if ever. The aim of the review is to highlight the current knowledge on antibiotic resistance in the neonatal population, the possible therapeutic choices, and the prevention strategies to adopt in order to reduce the emergency and spread of resistant strains. Copyright © 2015 Elsevier B.V. All rights reserved.

[Epidemiological characteristics of typhoid fever and antibiotic susceptibility testing of Salmonella Typhi isolates in Guangxi, 1994-2013].

PubMed

Wang, Mingliu; Kan, Biao; Yang, Jin; Lin, Mei; Yan, Meiying; Zeng, Jun; Quan, Yi; Liao, Hezhuang; Zhou, Lingyun; Jiang, Zhenling; Huang, Dehui

2014-08-01

Through analyzing the typhoid epidemics and to determine and monitor regional resistance characteristics of the shift of drug resistant profile on Salmonella (S.) Typhi, to understand the related epidemiological characteristics of typhoid fever and to provide evidence for the development of strategies, in Guangxi. Data of typhoid fever from surveillance and reporting system between 1994 to 2013 was collected and statistically analyzed epidemiologically. The susceptibility of 475 S. Typhi isolates from patients on ten antibiotics was tested by broth micro-dilution method and minimum inhibition concentration was obtained and interpreted based on the CLSI standard. From 1994 to 2013, a total of 57 928 cases of typhoid fever were reported in Guangxi province with an annual incidence of 6.29/100 000 and mortality as 0.03%. The higher incidence was observed in the population under 20 years of age. There was no significant difference on incidence between male and female, but farmers and students were among the hardest hit groups. More cases were seen from the northern part of the province. Cases appeared all year round with the peak from May to October. A total of 13 major outbreaks during 2001 to 2013 were reported and the main transmission route was water-borne. All the strains were sensitive to third generation cephalosporins cefotaxime and fluoroquinolones norfloxacin. The susceptibility rates to tetracycline, chloramphenicol, ampicillin and gentamicin was around 98% but relative lower susceptible rate to ciprofloxacin was seen as 89.89% . The lowest susceptibility was found for streptomycin and sulfamethoxazole agents, with the rates as 67.73% and 65.89% , respectively. One strain was found to have been resistant to ciprofloxacin and another 47 isolates with reduced susceptibility to ciprofloxacin. Twenty eight isolates were found to be resistant to multiple antibiotics and one displayed ampicillin, chloramphenicol, streptomycin, sulfamethoxazole tetracycline and nalidixic acid (ACSSxT-NAL) resistance profile. This was the first report in China. Multi-drug resistant strains were frequently isolated from small scale outbreaks of typhoid fever. The incidence of typhoid fever in Guangxi was still high and some strains showed multi-drug resistance and reduced susceptibility to ciprofloxacin, indicating that the surveillance and monitor programs on drug resistance of S. Typhi should be strengthened, to prevent large scale outbreaks of typhoid fever in this province.

Diversity of Multi-Drug Resistant Avian Pathogenic Escherichia coli (APEC) Causing Outbreaks of Colibacillosis in Broilers during 2012 in Spain.

PubMed

Solà-Ginés, Marc; Cameron-Veas, Karla; Badiola, Ignacio; Dolz, Roser; Majó, Natalia; Dahbi, Ghizlane; Viso, Susana; Mora, Azucena; Blanco, Jorge; Piedra-Carrasco, Nuria; González-López, Juan José; Migura-Garcia, Lourdes

2015-01-01

Avian pathogenic Escherichia coli (APEC) are the major cause of colibacillosis in poultry production. In this study, a total of 22 E. coli isolated from colibacillosis field cases and 10 avian faecal E. coli (AFEC) were analysed. All strains were characterised phenotypically by susceptibility testing and molecular typing methods such as pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The presence of 29 virulence genes associated to APEC and human extraintestinal pathogenic E. coli (ExPEC) was also evaluated. For cephalosporin resistant isolates, cephalosporin resistance genes, plasmid location and replicon typing was assessed. Avian isolates belonged to 26 O:H serotypes and 24 sequence types. Out of 22 APEC isolates, 91% contained the virulence genes predictors of APEC; iutA, hlyF, iss, iroN and ompT. Of all strains, 34% were considered ExPEC. PFGE analysis demonstrated a high degree of genetic polymorphism. All strains were multi-resistant, including those isolated from healthy animals. Eleven strains were resistant to cephalosporins; six contained blaCTX-M-14, two blaSHV-12, two blaCMY-2 and one blaSHV-2. Two strains harboured qnrA, and two qnrA together with aac(6')-Ib-cr. Additionally, the emergent clone O25b:H4-B2-ST131 was isolated from a healthy animal which harboured blaCMY-2 and qnrS genes. Cephalosporin resistant genes were mainly associated to the presence of IncK replicons. This study demonstrates a very diverse population of multi-drug resistant E. coli containing a high number of virulent genes. The E. coli population among broilers is a reservoir of resistance and virulence-associated genes that could be transmitted into the community through the food chain. More epidemiological studies are necessary to identify clonal groups and resistance mechanisms with potential relevance to public health.

Diversity of Multi-Drug Resistant Avian Pathogenic Escherichia coli (APEC) Causing Outbreaks of Colibacillosis in Broilers during 2012 in Spain

PubMed Central

Solà-Ginés, Marc; Cameron-Veas, Karla; Badiola, Ignacio; Dolz, Roser; Majó, Natalia; Dahbi, Ghizlane; Viso, Susana; Mora, Azucena; Blanco, Jorge; Piedra-Carrasco, Nuria; González-López, Juan José; Migura-Garcia, Lourdes

2015-01-01

Avian pathogenic Escherichia coli (APEC) are the major cause of colibacillosis in poultry production. In this study, a total of 22 E. coli isolated from colibacillosis field cases and 10 avian faecal E. coli (AFEC) were analysed. All strains were characterised phenotypically by susceptibility testing and molecular typing methods such as pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The presence of 29 virulence genes associated to APEC and human extraintestinal pathogenic E. coli (ExPEC) was also evaluated. For cephalosporin resistant isolates, cephalosporin resistance genes, plasmid location and replicon typing was assessed. Avian isolates belonged to 26 O:H serotypes and 24 sequence types. Out of 22 APEC isolates, 91% contained the virulence genes predictors of APEC; iutA, hlyF, iss, iroN and ompT. Of all strains, 34% were considered ExPEC. PFGE analysis demonstrated a high degree of genetic polymorphism. All strains were multi-resistant, including those isolated from healthy animals. Eleven strains were resistant to cephalosporins; six contained bla CTX-M-14, two bla SHV-12, two bla CMY-2 and one bla SHV-2. Two strains harboured qnrA, and two qnrA together with aac(6’)-Ib-cr. Additionally, the emergent clone O25b:H4-B2-ST131 was isolated from a healthy animal which harboured bla CMY-2 and qnrS genes. Cephalosporin resistant genes were mainly associated to the presence of IncK replicons. This study demonstrates a very diverse population of multi-drug resistant E. coli containing a high number of virulent genes. The E. coli population among broilers is a reservoir of resistance and virulence-associated genes that could be transmitted into the community through the food chain. More epidemiological studies are necessary to identify clonal groups and resistance mechanisms with potential relevance to public health. PMID:26600205

Stress and tinnitus—from bedside to bench and back

PubMed Central

Mazurek, Birgit; Haupt, Heidemarie; Olze, Heidi; Szczepek, Agnieszka J.

2012-01-01

The aim of this review is to focus the attention of clinicians and basic researchers on the association between psycho-social stress and tinnitus. Although tinnitus is an auditory symptom, its onset and progression often associates with emotional strain. Recent epidemiological studies have provided evidence for a direct relationship between the emotional status of subjects and tinnitus. In addition, studies of function, morphology, and gene and protein expression in the auditory system of animals exposed to stress support the notion that the emotional status can influence the auditory system. The data provided by clinical and basic research with use of animal stress models offers valuable clues for an improvement in diagnosis and more effective treatment of tinnitus. PMID:22701404

How direct competition shapes coexistence and vaccine effects in multi-strain pathogen systems.

PubMed

Gjini, Erida; Valente, Carina; Sá-Leão, Raquel; Gomes, M Gabriela M

2016-01-07

We describe an integrated modeling framework for understanding strain coexistence in polymorphic pathogen systems. Previous studies have debated the utility of neutral formulations and focused on cross-immunity between strains as a major stabilizing mechanism. Here we convey that direct competition for colonization mediates stable coexistence only when competitive abilities amongst pathogen clones satisfy certain pairwise asymmetries. We illustrate our ideas with nested SIS models of single and dual colonization, applied to polymorphic pneumococcal bacteria. By fitting the models to cross-sectional prevalence data from Portugal (before and after the introduction of a seven-valent pneumococcal conjugate vaccine), we are able to not only statistically compare neutral and non-neutral epidemiological formulations, but also estimate vaccine efficacy, transmission and competition parameters simultaneously. Our study highlights that the response of polymorphic pathogen populations to interventions holds crucial information about strain interactions, which can be extracted by suitable nested modeling. Copyright © 2015 Elsevier Ltd. All rights reserved.

Variable number of tandem repeats and pulsed-field gel electrophoresis cluster analysis of enterohemorrhagic Escherichia coli serovar O157 strains.

PubMed

Yokoyama, Eiji; Uchimura, Masako

2007-11-01

Ninety-five enterohemorrhagic Escherichia coli serovar O157 strains, including 30 strains isolated from 13 intrafamily outbreaks and 14 strains isolated from 3 mass outbreaks, were studied by pulsed-field gel electrophoresis (PFGE) and variable number of tandem repeats (VNTR) typing, and the resulting data were subjected to cluster analysis. Cluster analysis of the VNTR typing data revealed that 57 (60.0%) of 95 strains, including all epidemiologically linked strains, formed clusters with at least 95% similarity. Cluster analysis of the PFGE patterns revealed that 67 (70.5%) of 95 strains, including all but 1 of the epidemiologically linked strains, formed clusters with 90% similarity. The number of epidemiologically unlinked strains forming clusters was significantly less by VNTR cluster analysis than by PFGE cluster analysis. The congruence value between PFGE and VNTR cluster analysis was low and did not show an obvious correlation. With two-step cluster analysis, the number of clustered epidemiologically unlinked strains by PFGE cluster analysis that were divided by subsequent VNTR cluster analysis was significantly higher than the number by VNTR cluster analysis that were divided by subsequent PFGE cluster analysis. These results indicate that VNTR cluster analysis is more efficient than PFGE cluster analysis as an epidemiological tool to trace the transmission of enterohemorrhagic E. coli O157.

Molecular epidemiological investigation of Brucella melitensis circulating in Mongolia by MLVA16.

PubMed

Kang, Sung-Il; Her, Moon; Erdenebaataar, Janchivdorj; Vanaabaatar, Batbaatar; Cho, Hyorim; Sung, So-Ra; Lee, Jin Ju; Jung, Suk Chan; Park, Yong Ho; Kim, Ji-Yeon

2017-02-01

Mongolia has a high incidence of brucellosis in human and animals due to livestock husbandry. To investigate the genetic characteristics of Mongolian B. melitensis, an MLVA (multi-locus variable-number tandem-repeat analysis)-16 assay was performed with 94 B. melitensis isolates. They were identified as B. melitensis biovar (bv.) 1 (67), 3 (10) and Rev. 1 vaccine strains (17) using a classical biotyping and multiplex PCR. In genotyping, three human isolates were grouped at 2 genotypes with sheep isolates, and it implies that B. melitensis are cross-infected between human and livestock. In the parsimony analysis, Mongolian B. melitensis isolates had high genetic similarity with Chinese strains, likely due to the geographical proximity, clustered distinctively as compared with other foreign isolates. B. melitensis Rev. 1 vaccine strains were divided into 4 genotypes with 92% similarity. In the analysis of Rev.1 strains, the risk of mutation of vaccine strain might not be overlooked. Animal quarantines should be strengthened to prevent the spread of Brucella species among adjacent countries. Copyright © 2016 Elsevier Ltd. All rights reserved.

Characterizing the next-generation matrix and basic reproduction number in ecological epidemiology.

PubMed

Roberts, M G; Heesterbeek, J A P

2013-03-01

We address the interaction of ecological processes, such as consumer-resource relationships and competition, and the epidemiology of infectious diseases spreading in ecosystems. Modelling such interactions seems essential to understand the dynamics of infectious agents in communities consisting of interacting host and non-host species. We show how the usual epidemiological next-generation matrix approach to characterize invasion into multi-host communities can be extended to calculate R₀, and how this relates to the ecological community matrix. We then present two simple examples to illustrate this approach. The first of these is a model of the rinderpest, wildebeest, grass interaction, where our inferred dynamics qualitatively matches the observed phenomena that occurred after the eradication of rinderpest from the Serengeti ecosystem in the 1980s. The second example is a prey-predator system, where both species are hosts of the same pathogen. It is shown that regions for the parameter values exist where the two host species are only able to coexist when the pathogen is present to mediate the ecological interaction.

A Bayesian Inferential Approach to Quantify the Transmission Intensity of Disease Outbreak

PubMed Central

Kadi, Adiveppa S.; Avaradi, Shivakumari R.

2015-01-01

Background. Emergence of infectious diseases like influenza pandemic (H1N1) 2009 has become great concern, which posed new challenges to the health authorities worldwide. To control these diseases various studies have been developed in the field of mathematical modelling, which is useful tool for understanding the epidemiological dynamics and their dependence on social mixing patterns. Method. We have used Bayesian approach to quantify the disease outbreak through key epidemiological parameter basic reproduction number (R 0), using effective contacts, defined as sum of the product of incidence cases and probability of generation time distribution. We have estimated R 0 from daily case incidence data for pandemic influenza A/H1N1 2009 in India, for the initial phase. Result. The estimated R 0 with 95% credible interval is consistent with several other studies on the same strain. Through sensitivity analysis our study indicates that infectiousness affects the estimate of R 0. Conclusion. Basic reproduction number R 0 provides the useful information to the public health system to do some effort in controlling the disease by using mitigation strategies like vaccination, quarantine, and so forth. PMID:25784956

A MLVA Genotyping Scheme for Global Surveillance of the Citrus Pathogen Xanthomonas citri pv. citri Suggests a Worldwide Geographical Expansion of a Single Genetic Lineage

PubMed Central

Boyer, Karine; Leduc, Alice; Tourterel, Christophe; Drevet, Christine; Ravigné, Virginie; Gagnevin, Lionel; Guérin, Fabien; Chiroleu, Frédéric; Koebnik, Ralf; Verdier, Valérie; Vernière, Christian

2014-01-01

MultiLocus Variable number of tandem repeat Analysis (MLVA) has been extensively used to examine epidemiological and evolutionary issues on monomorphic human pathogenic bacteria, but not on bacterial plant pathogens of agricultural importance albeit such tools would improve our understanding of their epidemiology, as well as of the history of epidemics on a global scale. Xanthomonas citri pv. citri is a quarantine organism in several countries and a major threat for the citrus industry worldwide. We screened the genomes of Xanthomonas citri pv. citri strain IAPAR 306 and of phylogenetically related xanthomonads for tandem repeats. From these in silico data, an optimized MLVA scheme was developed to assess the global diversity of this monomorphic bacterium. Thirty-one minisatellite loci (MLVA-31) were selected to assess the genetic structure of 129 strains representative of the worldwide pathological and genetic diversity of X. citri pv. citri. Based on Discriminant Analysis of Principal Components (DAPC), four pathotype-specific clusters were defined. DAPC cluster 1 comprised strains that were implicated in the major geographical expansion of X. citri pv. citri during the 20th century. A subset of 12 loci (MLVA-12) resolved 89% of the total diversity and matched the genetic structure revealed by MLVA-31. MLVA-12 is proposed for routine epidemiological identification of X. citri pv. citri, whereas MLVA-31 is proposed for phylogenetic and population genetics studies. MLVA-31 represents an opportunity for international X. citri pv. citri genotyping and data sharing. The MLVA-31 data generated in this study was deposited in the Xanthomonas citri genotyping database (http://www.biopred.net/MLVA/). PMID:24897119

Molecular characterization of Shiga-toxigenic Escherichia coli isolated from diverse sources from India by multi-locus variable number tandem repeat analysis (MLVA).

PubMed

Kumar, A; Taneja, N; Sharma, R K; Sharma, H; Ramamurthy, T; Sharma, M

2014-12-01

In a first study from India, a diverse collection of 140 environmental and clinical non-O157 Shiga-toxigenic Escherichia coli strains from a large geographical area in north India was typed by multi-locus variable number tandem repeat analysis (MLVA). The distribution of major virulence genes stx1, stx2 and eae was found to be 78%, 70% and 10%, respectively; 15 isolates were enterohaemorrhagic E. coli (stx1 +/stx2 + and eae +). By MLVA analysis, 44 different alleles were obtained. Dendrogram analysis revealed 104 different genotypes and 19 MLVA-type complexes divided into two main lineages, i.e. mutton and animal stool. Human isolates presented a statistically significant greater odds ratio for clustering with mutton samples compared to animal stool isolates. Five human isolates clustered with animal stool strains suggesting that some of the human infections may be from cattle, perhaps through milk, contact or the environment. Further epidemiological studies are required to explore these sources in context with occurrence of human cases.

Genetic diversity of Brucella ovis isolates from Rio Grande do Sul, Brazil, by MLVA16

PubMed Central

2014-01-01

Background Ovine epididymitis is predominantly associated with Brucella ovis infection. Molecular characterization of Brucella spp. achieved by multi-locus variable number of tandem repeats (VNTR) analyses (MLVA) have proved to be a powerful tool for epidemiological trace-back studies. Thus, the aim of this study was to evaluate the genetic diversity of Brucella ovis isolates from Rio Grande do Sul State, Brazil, by MLVA16. Findings MLVA16 genotyping identified thirteen distinct genotypes and a Hunter-Gaston diversity index of 0.989 among the fourteen B. ovis genotyped strains. All B. ovis MLVA16 genotypes observed in the present study represented non-previously described profiles. Analyses of the eight conserved loci included in panel 1 (MLVA8) showed three different genotypes, two new and one already described for B. ovis isolates. Among ten B. ovis isolates from same herd only two strains had identical pattern, whereas the four isolates with no epidemiologic information exhibited a single MLVA16 pattern each. Analysis of minimal spanning tree, constructed using the fourteen B. ovis strains typed in this study together with all nineteen B. ovis MLVA16 genotypes available in the MLVAbank 2014, revealed the existence of two clearly distinct major clonal complexes. Conclusions In conclusion, the results of the present study showed a high genetic diversity among B. ovis field isolates from Rio Grande do Sul State, Brazil, by MLVA16. PMID:25015223

Genetic diversity of Brucella ovis isolates from Rio Grande do Sul, Brazil, by MLVA16.

PubMed

Dorneles, Elaine M S; Freire, Guilherme N; Dasso, Maurício G; Poester, Fernando P; Lage, Andrey P

2014-07-12

Ovine epididymitis is predominantly associated with Brucella ovis infection. Molecular characterization of Brucella spp. achieved by multi-locus variable number of tandem repeats (VNTR) analyses (MLVA) have proved to be a powerful tool for epidemiological trace-back studies. Thus, the aim of this study was to evaluate the genetic diversity of Brucella ovis isolates from Rio Grande do Sul State, Brazil, by MLVA16. MLVA16 genotyping identified thirteen distinct genotypes and a Hunter-Gaston diversity index of 0.989 among the fourteen B. ovis genotyped strains. All B. ovis MLVA16 genotypes observed in the present study represented non-previously described profiles. Analyses of the eight conserved loci included in panel 1 (MLVA8) showed three different genotypes, two new and one already described for B. ovis isolates. Among ten B. ovis isolates from same herd only two strains had identical pattern, whereas the four isolates with no epidemiologic information exhibited a single MLVA16 pattern each. Analysis of minimal spanning tree, constructed using the fourteen B. ovis strains typed in this study together with all nineteen B. ovis MLVA16 genotypes available in the MLVAbank 2014, revealed the existence of two clearly distinct major clonal complexes. In conclusion, the results of the present study showed a high genetic diversity among B. ovis field isolates from Rio Grande do Sul State, Brazil, by MLVA16.

Multiple-locus variable-number tandem-repeat analysis of the swine dysentery pathogen, Brachyspira hyodysenteriae.

PubMed

Hidalgo, Alvaro; Carvajal, Ana; La, Tom; Naharro, Germán; Rubio, Pedro; Phillips, Nyree D; Hampson, David J

2010-08-01

The spirochete Brachyspira hyodysenteriae is the causative agent of swine dysentery, a severe colonic infection of pigs that has a considerable economic impact in many swine-producing countries. In spite of its importance, knowledge about the global epidemiology and population structure of B. hyodysenteriae is limited. Progress in this area has been hampered by the lack of a low-cost, portable, and discriminatory method for strain typing. The aim of the current study was to develop and test a multiple-locus variable-number tandem-repeat analysis (MLVA) method that could be used in basic veterinary diagnostic microbiology laboratories equipped with PCR technology or in more advanced laboratories with access to capillary electrophoresis. Based on eight loci, and when performed on isolates from different farms in different countries, as well as type and reference strains, the MLVA technique developed was highly discriminatory (Hunter and Gaston discriminatory index, 0.938 [95% confidence interval, 0.9175 to 0.9584]) while retaining a high phylogenetic value. Using the technique, the species was shown to be diverse (44 MLVA types from 172 isolates and strains), although isolates were stable in herds over time. The population structure appeared to be clonal. The finding of B. hyodysenteriae MLVA type 3 in piggeries in three European countries, as well as other, related, strains in different countries, suggests that spreading of the pathogen via carrier pigs is likely. MLVA overcame drawbacks associated with previous typing techniques for B. hyodysenteriae and was a powerful method for epidemiologic and population structure studies on this important pathogenic spirochete.

Molecular Epidemiology of Community-Associated Methicillin-resistant Staphylococcus aureus in the genomic era: a Cross-Sectional Study

PubMed Central

Prosperi, Mattia; Veras, Nazle; Azarian, Taj; Rathore, Mobeen; Nolan, David; Rand, Kenneth; Cook, Robert L.; Johnson, Judy; Morris, J. Glenn; Salemi, Marco

2013-01-01

Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of healthcare-associated infections and significant contributor to healthcare cost. Community-associated-MRSA (CA-MRSA) strains have now invaded healthcare settings. A convenience sample of 97 clinical MRSA isolates was obtained from seven hospitals during a one-week period in 2010. We employed a framework integrating Staphylococcus protein A typing and full-genome next-generation sequencing. Single nucleotide polymorphisms were analyzed using phylodynamics. Twenty-six t002, 48 t008, and 23 other strains were identified. Phylodynamic analysis of 30 t008 strains showed ongoing exponential growth of the effective population size the basic reproductive number (R0) ranging from 1.24 to 1.34. No evidence of hospital clusters was identified. The lack of phylogeographic clustering suggests that community introduction is a major contributor to emergence of CA-MRSA strains within hospitals. Phylodynamic analysis provides a powerful framework to investigate MRSA transmission between the community and hospitals, an understanding of which is essential for control. PMID:23712667

Strategies for basic laboratory diagnostics of the hemoglobinopathies in multi-ethnic societies: interpretation of results and pitfalls.

PubMed

Giordano, P C

2013-10-01

The consistent multi-ethnic migrations of the last decades have considerably changed the epidemiology of the hemoglobinopathies. Healthy carriers of these conditions are present today in many nonendemic parts of the world, and severely affected children are now born where these diseases were previously rare or unknown. Improving the competence in carrier diagnostics at the laboratory level is one of the first concerns when introducing management and primary prevention of the severe conditions in nonendemic areas. This review describes how and when carriers should be correctly diagnosed and informed. The essential technologies needed for basic carrier diagnostics in different situations are summarized in some detail, and interpretation of the results and a number of related problems are discussed. The role of the hematology laboratory is essential, particularly in nonendemic areas where the first line of health care is often insufficiently aware of hemoglobinopathy management. Carriers living in nonendemic areas can be appropriately diagnosed and informed regarding genetic risk and prevention by well-organized laboratories. Both basic and specialized diagnostics are needed for the correct treatment for the anemic carriers, for primary prevention in couples at risk and for state-of-the art care of severely affected patients. © 2012 John Wiley & Sons Ltd.

Quantifying the dilution effect for models in ecological epidemiology.

PubMed

Roberts, M G; Heesterbeek, J A P

2018-03-01

The dilution effect , where an increase in biodiversity results in a reduction in the prevalence of an infectious disease, has been the subject of speculation and controversy. Conversely, an amplification effect occurs when increased biodiversity is related to an increase in prevalence. We explore the conditions under which these effects arise, using multi species compartmental models that integrate ecological and epidemiological interactions. We introduce three potential metrics for quantifying dilution and amplification, one based on infection prevalence in a focal host species, one based on the size of the infected subpopulation of that species and one based on the basic reproduction number. We introduce our approach in the simplest epidemiological setting with two species, and show that the existence and strength of a dilution effect is influenced strongly by the choices made to describe the system and the metric used to gauge the effect. We show that our method can be generalized to any number of species and to more complicated ecological and epidemiological dynamics. Our method allows a rigorous analysis of ecological systems where dilution effects have been postulated, and contributes to future progress in understanding the phenomenon of dilution in the context of infectious disease dynamics and infection risk. © 2018 The Author(s).

Physiological typing of Pseudallescheria and Scedosporium strains using Taxa Profile, a semi-automated, 384-well microtitre system.

PubMed

Horré, R; Schaal, K P; Marklein, G; de Hoog, G S; Reiffert, S-M

2011-10-01

During the last few decades, Pseudallescheria and Scedosporium infections in humans are noted with increasing frequency. Multi-drug resistance commonly occurring in this species complex interferes with adequate therapy. Rapid and correct identification of clinical isolates is of paramount significance for optimal treatment in the early stages of infection, while strain typing is necessary for epidemiological purposes. In view of the development of physiological diagnostic parameters, 570 physiological reactions were evaluated using the Taxa Profile Micronaut system, a semi-automatic, computer-assisted, 384-well microtitre platform. Thirty two strains of the Pseudallescheria and Scedosporium complex were analysed after molecular verification of correct species attribution. Of the compounds tested, 254 proved to be polymorphic. Cluster analysis was performed with the Micronaut profile software, which is linked to the ntsypc® program. The systemic opportunist S. prolificans was unambiguously separated from the remaining species. Within the P. boydii/P. apiosperma complex differentiation was noted at the level of individual strains, but no unambiguous parameters for species recognition were revealed. © 2011 Blackwell Verlag GmbH.

Current Practices in Teaching Introductory Epidemiology: How We Got Here, Where to Go

PubMed Central

Keyes, Katherine M.; Galea, Sandro

2014-01-01

The number of students and disciplines requiring basic instruction in epidemiologic methods is growing. As a field, we now have a lexicon of epidemiologic terminology and particular methods that have developed and become canonical through the historical development of the field. Yet, many of our basic concepts remain elusive to some students, particularly those not pursuing a career in epidemiology. Further, disagreement and redundancy across basic terms limit their utility in teaching epidemiology. Many approaches to teaching epidemiology generally start with labeling key concepts and then move on to explain them. We submit that an approach grounded not in labels but in foundational concepts may offer a useful adjunct to introductory epidemiology education. We propose 7 foundational steps in conducting an epidemiologic study and provide examples of how these steps can be operationalized, using simple graphics that articulate how populations are defined, samples are selected, and individuals are followed to count cases. A reorganization of introductory epidemiology around core first principles may be an effective way forward for educating the next generation of public health scientists. PMID:25190677

Mechanical behaviors of multi-filament twist superconducting strand under tensile and cyclic loading

NASA Astrophysics Data System (ADS)

Wang, Xu; Li, Yingxu; Gao, Yuanwen

2016-01-01

The superconducting strand, serving as the basic unit cell of the cable-in-conduit-conductors (CICCs), is a typical multi-filament twist composite which is always subjected to a cyclic loading under the operating condition. Meanwhile, the superconducting material Nb3Sn in the strand is sensitive to strain frequently relating to the performance degradation of the superconductivity. Therefore, a comprehensive study on the mechanical behavior of the strand helps understanding the superconducting performance of the strained Nb3Sn strands. To address this issue, taking the LMI (internal tin) strand as an example, a three-dimensional structural finite element model, named as the Multi-filament twist model, of the strand with the real configuration of the LMI strand is built to study the influences of the plasticity of the component materials, the twist of the filament bundle, the initial thermal residual stress and the breakage and its evolution of the filaments on the mechanical behaviors of the strand. The effective properties of superconducting filament bundle with random filament breakage and its evolution versus strain are obtained based on the damage theory of fiber-reinforced composite materials proposed by Curtin and Zhou. From the calculation results of this model, we find that the occurrence of the hysteresis loop in the cyclic loading curve is determined by the reverse yielding of the elastic-plastic materials in the strand. Both the initial thermal residual stress in the strand and the pitch length of the filaments have significant impacts on the axial and hysteretic behaviors of the strand. The damage of the filaments also affects the axial mechanical behavior of the strand remarkably at large axial strain. The critical current of the strand is calculated by the scaling law with the results of the Multi-filament twist model. The predicted results of the Multi-filament twist model show an acceptable agreement with the experiment.

Phylogenetic, epidemiological and functional analyses of the Streptococcus bovis/Streptococcus equinus complex through an overarching MLST scheme.

PubMed

Jans, Christoph; de Wouters, Tomas; Bonfoh, Bassirou; Lacroix, Christophe; Kaindi, Dasel Wambua Mulwa; Anderegg, Janine; Böck, Désirée; Vitali, Sabrina; Schmid, Thomas; Isenring, Julia; Kurt, Fabienne; Kogi-Makau, Wambui; Meile, Leo

2016-06-21

The Streptococcus bovis/Streptococcus equinus complex (SBSEC) comprises seven (sub)species classified as human and animal commensals, emerging opportunistic pathogens and food fermentative organisms. Changing taxonomy, shared habitats, natural competence and evidence for horizontal gene transfer pose difficulties for determining their phylogeny, epidemiology and virulence mechanisms. Thus, novel phylogenetic and functional classifications are required. An SBSEC overarching multi locus sequence type (MLST) scheme targeting 10 housekeeping genes was developed, validated and combined with host-related properties of adhesion to extracellular matrix proteins (ECM), activation of the immune responses via NF-KB and survival in simulated gastric juice (SGJ). Commensal and pathogenic SBSEC strains (n = 74) of human, animal and food origin from Europe, Asia, America and Africa were used in the MLST scheme yielding 66 sequence types and 10 clonal complexes differentiated into distinct habitat-associated and mixed lineages. Adhesion to ECMs collagen I and mucin type II was a common characteristic (23 % of strains) followed by adhesion to fibronectin and fibrinogen (19.7 %). High adhesion abilities were found for East African dairy and human blood isolate branches whereas commensal fecal SBSEC displayed low adhesion. NF-KB activation was observed for a limited number of dairy and blood isolates suggesting the potential of some pathogenic strains for reduced immune activation. Strains from dairy MLST clades displayed the highest relative survival to SGJ independently of dairy adaptation markers lacS/lacZ. Combining phylogenetic and functional analyses via SBSEC MLST enabled the clear delineation of strain clades to unravel the complexity of this bacterial group. High adhesion values shared between certain dairy and blood strains as well as the behavior of NF-KB activation are concerning for specific lineages. They highlighted the health risk among shared lineages and establish the basis to elucidate (zoonotic-) transmission, host specificity, virulence mechanisms and enhanced risk assessment as pathobionts in an overarching One Health approach.

Prolonged and mixed non-O157 Escherichia coli infection in an Australian household.

PubMed

Staples, M; Graham, R M A; Doyle, C J; Smith, H V; Jennison, A V

2012-05-01

An Australian family was identified through a Public Health follow up on a Shiga-toxigenic Escherichia coli (STEC) positive bloody diarrhoea case, with three of the four family members experiencing either symptomatic or asymptomatic STEC shedding. Bacterial isolates were submitted to stx sequence sub-typing, multi-locus variable number tandem repeat analysis (MLVA), multi-locus sequence typing (MLST) and binary typing. The analysis revealed that there were multiple strains of STEC being shed by the family members, with similar virulence gene profiles and the same serogroup but differing in their MLVA and MLST profiles. This study illustrates the potentially complicated nature of non-O157 STEC infections and the importance of molecular epidemiology in understanding disease clusters. © 2012 QUEENSLAND HEALTH. Clinical Microbiology and Infection © 2012 European Society of Clinical Microbiology and Infectious Diseases.

Social relationships and their biological correlates: Coronary Artery Risk Development in Young Adults (CARDIA) study.

PubMed

Seeman, Teresa E; Gruenewald, Tara L; Cohen, Sheldon; Williams, David R; Matthews, Karen A

2014-05-01

Analyses test the hypothesis that aspects of social relationships (quantity of ties, social support and social strain) are associated with differences in levels of biological risk across multiple major physiological regulatory systems and consequently overall multi-systems risk (i.e., allostatic load [AL]). Data are from the Coronary Artery Risk Development in Young Adults (CARDIA) study--a bi-ethnic, prospective, multi-center epidemiological study, initiated in 1985-1986 to track the development of cardiovascular risk in young adulthood (N=5115). At the year 15 follow-up when participants were between 32 and 45 years of age, additional social and biological data were collected; biological data used to assess AL were collected at the Oakland, CA and Chicago, IL sites (N=844). Social strains were most strongly and positively related to overall AL (Cohen's d=.79 for highest vs. lowest quartile), and to each of its component biological subsystems, independent of social ties and support as well as sociodemographics and health behaviors. Social ties and emotional support were also negatively related to AL (Cohen's d=.33 and d=.44 for lowest vs. highest quartiles of ties and support, respectively) though controls for social strains reduced these associations to non-significance. Social support and social strain were more strongly related to overall AL than to any of its component subscales while social ties were less strongly related to AL and to its component subscales. There was no evidence that effects differed by sex, age or ethnicity. Findings focus attention on the particularly strong relationship between social strains and profiles of biological risk and support the cumulative impact of social factors on biological risks, showing larger effects for cumulative AL than for any of the individual biological systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

Current methods for molecular epidemiology studies of implant infections.

PubMed

Campoccia, Davide; Montanaro, Lucio; Arciola, Carla Renata

2009-09-01

Over the last few decades, the number of surgical procedures involving prosthetic materials has greatly multiplied, along with the rising medical and economic impact of implant-associated infections. The need to appropriately counteract and deal with this phenomenon has led to growing efforts to elucidate the etiology, pathogenesis and epidemiology of these types of infections, characterized by opportunistic pathogens. Molecular epidemiology studies have progressively emerged as a leading multitask tool to identify and fingerprint bacterial strains, unveil the complex clonal nature of important pathogens, detect outbreak events, track the origin of the infections, assess the clinical significance of individual strain types, survey their distribution, recognize associations of strain types with specific virulence determinants and/or pathological conditions, assess the role played by the specific components of the virulon, and reveal the phylogeny and the mechanisms through which new strain types have emerged. Despite the many advances that have been made thanks to these flourishing new approaches to molecular epidemiology, a number of critical aspects remain challenging. In this paper, we briefly discuss the current limitations and possible developments of molecular epidemiology methods in the investigation and surveillance of implant infections.

Evidence for the existence of two new members of the family Chlamydiaceae and proposal of Chlamydia avium sp. nov. and Chlamydia gallinacea sp. nov.

PubMed

Sachse, Konrad; Laroucau, Karine; Riege, Konstantin; Wehner, Stefanie; Dilcher, Meik; Creasy, Heather Huot; Weidmann, Manfred; Myers, Garry; Vorimore, Fabien; Vicari, Nadia; Magnino, Simone; Liebler-Tenorio, Elisabeth; Ruettger, Anke; Bavoil, Patrik M; Hufert, Frank T; Rosselló-Móra, Ramon; Marz, Manja

2014-03-01

The family Chlamydiaceae with the recombined single genus Chlamydia currently comprises nine species, all of which are obligate intracellular organisms distinguished by a unique biphasic developmental cycle. Anecdotal evidence from epidemiological surveys in flocks of poultry, pigeons and psittacine birds have indicated the presence of non-classified chlamydial strains, some of which may act as pathogens. In the present study, phylogenetic analysis of ribosomal RNA and ompA genes, as well as multi-locus sequence analysis of 11 field isolates were conducted. All independent analyses assigned the strains into two different clades of monophyletic origin corresponding to pigeon and psittacine strains or poultry isolates, respectively. Comparative genome analysis involving the type strains of currently accepted Chlamydiaceae species and the designated type strains representing the two new clades confirmed that the latter could be classified into two different species as their average nucleotide identity (ANI) values were always below 94%, both with the closest relative species and between themselves. In view of the evidence obtained from the analyses, we propose the addition of two new species to the current classification: Chlamydia avium sp. nov. comprising strains from pigeons and psittacine birds (type strain 10DC88(T); DSMZ: DSM27005(T), CSUR: P3508(T)) and Chlamydia gallinacea sp. nov. comprising strains from poultry (type strain 08-1274/3(T); DSMZ: DSM27451(T), CSUR: P3509(T)). Copyright © 2014 Elsevier GmbH. All rights reserved.

10th International Conference on Malignancies in AIDS and Other Acquired Immunodeficiencies: Basic, Epidemiologic and Clinical Research

Cancer.gov

Summary of speakers and events from the 2006 ICMAOI conference, focused on presenting basic, epidemiologic, and clinical aspects of research on malignancies in HIV-infected and other immunosuppressed individuals.

5th International Conference on Malignancies in AIDS and Other Acquired Immunodeficiencies: Basic,Epidemiologic and Clinical Research

Cancer.gov

Summary of speakers and events from the 2005 ICMAOI conference, focused on presenting basic, epidemiologic, and clinical aspects of research on malignancies in HIV-infected and other immunosuppressed individuals.

6th International Conference on Malignancies in AIDS and Other Acquired Immunodeficiencies: Basic,Epidemiologic and Clinical Research

Cancer.gov

Summary of speakers and events from the 2002 ICMAOI conference, focused on presenting basic, epidemiologic, and clinical aspects of research on malignancies in HIV-infected and other immunosuppressed individuals.

9th International Conference on Malignancies in AIDS and Other Acquired Immunodeficiencies: Basic,Epidemiologic and Clinical Research

Cancer.gov

Summary of speakers and events from the 2005 ICMAOI conference, focused on presenting basic, epidemiologic, and clinical aspects of research on malignancies in HIV-infected and other immunosuppressed individuals.

7th International Conference on Malignancies in AIDS and Other Acquired Immunodeficiencies: Basic,Epidemiologic and Clinical Research

Cancer.gov

Summary of speakers and events from the 2003 ICMAOI conference, focused on presenting basic, epidemiologic, and clinical aspects of research on malignancies in HIV-infected and other immunosuppressed individuals.

4th International Conference on Malignancies in AIDS and Other Acquired Immunodeficiencies: Basic,Epidemiologic and Clinical Research

Cancer.gov

Summary of speakers and events from the 2000 ICMAOI conference, focused on presenting basic, epidemiologic, and clinical aspects of research on malignancies in HIV-infected and other immunosuppressed individuals.

3rd International Conference on Malignancies in AIDS and Other Acquired Immunodeficiencies: Basic,Epidemiologic and Clinical Research

Cancer.gov

Summary of speakers and events from the 1999 ICMAOI conference, focused on presenting basic, epidemiologic, and clinical aspects of research on malignancies in HIV-infected and other immunosuppressed individuals.

Risk assessments using the Strain Index and the TLV for HAL, Part II: Multi-task jobs and prevalence of CTS.

PubMed

Kapellusch, Jay M; Silverstein, Barbara A; Bao, Stephen S; Thiese, Mathew S; Merryweather, Andrew S; Hegmann, Kurt T; Garg, Arun

2018-02-01

The Strain Index (SI) and the American Conference of Governmental Industrial Hygienists (ACGIH) threshold limit value for hand activity level (TLV for HAL) have been shown to be associated with prevalence of distal upper-limb musculoskeletal disorders such as carpal tunnel syndrome (CTS). The SI and TLV for HAL disagree on more than half of task exposure classifications. Similarly, time-weighted average (TWA), peak, and typical exposure techniques used to quantity physical exposure from multi-task jobs have shown between-technique agreement ranging from 61% to 93%, depending upon whether the SI or TLV for HAL model was used. This study compared exposure-response relationships between each model-technique combination and prevalence of CTS. Physical exposure data from 1,834 workers (710 with multi-task jobs) were analyzed using the SI and TLV for HAL and the TWA, typical, and peak multi-task job exposure techniques. Additionally, exposure classifications from the SI and TLV for HAL were combined into a single measure and evaluated. Prevalent CTS cases were identified using symptoms and nerve-conduction studies. Mixed effects logistic regression was used to quantify exposure-response relationships between categorized (i.e., low, medium, and high) physical exposure and CTS prevalence for all model-technique combinations, and for multi-task workers, mono-task workers, and all workers combined. Except for TWA TLV for HAL, all model-technique combinations showed monotonic increases in risk of CTS with increased physical exposure. The combined-models approach showed stronger association than the SI or TLV for HAL for multi-task workers. Despite differences in exposure classifications, nearly all model-technique combinations showed exposure-response relationships with prevalence of CTS for the combined sample of mono-task and multi-task workers. Both the TLV for HAL and the SI, with the TWA or typical techniques, appear useful for epidemiological studies and surveillance. However, the utility of TWA, typical, and peak techniques for job design and intervention is dubious.

Encouraging primary care research: evaluation of a one-year, doctoral clinical epidemiology research course.

PubMed

Liira, Helena; Koskela, Tuomas; Thulesius, Hans; Pitkälä, Kaisu

2016-01-01

Research and PhDs are relatively rare in family medicine and primary care. To promote research, regular one-year research courses for primary care professionals with a focus on clinical epidemiology were started. This study explores the academic outcomes of the first four cohorts of research courses and surveys the participants' perspectives on the research course. An electronic survey was sent to the research course participants. All peer-reviewed scientific papers published by these students were retrieved by literature searches in PubMed. Primary care in Finland. A total of 46 research course participants who had finished the research courses between 2007 and 2012. Of the 46 participants 29 were physicians, eight nurses, three dentists, four physiotherapists, and two nutritionists. By the end of 2014, 28 of the 46 participants (61%) had published 79 papers indexed in PubMed and seven students (15%) had completed a PhD. The participants stated that the course taught them critical thinking, and provided basic research knowledge, inspiration, and fruitful networks for research. A one-year, multi-professional, clinical epidemiology based research course appeared to be successful in encouraging primary care research as measured by research publications and networking. Activating teaching methods, encouraging focus on own research planning, and support from peers and tutors helped the participants to embark on research projects that resulted in PhDs for 15% of the participants. Clinical research and PhDs are rare in primary care in Finland, which has consequences for the development of the discipline and for the availability of clinical lecturers at the universities. A clinical epidemiology oriented, one-year research course increased the activity in primary care research. Focus on own research planning and learning the challenges of research with peers appeared to enhance the success of a doctoral research course. A doctoral research course encouraged networking, and the course collaboration sometimes led to paper co-authoring. In the Nordic countries, the primary care health professionals are used to working in multi-professional teams. A multi-professional strategy also seems fruitful in doctoral research education.

Current practices in teaching introductory epidemiology: how we got here, where to go.

PubMed

Keyes, Katherine M; Galea, Sandro

2014-10-01

The number of students and disciplines requiring basic instruction in epidemiologic methods is growing. As a field, we now have a lexicon of epidemiologic terminology and particular methods that have developed and become canonical through the historical development of the field. Yet, many of our basic concepts remain elusive to some students, particularly those not pursuing a career in epidemiology. Further, disagreement and redundancy across basic terms limit their utility in teaching epidemiology. Many approaches to teaching epidemiology generally start with labeling key concepts and then move on to explain them. We submit that an approach grounded not in labels but in foundational concepts may offer a useful adjunct to introductory epidemiology education. We propose 7 foundational steps in conducting an epidemiologic study and provide examples of how these steps can be operationalized, using simple graphics that articulate how populations are defined, samples are selected, and individuals are followed to count cases. A reorganization of introductory epidemiology around core first principles may be an effective way forward for educating the next generation of public health scientists. © The Author 2014. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The impact of strain-specific immunity on Lyme disease incidence is spatially heterogeneous.

PubMed

Khatchikian, Camilo E; Nadelman, Robert B; Nowakowski, John; Schwartz, Ira; Wormser, Gary P; Brisson, Dustin

2017-12-01

Lyme disease, caused by the bacterium Borrelia burgdorferi, is the most common tick-borne infection in the US. Recent studies have demonstrated that the incidence of human Lyme disease would have been even greater were it not for the presence of strain-specific immunity, which protects previously infected patients against subsequent infections by the same B. burgdorferi strain. Here, spatial heterogeneity is incorporated into epidemiological models to accurately estimate the impact of strain-specific immunity on human Lyme disease incidence. The estimated reduction in the number of Lyme disease cases is greater in epidemiologic models that explicitly include the spatial distribution of Lyme disease cases reported at the county level than those that utilize nationwide data. strain-specific immunity has the greatest epidemiologic impact in geographic areas with the highest Lyme disease incidence due to the greater proportion of people that have been previously infected and have developed strain-specific immunity. Copyright © 2017 Elsevier Inc. All rights reserved.

Epidemiology of Transfusion-Transmitted Infections Among Multi-Transfused Patients in Seven Hospitals in Peru

DTIC Science & Technology

2005-01-01

locate jcv Epidemiology of transfusion-transmitted infections among multi-transfused patients in seven hospitals in Peru 1 VA. Laguna-Torres a...and risk factors associated with TTIs among a sample of multi-transfused adult patients in Peru Study design: A cross- sectional multi-center study...was conducted across seven major hospitals in Peru fi’om February 2003 to September 2004 Self-reported behavior lntbrmatlon (medical procedures

In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence.

PubMed

Laing, Chad R; Buchanan, Cody; Taboada, Eduardo N; Zhang, Yongxiang; Karmali, Mohamed A; Thomas, James E; Gannon, Victor Pj

2009-06-29

Many approaches have been used to study the evolution, population structure and genetic diversity of Escherichia coli O157:H7; however, observations made with different genotyping systems are not easily relatable to each other. Three genetic lineages of E. coli O157:H7 designated I, II and I/II have been identified using octamer-based genome scanning and microarray comparative genomic hybridization (mCGH). Each lineage contains significant phenotypic differences, with lineage I strains being the most commonly associated with human infections. Similarly, a clade of hyper-virulent O157:H7 strains implicated in the 2006 spinach and lettuce outbreaks has been defined using single-nucleotide polymorphism (SNP) typing. In this study an in silico comparison of six different genotyping approaches was performed on 19 E. coli genome sequences from 17 O157:H7 strains and single O145:NM and K12 MG1655 strains to provide an overall picture of diversity of the E. coli O157:H7 population, and to compare genotyping methods for O157:H7 strains. In silico determination of lineage, Shiga-toxin bacteriophage integration site, comparative genomic fingerprint, mCGH profile, novel region distribution profile, SNP type and multi-locus variable number tandem repeat analysis type was performed and a supernetwork based on the combination of these methods was produced. This supernetwork showed three distinct clusters of strains that were O157:H7 lineage-specific, with the SNP-based hyper-virulent clade 8 synonymous with O157:H7 lineage I/II. Lineage I/II/clade 8 strains clustered closest on the supernetwork to E. coli K12 and E. coli O55:H7, O145:NM and sorbitol-fermenting O157 strains. The results of this study highlight the similarities in relationships derived from multi-locus genome sampling methods and suggest a "common genotyping language" may be devised for population genetics and epidemiological studies. Future genotyping methods should provide data that can be stored centrally and accessed locally in an easily transferable, informative and extensible format based on comparative genomic analyses.

MEMS tunable optical filter based on multi-ring resonator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dessalegn, Hailu, E-mail: hailudessalegn@yahoo.com, E-mail: tsrinu@ece.iisc.ernet.in; Srinivas, T., E-mail: hailudessalegn@yahoo.com, E-mail: tsrinu@ece.iisc.ernet.in

We propose a novel MEMS tunable optical filter with a flat-top pass band based on multi-ring resonator in an electrostatically actuated microcantilever for communication application. The filter is basically structured on a microcantilever beam and built in optical integrated ring resonator which is placed in one end of the beam to gain maximum stress on the resonator. Thus, when a DC voltage is applied, the beam will bend, that induces a stress and strain in the ring, which brings a change in refractive index and perimeter of the rings leading to change in the output spectrum shift, providing the tenabilitymore » as high as 0.68nm/μN and it is capable of tuning up to 1.7nm.« less

Sub-typing of extended-spectrum-β-lactamase-producing isolates from a nosocomial outbreak: application of a 10-loci generic Escherichia coli multi-locus variable number tandem repeat analysis.

PubMed

Karami, Nahid; Helldal, Lisa; Welinder-Olsson, Christina; Ahrén, Christina; Moore, Edward R B

2013-01-01

Extended-spectrum β-lactamase producing Escherichia coli (ESBL-E. coli) were isolated from infants hospitalized in a neonatal, post-surgery ward during a four-month-long nosocomial outbreak and six-month follow-up period. A multi-locus variable number tandem repeat analysis (MLVA), using 10 loci (GECM-10), for 'generic' (i.e., non-STEC) E. coli was applied for sub-species-level (i.e., sub-typing) delineation and characterization of the bacterial isolates. Ten distinct GECM-10 types were detected among 50 isolates, correlating with the types defined by pulsed-field gel electrophoresis (PFGE), which is recognized to be the 'gold-standard' method for clinical epidemiological analyses. Multi-locus sequence typing (MLST), multiplex PCR genotyping of bla CTX-M, bla TEM, bla OXA and bla SHV genes and antibiotic resistance profiling, as well as a PCR assay specific for detecting isolates of the pandemic O25b-ST131 strain, further characterized the outbreak isolates. Two clusters of isolates with distinct GECM-10 types (G06-04 and G07-02), corresponding to two major PFGE types and the MLST-based sequence types (STs) 131 and 1444, respectively, were confirmed to be responsible for the outbreak. The application of GECM-10 sub-typing provided reliable, rapid and cost-effective epidemiological characterizations of the ESBL-producing isolates from a nosocomial outbreak that correlated with and may be used to replace the laborious PFGE protocol for analyzing generic E. coli.

Epidemiologic Consequences of Microvariation in Mycobacterium tuberculosis

PubMed Central

Mathema, Barun; Kurepina, Natalia; Yang, Guibin; Shashkina, Elena; Manca, Claudia; Mehaffy, Carolina; Bielefeldt-Ohmann, Helle; Ahuja, Shama; Fallows, Dorothy A.; Izzo, Angelo; Bifani, Pablo; Dobos, Karen; Kaplan, Gilla

2012-01-01

Background. Evidence from genotype-phenotype studies suggests that genetic diversity in pathogens have clinically relevant manifestations that can impact outcome of infection and epidemiologic success. We studied 5 closely related Mycobacterium tuberculosis strains that collectively caused extensive disease (n = 862), particularly among US-born tuberculosis patients. Methods. Representative isolates were selected using population-based genotyping data from New York City and New Jersey. Growth and cytokine/chemokine response were measured in infected human monocytes. Survival was determined in aerosol-infected guinea pigs. Results. Multiple genotyping methods and phylogenetically informative synonymous single nucleotide polymorphisms showed that all strains were related by descent. In axenic culture, all strains grew similarly. However, infection of monocytes revealed 2 growth phenotypes, slower (doubling ∼55 hours) and faster (∼25 hours). The faster growing strains elicited more tumor necrosis factor α and interleukin 1β than the slower growing strains, even after heat killing, and caused accelerated death of infected guinea pigs (∼9 weeks vs 24 weeks) associated with increased lung inflammation/pathology. Epidemiologically, the faster growing strains were associated with human immunodeficiency virus and more limited in spread, possibly related to their inherent ability to induce a strong protective innate immune response in immune competent hosts. Conclusions. Natural variation, with detectable phenotypic changes, among closely related clinical isolates of M. tuberculosis may alter epidemiologic patterns in human populations. PMID:22315279

Genetic Relatedness among Hepatitis A Virus Strains Associated with Food-Borne Outbreaks

PubMed Central

Vaughan, Gilberto; Xia, Guoliang; Forbi, Joseph C.; Purdy, Michael A.; Rossi, Lívia Maria Gonçalves; Spradling, Philip R.; Khudyakov, Yury E.

2013-01-01

The genetic characterization of hepatitis A virus (HAV) strains is commonly accomplished by sequencing subgenomic regions, such as the VP1/P2B junction. HAV genome is not extensively variable, thus presenting opportunity for sharing sequences of subgenomic regions among genetically unrelated isolates. The degree of misrepresentation of phylogenetic relationships by subgenomic regions is especially important for tracking transmissions. Here, we analyzed whole-genome (WG) sequences of 101 HAV strains identified from 4 major multi-state, food-borne outbreaks of hepatitis A in the Unites States and from 14 non-outbreak-related HAV strains that shared identical VP1/P2B sequences with the outbreak strains. Although HAV strains with an identical VP1/P2B sequence were specific to each outbreak, WG were different, with genetic diversity reaching 0.31% (mean 0.09%). Evaluation of different subgenomic regions did not identify any other section of the HAV genome that could accurately represent phylogenetic relationships observed using WG sequences. The identification of 2–3 dominant HAV strains in 3 out of 4 outbreaks indicates contamination of the implicated food items with a heterogeneous HAV population. However, analysis of intra-host HAV variants from eight patients involved in one outbreak showed that only a single sequence variant established infection in each patient. Four non-outbreak strains were found closely related to strains from 2 outbreaks, whereas ten were genetically different from the outbreak strains. Thus, accurate tracking of HAV strains can be accomplished using HAV WG sequences, while short subgenomic regions are useful for identification of transmissions only among cases with known epidemiological association. PMID:24223112

Endotheliotropic elephant herpes virus (EEHV) infection. The first PCR-confirmed fatal case in Asia.

PubMed

Reid, C E; Hildebrandt, T B; Marx, N; Hunt, M; Thy, N; Reynes, J M; Schaftenaar, W; Fickel, J

2006-06-01

Since 1995, 4 suspected cases of Endotheliotropic Elephant Herpes Virus (EEHV) infection, i.e. based on clinical presentation, have occurred in Asia without resulting in epidemic outbreaks as expected. In order to confirm the presence of EEHV on the continent of Asia, viral DNA particles from liver samples of a wild-caught 3-year-old elephant found dead at a Cambodian elephant sanctuary and clinically diagnosed with EEHV, were PCR processed using known EEHV strain primers. The presence of EEHV viral nucleic acids was confirmed and the nucleic acids had a 99% sequence similarity to the U.S.A strain (gene bank locus: AF117265) and 97% sequence similarity to the European strain (gene bank locus: AF354746) assigning this case to the EEHV-1 cluster. More than the confirmation of EEHV on the continent of Asia, is the phylogenic relationship to the USA and European strains with no corresponding contact or transport of USA or European elephants to Asia. Thus, this brings many of the traditional theories into question. Although almost forgotten, this disease is still ramped in captive elephant populations worldwide and continues to devastate particularly the neonatal and weaning-age population. Special attention and continued research are needed specifically in the area of basic virology and epidemiology.

[Development of the influenza epidemic in season 2011-2012 in some areas of Russia: results of activity of the Influenza Etiology and Epidemiology Center of the Ivanovsky Institute of Virology].

PubMed

L'vov, D K; Burtseva, E I; Kolobukhina, L V; Feodoritova, E L; Shevchenko, E S; Ivanova, V T; Lavrishcheva, V V; Breslav, N V; Trushakova, S V; Merkulova, L N; Vartanian, R V; Kisteneva, L B; Oskerko, T A; Al'khovskiĭ, S V; Siluianova, É V; Mukasheva, E A; Krasnoslobodtsev, K G; Prilipov, A G; Beliaev, A L; Samokhvalov, E I; Shchelkanov, M Iu; Malyshev, N A

2013-01-01

The results of analysis of the peculiarities of the epidemic 2011-2012 development in the areas of 10 cities of Russia obtained by basic laboratories of IEES on the base of D.I. Ivanovsky Research Institute of Virology, Ministry of Public Health and Social Development of Russia, are presented. The increasing ARD morbidity caused by the influenza viruses was detected rather late--in February-March 2012. The highest indices of the morbidity were detected during weeks 10-13 followed by decreasing to threshold levels by week 27. Children 0-2 and 3-6 years old were involved the most, meantime the high rate of hospitalization was found for 15-64 years old aged group (25%). Influenza A(H3N2) and B viruses were the cause of the epidemic. The results of studies of the antigenic and genetic properties of the influenza strains showed most of them to be close relatives to the vaccine strains. Some heterogeneity of circulating strains and their drift variants were found as well. All tested strains were sensitive to arbidol, oseltamivir and zanamivir, and saved resistance to rimantadine. The ratio of ARD viruses was comparable with the last epidemic seasons.

[Development of Staphylococcus Haemolyticus multilocus sequencing scheme and its use for molecular-epidemiologic analysis of strains isolated in hospitals in Russian federation in 2009-2010].

PubMed

Voronina, O L; Kunda, M S; Dmitrenko, O A; Lunin, V G; Gintsburg, A L

2011-01-01

Development of Staphylococcus haemolyticus strain typing method based on multilocus sequencing for resolving problems of molecular epidemiology. 102 strains of coagulase negative staphylococci (CNS) isolated in hospitals of various specialization in N. Novgorod and Moscow were studied. Species identification of strain was performed by using tuf gene fragment sequencing, S. haemolyticus strain differentiation--by MLST results. eBURST approach was used for cluster analysis of MLST data; structural changes in tagatose-6-phosphate kinase were studied by using InterProScan platform and SWISS-MODEL site programs; MLST scheme gene allele variability analysis was performed by using MEGA4.0 program package. In the 102 strains sampled CNS was detected in 28 strains of the S. haemolyticus species. The MLST scheme developed for the first time for S. haemolyticus including mvaK, rphE, tphK, gtr, arcC, triA, aroE genes allowed the differentiation of the sampled strains by 11 genotypes. Strains with ST 3, 8, 6, 1, 4, 5 and 11 differed by highest epidemiologic significance. Cluster and phylogenetic analysis of the data obtained showed a high adaptive ability of the nosocomial S. haemolyticus strains. Multiresistance to antibacterial preparations was detected in the analyzed strains. The MLST method developed was effective in the differentiation of S. haemolyticus strains that circulate in hospitals and threaten both neonates and hospitalized adult patients.

[Molecular epidemiology and transmission of HIV-1 infection in Zhejiang province, 2015].

PubMed

Yang, J Z; Chen, W J; Zhang, W J; He, L; Zhang, J F; Pan, X H

2017-11-10

Objective: To understand the distribution of HIV-1 subtype diversity and its transmission characteristics in Zhejiang province. Methods: A total of 302 newly diagnosed HIV-1 positive patients were selected through stratified random sampling in Zhejiang in 2015. HIV-1 pol genes were sequenced successfully with reverse transcription PCR/nested PCR and phylogenetic analysis was conducted for 276 patients. Then a molecular epidemiologic study was performed combined with field epidemiological investigation. Results: Of 276 sequence samples analyzed, 122 CRF07_BC strains (44.2%), 103 CRF01_AE strains (37.3%), 17 CRF08_BC strains (6.1%), 9 B strains (3.2%), 6 CRF55_01B strains (2.2%), 5 C strains (1.8%), 1 CRF59_01B strain (0.4%), 1 CRF67_01B strain (0.4%), 1 A1 strain (0.4%), and 11 URFs strains (4.0%) were identified. Phylogenetic analysis revealed 16 clusters with only 15.1% (34/225) sequences involved among CRF07_BC and CRF01_AE strains. The clustered cases in MSM were higher than that in populations with other transmission routes. And clusters existed between the populations with different transmission routes. Conclusion: The major strains of HIV-1 in Zhejiang are CRF07_BC and CRF01_AE. The HIV subtypes showed more complexity in Zhejiang. It is necessary to strengthen the surveillance for HIV subtypes, carry out classified management and conduct effective prevention and control in the population at high risk.

Genomic Characterization Helps Dissecting an Outbreak of Listeriosis in Northern Italy.

PubMed

Comandatore, Francesco; Corbella, Marta; Andreoli, Giuseppina; Scaltriti, Erika; Aguzzi, Massimo; Gaiarsa, Stefano; Mariani, Bianca; Morganti, Marina; Bandi, Claudio; Fabbi, Massimo; Marone, Piero; Pongolini, Stefano; Sassera, Davide

2017-07-06

Listeria monocytogenes (Lm) is a bacterium widely distributed in nature and able to contaminate food processing environments, including those of dairy products. Lm is a primary public health issue, due to the very low infectious dose and the ability to produce severe outcomes, in particular in elderly, newborns, pregnant women and immunocompromised patients. In the period between April and July 2015, an increased number of cases of listeriosis was observed in the area of Pavia, Northern Italy. An epidemiological investigation identified a cheesemaking small organic farm as the possible origin of the outbreak. In this work we present the results of the retrospective epidemiological study that we performed using molecular biology and genomic epidemiology methods. The strains sampled from patients and those from the target farm's cheese were analyzed using PFGE and whole genome sequencing (WGS) based methods. The performed WGS based analyses included: a) in-silico MLST typing; b) SNPs calling and genetic distance evaluation; c) determination of the resistance and virulence genes profiles; d) SNPs based phylogenetic reconstruction. Three of the patient strains and all the cheese strains resulted to belong to the same phylogenetic cluster, in Sequence Type 29. A further accurate SNPs analysis revealed that two of the three patient strains and all the cheese strains were highly similar (0.8 SNPs of average distance) and exhibited a higer distance from the third patient isolate (9.4 SNPs of average distance). Despite the global agreement among the results of the PFGE and WGS epidemiological studies, the latter approach agree with epidemiological data in indicating that one the patient strains could have originated from a different source. This result highlights that WGS methods can allow to better.

Genomic Characterization Helps Dissecting an Outbreak of Listeriosis in Northern Italy

PubMed Central

Comandatore, Francesco; Corbella, Marta; Andreoli, Giuseppina; Scaltriti, Erika; Aguzzi, Massimo; Gaiarsa, Stefano; Mariani, Bianca; Morganti, Marina; Bandi, Claudio; Fabbi, Massimo; Marone, Piero; Pongolini, Stefano; Sassera, Davide

2017-01-01

Introduction Listeria monocytogenes (Lm) is a bacterium widely distributed in nature and able to contaminate food processing environments, including those of dairy products. Lm is a primary public health issue, due to the very low infectious dose and the ability to produce severe outcomes, in particular in elderly, newborns, pregnant women and immunocompromised patients. Methods In the period between April and July 2015, an increased number of cases of listeriosis was observed in the area of Pavia, Northern Italy. An epidemiological investigation identified a cheesemaking small organic farm as the possible origin of the outbreak. In this work we present the results of the retrospective epidemiological study that we performed using molecular biology and genomic epidemiology methods. The strains sampled from patients and those from the target farm's cheese were analyzed using PFGE and whole genome sequencing (WGS) based methods. The performed WGS based analyses included: a) in-silico MLST typing; b) SNPs calling and genetic distance evaluation; c) determination of the resistance and virulence genes profiles; d) SNPs based phylogenetic reconstruction. Results Three of the patient strains and all the cheese strains resulted to belong to the same phylogenetic cluster, in Sequence Type 29. A further accurate SNPs analysis revealed that two of the three patient strains and all the cheese strains were highly similar (0.8 SNPs of average distance) and exhibited a higer distance from the third patient isolate (9.4 SNPs of average distance). Discussion Despite the global agreement among the results of the PFGE and WGS epidemiological studies, the latter approach agree with epidemiological data in indicating that one the patient strains could have originated from a different source. This result highlights that WGS methods can allow to better PMID:28856063

Microbial Forensics: A Scientific Assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keim, Paul

2003-02-17

Microorganisms have been used as weapons in criminal acts, most recently highlighted by the terrorist attack using anthrax in the fall of 2001. Although such ''biocrimes'' are few compared with other crimes, these acts raise questions about the ability to provide forensic evidence for criminal prosecution that can be used to identify the source of the microorganisms used as a weapon and, more importantly, the perpetrator of the crime. Microbiologists traditionally investigate the sources of microorganisms in epidemiological investigations, but rarely have been asked to assist in criminal investigations. A colloquium was convened by the American Academy of Microbiology inmore » Burlington, Vermont, on June 7-9, 2002, in which 25 interdisciplinary, expert scientists representing evolutionary microbiology, ecology, genomics, genetics, bioinformatics, forensics, chemistry, and clinical microbiology, deliberated on issues in microbial forensics. The colloquium's purpose was to consider issues relating to microbial forensics, which included a detailed identification of a microorganism used in a bioattack and analysis of such a microorganism and related materials to identify its forensically meaningful source--the perpetrators of the bioattack. The colloquium examined the application of microbial forensics to assist in resolving biocrimes with a focus on what research and education are needed to facilitate the use of microbial forensics in criminal investigations and the subsequent prosecution of biocrimes, including acts of bioterrorism. First responders must consider forensic issues, such as proper collection of samples to allow for optimal laboratory testing, along with maintaining a chain of custody that will support eventual prosecution. Because a biocrime may not be immediately apparent, a linkage must be made between routine diagnosis, epidemiological investigation, and criminal investigation. There is a need for establishing standard operating procedures and training to meet these initial challenges so as minimize disturbance of the evidence. While epidemiology and forensics are similar sciences with similar goals when applied to biocrimes, forensics has additional and more stringent requirements. Maintaining a chain of custody on evidentiary samples is one example of an extra requirement imposed on an investigation of a biocrime. Another issue is the intent in microbial forensics to identify a bioattack organism in greatest detail. If possible, forensic investigations will strive to identify the precise strain and substrain, rather than just to the species level, which might be sufficient in an epidemiological investigation. Although multiple groups have developed lists of bioterrorism target pathogens, these lists are too narrow. An expansion of microorganisms relevant to food and water threats should be considered. Computerized networks should be established to track infectious disease outbreaks in real time. These systems could alert public health and agricultural officials to the existence of a potential bioattack earlier than simply waiting for a report of a suspicious cluster of similar patients. Once a biocrime is suspected, a wide variety of methods are available to identify the microorganism used in the bioattack and to analyze features that might lead to the source of the event. A multi-pronged approach to such an investigation may be preferable, using many available methods-ranging from genomics to sequencing to physiology to analysis of substances in the sample. Microbial forensics will be most effective if there is sufficient basic scientific information concerning microbial genetics, evolution, physiology, and ecology. Strain subtyping analysis will be difficult to interpret if we do not understand some of the basic evolutionary mechanisms and population diversity of pathogens. Phenotypic features associated with evidentiary pathogens also may provide investigative leads, but full exploitation of these features can only be accomplished if we understand basic principles that control microbial physiology. Finally, the more precise and refined a microbial forensic system becomes, the more proper guidelines for handling and storage will be defined. Thus, improper dissemination or use of the pathogens will be reduced and inadvertent release will be minimized. An additional outcome of establishing these guidelines or rules is that the legitimate investigator will be protected to pursue research without unnecessary intrusion. Colloquium participants identified a variety of needs and directions in the following areas: sample handling and collection, detection, research direction, data access, QA/QC, and education. General recommendations are provided for direction or insight for the scientific community, law enforcement community, legal community, and the public.« less

Identification of non-streptococcal organisms from human dental plaque grown on the Streptococcus-selective medium mitis-salivarius agar.

PubMed

Kim, Yeon-Hee; Lee, Si Young

2015-02-01

Mitis-salivarius (MS) agar has been used widely in microbial epidemiological studies because oral viridans streptococci can be selectively grown on this medium. Even though the previous findings reported the limited selecting power of MS agar for streptococcus strains, the identities of non-streptococcal strains from human oral samples which can grow on this medium are not clear yet. In this study, we identified non-streptococcal organisms grown on MS agar plates by polymerase chain reaction (PCR) amplification and sequencing of the 16S ribosomal RNA (rRNA) gene. Eighty bacterial colonies on MS plates were isolated from plaque samples, and bacterial identification was achieved with the rapid ID 32 Strep system and mini API reader. The bacterial colonies identified as non-streptococci by the API system were selected for further identification. The 16S rRNA gene was amplified by PCR and verified using DNA sequencing analysis for identification. Sequences were compared with those of reference organisms in the genome database of the National Center for Biotechnology Information using the Basic Local Alignment Search Tool (BLAST). Among the 11 isolated non-streptococcal strains on MS plates, 3 strains were identified as Actinomyces naeslundii, 7 strains were identified as Actinomyces oris and 1 strain were identified as Actinomyces sp. using Blastn. In this study, we showed that some oral Actinomyces species can grow on Streptococcus-selective MS agar plates. Copyright © 2014 Elsevier Ltd. All rights reserved.

An Efficient Implementation of the GMC Micromechanics Model for Multi-Phased Materials with Complex Microstructures

NASA Technical Reports Server (NTRS)

Pindera, Marek-Jerzy; Bednarcyk, Brett A.

1997-01-01

An efficient implementation of the generalized method of cells micromechanics model is presented that allows analysis of periodic unidirectional composites characterized by repeating unit cells containing thousands of subcells. The original formulation, given in terms of Hill's strain concentration matrices that relate average subcell strains to the macroscopic strains, is reformulated in terms of the interfacial subcell tractions as the basic unknowns. This is accomplished by expressing the displacement continuity equations in terms of the stresses and then imposing the traction continuity conditions directly. The result is a mixed formulation wherein the unknown interfacial subcell traction components are related to the macroscopic strain components. Because the stress field throughout the repeating unit cell is piece-wise uniform, the imposition of traction continuity conditions directly in the displacement continuity equations, expressed in terms of stresses, substantially reduces the number of unknown subcell traction (and stress) components, and thus the size of the system of equations that must be solved. Further reduction in the size of the system of continuity equations is obtained by separating the normal and shear traction equations in those instances where the individual subcells are, at most, orthotropic. The reformulated version facilitates detailed analysis of the impact of the fiber cross-section geometry and arrangement on the response of multi-phased unidirectional composites with and without evolving damage. Comparison of execution times obtained with the original and reformulated versions of the generalized method of cells demonstrates the new version's efficiency.

Genomic diversity of necrotic enteritis-associated strains of Clostridium perfringens: a review.

PubMed

Lacey, Jake A; Johanesen, Priscilla A; Lyras, Dena; Moore, Robert J

2016-06-01

The investigation of genomic variation between Clostridium perfringens isolates from poultry has been an important tool to enhance our understanding of the genetic basis of strain pathogenicity and the epidemiology of virulent and avirulent strains within the context of necrotic enteritis (NE). The earliest studies used whole genome profiling techniques such as pulsed-field gel electrophoresis to differentiate isolates and determine their relative levels of relatedness. DNA sequencing has been used to investigate genetic variation in (a) individual genes, such as those encoding the alpha and NetB toxins; (b) panels of housekeeping genes for multi-locus sequence typing and (c) most recently whole genome sequencing to build a more complete picture of genomic differences between isolates. Conclusions drawn from these studies include: differential carriage of large conjugative plasmids accounts for a large proportion of inter-strain differences; plasmid-encoded genes are more highly conserved than chromosomal genes, perhaps indicating a relatively recent origin for the plasmids; isolates from NE-affected birds fall into three distinct sequence-based clades while non-pathogenic isolates from healthy birds tend to be more genomically diverse. Overall, the NE causing strains are closely related to C. perfringens isolates from other birds and other diseases whereas the non-pathogenic poultry strains are generally more remotely related to either the pathogenic strains or the strains from other birds. Genomic analysis has indicated that genes in addition to netB are associated with NE pathogenic isolates. Collectively, this work has resulted in a deeper understanding of the pathogenesis of this important poultry disease.

Multi-fiber strains measured by micro-Raman spectroscopy: Principles and experiments

NASA Astrophysics Data System (ADS)

Lei, Zhenkun; Wang, Yunfeng; Qin, Fuyong; Qiu, Wei; Bai, Ruixiang; Chen, Xiaogang

2016-02-01

Based on widely used axial strain measurement method of Kevlar single fiber, an original theoretical model and measurement principle of application of micro-Raman spectroscopy to multi-fiber strains in a fiber bundle were established. The relationship between the nominal Raman shift of fiber bundle and the multi-fiber strains was deduced. The proposed principle for multi-fiber strains measurement is consistent with two special cases: single fiber deformation and multi-fiber deformation under equal strain. It is found experimentally that the distribution of Raman scattering intensity of a Kevlar 49 fiber as a function of distance between a fiber and the laser spot center follows a Gaussian function. Combining the Raman-shift/strain relationship of the Kevlar 49 single fiber and the uniaxial tension measured by micro-Raman spectroscopy, the Raman shift as a function of strain was obtained. Then the Raman peak at 1610 cm-1 for the Kevlar 49 fiber was fitted to a Lorentzian function and the FWHM showed a quadratic increase with the fiber strain. Finally, a dual-fiber tensile experiment was performed to verify the adequacy of the Raman technique for the measurement of multi-fiber strains.

NCI 1st International Workshop on the Biology, Prevention, and Treatment of Relapse After Allogeneic Hematopoietic Stem Cell Transplantation: Summary and Recommendations from the Organizing Committee

PubMed Central

Bishop, Michael R.; Alyea, Edwin P.; Cairo, Mitchell S.; Falkenburg, J.H. Frederik; June, Carl H.; Kröger, Nicolaus; Little, Richard F.; Miller, Jeffrey S.; Pavletic, Steven Z.; Porter, David L.; Riddell, Stanley R.; van Besien, Koen; Wayne, Alan S.; Weisdorf, Daniel J.; Wu, Roy S.; Giralt, Sergio

2011-01-01

The First International Workshop on The Biology, Prevention, and Treatment of Relapse After Allogeneic Hematopoietic Stem Cell Transplantation was organized and convened to identify, prioritize, and coordinate future research activities related to relapse after allogeneic hematopoietic stem cell transplantation (alloHSCT). Each of the Workshop’s six working committees have published individual reports of ongoing basic, translational and clinical research and recommended areas for future research related to the areas of relapse biology, epidemiology, prevention and treatment. This document summarizes each of the committees’ recommendations and suggests three major initiatives for a coordinated research effort to address the problem of relapse after alloHSCT. The first is the need to establish multi-center correlative and clinical trials networks for basic/translational, epidemiological, and clinical research. Second, there is a need for a network of biorepositories for the collection of samples pre- and post-alloHSCT to aid in laboratory and clinical studies. Third, there should be further refinement, implementation, and study of the proposed Workshop disease-specific response and relapse definitions and the recommendations for monitoring of minimal residual disease. These recommendations, in coordination with ongoing research initiatives and transplant organizations, provide a research framework to rapidly and efficiently address the significant problem of relapse following alloHSCT. PMID:21224011

Structural and Practical Identifiability Issues of Immuno-Epidemiological Vector-Host Models with Application to Rift Valley Fever.

PubMed

Tuncer, Necibe; Gulbudak, Hayriye; Cannataro, Vincent L; Martcheva, Maia

2016-09-01

In this article, we discuss the structural and practical identifiability of a nested immuno-epidemiological model of arbovirus diseases, where host-vector transmission rate, host recovery, and disease-induced death rates are governed by the within-host immune system. We incorporate the newest ideas and the most up-to-date features of numerical methods to fit multi-scale models to multi-scale data. For an immunological model, we use Rift Valley Fever Virus (RVFV) time-series data obtained from livestock under laboratory experiments, and for an epidemiological model we incorporate a human compartment to the nested model and use the number of human RVFV cases reported by the CDC during the 2006-2007 Kenya outbreak. We show that the immunological model is not structurally identifiable for the measurements of time-series viremia concentrations in the host. Thus, we study the non-dimensionalized and scaled versions of the immunological model and prove that both are structurally globally identifiable. After fixing estimated parameter values for the immunological model derived from the scaled model, we develop a numerical method to fit observable RVFV epidemiological data to the nested model for the remaining parameter values of the multi-scale system. For the given (CDC) data set, Monte Carlo simulations indicate that only three parameters of the epidemiological model are practically identifiable when the immune model parameters are fixed. Alternatively, we fit the multi-scale data to the multi-scale model simultaneously. Monte Carlo simulations for the simultaneous fitting suggest that the parameters of the immunological model and the parameters of the immuno-epidemiological model are practically identifiable. We suggest that analytic approaches for studying the structural identifiability of nested models are a necessity, so that identifiable parameter combinations can be derived to reparameterize the nested model to obtain an identifiable one. This is a crucial step in developing multi-scale models which explain multi-scale data.

Nosocomial outbreak of staphyloccocal scalded skin syndrome in neonates in England, December 2012 to March 2013.

PubMed

Paranthaman, K; Bentley, A; Milne, L M; Kearns, A; Loader, S; Thomas, A; Thompson, F; Logan, M; Newitt, S; Puleston, R

2014-08-21

Staphylococcal scalded skin syndrome (SSSS) is a blistering skin condition caused by exfoliative toxin-producing strains of Staphylococcus aureus. Outbreaks of SSSS in maternity settings are rarely reported. We describe an outbreak of SSSS that occurred among neonates born at a maternity unit in England during December 2012 to March 2013. Detailed epidemiological and microbiological investigations were undertaken. Eight neonates were found to be infected with the outbreak strain of S. aureus, of spa type t346, representing a single pulsotype. All eight isolates contained genes encoding exfoliative toxin A (eta) and six of them contained genes encoding toxin B (etb). Nasal swabs taken during targeted staff screening yielded a staphylococcal carriage rate of 21% (17/80), but none contained the outbreak strain. Mass screening involving multi-site swabbing and pooled, enrichment culture identified a healthcare worker (HCW) with the outbreak strain. This HCW was known to have a chronic skin condition and their initial nasal screen was negative. The outbreak ended when they were excluded from work. This outbreak highlights the need for implementing robust swabbing and culture methodswhen conventional techniques are unsuccessful in identifying staff carrier(s). This study adds to the growing body of evidence on the role of HCWs in nosocomial transmission of S. aureus.

First clinical and microbiological characterization of Clostridium difficile infection in a Croatian University Hospital.

PubMed

Novak, Anita; Spigaglia, Patrizia; Barbanti, Fabrizio; Goic-Barisic, Ivana; Tonkic, Marija

2014-12-01

Clinical background and molecular epidemiology of Clostridium difficile infection (CDI) in the University Hospital Centre Split were investigated from January 2010 to December 2011. In total, 54 patients with first episode of CDI were consecutively included in the study based on the positive EIA test specific for A and B toxins. Demographic and clinical data were prospectively analyzed from medical records. CDI incidence rate was 0.6 per 10,000 patient-days. Thirty six cases (70.6%) were healthcare-associated, twelve cases (23.5%) were community-associated and three (5.9%) were indeterminate. Six patients (11.7%) had suffered one or more recurrences and 37 patients (72.5%) showed severe CDI. Prior therapy with third generation cephalosporin was significantly associated with severe CDI (P<0.021). Fifty four toxigenic C. difficile strains were isolated and 50 of them were available for PCR-ribotyping. Sixteen different PCR-ribotypes were identified. The most prevalent were PCR-ribotype 001 (27.8%) and 014/020 (24.1%). Twenty three strains were resistant to at least one of the antibiotics tested. Among resistant strains, three (13.0%)--all PCR-ribotype 001--were multi-resistant. Resistance to fluoroquinolones was significantly higher in strains that caused infection after previous use of fluoroquinolones (P=0.04). Copyright © 2014 Elsevier Ltd. All rights reserved.

[Molecular-genetic characterization of shiga-toxin producing Escherichia coli isolated during a food-borne outbreak in St. Petersburg in 2013].

PubMed

Onishchenko, G G; Dyatlov, I A; Svetoch, E A; Volozhantsev, N V; Bannov, V A; Kartsev, N N; Borzenkov, V N; Fursova, N K; Shemyakin, I G; Bogun, A G; Kislichkina, A A; Popova, A V; Myakinina, V P; Teimurazov, M G; Polosenko, O V; Kaftyreva, L A; Makarova, M A; Matveeva, Z N; Grechaninova, T A; Grigor'eva, N S; Kicha, E V; Zabalueva, G V; Kutasova, T B; Korzhaev, Yu N; Bashketova, N S; Bushmanova, O N; Stalevskaya, A V; Tchinjeria, I G; Zhebrun, F B

2015-01-01

Shiga toxin-producing Escherichia coli (STEC) food-borne infections are reported worldwide and represent a serious problem for public healthcare. In the Russian Federation there is little information on epidemiology and etiology of STEC-infections as well as on molecular-genetic peculiarities of STEC pathogens. Our aim was to describe a food-borne outbreak as hemorrhagic colitis (HC) along with hemolytic uremic syndrome (HUS), enterocolitis, and acute gastroenteritis in children in St. Petersburg in 2013. Epidemiological, microbiological, molecular-genetic and bioinformatic methods were applied. Objects to study were clinical specimens, milk and food samples, as well as STEC strains isolated during the outbreak. The outbreak of food-borne infection was found to be caused by STEC-contaminated raw milk as confirmed by epidemiological analysis, detection of STEC DNA and isolation of relevant pathogens in milk and sick children fecal specimens. The whole-genome sequencing revealed two groups ofpathogens, E. coli O157:H7 and E. coli O101:H33 among collected strains. Group I strains were attributed to the previously known sequence type ST24, while group II strains belonged to the previously non-described sequence type ST145. In strain genomes of both groups there were identified nucleotide sequences of VT2-like prophage carrying stx2c gene, plasmid enterohemolysin gene, and gene of the STEC main adhesion factor intimin. Gene of intimin gamma was identified in E. coli O157:H7 strains and intimin iota 2 in E. coli O101:H33 strains. The latter previously was identified only in enteropathogenic E. coli (EPEC) strains. The additional knowledge of epidemiology and biology of STEC pathogens would assist clinicians and epidemiologists in diagnosing, treating and preventing hemorrhagic colitis.

Human Brucellosis in Maghreb: Existence of a Lineage Related to Socio-Historical Connections with Europe

PubMed Central

Lounes, Nedjma; Cherfa, Moulay-Ali; Le Carrou, Gilles; Bouyoucef, Abdellah; Jay, Maryne; Garin-Bastuji, Bruno; Mick, Virginie

2014-01-01

Despite control/eradication programs, brucellosis, major worldwide zoonosis due to the Brucella genus, is endemic in Northern Africa and remains a major public health problem in the Maghreb region (Algeria/Morocco/Tunisia). Brucella melitensis biovar 3 is mostly involved in human infections and infects mainly small ruminants. Human and animal brucellosis occurrence in the Maghreb seems still underestimated and its epidemiological situation remains hazy. This study summarizes official data, regarding Brucella melitensis infections in Algeria, from 1989 to 2012, with the purpose to provide appropriate insights concerning the epidemiological situation of human and small ruminant brucellosis in Maghreb. Algeria and Europe are closely linked for historical and economical reasons. These historical connections raise the question of their possible impact on the genetic variability of Brucella strains circulating in the Maghreb. Other purpose of this study was to assess the genetic diversity among Maghreb B. melitensis biovar 3 strains, and to investigate their possible epidemiological relationship with European strains, especially with French strains. A total of 90 B. melitensis biovar 3 Maghreb strains isolated over a 25 year-period (1989–2014), mainly from humans, were analysed by MLVA-16. The obtained results were compared with genotypes of European B. melitensis biovar 3 strains. Molecular assays showed that Algerian strains were mainly distributed into two distinct clusters, one Algerian cluster related to European sub-cluster. These results led to suggest the existence of a lineage resulting from socio-historical connections between Algeria and Europe that might have evolved distinctly from the Maghreb autochthonous group. This study provides insights regarding the epidemiological situation of human brucellosis in the Maghreb and is the first molecular investigation regarding B. melitensis biovar 3 strains circulating in the Maghreb. PMID:25517901

Molecular characterization of measles viruses in Turkey (2010-2011): first report of genotype D9 involved in an outbreak in 2011.

PubMed

Kalaycioglu, Atila T; Baykal, Atakan; Guldemir, Dilek; Bakkaloglu, Zekiye; Korukluoglu, Gulay; Coskun, Aslihan; Torunoglu, Mehmet Ali; Ertek, Mustafa; Durmaz, Riza

2013-12-01

Genetic characterization of measles viruses (MVs) combined with acquisition of epidemiologic information is essential for measles surveillance programs used in determining transmission pathways. This study describes the molecular characterization of 26 MV strains (3 from 2010, 23 from 2011) obtained from urine or throat swabs harvested from patients in Turkey. MV RNA samples (n = 26) were subjected to sequence analysis of 450 nucleotides comprising the most variable C-terminal region of the nucleoprotein (N) gene. Phylogenetic analysis revealed 20 strains from 2011 belonged to genotype D9, 3 to D4, 2 strains from 2010 to genotype D4 and 1 to genotype B3. This study represents the first report describing the involvement of MV genotype D9 in an outbreak in Turkey. The sequence of the majority of genotype D9 strains was identical to those identified in Russia, Malaysia, Japan, and the UK. Despite lack of sufficient epidemiologic information, the presence of variants observed following phylogenetic analysis suggested that exposure to genotype D9 might have occurred due to importation more than once. Phylogenetic analysis of five genotype D4 strains revealed the presence of four variants. Epidemiological information and phylogenetic analysis suggested that three genotype D4 strains and one genotype B3 strain were associated with importation. This study suggests the presence of pockets of unimmunized individuals making Turkey susceptible to outbreaks. Continuing molecular surveillance of measles strains in Turkey is essential as a means of acquiring epidemiologic information to define viral transmission patterns and determine the effectiveness of measles vaccination programs designed to eliminate this virus. © 2013 Wiley Periodicals, Inc.

Clinical and microbiological characterization of Clostridium difficile infection in a tertiary care hospital in Shanghai, China.

PubMed

Dong, Danfeng; Peng, Yibing; Zhang, Lihua; Jiang, Cen; Wang, Xuefeng; Mao, Enqiang

2014-01-01

Over the last decade, Clostridium difficile infection (CDI) has emerged as a significant nosocomial infection, yet little has been reported from China. This study aimed to characterize the clinical and microbiological features of CDI from a hospital in Shanghai. Patients with CDI seen between December 2010 and March 2013 were included in this study, of which clinical data were retrospectively collected. The microbiological features of corresponding isolates were analyzed including genotype by multi-locus sequence typing (MLST), antimicrobial susceptibility, toxin production, sporulation capacity, biofilm formation, and motility. Ninety-four cases of CDI were included during this study period, 12 of whom were severe cases. By reviewing the clinical data, all patients were treated empirically with proton pump inhibitor or antibiotics or both, and they were distributed widely across various wards, most frequently to the digestive ward (28/94, 29.79%). Comparing the severe with mild cases, no significant differences were found in the basic epidemiological data or the microbiological features. Among the 94 isolates, 31 were toxin A-negative toxin B-positive all genotyped as ST37. They generated fewer toxins and spores, as well as similar amounts of biofilm and motility percentages, but exhibited highest drug resistance to cephalosporins, quinolones, macrolide-lincosamide and streptogramin (MLSB), and tetracycline. No specific clinical genotype or microbiological features were found in severe cases; antimicrobial resistance could be the primary reason for epidemic strains leading to the dissemination and persistence of CDI.

Epidemiological analysis of Leishmania tropica strains and giemsa-stained smears from Syrian and Turkish leishmaniasis patients using multilocus microsatellite typing (MLMT)

PubMed Central

Nasereddin, Abed; Onay, Hüseyin; Karaca, Emin; Özkeklikçi, Ahmet; Jaffe, Charles L.; Kuhls, Katrin; Özbilgin, Ahmet; Ertabaklar, Hatice; Demir, Samiye; Özbel, Yusuf; Töz, Seray

2017-01-01

Turkey is located in an important geographical location, in terms of the epidemiology of vector-borne diseases, linking Asia and Europe. Cutaneous leishmaniasis (CL) is one of the endemic diseases in a Turkey and according to the Ministry Health of Turkey, 45% of CL patients originate from Şanlıurfa province located in southeastern Turkey. Herein, the epidemiological status of CL, caused by L. tropica, in Turkey was examined using multilocus microsatellite typing (MLMT) of strains obtained from Turkish and Syrian patients. A total of 38 cryopreserved strains and 20 Giemsa-stained smears were included in the present study. MLMT was performed using 12 highly specific microsatellite markers. Delta K (ΔK) calculation and Bayesian statistics were used to determine the population structure. Three main populations (POP A, B and C) were identified and further examination revealed the presence of three subpopulations for POP B and C. Combined analysis was performed using the data of previously typed L. tropica strains and Mediterranean and Şanlıurfa populations were identified. This finding suggests that the epidemiological status of L. tropica is more complicated than expected when compared to previous studies. A new population, comprised of Syrian L. tropica samples, was reported for the first time in Turkey, and the data presented here will provide new epidemiological information for further studies. PMID:28403153

[Genetic subtype and epidemiological feature of HIV-1 circulating strains among recently infected patients in Fujian province].

PubMed

Deng, Yongyue; Zhang, Chunyang; Yan, Yansheng; Yan, Pingping; Wu, Shouli

2014-06-01

In order to evaluate the distribution of genetic subtypes and epidemiological feature of HIV-1 circulating strains in Fujian province. Blood samples and epidemiological data were collected from 104 newly infected patients who were distinguished by BED-CEIA methodology, during 2011-2012. Viral sequences(n = 81) of HIV-1 gag, env, and pol segments were amplified by nested PCR. Subtypes B and four Circulating Recombinant Forms, (CRF01_AE, CRF07_BC, CRF08_BC and CRF55_01B) were found in the samples, CRF01_AE(45.68%)and CRF07_BC(35.80%) were the two main HIV-1 strains in Fujian province. Compared with previous data, the proportion of CRF07_BC rose significantly while it gradually decreased in CRF01_AE. Heterosexual contact was still the principal transmission route in Fujian province, but the number of infection among men-who-have-sex-with- men grew rapidly. Results from this study suggested that different subtypes of HIV-1 strain existed in Fujian province. The distribution of subtypes and the mode of transmission were changing with the progress of epidemic. Dynamic monitoring of the molecular epidemiology trends of HIV-1 infection should be enhanced.

Prevalence and Molecular Characterization of S. aureus and MRSA on Children's Playgrounds.

PubMed

Thapaliya, Dipendra; Kadariya, Jhalka; Capuano, Mike; Rush, Haleigh; Yee, Clair; Oet, Mark; Lohani, Sapana; Smith, Tara C

2018-05-09

Staphylococcus aureus is a major public health concern due to the emergence of virulent and drug resistant strains such as methicillin-resistant Staphylococcus aureus (MRSA). Although numerous studies have been conducted to assess the environmental contamination of S. aureus in health-care and household settings, little is known about the prevalence and epidemiology of S. aureus, including MRSA, on environmental surfaces of children's playgrounds. This study investigated the prevalence and molecular epidemiology of S. aureus and MRSA at playgrounds in northeast Ohio (NEO). A total of 280 environmental samples were collected from 10 playgrounds in NEO in July 2016. Sampling sites were selected based on playground size and availability of equipment located in both small and large cities and their suburbs. Samples were analyzed using established microbiology methods, and resulting S. aureus isolates were typed by spa typing. PCR was used to detect the presence of the Panton-Valentine leukocidin (PVL) and mecA genes. Antibiotic susceptibility was tested via the Vitek-2 System. The overall prevalence of S. aureus and MRSA was 31.8% (89/280) and 3.9% (11/280) respectively. A total of 43 spa types were detected from 257 S. aureus isolates. Overall, t189 was the most common spa type, accounting for 15.6% (40/257) of the isolates. Sixteen isolates (6.2%) were t002 (ST5/USA100), a common hospital-associated strain, and 11 isolates (4.3%) were t008 (ST8/USA300), a common community-associated strain. Five livestock-associated strain (t571/ST398) were also identified. Twenty-nine (11.3%) isolates were resistant to oxacillin, and sixty-six (25.7%) were multi-drug resistant S. aureus. The results of this study indicate that environmental surfaces of playgrounds in northeastern Ohio were contaminated with S. aureus and MRSA. These data reinforce the need for implementing effective prevention strategies to mitigate the risk imposed to children by environmental contamination of MRSA.

Comparison of Genomic Methods for Differentiating Strains of Enterococcus faecium: Assessment Using Clinical Epidemiologic Data

PubMed Central

Savor, Connie; Pfaller, Michael A.; Kruszynski, Julie A.; Hollis, Richard J.; Noskin, Gary A.; Peterson, Lance R.

1998-01-01

Genomic DNA extracted from 45 vancomycin-resistant Enterococcus faecium (VRE) isolates was cleaved with HindIII and HaeIII and subjected to agarose gel electrophoresis. The ability of this method (restriction endonuclease analysis [REA]) to distinguish strains at the subspecies level was compared with results previously determined by pulsed-field gel electrophoresis (PFGE). Chart reviews were performed to provide a clinical correlation of possible epidemiologic relatedness. A likely clinical association was found for 29 patients as part of two outbreaks. REA found 21 of 21 isolates were the same type in the first outbreak, with PFGE calling 19 strains the same type. In the second outbreak with eight patient isolates, HindIII found six were the same type and two were unique types. HaeIII found three strains were the same type, two strains were a separate type, and three more strains were unique types, while PFGE found three were the same type and five were unique types. No single “ideal” method can be used without clinical epidemiologic investigation, but any of these techniques is helpful in providing focus to infection control practitioners assessing possible outbreaks of nosocomial infection. PMID:9774587

Quantitative assessment of viable cells of Lactobacillus plantarum strains in single, dual and multi-strain biofilms.

PubMed

Fernández Ramírez, Mónica D; Kostopoulos, Ioannis; Smid, Eddy J; Nierop Groot, Masja N; Abee, Tjakko

2017-03-06

Biofilms of Lactobacillus plantarum are a potential source for contamination and recontamination of food products. Although biofilms have been mostly studied using single species or even single strains, it is conceivable that in a range of environmental settings including food processing areas, biofilms are composed of multiple species with each species represented by multiple strains. In this study six spoilage related L. plantarum strains FBR1-FBR6 and the model strain L. plantarum WCFS1 were characterised in single, dual and multiple strain competition models. A quantitative PCR approach was used with added propidium monoazide (PMA) enabling quantification of intact cells in the biofilm, representing the viable cell fraction that determines the food spoilage risk. Our results show that the performance of individual strains in multi-strain cultures generally correlates with their performance in pure culture, and relative strain abundance in multi-strain biofilms positively correlated with the relative strain abundance in suspended (planktonic) cultures. Performance of individual strains in dual-strain biofilms was highly influenced by the presence of the secondary strain, and in most cases no correlation between the relative contributions of viable planktonic cells and viable cells in the biofilm was noted. The total biofilm quantified by CV staining of the dual and multi-strain biofilms formed was mainly correlated to CV values of the dominant strain obtained in single strain studies. However, the combination of strain FBR5 and strain WCFS1 showed significantly higher CV values compared to the individual performances of both strains indicating that total biofilm formation was higher in this specific condition. Notably, L. plantarum FBR5 was able to outgrow all other strains and showed the highest relative abundance in dual and multi-strain biofilms. All the dual and multi-strain biofilms contained a considerable number of viable cells, representing a potential source of contamination. Copyright © 2016 Elsevier B.V. All rights reserved.

Complete Circular Genome Sequence of Successful ST8/SCCmecIV Community-Associated Methicillin-Resistant Staphylococcus aureus (OC8) in Russia: One-Megabase Genomic Inversion, IS256’s Spread, and Evolution of Russia ST8-IV

PubMed Central

Wan, Tsai-Wen; Higuchi, Wataru; Hung, Wei-Chun; Reva, Ivan V.; Singur, Olga A.; Gostev, Vladimir V.; Sidorenko, Sergey V.; Peryanova, Olga V.; Salmina, Alla B.; Reva, Galina V.; Teng, Lee-Jene; Yamamoto, Tatsuo

2016-01-01

ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has been a common threat, with large USA300 epidemics in the United States. The global geographical structure of ST8/SCCmecIV has not yet been fully elucidated. We herein determined the complete circular genome sequence of ST8/SCCmecIVc strain OC8 from Siberian Russia. We found that 36.0% of the genome was inverted relative to USA300. Two IS256, oppositely oriented, at IS256-enriched hot spots were implicated with the one-megabase genomic inversion (MbIN) and vSaβ split. The behavior of IS256 was flexible: its insertion site (att) sequences on the genome and junction sequences of extrachromosomal circular DNA were all divergent, albeit with fixed sizes. A similar multi-IS256 system was detected, even in prevalent ST239 healthcare-associated MRSA in Russia, suggesting IS256’s strong transmission potential and advantage in evolution. Regarding epidemiology, all ST8/SCCmecIVc strains from European, Siberian, and Far Eastern Russia, examined had MbIN, and geographical expansion accompanied divergent spa types and resistance to fluoroquinolones, chloramphenicol, and often rifampicin. Russia ST8/SCCmecIVc has been associated with life-threatening infections such as pneumonia and sepsis in both community and hospital settings. Regarding virulence, the OC8 genome carried a series of toxin and immune evasion genes, a truncated giant surface protein gene, and IS256 insertion adjacent to a pan-regulatory gene. These results suggest that unique single ST8/spa1(t008)/SCCmecIVc CA-MRSA (clade, Russia ST8-IVc) emerged in Russia, and this was followed by large geographical expansion, with MbIN as an epidemiological marker, and fluoroquinolone resistance, multiple virulence factors, and possibly a multi-IS256 system as selective advantages. PMID:27741255

Complete Circular Genome Sequence of Successful ST8/SCCmecIV Community-Associated Methicillin-Resistant Staphylococcus aureus (OC8) in Russia: One-Megabase Genomic Inversion, IS256's Spread, and Evolution of Russia ST8-IV.

PubMed

Wan, Tsai-Wen; Khokhlova, Olga E; Iwao, Yasuhisa; Higuchi, Wataru; Hung, Wei-Chun; Reva, Ivan V; Singur, Olga A; Gostev, Vladimir V; Sidorenko, Sergey V; Peryanova, Olga V; Salmina, Alla B; Reva, Galina V; Teng, Lee-Jene; Yamamoto, Tatsuo

2016-01-01

ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has been a common threat, with large USA300 epidemics in the United States. The global geographical structure of ST8/SCCmecIV has not yet been fully elucidated. We herein determined the complete circular genome sequence of ST8/SCCmecIVc strain OC8 from Siberian Russia. We found that 36.0% of the genome was inverted relative to USA300. Two IS256, oppositely oriented, at IS256-enriched hot spots were implicated with the one-megabase genomic inversion (MbIN) and vSaβ split. The behavior of IS256 was flexible: its insertion site (att) sequences on the genome and junction sequences of extrachromosomal circular DNA were all divergent, albeit with fixed sizes. A similar multi-IS256 system was detected, even in prevalent ST239 healthcare-associated MRSA in Russia, suggesting IS256's strong transmission potential and advantage in evolution. Regarding epidemiology, all ST8/SCCmecIVc strains from European, Siberian, and Far Eastern Russia, examined had MbIN, and geographical expansion accompanied divergent spa types and resistance to fluoroquinolones, chloramphenicol, and often rifampicin. Russia ST8/SCCmecIVc has been associated with life-threatening infections such as pneumonia and sepsis in both community and hospital settings. Regarding virulence, the OC8 genome carried a series of toxin and immune evasion genes, a truncated giant surface protein gene, and IS256 insertion adjacent to a pan-regulatory gene. These results suggest that unique single ST8/spa1(t008)/SCCmecIVc CA-MRSA (clade, Russia ST8-IVc) emerged in Russia, and this was followed by large geographical expansion, with MbIN as an epidemiological marker, and fluoroquinolone resistance, multiple virulence factors, and possibly a multi-IS256 system as selective advantages.

Extended-spectrum beta-lactamase-producing Escherichia coli infections in children: are community-acquired strains different from nosocomial strains?

PubMed

Morgand, Marjolaine; Vimont, Sophie; Bleibtreu, Alexandre; Boyd, Anders; Thien, Hoang Vu; Zahar, Jean-Ralph; Denamur, Erick; Arlet, Guillaume

2014-11-01

Infections caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are an important cause of morbidity and mortality, especially in children. We compared 58 epidemiologically unrelated ESBL-producing E. coli strains that caused infections. They were isolated between 2008 and 2012 in two Parisian pediatric hospitals and grouped according to their origin into either community-acquired (CA) (n=37) or nosocomially acquired (NA) (n=21) strains. Molecular characteristics of the ESBLs, phylogenetic traits of the strains including their belonging to clone O25b-ST131, prevalence of associated virulence genes, growth capacities in different media, metabolic phenotype and biofilm formation abilities were studied. ESBL type, associated resistance and distribution of phylogenetic groups were similar in the CA and NA groups. More than 60% of the B2 phylogroup strains in both groups belonged to the ST131 clone. Interestingly, CA strains possessed more genes encoding virulence factors and the distribution of these genes differed significantly between the two groups: fyuA, hlyC, papC and papGII were more frequent in the CA group, whereas iroN was more frequent in the NA group. CA strains also showed enhanced growth capacities in Luria Bertani rich medium. They tended to produce more biofilm but the difference was not significant. This study confirms the wide spread of clone ST131 among infected children, regardless of whether their infections were community- or nosocomially acquired. It highlights genotypic and phenotypic differences according to the origin of the strains that could indicate adaptability of these multi-resistant bacteria to specific environmental and host factors. Copyright © 2014 Elsevier GmbH. All rights reserved.

Molecular epidemiology of Plum pox virus in Japan.

PubMed

Maejima, Kensaku; Himeno, Misako; Komatsu, Ken; Takinami, Yusuke; Hashimoto, Masayoshi; Takahashi, Shuichiro; Yamaji, Yasuyuki; Oshima, Kenro; Namba, Shigetou

2011-05-01

For a molecular epidemiological study based on complete genome sequences, 37 Plum pox virus (PPV) isolates were collected from the Kanto region in Japan. Pair-wise analyses revealed that all 37 Japanese isolates belong to the PPV-D strain, with low genetic diversity (less than 0.8%). In phylogenetic analysis of the PPV-D strain based on complete nucleotide sequences, the relationships of the PPV-D strain were reconstructed with high resolution: at the global level, the American, Canadian, and Japanese isolates formed their own distinct monophyletic clusters, suggesting that the routes of viral entry into these countries were independent; at the local level, the actual transmission histories of PPV were precisely reconstructed with high bootstrap support. This is the first description of the molecular epidemiology of PPV based on complete genome sequences.

Genome organization of epidemic Acinetobacter baumannii strains.

PubMed

Di Nocera, Pier Paolo; Rocco, Francesco; Giannouli, Maria; Triassi, Maria; Zarrilli, Raffaele

2011-10-10

Acinetobacter baumannii is an opportunistic pathogen responsible for hospital-acquired infections. A. baumannii epidemics described world-wide were caused by few genotypic clusters of strains. The occurrence of epidemics caused by multi-drug resistant strains assigned to novel genotypes have been reported over the last few years. In the present study, we compared whole genome sequences of three A. baumannii strains assigned to genotypes ST2, ST25 and ST78, representative of the most frequent genotypes responsible for epidemics in several Mediterranean hospitals, and four complete genome sequences of A. baumannii strains assigned to genotypes ST1, ST2 and ST77. Comparative genome analysis showed extensive synteny and identified 3068 coding regions which are conserved, at the same chromosomal position, in all A. baumannii genomes. Genome alignments also identified 63 DNA regions, ranging in size from 4 o 126 kb, all defined as genomic islands, which were present in some genomes, but were either missing or replaced by non-homologous DNA sequences in others. Some islands are involved in resistance to drugs and metals, others carry genes encoding surface proteins or enzymes involved in specific metabolic pathways, and others correspond to prophage-like elements. Accessory DNA regions encode 12 to 19% of the potential gene products of the analyzed strains. The analysis of a collection of epidemic A. baumannii strains showed that some islands were restricted to specific genotypes. The definition of the genome components of A. baumannii provides a scaffold to rapidly evaluate the genomic organization of novel clinical A. baumannii isolates. Changes in island profiling will be useful in genomic epidemiology of A. baumannii population.

Multiple-locus variable-number tandem repeat analysis potentially reveals the existence of two groups of Anaplasma phagocytophilum circulating in cattle in France with different wild reservoirs.

PubMed

Dugat, Thibaud; Zanella, Gina; Véran, Luc; Lesage, Céline; Girault, Guillaume; Durand, Benoît; Lagrée, Anne-Claire; Boulouis, Henri-Jean; Haddad, Nadia

2016-11-22

Anaplasma phagocytophilum is the causative agent of tick-borne fever, a disease with high economic impact for domestic ruminants in Europe. Epidemiological cycles of this species are complex, and involve different ecotypes circulating in various host species. To date, these epidemiological cycles are poorly understood, especially in Europe, as European reservoir hosts (i.e. vertebrate hosts enabling long-term maintenance of the bacterium in the ecosystem), of the bacterium have not yet been clearly identified. In this study, our objective was to explore the presence, the prevalence, and the genetic diversity of A. phagocytophilum in wild animals, in order to better understand their implications as reservoir hosts of this pathogen. The spleens of 101 wild animals were collected from central France and tested for the presence of A. phagocytophilum DNA by msp2 qPCR. Positive samples were then typed by multi-locus variable-number tandem repeat (VNTR) analysis (MLVA), and compared to 179 previously typed A. phagocytophilum samples. Anaplasma phagocytophilum DNA was detected in 82/101 (81.2%) animals including 48/49 red deer (98%), 20/21 roe deer (95.2%), 13/29 wild boars (44.8%), and 1/1 red fox. MLVA enabled the discrimination of two A. phagocytophilum groups: group A contained the majority of A. phagocytophilum from red deer and two thirds of those from cattle, while group B included a human strain and variants from diverse animal species, i.e. sheep, dogs, a horse, the majority of variants from roe deer, and the remaining variants from cattle and red deer. Our results suggest that red deer and roe deer are promising A. phagocytophilum reservoir host candidates. Moreover, we also showed that A. phagocytophilum potentially circulates in at least two epidemiological cycles in French cattle. The first cycle may involve red deer as reservoir hosts and cattle as accidental hosts for Group A strains, whereas the second cycle could involve roe deer as reservoir hosts and at least domestic ruminants, dogs, horses, and humans as accidental hosts for Group B strains.

[Properties of Salmonella isolates in the Czech Republic].

PubMed

Srámová, H; Karpísková, R; Dĕdicová, D; Sisák, F; Rychlík, I

1999-08-01

Based on a grant project "Use and importance of epidemiological markers in Salmonella enteritidis and Salmonella typhimurium in the spread of salmonelloses in children under two years of age" implemented in 1995 to 1997, the authors investigated epidemiological markers in 1,186 salmonella isolates; the strains were isolated from faeces of 838 sick children, from 266 faeces of their contacts, from 49 specimens of incriminated foods and from 33 smears from the children's environment. Of 1,186 Salmonella isolates 999 were strains of S. enteritidis, 39 strains of S. typhimurium and 148 strains were not identified. The markers of Salmonella isolates were investigated from the aspect of biotyping--98% S. enteritidis were formed by the biovar Jena. 2% by biovar Essen; sensitivity to antibiotics--94.5% Salmonella strains were sensitive to 12 selected antibiotics, 2.9% were resistant and in 2.6% the resistance was in the intermediate zone; phagotyping--in 808 strains of S. enteritidis PT 8--88% predominated, in S. typhimurium DT 104 and DT 141; assessment of plasmid profiles--in strains of S. enteritidis plasmid 55 kb predominated, in three strains of S. typhimurium a plasmid size 95 kb; virulence--was compared in 43 strains isolated from hospitalized children with a severe clinical course with 39 strains from children treated at home. In vitro tests revealed that hospitalization of affected children was associated with virulence of the strains (SE phagotype 8) and not with age. The presented results are discussed with regard to the epidemiological situation in the Czech Republic and in the world.

Comparison of four molecular methods to type Salmonella Enteritidis strains.

PubMed

Campioni, Fábio; Pitondo-Silva, André; Bergamini, Alzira M M; Falcão, Juliana P

2015-05-01

This study compared the pulsed-field gel electrophoresis (PFGE), enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR), multilocus variable-number of tanden-repeat analysis (MLVA), and multilocus sequence typing (MLST) methods for typing 188 Salmonella Enteritidis strains from different sources isolated over a 24-year period in Brazil. PFGE and ERIC-PCR were more efficient than MLVA for subtyping the strains. However, MLVA provided additional epidemiological information for those strains. In addition, MLST showed the Brazilian strains as belonging to the main clonal complex of S. Enteritidis, CC11, and provided the first report of two new STs in the S. enterica database but could not properly subtype the strains. Our results showed that the use of PFGE or ERIC-PCR together with MLVA is suitable to efficiently subtype S. Enteritidis strains and provide important epidemiological information. © 2015 APMIS. Published by John Wiley & Sons Ltd.

A complex scenario of tuberculosis transmission is revealed through genetic and epidemiological surveys in Porto.

PubMed

Rito, Teresa; Matos, Carlos; Carvalho, Carlos; Machado, Henrique; Rodrigues, Gabriela; Oliveira, Olena; Ferreira, Eduarda; Gonçalves, Jorge; Maio, Lurdes; Morais, Clara; Ramos, Helena; Guimarães, João Tiago; Santos, Catarina L; Duarte, Raquel; Correia-Neves, Margarida

2018-01-25

Tuberculosis (TB) incidence is decreasing worldwide and eradication is becoming plausible. In low-incidence countries, intervention on migrant populations is considered one of the most important strategies for elimination. However, such measures are inappropriate in European areas where TB is largely endemic, such as Porto in Portugal. We aim to understand transmission chains in Porto through a genetic characterization of Mycobacterium tuberculosis strains and through a detailed epidemiological evaluation of cases. We genotyped the M. tuberculosis strains using the MIRU-VNTR system. We performed an evolutionary reconstruction of the genotypes with median networks, used in this context for the first time. TB cases from a period of two years were evaluated combining genetic, epidemiological and georeferencing information. The data reveal a unique complex scenario in Porto where the autochthonous population acts as a genetic reservoir of M. tuberculosis diversity with discreet episodes of transmission, mostly undetected using classical epidemiology alone. Although control policies have been successful in decreasing incidence in Porto, the discerned complexity suggests that, for elimination to be a realistic goal, strategies need to be adjusted and coupled with a continuous genetic characterization of strains and detailed epidemiological evaluation, in order to successfully identify and interrupt transmission chains.

Age-Adjustment and Related Epidemiology Rates in Education and Research

ERIC Educational Resources Information Center

Baker, John D.; Kruckman, Laurence; George, Joyce

2006-01-01

A quick review of introductory textbooks reveals that while gerontology authors and instructors introduce some aspect of demography and epidemiology data, there is limited focus on age adjustment or other important epidemiology rates. The goal of this paper is to reintroduce a variety of basic epidemiology strategies such as incidence, prevalence,…

Urgent Implementation in a Hospital Setting of a Strategy To Rule Out Secondary Cases Caused by Imported Extensively Drug-Resistant Mycobacterium tuberculosis Strains at Diagnosis

PubMed Central

Pérez-Lago, Laura; Martínez-Lirola, Miguel; García, Sergio; Herranz, Marta; Mokrousov, Igor; Comas, Iñaki; Martínez-Priego, Llúcia; Bouza, Emilio

2016-01-01

Current migratory movements require new strategies for rapidly tracking the transmission of high-risk imported Mycobacterium tuberculosis strains. Whole-genome sequencing (WGS) enables us to identify single-nucleotide polymorphisms (SNPs) and therefore design PCRs to track specific relevant strains. However, fast implementation of these strategies in the hospital setting is difficult because professionals working in diagnostics, molecular epidemiology, and genomics are generally at separate institutions. In this study, we describe the urgent implementation of a system that integrates genomics and molecular tools in a genuine high-risk epidemiological alert involving 2 independent importations of extensively drug resistant (XDR) and pre-XDR Beijing M. tuberculosis strains from Russia into Spain. Both cases involved commercial sex workers with long-standing tuberculosis (TB). The system was based on strain-specific PCRs tailored from WGS data that were transferred to the local node that was managing the epidemiological alert. The optimized tests were available for prospective implementation in the local node 33 working days after receiving the primary cultures of the XDR strains and were applied to all 42 new incident cases. An interpretable result was obtained in each case (directly from sputum for 27 stain-positive cases) and corresponded to the amplification profiles for strains other than the targeted pre-XDR and XDR strains, which made it possible to prospectively rule out transmission of these high-risk strains at diagnosis. PMID:27682128

Urgent Implementation in a Hospital Setting of a Strategy To Rule Out Secondary Cases Caused by Imported Extensively Drug-Resistant Mycobacterium tuberculosis Strains at Diagnosis.

PubMed

Pérez-Lago, Laura; Martínez-Lirola, Miguel; García, Sergio; Herranz, Marta; Mokrousov, Igor; Comas, Iñaki; Martínez-Priego, Llúcia; Bouza, Emilio; García-de-Viedma, Darío

2016-12-01

Current migratory movements require new strategies for rapidly tracking the transmission of high-risk imported Mycobacterium tuberculosis strains. Whole-genome sequencing (WGS) enables us to identify single-nucleotide polymorphisms (SNPs) and therefore design PCRs to track specific relevant strains. However, fast implementation of these strategies in the hospital setting is difficult because professionals working in diagnostics, molecular epidemiology, and genomics are generally at separate institutions. In this study, we describe the urgent implementation of a system that integrates genomics and molecular tools in a genuine high-risk epidemiological alert involving 2 independent importations of extensively drug resistant (XDR) and pre-XDR Beijing M. tuberculosis strains from Russia into Spain. Both cases involved commercial sex workers with long-standing tuberculosis (TB). The system was based on strain-specific PCRs tailored from WGS data that were transferred to the local node that was managing the epidemiological alert. The optimized tests were available for prospective implementation in the local node 33 working days after receiving the primary cultures of the XDR strains and were applied to all 42 new incident cases. An interpretable result was obtained in each case (directly from sputum for 27 stain-positive cases) and corresponded to the amplification profiles for strains other than the targeted pre-XDR and XDR strains, which made it possible to prospectively rule out transmission of these high-risk strains at diagnosis. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Genetic evolution of Mycoplasma capricolum subsp. capripneumoniae strains and molecular epidemiology of contagious caprine pleuropneumonia by sequencing of locus H2.

PubMed

Lorenzon, S; Wesonga, H; Ygesu, Laikemariam; Tekleghiorgis, Tesfaalem; Maikano, Y; Angaya, M; Hendrikx, P; Thiaucourt, F

2002-03-01

Contagious caprine pleuropneumonia (CCPP) is a major threat to goat farming in developing countries. Its exact distribution is not well known, despite the fact that new diagnostic tools such as PCR and competitive ELISA are now available. The authors developed a study of the molecular epidemiology of the disease, based on the amplification of a 2400 bp long fragment containing two duplicated gene coding for a putative membrane protein. The sequence of this fragment, obtained on 19 Mycoplasma capricolum subsp. capripneumoniae (Mccp) strains from various geographical locations, gave 11 polymorphic positions. The three mutations found on gene H2prim were silent and did not appear to induce any amino acid modifications in the putative translated protein. The second gene may be a pseudogene not translated in vivo, as it bore a deletion of the ATG codon found in the other members of the "Mycoplasma mycoides cluster" and as the six mutations evidenced in the Mccp strains would induce modifications in the translated amino acids. In addition, an Mccp strain isolated in the United Arab Emirates showed a deletion of the whole pseudogene, a further indication that this gene is not compulsory for mycoplasma growth. Four lineages were defined, based on the nucleotide sequence. These correlated relatively well with the geographical origin of the strains: North, Central or East Africa. The strain of Turkish origin had a sequence similar to that found in North African strains, while strains isolated in Oman had sequences similar to those of North or East African strains. The latter is possibly due to the regular import of goats of various origins. Similar molecular epidemiology tools have been developed by sequencing the two operons of the 16S rRNA gene or by AFLP. All these various techniques give complementary results. One (16S rRNA) offers the likelihood of a finer identification of strains circulating in a region, another (H2) of determining the geographical origin of the strains. These tools can make a very useful contribution to understanding the epidemiology of CCPP.

Syphilis epidemiology in 1994-2013, molecular epidemiological strain typing and determination of macrolide resistance in Treponema pallidum in 2013-2014 in Tuva Republic, Russia.

PubMed

Khairullin, Rafil; Vorobyev, Denis; Obukhov, Andrey; Kuular, Ural-Herel; Kubanova, Anna; Kubanov, Alexey; Unemo, Magnus

2016-07-01

The incidence of syphilis in the Tuva Republic (geographical centre of Asia), Russia has been exceedingly high historically. No detailed examinations and no molecular investigations of Treponema pallidum strains transmitted in the Tuva Republic, or in general, in Russia, were published internationally. We examined the syphilis epidemiology in 1994-2013, and the molecular epidemiology and macrolide resistance in T. pallidum strains in 2013-2014 in the Tuva Republic. Among 95 mainly primary or secondary syphilis patients, the arp, tpr, tp0548 and 23S rRNA genes in 85 polA gene-positive genital ulcer specimens were characterized. The syphilis incidence in Tuva Republic peaked in 1998 (1562), however declined to 177 in 2013. Among the 70 (82%) completely genotyped specimens, six molecular strain types were found. Strain type 14d/f accounted for 91%, but also 14c/f, 14d/g, 14b/f, 14i/f, 9d/f, and 4d/f were identified. Two (2.4%) specimens contained the 23S rRNA A2058G macrolide resistance mutation. This is the first internationally published typing study regarding T. pallidum in Russia, performed in the Tuva Republic with the highest syphilis incidence in Russia. The two molecular strain types 4d/f and 9d/f have previously been described only in Eastern and Northern China and for the first time, macrolide-resistant syphilis was described in Russia. © 2016 APMIS. Published by John Wiley & Sons Ltd.

Stenotrophomonas maltophilia in a university hospital of traditional Chinese medicine: molecular epidemiology and antimicrobial resistance.

PubMed

Zhao, S; Yang, L; Liu, H; Gao, F

2017-07-01

Stenotrophomona maltophilia has emerged as an important opportunistic pathogen that is highly antibiotic resistant. Analysis of antibiotic susceptibilities, drug-resistant gene profiles and molecular typing of S. maltophilia was undertaken in a university hospital of traditional Chinese medicine in East China. Resistance to sulphamethoxazole (SXT) was found to be an indicator of multi-drug resistance. SXT resistance was mediated by sul and dfrA genes in integrons, especially class 1. Some evidence of clonal dissemination was found, indicating the occurrence of cross-transmission of antibiotic-resistant strains within the hospital. This underscores the need for effective control and prevention measures in hospitals. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Molecular Epidemiology of Pulmonary Tuberculosis in Belgrade, Central Serbia

PubMed Central

Vuković, Dragana; Rüsch-Gerdes, Sabine; Savić, Branislava; Niemann, Stefan

2003-01-01

In order to gain precise data on the actual epidemiology of tuberculosis (TB) in Belgrade, central Serbia, we conducted the molecular epidemiological investigation described herein. IS6110 restriction fragment length polymorphism (RFLP) typing of 176 Mycobacterium tuberculosis isolates was performed. These strains were obtained from 48.4% of all patients diagnosed with culture-proven pulmonary TB from April through September 1998 and from May through October 1999. Clusters containing strains with identical RFLP IS6110 patterns were assumed to have arisen from recent transmission. Of the 176 cases, 55 (31.2%) were grouped into 23 clusters ranging in size from two to six patients. Nearly 80% of clustered patients were directly interviewed, and transmission between family-unrelated contacts was found to be predominant in the study population. Classical contact investigation identified only 2 (3.6%) of the 55 clustered patients. The clustering of TB patients was not associated with any demographic or clinical characteristic other than infection with multidrug-resistant (MDR) M. tuberculosis strains. Nearly 70% of MDR strains were clustered, which indicates active transmission of MDR TB in Belgrade. However, this was not observed by conventional epidemiologic surveillance. In conclusion, the first molecular epidemiologic analysis of TB in the region revealed frequent recent transmission of TB and pointed out significant shortcomings of the current concept for conventional contact tracing. The results presented also demonstrate that transmission of MDR TB in Belgrade is not optimally controlled, and they provide support for the development of improved control strategies, including application of molecular methods. PMID:12958271

Quantifying Transmission of Highly Pathogenic and Low Pathogenicity H7N1 Avian Influenza in Turkeys

PubMed Central

Saenz, Roberto A.; Essen, Steve C.; Brookes, Sharon M.; Iqbal, Munir; Wood, James L. N.; Grenfell, Bryan T.; McCauley, John W.; Brown, Ian H.; Gog, Julia R.

2012-01-01

Outbreaks of avian influenza in poultry can be devastating, yet many of the basic epidemiological parameters have not been accurately characterised. In 1999–2000 in Northern Italy, outbreaks of H7N1 low pathogenicity avian influenza virus (LPAI) were followed by the emergence of H7N1 highly pathogenic avian influenza virus (HPAI). This study investigates the transmission dynamics in turkeys of representative HPAI and LPAI H7N1 virus strains from this outbreak in an experimental setting, allowing direct comparison of the two strains. The fitted transmission rates for the two strains are similar: 2.04 (1.5–2.7) per day for HPAI, 2.01 (1.6–2.5) per day for LPAI. However, the mean infectious period is far shorter for HPAI (1.47 (1.3–1.7) days) than for LPAI (7.65 (7.0–8.3) days), due to the rapid death of infected turkeys. Hence the basic reproductive ratio, is significantly lower for HPAI (3.01 (2.2–4.0)) than for LPAI (15.3 (11.8–19.7)). The comparison of transmission rates and are critically important in relation to understanding how HPAI might emerge from LPAI. Two competing hypotheses for how transmission rates vary with population size are tested by fitting competing models to experiments with differing numbers of turkeys. A model with frequency-dependent transmission gives a significantly better fit to experimental data than density-dependent transmission. This has important implications for extrapolating experimental results from relatively small numbers of birds to the commercial poultry flock size, and for how control, including vaccination, might scale with flock size. PMID:23028760

Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches.

PubMed

Schürch, A C; Arredondo-Alonso, S; Willems, R J L; Goering, R V

2018-04-01

Whole genome sequence (WGS)-based strain typing finds increasing use in the epidemiologic analysis of bacterial pathogens in both public health as well as more localized infection control settings. This minireview describes methodologic approaches that have been explored for WGS-based epidemiologic analysis and considers the challenges and pitfalls of data interpretation. Personal collection of relevant publications. When applying WGS to study the molecular epidemiology of bacterial pathogens, genomic variability between strains is translated into measures of distance by determining single nucleotide polymorphisms in core genome alignments or by indexing allelic variation in hundreds to thousands of core genes, assigning types to unique allelic profiles. Interpreting isolate relatedness from these distances is highly organism specific, and attempts to establish species-specific cutoffs are unlikely to be generally applicable. In cases where single nucleotide polymorphism or core gene typing do not provide the resolution necessary for accurate assessment of the epidemiology of bacterial pathogens, inclusion of accessory gene or plasmid sequences may provide the additional required discrimination. As with all epidemiologic analysis, realizing the full potential of the revolutionary advances in WGS-based approaches requires understanding and dealing with issues related to the fundamental steps of data generation and interpretation. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent.

PubMed

Alfonso-Morales, Abdulahi; Rios, Liliam; Martínez-Pérez, Orlando; Dolz, Roser; Valle, Rosa; Perera, Carmen L; Bertran, Kateri; Frías, Maria T; Ganges, Llilianne; Díaz de Arce, Heidy; Majó, Natàlia; Núñez, José I; Pérez, Lester J

2015-01-01

Infectious bursal disease (IBD) is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV) strains worldwide. Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population. This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain information about both genome segments of IBDV for molecular epidemiology studies.

Radii effect on the translation spring constant of force transducer beams

NASA Technical Reports Server (NTRS)

Scott, C. E.

1992-01-01

Multi-component strain-gage force transducer design requires the designer to determine the spring constant of the numerous beams or flexures incorporated in the transducer. The classical beam deflection formulae that are used in calculating these spring constants typically assume that the beam has a uniform moment of inertia along the entire beam length. In practice all beams have a radius at the end where the beam interfaces with the shoulder of the transducer, and on short beams in particular this increases the beam spring constant considerably. A Basic computer program utilizing numerical integration is presented to determine this effect.

[Serotype and phage type distribution of human Salmonella strains isolated in Spain, 1997-2001].

PubMed

Echeita, María Aurora; Aladueña, Ana María; Díez, Rosa; Arroyo, Margarita; Cerdán, Francisca; Gutiérrez, Rafaela; de la Fuente, Manuela; González-Sanz, Rubén; Herrera-León, Silvia; Usera, Miguel Angel

2005-03-01

Salmonellosis is one of the most frequent causes of gastroenteritis in Spain. Serotyping is the gold standard epidemiological marker for subdividing Salmonella spp. strains. A small number of serotypes are very frequently isolated, reducing the discriminatory power of serotyping. Thus, to increase our knowledge of Salmonella spp. epidemiology, additional epidemiological markers, such as phage typing, should be used for this purpose. Salmonella spp. strains of human origin sent to the Laboratorio Nacional de Referencia de Salmonella y Shigella (LNRSSE, Spanish Reference Laboratory for Salmonella and Shigella) between 1997 and 2001 were serotyped using conventional agglutination methods, and Enteritidis, Typhimurium, Hadar, Virchow and Typhi serotypes were additionally phage typed according to internationally-developed schemes. A total of 30,856 Salmonella spp. strains, isolated in the majority of Spanish Autonomous Communities, were analyzed. Enteritidis (51%) and Typhimurium (24%) were the most frequently isolated serotypes. The following were the most frequent serotype/phage type combinations: Enteritidis/PT1 (18%), Enteritidis/PT4 (15%), Enteritidis/PT6a (5%), Typhimurium/DT104 (5%) and Enteritidis/PT6 (3%). The serotype Enteritidis/PT1 showed the greatest increase over the period studied, from 11.61% in 1997 to 24.74% in 2001. A hierarchical typing approach for Salmonella spp., using serotyping coupled with phage typing allowed a higher level of discrimination among Salmonella serotypes. Application of this approach in epidemiological studies could be highly useful for early characterization of related strains.

Systematic review and meta-analysis: Multi-strain probiotics as adjunct therapy for Helicobacter pylori eradication and prevention of adverse events

PubMed Central

Huang, Ying; Wang, Lin; Malfertheiner, Peter

2015-01-01

Background Eradication rates with triple therapy for Helicobacter pylori infections have currently declined to unacceptable levels worldwide. Newer quadruple therapies are burdened with a high rate of adverse events. Whether multi-strain probiotics can improve eradication rates or diminish adverse events remains uncertain. Methods Relevant publications in which patients with H. pylori infections were randomized to a multi-strain probiotic or control were identified in PubMed, Cochrane Databases, and other sources from 1 January 1960–3 June 2015. Primary outcomes included eradication rates, incidence of any adverse event and the incidence of antibiotic-associated diarrhea. As probiotic efficacy is strain-specific, pooled relative risks and 95% confidence intervals were calculated using meta-analysis stratified by similar multi-strain probiotic mixtures. Results A total of 19 randomized controlled trials (20 treatment arms, n = 2730) assessing one of six mixtures of strains of probiotics were included. Four multi-strain probiotics significantly improved H. pylori eradication rates, five significantly prevented any adverse reactions and three significantly reduced antibiotic-associated diarrhea. Only two probiotic mixtures (Lactobacillus acidophilus/Bifidobacterium animalis and an eight-strain mixture) had significant efficacy for all three outcomes. Conclusions Our meta-analysis found adjunctive use of some multi-strain probiotics may improve H. pylori eradication rates and prevent the development of adverse events and antibiotic-associated diarrhea, but not all mixtures were effective. PMID:27536365

Comparative Genomics Study of Multi-Drug-Resistance Mechanisms in the Antibiotic-Resistant Streptococcus suis R61 Strain

PubMed Central

Zhang, Anding; Wu, Jiayan; Chen, Bo; Hua, Yafeng; Yu, Jun; Chen, Huanchun; Xiao, Jingfa; Jin, Meilin

2011-01-01

Background Streptococcus suis infections are a serious problem for both humans and pigs worldwide. The emergence and increasing prevalence of antibiotic-resistant S. suis strains pose significant clinical and societal challenges. Results In our study, we sequenced one multi-drug-resistant S. suis strain, R61, and one S. suis strain, A7, which is fully sensitive to all tested antibiotics. Comparative genomic analysis revealed that the R61 strain is phylogenetically distinct from other S. suis strains, and the genome of R61 exhibits extreme levels of evolutionary plasticity with high levels of gene gain and loss. Our results indicate that the multi-drug-resistant strain R61 has evolved three main categories of resistance. Conclusions Comparative genomic analysis of S. suis strains with diverse drug-resistant phenotypes provided evidence that horizontal gene transfer is an important evolutionary force in shaping the genome of multi-drug-resistant strain R61. In this study, we discovered novel and previously unexamined mutations that are strong candidates for conferring drug resistance. We believe that these mutations will provide crucial clues for designing new drugs against this pathogen. In addition, our work provides a clear demonstration that the use of drugs has driven the emergence of the multi-drug-resistant strain R61. PMID:21966396

Comparative genomics study of multi-drug-resistance mechanisms in the antibiotic-resistant Streptococcus suis R61 strain.

PubMed

Hu, Pan; Yang, Ming; Zhang, Anding; Wu, Jiayan; Chen, Bo; Hua, Yafeng; Yu, Jun; Chen, Huanchun; Xiao, Jingfa; Jin, Meilin

2011-01-01

Streptococcus suis infections are a serious problem for both humans and pigs worldwide. The emergence and increasing prevalence of antibiotic-resistant S. suis strains pose significant clinical and societal challenges. In our study, we sequenced one multi-drug-resistant S. suis strain, R61, and one S. suis strain, A7, which is fully sensitive to all tested antibiotics. Comparative genomic analysis revealed that the R61 strain is phylogenetically distinct from other S. suis strains, and the genome of R61 exhibits extreme levels of evolutionary plasticity with high levels of gene gain and loss. Our results indicate that the multi-drug-resistant strain R61 has evolved three main categories of resistance. Comparative genomic analysis of S. suis strains with diverse drug-resistant phenotypes provided evidence that horizontal gene transfer is an important evolutionary force in shaping the genome of multi-drug-resistant strain R61. In this study, we discovered novel and previously unexamined mutations that are strong candidates for conferring drug resistance. We believe that these mutations will provide crucial clues for designing new drugs against this pathogen. In addition, our work provides a clear demonstration that the use of drugs has driven the emergence of the multi-drug-resistant strain R61.

Dissemination and genetic support of broad-spectrum beta-lactam-resistant Escherichia coli strain isolated from two Tunisian hospitals during 2004-2012.

PubMed

Ayari, Khaoula; Bourouis, Amel; Chihi, Hela; Mahrouki, Sihem; Naas, Thierry; Belhadj, Omrane

2017-06-01

The dissemination of extended-spectrum β-lactamase (ESBL)-producing bacteria presented a great concern worldwide. Gram-negative organisms such as Escherichia coli and Klebsiella pneumoniae are the most frequently isolated pathogens responsible for nosocomial infections. The aim of this study was to investigate and to follow the emergence of resistance and the characterization of Extended-Spectrum Beta-Lactamases (ESBL) among broad-spectrum beta-lactam- Escherichia coli clinical isolates recovered from the military hospital and Habib Thameur hospital in Tunisia. A total of 113 E.coli isolates obtained during the period 2004 through 2012 showed a significant degree of multi-resistance. Among these strains, the double-disk synergy test confirmed the ESBL phenotype in 46 isolates. These included 32(70%) strains from Hospital A and 14(30%) from Hospital B. The ESBL was identified as CTX-M-15. The ESBL resistance was transferred by a 60 kb plasmid CTXM-15-producing isolates were unrelated according to the PFGE analysis and characterization of the regions surrounding the blaCTX-M-15 showed the ISEcp1 elements located in the upstream region of the bla gene and 20 of them truncated by IS26. ESBL producing E. coli strains are a serious threat in the community in Tunisia and we should take into consideration any possible spread of such epidemiological resistance.

FDA Escherichia coli Identification (FDA-ECID) Microarray: a Pangenome Molecular Toolbox for Serotyping, Virulence Profiling, Molecular Epidemiology, and Phylogeny

PubMed Central

Patel, Isha R.; Gangiredla, Jayanthi; Lacher, David W.; Mammel, Mark K.; Jackson, Scott A.; Lampel, Keith A.

2016-01-01

ABSTRACT Most Escherichia coli strains are nonpathogenic. However, for clinical diagnosis and food safety analysis, current identification methods for pathogenic E. coli either are time-consuming and/or provide limited information. Here, we utilized a custom DNA microarray with informative genetic features extracted from 368 sequence sets for rapid and high-throughput pathogen identification. The FDA Escherichia coli Identification (FDA-ECID) platform contains three sets of molecularly informative features that together stratify strain identification and relatedness. First, 53 known flagellin alleles, 103 alleles of wzx and wzy, and 5 alleles of wzm provide molecular serotyping utility. Second, 41,932 probe sets representing the pan-genome of E. coli provide strain-level gene content information. Third, approximately 125,000 single nucleotide polymorphisms (SNPs) of available whole-genome sequences (WGS) were distilled to 9,984 SNPs capable of recapitulating the E. coli phylogeny. We analyzed 103 diverse E. coli strains with available WGS data, including those associated with past foodborne illnesses, to determine robustness and accuracy. The array was able to accurately identify the molecular O and H serotypes, potentially correcting serological failures and providing better resolution for H-nontypeable/nonmotile phenotypes. In addition, molecular risk assessment was possible with key virulence marker identifications. Epidemiologically, each strain had a unique comparative genomic fingerprint that was extended to an additional 507 food and clinical isolates. Finally, a 99.7% phylogenetic concordance was established between microarray analysis and WGS using SNP-level data for advanced genome typing. Our study demonstrates FDA-ECID as a powerful tool for epidemiology and molecular risk assessment with the capacity to profile the global landscape and diversity of E. coli. IMPORTANCE This study describes a robust, state-of-the-art platform developed from available whole-genome sequences of E. coli and Shigella spp. by distilling useful signatures for epidemiology and molecular risk assessment into one assay. The FDA-ECID microarray contains features that enable comprehensive molecular serotyping and virulence profiling along with genome-scale genotyping and SNP analysis. Hence, it is a molecular toolbox that stratifies strain identification and pathogenic potential in the contexts of epidemiology and phylogeny. We applied this tool to strains from food, environmental, and clinical sources, resulting in significantly greater phylogenetic and strain-specific resolution than previously reported for available typing methods. PMID:27037122

Genomic Sequencing of Bordetella pertussis for Epidemiology and Global Surveillance of Whooping Cough.

PubMed

Bouchez, Valérie; Guglielmini, Julien; Dazas, Mélody; Landier, Annie; Toubiana, Julie; Guillot, Sophie; Criscuolo, Alexis; Brisse, Sylvain

2018-06-01

Bordetella pertussis causes whooping cough, a highly contagious respiratory disease that is reemerging in many world regions. The spread of antigen-deficient strains may threaten acellular vaccine efficacy. Dynamics of strain transmission are poorly defined because of shortcomings in current strain genotyping methods. Our objective was to develop a whole-genome genotyping strategy with sufficient resolution for local epidemiologic questions and sufficient reproducibility to enable international comparisons of clinical isolates. We defined a core genome multilocus sequence typing scheme comprising 2,038 loci and demonstrated its congruence with whole-genome single-nucleotide polymorphism variation. Most cases of intrafamilial groups of isolates or of multiple isolates recovered from the same patient were distinguished from temporally and geographically cocirculating isolates. However, epidemiologically unrelated isolates were sometimes nearly undistinguishable. We set up a publicly accessible core genome multilocus sequence typing database to enable global comparisons of B. pertussis isolates, opening the way for internationally coordinated surveillance.

19-VNTR loci used in genotyping Chinese clinical Mycobacterium tuberculosis complex strains and in association with spoligotyping.

PubMed

Jiang, Yi; Liu, Hai-can; Zheng, Huajun; Dou, Xiangfeng; Tang, Biao; Zhao, Xiu-qin; Zhu, Yongqiang; Lu, Bing; Wang, Shengyue; Dong, Hai-yan; Zhang, Yuan-yuan; Zhao, Guoping; Wan, Kanglin

2013-07-01

Recently, tandem repeat typing has emerged as a rapid and easy method for the molecular epidemiology of the Mycobacterium tuberculosis (M. tuberculosis) complex. In this study, a collection of 19 VNTRs incorporating 15 previously described loci and 4 newly evaluated markers were used to genotype 206 Chinese M. tuberculosis isolates and 9 BCG strains. The discriminatory power was evaluated and compared with that obtained by Spoligotyping. It turned out that 15-locus VNTR could be very useful in M. tuberculosis complex strains genotyping in China. The 4 newly evaluated loci were proved informative and could be useful for future epidemiology studies, especially in Beijing family strains. In addition, a unique pattern of the latter 4 loci were found in Chinese BCG strains. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular epidemiology of duck hepatitis a virus types 1 and 3 in China, 2010-2015.

PubMed

Wen, X; Zhu, D; Cheng, A; Wang, M; Chen, S; Jia, R; Liu, M; Sun, K; Zhao, X; Yang, Q; Wu, Y; Chen, X

2018-02-01

Duck hepatitis A virus (DHAV) is the most common aetiologic agent of duck virus hepatitis (DVH), causing substantial economic losses in the duck industry worldwide. In China, officially approved DHAV-1 live-attenuated vaccines have been used widely to vaccinate breeder ducks since 2013. However, following the reports of DVH outbreaks, it has become necessary to assess the epidemiological situation of this virus in China. We conducted molecular epidemiological analyses of 32 DHAV field isolates while analysing the samples from ducks suspected of having hepatitis collected from commercial duck farms in China between May 2010 and December 2015. Considerable changes were observed in the epidemiology of DHAV-1 and DHAV-3 in China over time. A higher number of DHAV-1 strains were isolated during 2010-2012, coinciding with the widespread use of officially approved DHAV-1 live vaccine strains beginning in 2013. In contrast, a higher rate of DHAV-3 causing DHAV infections was observed between 2013 and 2015. Phylogenetic analyses based on the full-length VP1 gene were performed on these field isolates and using reference strains available in GenBank. DHAV-1 field isolates were evaluated in two groups: one group closely related to prototype strains and circulating in China between 2010 and 2012 and another group exhibiting genetic and serological differences from prototype strains. All DHAV-3 strains isolated in this study were grouped as monophyletic, which has become the predominant viral type, particularly in Shandong and Sichuan provinces, since 2013. In conclusion, these data provide updated information on the genetic and serological diversity of DHAV-1 and DHAV-3, and our findings may serve as a foundation for the prevention of, and vaccine development for, DHAV in China. © 2017 Blackwell Verlag GmbH.

Understanding the molecular epidemiology and global relationships of Brachyspira hyodysenteriae from swine herds in the United States: a multi-locus sequence typing approach.

PubMed

Mirajkar, Nandita S; Gebhart, Connie J

2014-01-01

Outbreaks of mucohemorrhagic diarrhea in pigs caused by Brachyspira hyodysenteriae in the late 2000s indicated the re-emergence of Swine Dysentery (SD) in the U.S. Although the clinical disease was absent in the U.S. since the early 1990s, it continued to cause significant economic losses to other swine rearing countries worldwide. This study aims to fill the gap in knowledge pertaining to the re-emergence and epidemiology of B. hyodysenteriae in the U.S. and its global relationships using a multi-locus sequence typing (MLST) approach. Fifty-nine post re-emergent isolates originating from a variety of sources in the U.S. were characterized by MLST, analyzed for epidemiological relationships (within and between multiple sites of swine systems), and were compared with pre re-emergent isolates from the U.S. Information for an additional 272 global isolates from the MLST database was utilized for international comparisons. Thirteen nucleotide sequence types (STs) including a predominant genotype (ST93) were identified in the post re-emergent U.S. isolates; some of which showed genetic similarity to the pre re-emergent STs thereby suggesting its likely role in the re-emergence of SD. In the U.S., in general, no more than one ST was found on a site; multiple sites of a common system shared a ST; and STs found in the U.S. were distinct from those identified globally. Of the 110 STs characterized from ten countries, only two were found in more than one country. The U.S. and global populations, identified as clonal and heterogeneous based on STs, showed close relatedness based on amino acid types (AATs). One predicted founder type (AAT9) and multiple predicted subgroup founder types identified for both the U.S. and the global population indicate the potential microevolution of this pathogen. This study elucidates the strain diversity and microevolution of B. hyodysenteriae, and highlights the utility of MLST for epidemiological and surveillance studies.

Whole-Genome-Sequencing characterization of bloodstream infection-causing hypervirulent Klebsiella pneumoniae of capsular serotype K2 and ST374.

PubMed

Wang, Xiaoli; Xie, Yingzhou; Li, Gang; Liu, Jialin; Li, Xiaobin; Tian, Lijun; Sun, Jingyong; Ou, Hong-Yu; Qu, Hongping

2018-01-01

Hypervirulent K. pneumoniae variants (hvKP) have been increasingly reported worldwide, causing metastasis of severe infections such as liver abscesses and bacteremia. The capsular serotype K2 hvKP strains show diverse multi-locus sequence types (MLSTs), but with limited genetics and virulence information. In this study, we report a hypermucoviscous K. pneumoniae strain, RJF293, isolated from a human bloodstream sample in a Chinese hospital. It caused a metastatic infection and fatal septic shock in a critical patient. The microbiological features and genetic background were investigated with multiple approaches. The Strain RJF293 was determined to be multilocis sequence type (ST) 374 and serotype K2, displayed a median lethal dose (LD50) of 1.5 × 10 2 CFU in BALB/c mice and was as virulent as the ST23 K1 serotype hvKP strain NTUH-K2044 in a mouse lethality assay. Whole genome sequencing revealed that the RJF293 genome codes for 32 putative virulence factors and exhibits a unique presence/absence pattern in comparison to the other 105 completely sequenced K. pneumoniae genomes. Whole genome SNP-based phylogenetic analysis revealed that strain RJF293 formed a single clade, distant from those containing either ST66 or ST86 hvKP. Compared to the other sequenced hvKP chromosomes, RJF293 contains several strain-variable regions, including one prophage, one ICEKp1 family integrative and conjugative element and six large genomic islands. The sequencing of the first complete genome of an ST374 K2 hvKP clinical strain should reinforce our understanding of the epidemiology and virulence mechanisms of this bloodstream infection-causing hvKP with clinical significance.

Whole-Genome-Sequencing characterization of bloodstream infection-causing hypervirulent Klebsiella pneumoniae of capsular serotype K2 and ST374

PubMed Central

Wang, Xiaoli; Xie, Yingzhou; Li, Gang; Liu, Jialin; Li, Xiaobin; Tian, Lijun; Sun, Jingyong; Qu, Hongping

2018-01-01

ABSTRACT Hypervirulent K. pneumoniae variants (hvKP) have been increasingly reported worldwide, causing metastasis of severe infections such as liver abscesses and bacteremia. The capsular serotype K2 hvKP strains show diverse multi-locus sequence types (MLSTs), but with limited genetics and virulence information. In this study, we report a hypermucoviscous K. pneumoniae strain, RJF293, isolated from a human bloodstream sample in a Chinese hospital. It caused a metastatic infection and fatal septic shock in a critical patient. The microbiological features and genetic background were investigated with multiple approaches. The Strain RJF293 was determined to be multilocis sequence type (ST) 374 and serotype K2, displayed a median lethal dose (LD50) of 1.5 × 102 CFU in BALB/c mice and was as virulent as the ST23 K1 serotype hvKP strain NTUH-K2044 in a mouse lethality assay. Whole genome sequencing revealed that the RJF293 genome codes for 32 putative virulence factors and exhibits a unique presence/absence pattern in comparison to the other 105 completely sequenced K. pneumoniae genomes. Whole genome SNP-based phylogenetic analysis revealed that strain RJF293 formed a single clade, distant from those containing either ST66 or ST86 hvKP. Compared to the other sequenced hvKP chromosomes, RJF293 contains several strain-variable regions, including one prophage, one ICEKp1 family integrative and conjugative element and six large genomic islands. The sequencing of the first complete genome of an ST374 K2 hvKP clinical strain should reinforce our understanding of the epidemiology and virulence mechanisms of this bloodstream infection-causing hvKP with clinical significance. PMID:29338592

Genetic Diversity and Population Structure of Leishmania infantum from Southeastern France: Evaluation Using Multi-Locus Microsatellite Typing

PubMed Central

Pomares, Christelle; Marty, Pierre; Bañuls, Anne Laure; Lemichez, Emmanuel; Pratlong, Francine; Faucher, Benoît; Jeddi, Fakhri; Moore, Sandy; Michel, Grégory; Aluru, Srikanth; Piarroux, Renaud; Hide, Mallorie

2016-01-01

In the south of France, Leishmania infantum is responsible for numerous cases of canine leishmaniasis (CanL), sporadic cases of human visceral leishmaniasis (VL) and rare cases of cutaneous and muco-cutaneous leishmaniasis (CL and MCL, respectively). Several endemic areas have been clearly identified in the south of France including the Pyrénées-Orientales, Cévennes (CE), Provence (P), Alpes-Maritimes (AM) and Corsica (CO). Within these endemic areas, the two cities of Nice (AM) and Marseille (P), which are located 150 km apart, and their surroundings, concentrate the greatest number of French autochthonous leishmaniasis cases. In this study, 270 L. infantum isolates from an extended time period (1978–2011) from four endemic areas, AM, P, CE and CO, were assessed using Multi-Locus Microsatellite Typing (MLMT). MLMT revealed a total of 121 different genotypes with 91 unique genotypes and 30 repeated genotypes. Substantial genetic diversity was found with a strong genetic differentiation between the Leishmania populations from AM and P. However, exchanges were observed between these two endemic areas in which it seems that strains spread from AM to P. The genetic differentiations in these areas suggest strong epidemiological structuring. A model-based analysis using STRUCTURE revealed two main populations: population A (consisting of samples primarily from the P and AM endemic areas with MON-1 and non-MON-1 strains) and population B consisting of only MON-1 strains essentially from the AM endemic area. For four patients, we observed several isolates from different biological samples which provided insight into disease relapse and re-infection. These findings shed light on the transmission dynamics of parasites in humans. However, further data are required to confirm this hypothesis based on a limited sample set. This study represents the most extensive population analysis of L. infantum strains using MLMT conducted in France. PMID:26808522

Global stability analysis of two-strain epidemic model with bilinear and non-monotone incidence rates

NASA Astrophysics Data System (ADS)

Baba, Isa Abdullahi; Hincal, Evren

2017-05-01

In this article we studied an epidemic model consisting of two strains with different types of incidence rates; bilinear and non-monotone. The model consists of four equilibrium points: disease-free equilibrium, endemic with respect to strain 1, endemic with respect to strain 2, and endemic with respect to both strains. The global stability analysis of the equilibrium points was carried out through the use of Lyapunov functions. Two basic reproduction ratios R 1 0 and R 2 0 are found, and we have shown that if both are less than one, the disease dies out, and if both are greater than one epidemic occurs. Furthermore, epidemics occur with respect to any strain with a basic reproduction ratio greater than one and disease dies out with respect to any strain with a basic reproduction ratio less than one. It was also shown that any strain with highest basic reproduction ratio will automatically outperform the other strain, thereby eliminating it. Numerical simulations were carried out to support the analytic result and to show the effect of the parameter k in the non-monotone incidence rate, which describes the psychological effect of general public towards infection.

[Update on the epidemiology of hydatidosis. Hydatid echinococci: species; life cycles; epidemiologic consequences].

PubMed

Euzéby, J

1990-05-01

Human hydatidosis results from infestation by two species of Echinococcus. (1) E. vogeli, the life-cycle of which occurs in amazonian forests and involves wild canidae and cuniculidae. (2) E. granulosus, which includes two geographical groups: (a) Northern group, with two sub-species E. g borelis and E. g. canadensis, the life-cycle of which is sylvatic and that are agents of a pulmonary hydatidosis which may affect Man. (b) "European" (actually cosmopolitan) form, with two sub-species: (1) E. q. equinus (equine strain) occurring between dogs and horses and unable to infect Man; (2) E. g. granulosus, with several strains and clones according to the species of their intermediate hosts and which are the agents of synanthropic or sylvatic life-cycles. Man may enter into some of these life cycles, but not into all of them: ovine strains, chiefly, but pig and camel strains also, have a zoonotic incidence. From these data, the author emphasizes the epidemiological features of human hydatidosis, which over-runs the classical rural one, resulting from the drog-sheep life-cycle.

Study of Resource Recovery and Epidemiology in an Anaerobic Digester

NASA Technical Reports Server (NTRS)

Li, K. Y.; Cao, Song; Hunt, M. D.; Fu, Xuping

1995-01-01

Three 4-liter packed bed anaerobic digesters were fabricated and operated at 35 degrees C, pH around 7, and hydraulic retention time (HRT) of 20, 10 and 5 days to study the resource recovery and epidemiology in a controlled ecological life support system (CELSS). A simulated wastewater, consisted of shower water, clothwash water, dishwasher water, handwash water, and urine flush water was used as the feeding solution. Under steady-state operation, chemical oxygen demand (COD), total organic carbon (TOC), pH, nitrogen, phosphorus, and potassium wer monitored in the digester input and output solutions. The volume and the CH4/CO2 ratios in the biogas produced from the anaerobic digesters were measured. The results indicate about 90 percent of TOC is converted while only 5-8 percent of N-P-K are consumed in the digester. A multi-drug resistant strain of Salmonella choleraesuis was used as the indicator bacterium in the epidemiology study. The levels of Salmonella choleraesuis in the influent and the effluent wer determined and decimal decay rate constants, k(d), were estimated. The k(d) values were greater at higher initial doses than lower doses for the same HR, and greater for batch digestion (7.89/d) than for continuous digestion (4.28, 3.82, and 3.82/d for 20, 10, and 5 d HRT, respectively).

Crack width monitoring of concrete structures based on smart film

NASA Astrophysics Data System (ADS)

Zhang, Benniu; Wang, Shuliang; Li, Xingxing; Zhang, Xu; Yang, Guang; Qiu, Minfeng

2014-04-01

Due to its direct link to structural security, crack width is thought to be one of the most important parameters reflecting damage conditions of concrete structures. However, the width problem is difficult to solve with the existing structural health monitoring methods. In this paper, crack width monitoring by means of adhering enameled copper wires with different ultimate strains on the surface of structures is proposed, based on smart film crack monitoring put forward by the present authors. The basic idea of the proposed method is related to a proportional relationship between the crack width and ultimate strain of the broken wire. Namely, when a certain width of crack passes through the wire, some low ultimate strain wires will be broken and higher ultimate strain wires may stay non-broken until the crack extends to a larger scale. Detection of the copper wire condition as broken or non-broken may indicate the width of the structural crack. Thereafter, a multi-layered stress transfer model and specimen experiment are performed to quantify the relationship. A practical smart film is then redesigned with this idea and applied to Chongqing Jiangjin Yangtze River Bridge.

MLVA for Salmonella enterica subsp. enterica Serovar Dublin: Development of a Method Suitable for Inter-Laboratory Surveillance and Application in the Context of a Raw Milk Cheese Outbreak in France in 2012

PubMed Central

Vignaud, Marie-Léone; Cherchame, Emeline; Marault, Muriel; Chaing, Emilie; Le Hello, Simon; Michel, Valerie; Jourdan-Da Silva, Nathalie; Lailler, Renaud; Brisabois, Anne; Cadel-Six, Sabrina

2017-01-01

Salmonella enterica subspecies enterica serovar Dublin (S. Dublin) figures among the most frequently isolated Salmonella strains in humans in France. This serovar may affect production and animal health mainly in cattle herds with corresponding high economic losses. Given that the current gold standard method, pulsed-field gel electrophoresis (PFGE), provides insufficient discrimination for epidemiological investigations, we propose a standard operating procedure in this study for multiple-locus variable number tandem repeat analysis (MLVA) of S. Dublin, suitable for inter-laboratory surveillance. An in silico analysis on the genome of S. Dublin strains CT_02021853 was performed to identify appropriate microsatellite regions. Of 21 VNTR loci screened, six were selected and 401 epidemiologically unrelated and related strains, isolated from humans, food and animals were analyzed to assess performance criteria such as typeability, discriminatory power and epidemiological concordance. The MLVA scheme developed was applied to an outbreak involving Saint-Nectaire cheese for which investigations were conducted in France in 2012, making it possible to discriminate between epidemiologically related strains and sporadic case strains, while PFGE assigned only a single profile. The six loci selected were sequenced on a large set of strains to determine the sequence of the repeated units and flanking regions, and their stability was evaluated in vivo through the analysis of the strains investigated from humans, food and the farm environment during the outbreak. The six VNTR selected were found to be stable and the discriminatory power of the MLVA method developed was calculated to be 0.954 compared with that for PFGE, which was only 0.625. Twenty-four reference strains were selected from the 401 examined strains in order to represent most of the allele diversity observed for each locus. This reference set can be used to harmonize MLVA results and allow data exchange between laboratories. This original MLVA protocol could be used easily and routinely for monitoring of serovar Dublin isolates and for conducting outbreak investigations. PMID:28289408

Antagonistic Pleiotropy and Fitness Trade-Offs Reveal Specialist and Generalist Traits in Strains of Canine Distemper Virus

PubMed Central

Nikolin, Veljko M.; Osterrieder, Klaus; von Messling, Veronika; Hofer, Heribert; Anderson, Danielle; Dubovi, Edward; Brunner, Edgar; East, Marion L.

2012-01-01

Theoretically, homogeneous environments favor the evolution of specialists whereas heterogeneous environments favor generalists. Canine distemper is a multi-host carnivore disease caused by canine distemper virus (CDV). The described cell receptor of CDV is SLAM (CD150). Attachment of CDV hemagglutinin protein (CDV-H) to this receptor facilitates fusion and virus entry in cooperation with the fusion protein (CDV-F). We investigated whether CDV strains co-evolved in the large, homogeneous domestic dog population exhibited specialist traits, and strains adapted to the heterogeneous environment of smaller populations of different carnivores exhibited generalist traits. Comparison of amino acid sequences of the SLAM binding region revealed higher similarity between sequences from Canidae species than to sequences from other carnivore families. Using an in vitro assay, we quantified syncytia formation mediated by CDV-H proteins from dog and non-dog CDV strains in cells expressing dog, lion or cat SLAM. CDV-H proteins from dog strains produced significantly higher values with cells expressing dog SLAM than with cells expressing lion or cat SLAM. CDV-H proteins from strains of non-dog species produced similar values in all three cell types, but lower values in cells expressing dog SLAM than the values obtained for CDV-H proteins from dog strains. By experimentally changing one amino acid (Y549H) in the CDV-H protein of one dog strain we decreased expression of specialist traits and increased expression of generalist traits, thereby confirming its functional importance. A virus titer assay demonstrated that dog strains produced higher titers in cells expressing dog SLAM than cells expressing SLAM of non-dog hosts, which suggested possible fitness benefits of specialization post-cell entry. We provide in vitro evidence for the expression of specialist and generalist traits by CDV strains, and fitness trade-offs across carnivore host environments caused by antagonistic pleiotropy. These findings extend knowledge on CDV molecular epidemiology of particular relevance to wild carnivores. PMID:23239996

[Antibiotic resistance of Campylobacter and its epidemiologic significance].

PubMed

Aleksandrova, N Z; Minaev, V I; Gorelov, A V

1990-03-01

Sensitivity of 179 strains of thermophilic Campylobacter to 21 chemotherapeutic drugs was studied. Activity of the antibacterial agents against the pathogens was estimated by the MICs. The MIC50 and MIC90 were also determined. All the Campylobacter strains were sensitive to gentamicin, chloramphenicol, neomycin, furazolidone and furagin and resistant to cefazolin, polymyxin E, rifampicin, vancomycin and bacitracin. Differences in the attitude of the Campylobacter isolates from various sources and patients of various age groups to the chemotherapeutic drugs were detected. Possible consideration of the results of comparison of R spectra of Campylobacter strains and the levels of their resistance to antimicrobial drugs as epidemiological markers is discussed.

Translational Epidemiology in Psychiatry

PubMed Central

Weissman, Myrna M.; Brown, Alan S.; Talati, Ardesheer

2012-01-01

Translational research generally refers to the application of knowledge generated by advances in basic sciences research translated into new approaches for diagnosis, prevention, and treatment of disease. This direction is called bench-to-bedside. Psychiatry has similarly emphasized the basic sciences as the starting point of translational research. This article introduces the term translational epidemiology for psychiatry research as a bidirectional concept in which the knowledge generated from the bedside or the population can also be translated to the benches of laboratory science. Epidemiologic studies are primarily observational but can generate representative samples, novel designs, and hypotheses that can be translated into more tractable experimental approaches in the clinical and basic sciences. This bedside-to-bench concept has not been explicated in psychiatry, although there are an increasing number of examples in the research literature. This article describes selected epidemiologic designs, providing examples and opportunities for translational research from community surveys and prospective, birth cohort, and family-based designs. Rapid developments in informatics, emphases on large sample collection for genetic and biomarker studies, and interest in personalized medicine—which requires information on relative and absolute risk factors—make this topic timely. The approach described has implications for providing fresh metaphors to communicate complex issues in interdisciplinary collaborations and for training in epidemiology and other sciences in psychiatry. PMID:21646577

[Epidemiology and etiology of bacillary dysentery in Xinjiang Uigur Autonomous Region, 2004-2014].

PubMed

Zhang, J; Mahemuti, Mahemuti; Xia, Y D; Mutalifu, Mutalifu; Muheyati, Muheyati; Li, F; Gu, B S; Li, X L

2016-11-10

Objective: To understand the epidemiological and etiological characteristics of bacillary dysentery in Xinjiang Uigur Autonomous Region (Xinjiang) during 2004-2014, and provide evidence for the prevention and control of bacillary dysentery. Methods: Descriptive epidemiological analysis was conducted by using the incidence data of bacillary dysentery in Xinjiang during 2004-2014 and the serotyping and the antibiotic susceptibility test of the pathogens isolated were performed. Results: A total of 123 238 cases of bacillary dysentery were reported in Xinjiang from 2004 to 2014. The average annual incidence of bacillary dysentery ranged from 25.91 per 100 000 to 76.04 per 100 000 and the average annual mortality ranged from 0.00 to 46.90 per 100 000. The incidence of bacillary dysentery was higher in eastern Xinjiang than other areas. The incidence peak was during July-September. The incidence of bacillary dysentery in males was higher than that in females. The incidence was highest in infants and young children under five years old. Most cases were children outside child care settings, farmers and students. Shigella flexneri was the predominant pathogen and F2a was the most frequently detected subtype. The isolated strains were highly resistant to streptomycin, penicillin, doxycycline and tetracycline. The resistant rates to penicillin, tetracycline, doxycycline and streptomycin increased with year. Up to 71.43% of the strains were resistant to more than five antibiotics. Conclusion: The incidence of bacillary dysentery was in decrease in Xinjiang from 2004 to 2014, but in some area, the incidence of bacterial dysentery was higher than national average level. It is necessary to strengthen the surveillance and conduct targeted prevention and control in areas and population at high risk and in season with high incidence. The serious drug resistance and multi drug resistance of the pathogens have posed challenge to the prevention and treatment of bacillary dysentery in Xinjiang.

Basic glossary on genetic epidemiology.

PubMed

Malats, N; Calafell, F

2003-07-01

This is the second of a series of three glossaries on genetic concepts used in epidemiological research that the journal is publishing with the objective of helping the reader "walk" around the journal.

Global epidemiology of capsular group W meningococcal disease (1970-2015): Multifocal emergence and persistence of hypervirulent sequence type (ST)-11 clonal complex.

PubMed

Mustapha, Mustapha M; Marsh, Jane W; Harrison, Lee H

2016-03-18

Following an outbreak in Mecca Saudi Arabia in 2000, meningococcal strains expressing capsular group W (W) emerged as a major cause of invasive meningococcal disease (IMD) worldwide. The Saudi Arabian outbreak strain (Hajj clone) belonging to the ST-11 clonal complex (cc11) is similar to W cc11 causing occasional sporadic disease before 2000. Since 2000, W cc11 has caused large meningococcal disease epidemics in the African meningitis belt and endemic disease in South America, Europe and China. Traditional molecular epidemiologic typing suggested that a majority of current W cc11 burden represented global spread of the Hajj clone. However, recent whole genome sequencing (WGS) analyses revealed significant genetic heterogeneity among global W cc11 strains. While continued spread of the Hajj clone occurs in the Middle East, the meningitis belt and South Africa have co-circulation of the Hajj clone and other unrelated W cc11 strains. Notably, South America, the UK, and France share a genetically distinct W cc11 strain. Other W lineages persist in low numbers in Europe, North America and the meningitis belt. In summary, WGS is helping to unravel the complex genomic epidemiology of group W meningococcal strains. Wider application of WGS and strengthening of global IMD surveillance is necessary to monitor the continued evolution of group W lineages. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular Epidemiology of Human Rhinoviruses and Enteroviruses Highlights Their Diversity in Sub-Saharan Africa

PubMed Central

L’Huillier, Arnaud G.; Kaiser, Laurent; Petty, Tom J.; Kilowoko, Mary; Kyungu, Esther; Hongoa, Philipina; Vieille, Gaël; Turin, Lara; Genton, Blaise; D’Acremont, Valérie; Tapparel, Caroline

2015-01-01

Human rhinoviruses (HRVs) and enteroviruses (HEVs) belong to the Enterovirus genus and are the most frequent cause of infection worldwide, but data on their molecular epidemiology in Africa are scarce. To understand HRV and HEV molecular epidemiology in this setting, we enrolled febrile pediatric patients participating in a large prospective cohort assessing the causes of fever in Tanzanian children. Naso/oropharyngeal swabs were systematically collected and tested by real-time RT-PCR for HRV and HEV. Viruses from positive samples were sequenced and phylogenetic analyses were then applied to highlight the HRV and HEV types as well as recombinant or divergent strains. Thirty-eight percent (378/1005) of the enrolled children harboured an HRV or HEV infection. Although some types were predominant, many distinct types were co-circulating, including a vaccinal poliovirus, HEV-A71 and HEV-D68. Three HRV-A recombinants were identified: HRV-A36/HRV-A67, HRV-A12/HRV-A67 and HRV-A96/HRV-A61. Four divergent HRV strains were also identified: one HRV-B strain and three HRV-C strains. This is the first prospective study focused on HRV and HEV molecular epidemiology in sub-Saharan Africa. This systematic and thorough large screening with careful clinical data management confirms the wide genomic diversity of these viruses, brings new insights about their evolution and provides data about associated symptoms. PMID:26670243

Molecular Epidemiology of Human Rhinoviruses and Enteroviruses Highlights Their Diversity in Sub-Saharan Africa.

PubMed

L'Huillier, Arnaud G; Kaiser, Laurent; Petty, Tom J; Kilowoko, Mary; Kyungu, Esther; Hongoa, Philipina; Vieille, Gaël; Turin, Lara; Genton, Blaise; D'Acremont, Valérie; Tapparel, Caroline

2015-12-08

Human rhinoviruses (HRVs) and enteroviruses (HEVs) belong to the Enterovirus genus and are the most frequent cause of infection worldwide, but data on their molecular epidemiology in Africa are scarce. To understand HRV and HEV molecular epidemiology in this setting, we enrolled febrile pediatric patients participating in a large prospective cohort assessing the causes of fever in Tanzanian children. Naso/oropharyngeal swabs were systematically collected and tested by real-time RT-PCR for HRV and HEV. Viruses from positive samples were sequenced and phylogenetic analyses were then applied to highlight the HRV and HEV types as well as recombinant or divergent strains. Thirty-eight percent (378/1005) of the enrolled children harboured an HRV or HEV infection. Although some types were predominant, many distinct types were co-circulating, including a vaccinal poliovirus, HEV-A71 and HEV-D68. Three HRV-A recombinants were identified: HRV-A36/HRV-A67, HRV-A12/HRV-A67 and HRV-A96/HRV-A61. Four divergent HRV strains were also identified: one HRV-B strain and three HRV-C strains. This is the first prospective study focused on HRV and HEV molecular epidemiology in sub-Saharan Africa. This systematic and thorough large screening with careful clinical data management confirms the wide genomic diversity of these viruses, brings new insights about their evolution and provides data about associated symptoms.

Comparison of epidemiological and antibiotic susceptibility pattern of metallo-Beta-lactamase-positive and metallo-Beta-lactamase-negative strains of pseudomonas aeruginosa.

PubMed

Ranjan, Shikha; Banashankari, Gs; Babu, Pr Sreenivasa

2014-07-01

The infections caused by metallo-beta-lactamases (MBLs) producing Pseudomonas aeruginosa are associated with higher rates of mortality, morbidity, and overall healthcare costs compared to non-MBL P. aeruginosa infections. To compare the epidemiologic factors and antibiograms of MBL-positive and MBL-negative P. aeruginosa isolates in a tertiary care hospital. In an observational study, from January 2011 to December 2012, all non-duplicate P. aeruginosa isolates were subjected to an antimicrobial sensitivity test against 10 antibiotics of five different classes. All P. aeruginosa strains showing resistance to at least one of the carbapenems were subjected to the MBL-E test. Epidemiological features and antibiograms of MBL-positive and MBL-negative strains were compared and statistically analyzed. Out of 350 isolates (total sample = 5330) of P. aeruginosa, MBL was detected in 58 isolates by the E-test, resulting in a prevalence of 16.57%. Resistance to most of the antibiotics was significantly higher in the MBL-positive strains with 100% resistance to ciprofloxacin, tobramycin, and meropenem, followed by imipenem (93.10%) and gentamicin (89.66%). The prevalence of multidrug-resistant and pandrug-resistant strains was significantly higher among the MBL group as compared to that in the non-MBL group ((55.17 vs. 7.88% (P < 0.0001) and 8.62 vs. 0.68% (P = 0.0006)), respectively. MBL-positive P. aeruginosa strains showed very high resistance to various antibiotics, as compared to the non-MBL strains. Increasing prevalence of MBL-producing isolates in hospital settings makes it important to perform routine detection of MBL-positive P. aeruginosa strains by in vitro testing before antibiotic use, for the purposes of infection prevention, and control, and for minimizing the adverse outcomes of infections with MBL-producing strains.

Diversity and Evolution of Mycobacterium tuberculosis: Moving to Whole-Genome-Based Approaches

PubMed Central

Niemann, Stefan; Supply, Philip

2014-01-01

Genotyping of clinical Mycobacterium tuberculosis complex (MTBC) strains has become a standard tool for epidemiological tracing and for the investigation of the local and global strain population structure. Of special importance is the analysis of the expansion of multidrug (MDR) and extensively drug-resistant (XDR) strains. Classical genotyping and, more recently, whole-genome sequencing have revealed that the strains of the MTBC are more diverse than previously anticipated. Globally, several phylogenetic lineages can be distinguished whose geographical distribution is markedly variable. Strains of particular (sub)lineages, such as Beijing, seem to be more virulent and associated with enhanced resistance levels and fitness, likely fueling their spread in certain world regions. The upcoming generalization of whole-genome sequencing approaches will expectedly provide more comprehensive insights into the molecular and epidemiological mechanisms involved and lead to better diagnostic and therapeutic tools. PMID:25190252

Identification and development of a promising novel mumps vaccine candidate strain.

PubMed

Liang, Yan; Ma, Shaohui; Liu, Longding; Zhao, Hongling; Wang, Lichun; Jiang, Li; Xie, Zhongping; Dong, Chenghong; Li, Qihan

2010-12-01

Mumps epidemics are usually caused by airborne transmission of mumps virus (MuV) and have high morbidity in non-immunized children. Epidemiological studies in many regions of China show that the genotype F viral strain is the most prevalent. However, the genotype A strain is currently used to prepare vaccines. Regional epidemiological MuV data suggest a significant application for the development of live attenuated mumps vaccines targeting specific genotypes. This article reports the isolation and culture of a genotype F MuV candidate strain that could be used to prepare a live attenuated mumps vaccine. This strain is shown to have good immunological efficacy and stability in neurovirulence evaluations. This work should facilitate the implementation of mumps vaccination in mainland China by targeting the most prevalent MuV genotype, genotype F. Copyright © 2010 Institut Pasteur. Published by Elsevier SAS. All rights reserved.

Nonlinear mechanics of a ring structure subjected to multi-pairs of evenly distributed equal radial forces

NASA Astrophysics Data System (ADS)

Chen, Q.; Sun, F.; Li, Z. Y.; Taxis, L.; Pugno, N.

2017-10-01

Combining the elastica theory, finite element (FE) analysis, and a geometrical topological experiment, we studied the mechanical behavior of a ring subjected to multi-pairs of evenly distributed equal radial forces by looking at its seven distinct states. The results showed that the theoretical predictions of the ring deformation and strain energy matched the FE results very well, and that the ring deformations were comparable to the topological experiment. Moreover, no matter whether the ring was compressed or tensioned by N-pairs of forces, the ring always tended to be regular polygons with 2 N sides as the force increased, and a proper compressive force deformed the ring into exquisite flower-like patterns. The present study solves a basic mechanical problem of a ring subjected to lateral forces, which can be useful for studying the relevant mechanical behavior of ring structures from the nano- to the macro-scale.

Outbreak of Vibrio cholerae serogroup O1, serotype Ogawa, biotype El Tor strain--La Huasteca Region, Mexico, 2013.

PubMed

Díaz-Quiñonez, Alberto; Hernández-Monroy, Irma; Montes-Colima, Norma; Moreno-Pérez, Asunción; Galicia-Nicolás, Adriana; Martínez-Rojano, Hugo; Carmona-Ramos, Concepción; Sánchez-Mendoza, Miroslava; Rodríguez-Martínez, José Cruz; Suárez-Idueta, Lorena; Jiménez-Corona, María Eugenia; Ruiz-Matus, Cuitláhuac; Kuri-Morales, Pablo

2014-06-27

On September 2 and 6, 2013, Mexico's National System of Epidemiological Surveillance identified two cases of cholera in Mexico City. Rectal swab cultures from both patients were confirmed as toxigenic Vibrio cholerae serogroup O1, serotype Ogawa, biotype El Tor. Pulsed-field gel electrophoresis and virulence gene amplification (ctxA, ctxB, zot, and ace) demonstrated that the strains were identical to one another but different from strains circulating in Mexico previously. The strains were indistinguishable from the strain that has caused outbreaks in Haiti, the Dominican Republic, and Cuba. The strain was susceptible to doxycycline, had intermediate susceptibility to ampicillin and chloramphenicol, was less than fully susceptible to ciprofloxacin, and was resistant to furazolidone and trimethoprim-sulfamethoxazole. An investigation failed to identify a common source of infection, additional cases, or any epidemiologic link between the cases. Both patients were treated with a single, 300-mg dose of doxycycline, and their symptoms resolved.

Basic Reproduction Number and Transmission Dynamics of Common Serogroups of Enterohemorrhagic Escherichia coli.

PubMed

Chen, Shi; Sanderson, Michael W; Lee, Chihoon; Cernicchiaro, Natalia; Renter, David G; Lanzas, Cristina

2016-09-15

Understanding the transmission dynamics of pathogens is essential to determine the epidemiology, ecology, and ways of controlling enterohemorrhagic Escherichia coli (EHEC) in animals and their environments. Our objective was to estimate the epidemiological fitness of common EHEC strains in cattle populations. For that purpose, we developed a Markov chain model to characterize the dynamics of 7 serogroups of enterohemorrhagic Escherichia coli (O26, O45, O103, O111, O121, O145, and O157) in cattle production environments based on a set of cross-sectional data on infection prevalence in 2 years in two U.S. states. The basic reproduction number (R0) was estimated using a Bayesian framework for each serogroup based on two criteria (using serogroup alone [the O-group data] and using O serogroup, Shiga toxin gene[s], and intimin [eae] gene together [the EHEC data]). In addition, correlations between external covariates (e.g., location, ambient temperature, dietary, and probiotic usage) and prevalence/R0 were quantified. R0 estimates varied substantially among different EHEC serogroups, with EHEC O157 having an R0 of >1 (∼1.5) and all six other EHEC serogroups having an R0 of less than 1. Using the O-group data substantially increased R0 estimates for the O26, O45, and O103 serogroups (R0 > 1) but not for the others. Different covariates had distinct influences on different serogroups: the coefficients for each covariate were different among serogroups. Our modeling and analysis of this system can be readily expanded to other pathogen systems in order to estimate the pathogen and external factors that influence spread of infectious agents. In this paper we describe a Bayesian modeling framework to estimate basic reproduction numbers of multiple serotypes of Shiga toxin-producing Escherichia coli according to a cross-sectional study. We then coupled a compartmental model to reconstruct the infection dynamics of these serotypes and quantify their risk in the population. We incorporated different sensitivity levels of detecting different serotypes and evaluated their potential influence on the estimation of basic reproduction numbers. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Basic Reproduction Number and Transmission Dynamics of Common Serogroups of Enterohemorrhagic Escherichia coli

PubMed Central

Sanderson, Michael W.; Lee, Chihoon; Cernicchiaro, Natalia; Renter, David G.; Lanzas, Cristina

2016-01-01

ABSTRACT Understanding the transmission dynamics of pathogens is essential to determine the epidemiology, ecology, and ways of controlling enterohemorrhagic Escherichia coli (EHEC) in animals and their environments. Our objective was to estimate the epidemiological fitness of common EHEC strains in cattle populations. For that purpose, we developed a Markov chain model to characterize the dynamics of 7 serogroups of enterohemorrhagic Escherichia coli (O26, O45, O103, O111, O121, O145, and O157) in cattle production environments based on a set of cross-sectional data on infection prevalence in 2 years in two U.S. states. The basic reproduction number (R0) was estimated using a Bayesian framework for each serogroup based on two criteria (using serogroup alone [the O-group data] and using O serogroup, Shiga toxin gene[s], and intimin [eae] gene together [the EHEC data]). In addition, correlations between external covariates (e.g., location, ambient temperature, dietary, and probiotic usage) and prevalence/R0 were quantified. R0 estimates varied substantially among different EHEC serogroups, with EHEC O157 having an R0 of >1 (∼1.5) and all six other EHEC serogroups having an R0 of less than 1. Using the O-group data substantially increased R0 estimates for the O26, O45, and O103 serogroups (R0 > 1) but not for the others. Different covariates had distinct influences on different serogroups: the coefficients for each covariate were different among serogroups. Our modeling and analysis of this system can be readily expanded to other pathogen systems in order to estimate the pathogen and external factors that influence spread of infectious agents. IMPORTANCE In this paper we describe a Bayesian modeling framework to estimate basic reproduction numbers of multiple serotypes of Shiga toxin-producing Escherichia coli according to a cross-sectional study. We then coupled a compartmental model to reconstruct the infection dynamics of these serotypes and quantify their risk in the population. We incorporated different sensitivity levels of detecting different serotypes and evaluated their potential influence on the estimation of basic reproduction numbers. PMID:27401976

[Flesh-eating bacteria infection of an immunocompromised patient].

PubMed

Slavei, K; Hauser, B; Pénzes, I; Ondrejka, P; Faller, J

2001-10-01

After years of steadily declining morbidity and mortality due to group A streptococcal infections, a resurgence of severe, invasive disease has been ongoing since 1980, leading to the recognition of streptococcal shock syndrome (STSS), necrotizing fasciitis, the most severe form of invasive infection. The patients suffer from rapid local deep soft tissue destruction, severe septic shock and multi organ failure. The increased incidence of these infections has been accompanied by remarkable vigor in virulence and severity of the disease. The reason for this impressive change in the epidemiology and clinical manifestation of group A streptococcal infections remains unknown. The possible etiological factor is changing in virulence factor or the lack of protective immunity of the population (immunocompromise) against the invasive strains. We describe a severe necrotizing fasciitis of a 41-year-old previously immunocompromised woman. The patient developed severe septic shock, multi organ failure and perineal and lower abdominal skin, fat and fascia necrosis due to mixed GAS (aerob, anaerob) infection of the perineum and the Bartholini glands. After an aggressive surgical debridement, antibiotic and supportive therapy the generalised and local infection was treated.

The changing role and legitimate boundaries of epidemiology: community-based prevention programmes.

PubMed

Tuomilehto, J; Puska, P

1987-01-01

Epidemiology is the basic science of public health. It combines medical and social sciences, both of which are developing with new inventions. Therefore, the role of epidemiology and its boundaries are also changing over time. An important role of epidemiology is to develop and implement community-based control programmes for major diseases in the community. Such programmes are essential for large scale public health policy. It is necessary that epidemiological research can as freely as possible test new methods of disease prevention and health promotion. The first community-based control programme for cardiovascular diseases, the North Karelia Project is reviewed against this background. At present, it is still possible to define the boundaries of epidemiology geographically and culturally, but in the future, however, it will become more difficult. There is no doubt that epidemiology will remain as the basic science of public health but the scope of public health problems are growing much wider. These include the prevention of the final epidemic--the destruction of our planet by nuclear bombs. In the control of the existing epidemics and in the prevention of new ones the boundaries of epidemiology cannot stay rigid but they must be changing as new facts about the emerging public health problems are identified.

Strain Interactions as a Mechanism for Dominant Strain Alternation and Incidence Oscillation in Infectious Diseases: Seasonal Influenza as a Case Study

PubMed Central

Zhang, Xu-Sheng

2015-01-01

Background Many human infectious diseases are caused by pathogens that have multiple strains and show oscillation in infection incidence and alternation of dominant strains which together are referred to as epidemic cycling. Understanding the underlying mechanisms of epidemic cycling is essential for forecasting outbreaks of epidemics and therefore important for public health planning. Current theoretical effort is mainly focused on the factors that are extrinsic to the pathogens themselves (“extrinsic factors”) such as environmental variation and seasonal change in human behaviours and susceptibility. Nevertheless, co-circulation of different strains of a pathogen was usually observed and thus strains interact with one another within concurrent infection and during sequential infection. The existence of these intrinsic factors is common and may be involved in the generation of epidemic cycling of multi-strain pathogens. Methods and Findings To explore the mechanisms that are intrinsic to the pathogens themselves (“intrinsic factors”) for epidemic cycling, we consider a multi-strain SIRS model including cross-immunity and infectivity enhancement and use seasonal influenza as an example to parameterize the model. The Kullback-Leibler information distance was calculated to measure the match between the model outputs and the typical features of seasonal flu (an outbreak duration of 11 weeks and an annual attack rate of 15%). Results show that interactions among strains can generate seasonal influenza with these characteristic features, provided that: the infectivity of a single strain within concurrent infection is enhanced 2−7 times that within a single infection; cross-immunity as a result of past infection is 0.5–0.8 and lasts 2–9 years; while other parameters are within their widely accepted ranges (such as a 2–3 day infectious period and the basic reproductive number of 1.8–3.0). Moreover, the observed alternation of the dominant strain among epidemics emerges naturally from the best fit model. Alternative modelling that also includes seasonal forcing in transmissibility shows that both external mechanisms (i.e. seasonal forcing) and the intrinsic mechanisms (i.e., strain interactions) are equally able to generate the observed time-series in seasonal flu. Conclusions The intrinsic mechanism of strain interactions alone can generate the observed patterns of seasonal flu epidemics, but according to Kullback-Leibler information distance the importance of extrinsic mechanisms cannot be excluded. The intrinsic mechanism illustrated here to explain seasonal flu may also apply to other infectious diseases caused by polymorphic pathogens. PMID:26562668

Epidemiology of Modern Battlefield Colorectal Trauma: A Review of 977 Coalition Casualties

DTIC Science & Technology

2012-01-01

records, the ongoing Joint Surgical Transcolonic Injury or Ostomy Multi-theater Assessment project quantifies epidemiologic trends in colon injury...Transcolonic Injury or Ostomy Multi-theater Assessment (J-STOMA) project is an ongoing initiative to examine outcomes from OIF/OEF specific to co... ostomy reversal; (4) quality of life in injured US Service members who require fecal diversion (temporary or permanent); and (5) incidence and outcomes

[Mexican phenotype and genotype Vibrio cholerae 01].

PubMed

Giono, S; Gutiérrez Cogno, L; Rodríguez Angeles, G; del Rio Zolezzi, A; Valdespino González, J L; Sepúlveda Amor, J

1995-01-01

This paper presents the phenotypical and genotypical characterization of 26922 Vibrio cholerae 01 strains isolated in Mexico from 1991 to 1993. All strains isolated were El Tor biovar. Strains were sensitive to antibiotics excluding furazolidone, streptomycin and sulfisoxasole to which we found resistance in 97% and we are using this characteristic as epidemiological markers. We detected a marked change in frequency of Inaba serotype from 1991, when it was dominant, with 99.5%, until 1992 when Ogawa serotype turned to be dominant with 95% of isolates. All Vibrio cholerae 01 strains, except one Ogawa strain, were to igenic, and V. choleraeno 01 were not toxigenic by ELISA, PCR and cell culture tests. Dominant ribotype was 5, but we found some strains with 6a pattern and two with ribotype 12. We are searching for ribotype 2 among hemolytic strains in order to learn if there is any relation to Gulf Coast strains prevalent in the USA, but until now we have not found any V. cholerae ribotype 2 in our isolates. Even if rapid tests are recommended for immediate diagnosis of cholera, it is necessary to continue bacterial isolation in order to have strains for phenotyping and genotyping studies that may support epidemiological analysis.

[Epidemiology of food insecurity in Mexico].

PubMed

Mundo-Rosas, Verónica; Shamah-Levy, Teresa; Rivera-Dommarco, Juan A

2013-01-01

To estimate the proportion of Mexican households in food insecurity (FI) and their distribution in relation to nutrition and socioeconomic conditions. We evaluated information from 40 809 households. FI was measured using a harmonized version for Mexico of the Latin American and Caribbean food Security Scale. Households were classified according to the level of food insecurity as follows: Food security, mild, moderate and severe FI. We describe the distribution of FI according to some household socioeconomic variables. Nationally, 28.2% of households had moderate or severe FI. Rural, indigenous ethnicity and household deprivation were risk factors moderate to severe FI (35.4, 42.2 and 45.9%, respectively). Severe FI was also associated with lower children height and weight. Multi-sectorial actions are needed to address the basic needs of households with moderate and severe FI.

From the Macro to the Micro: Gel Mapping to Differentiate between Sporozoites of Two Immunologically Distinct Strains of Eimeria maxima (Strains M6 and Guelph)

PubMed Central

Liu, Hongbin; Al Nasr, Ibrahim; Liu, Xianyong; Suo, Xun; Barta, John

2015-01-01

Two immunologically distinct strains of E. maxima were examined in this study: the M6 strain and the Guelph strain. The differential expression between the sporozoites of the two strains of E. maxima was determined by image analysis of 100 μg of protein from each strain separated by standard one- and conventional two-dimensional polyacrylamide gel electrophoresis. In addition to differences in both molecular weight and the electrophoretic mobility, differences in the intensity of polypeptide bands for example, GS 136.4 and M6 169 were explored. Pooled gels were prepared from each strain. A representative 2D-PAGE gel spanning a non-linear pH range of 3–10 of E. maxima strain M6 consisted of approximately 694 polypeptide spots with about 67 (9.6%) of the polypeptide spots being unique relative to the other strain. E. maxima strain GS had about 696 discernable polypeptide spots with 69 spots (9.9%) that differed from those of the M6 strain. In-depth characterization of the variable polypeptide spots; unique polypeptide spots (absence or presence) and shared polypeptide spots with modifications may lead to novel vaccine target in the form of multi-component, multi-stage, multi-immunovariant strains, multi-species subunit vaccine, and diagnostic probe for E. maxima. PMID:26641262

From the Macro to the Micro: Gel Mapping to Differentiate between Sporozoites of Two Immunologically Distinct Strains of Eimeria maxima (Strains M6 and Guelph).

PubMed

El-Ashram, Saeed; Yin, Qing; Liu, Hongbin; Al Nasr, Ibrahim; Liu, Xianyong; Suo, Xun; Barta, John

2015-01-01

Two immunologically distinct strains of E. maxima were examined in this study: the M6 strain and the Guelph strain. The differential expression between the sporozoites of the two strains of E. maxima was determined by image analysis of 100 μg of protein from each strain separated by standard one- and conventional two-dimensional polyacrylamide gel electrophoresis. In addition to differences in both molecular weight and the electrophoretic mobility, differences in the intensity of polypeptide bands for example, GS 136.4 and M6 169 were explored. Pooled gels were prepared from each strain. A representative 2D-PAGE gel spanning a non-linear pH range of 3-10 of E. maxima strain M6 consisted of approximately 694 polypeptide spots with about 67 (9.6%) of the polypeptide spots being unique relative to the other strain. E. maxima strain GS had about 696 discernable polypeptide spots with 69 spots (9.9%) that differed from those of the M6 strain. In-depth characterization of the variable polypeptide spots; unique polypeptide spots (absence or presence) and shared polypeptide spots with modifications may lead to novel vaccine target in the form of multi-component, multi-stage, multi-immunovariant strains, multi-species subunit vaccine, and diagnostic probe for E. maxima.

Molecular epidemiology of tuberculosis: achievements and challenges to current knowledge.

PubMed Central

Murray, Megan; Nardell, Edward

2002-01-01

Over the past 10 years, molecular methods have become available with which to strain-type Mycobacterium tuberculosis. They have allowed researchers to study certain important but previously unresolved issues in the epidemiology of tuberculosis (TB). For example, some unsuspected microepidemics have been revealed and it has been shown that the relative contribution of recently acquired disease to the TB burden in many settings is far greater than had been thought. These findings have led to the strengthening of TB control. Other research has demonstrated the existence and described the frequency of exogenous reinfection in areas of high incidence. Much recent work has focused on the phenotypic variation among strains and has evaluated the relative transmissibility, virulence, and immunogenicity of different lineages of the organism. We summarize the recent achievements in TB epidemiology associated with the introduction of DNA fingerprinting techniques, and consider the implications of this technology for the design and analysis of epidemiological studies. PMID:12132006

Establishment of a national database to link epidemiological and molecular data from norovirus outbreaks in Ireland.

PubMed

Kelly, S; Foley, B; Dunford, L; Coughlan, S; Tuite, G; Duffy, M; Mitchell, S; Smyth, B; O'Neill, H; McKeown, P; Hall, W; Lynch, M

2008-11-01

A prospective study of norovirus outbreaks in Ireland was carried out over a 1-year period from 1 October 2004 to 30 September 2005. Epidemiological and molecular data on norovirus outbreaks in the Republic of Ireland (ROI) and Northern Ireland (NI) were collected and combined in real time in a common database. Most reported outbreaks occurred in hospitals and residential institutions and person-to-person spread was the predominant mode of transmission. The predominant circulating norovirus strain was the GII.4-2004 strain with a small number of outbreaks due to GII.2. This study represents the first time that enhanced epidemiological and virological data on norovirus outbreaks in Ireland have been described. The link established between the epidemiological and virological institutions during the course of this study has been continued and the data is being used as a source of data for the Foodborne Viruses in Europe Network (DIVINE-NET).

Legionnaires' disease from a cooling tower in a community outbreak in Lidköping, Sweden- epidemiological, environmental and microbiological investigation supported by meteorological modelling.

PubMed

Ulleryd, Peter; Hugosson, Anna; Allestam, Görel; Bernander, Sverker; Claesson, Berndt E B; Eilertz, Ingrid; Hagaeus, Anne-Christine; Hjorth, Martin; Johansson, Agneta; de Jong, Birgitta; Lindqvist, Anna; Nolskog, Peter; Svensson, Nils

2012-11-21

An outbreak of Legionnaires' Disease took place in the Swedish town Lidköping on Lake Vänern in August 2004 and the number of pneumonia cases at the local hospital increased markedly. As soon as the first patients were diagnosed, health care providers were informed and an outbreak investigation was launched. Classical epidemiological investigation, diagnostic tests, environmental analyses, epidemiological typing and meteorological methods. Thirty-two cases were found. The median age was 62 years (range 36 - 88) and 22 (69%) were males. No common indoor exposure was found. Legionella pneumophila serogroup 1 was found at two industries, each with two cooling towers. In one cooling tower exceptionally high concentrations, 1.2 × 109 cfu/L, were found. Smaller amounts were also found in the other tower of the first industry and in one tower of the second plant. Sero- and genotyping of isolated L. pneumophila serogroup 1 from three patients and epidemiologically suspected environmental strains supported the cooling tower with the high concentration as the source. In all, two L. pneumophila strains were isolated from three culture confirmed cases and both these strains were detected in the cooling tower, but one strain in another cooling tower as well. Meteorological modelling demonstrated probable spread from the most suspected cooling tower towards the town centre and the precise location of four cases that were stray visitors to Lidköping. Classical epidemiological, environmental and microbiological investigation of an LD outbreak can be supported by meteorological modelling methods.The broad competence and cooperation capabilities in the investigation team from different authorities were of paramount importance in stopping this outbreak.

Legionnaires’ disease from a cooling tower in a community outbreak in Lidköping, Sweden- epidemiological, environmental and microbiological investigation supported by meteorological modelling

PubMed Central

2012-01-01

Background An outbreak of Legionnaires’ Disease took place in the Swedish town Lidköping on Lake Vänern in August 2004 and the number of pneumonia cases at the local hospital increased markedly. As soon as the first patients were diagnosed, health care providers were informed and an outbreak investigation was launched. Methods Classical epidemiological investigation, diagnostic tests, environmental analyses, epidemiological typing and meteorological methods. Results Thirty-two cases were found. The median age was 62 years (range 36 – 88) and 22 (69%) were males. No common indoor exposure was found. Legionella pneumophila serogroup 1 was found at two industries, each with two cooling towers. In one cooling tower exceptionally high concentrations, 1.2 × 109 cfu/L, were found. Smaller amounts were also found in the other tower of the first industry and in one tower of the second plant. Sero- and genotyping of isolated L. pneumophila serogroup 1 from three patients and epidemiologically suspected environmental strains supported the cooling tower with the high concentration as the source. In all, two L. pneumophila strains were isolated from three culture confirmed cases and both these strains were detected in the cooling tower, but one strain in another cooling tower as well. Meteorological modelling demonstrated probable spread from the most suspected cooling tower towards the town centre and the precise location of four cases that were stray visitors to Lidköping. Conclusions Classical epidemiological, environmental and microbiological investigation of an LD outbreak can be supported by meteorological modelling methods. The broad competence and cooperation capabilities in the investigation team from different authorities were of paramount importance in stopping this outbreak. PMID:23171054

Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent

PubMed Central

Martínez-Pérez, Orlando; Dolz, Roser; Valle, Rosa; Perera, Carmen L.; Bertran, Kateri; Frías, Maria T.; Ganges, Llilianne; Díaz de Arce, Heidy; Majó, Natàlia; Núñez, José I.; Pérez, Lester J.

2015-01-01

Background Infectious bursal disease (IBD) is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV) strains worldwide. Methodology/Principal Findings Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population. Conclusions/Significance This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain information about both genome segments of IBDV for molecular epidemiology studies. PMID:25946336

Epidemiology and molecular characterization of methicillin-resistant Staphylococcus aureus nasal carriage isolates from bovines

PubMed Central

2014-01-01

Background Staphylococcus aureus is a common bacterium usually found on skin and mucous membranes of warm blooded animals. Resistance in S. aureus has been increasingly reported though depending on the clonal lineage. Indeed, while hospital acquired (HA)-methicillin resistant S. aureus (MRSA) are typically multi-resistant, community associated (CA)-MRSA are by large more susceptible to many antibiotics. Although S. aureus isolated from animals are often susceptible to most antibiotics, multi-resistant livestock associated (LA)-MRSA have been recovered from bovine mastitis. In this study, we investigated the prevalence and types of MRSA present in the nose of healthy bovines of different age groups and rearing practices. Since no validated methods for MRSA isolation from nasal swabs were available, we compared two isolation methods. Molecular characterization was performed by means of spa-typing, MLST, SCCmec typing and microarray analysis for the detection of antimicrobial resistance and virulence genes. Results MRSA between herd prevalence in bovines was estimated at 19.8%. There was a marked difference between rearing practices with 9.9%, 10.2% and 46.1% of the dairy, beef and veal calve farms respectively being MRSA positive. No significant difference was observed between both isolation methods tested. Most isolates were ST398 spa type t011 or closely related spa types. Few ST239 spa type t037 and t388 and ST8 spa type t121 were also found. SCCmec types carried by these strains were mainly type IV(2B), IV(2B&5) and type V. Type III and non-typeable SCCmec were recovered to a lesser extent. All isolates were multi-resistant to at least two antimicrobials in addition to the expected cefoxitin and penicillin resistance, with an average of resistance to 9.5 different antimicrobials. Isolates selected for microarray analysis carried a broad range of antimicrobial resistance and virulence genes. Conclusion MRSA were mainly present in veal farms, compared to the lower prevalence in dairy or beef farms. Multi-resistance in these strains was high. Though mainly CC398 spa t011 was found, the genetic diversity was higher than what was found for pigs in Belgium. CC8 strains, a typically human lineage but also recently found also in association with bovines, has been retrieved here also. PMID:25011427

Population analysis of clinical and environmental Vibrio parahaemolyticus isolated from eastern provinces in China by removing the recombinant SNPs in the MLST loci.

PubMed

Lu, Xin; Zhou, Haijian; Du, Xiaoli; Liu, Sha; Xu, Jialiang; Cui, Zhigang; Pang, Bo; Kan, Biao

2016-11-01

Vibrio parahaemolyticus is a common seafood-borne pathogenic bacterium which causes gastroenteritis in humans. Continuous surveillance on the molecular characters of the clinical and environmental V. parahaemolyticus strains needs to be conducted for the epidemiological and genetic purposes. To generate a picture of the population distribution of V. parahaemolyticus in eastern China isolated from clinical cases of gastroenteritis and environmental samples, we investigated the genetic and evolutionary relationships of the strains using the commonly used multi-locus sequence typing (MLST, in which seven house-keeping genes are used in the protocol). A highly genetic diversity within the V. parahaemolyticus population was observed but ST3 was still dominant in the clinical strains, and 103 new sequence types (ST) were found in the clinical strains by searching in the global V. parahaemolyticus MLST database. With these genetically diverse strains, we estimated the recombination rates of the loci in MLST analysis. The locus recA was found to be subject to exceptionally high rate of recombination, and the recombinant single nucleotide polymorphisms (SNPs) were also identified within the seven loci. The phylogenetic tree of the strains was re-constructed using the maximum likelihood method by removing the recombination SNPs of the seven loci, and the minimum spanning tree was re-constructed with the six loci without recA. Some changes were observed in comparison with the previously used methods, suggesting that the homologous recombination has roles in shaping the clonal structure of V. parahaemolyticus. We propose the recombination-free SNPs strategy in the clonality analysis of V. parahaemolyticus, especially when using the maximum likelihood method. Copyright © 2016. Published by Elsevier B.V.

The dynamics of pulmonary tuberculosis in Colima, Mexico (1999-2002).

PubMed

Chowell, Gerardo; Diaz-Dueñas, Porfirio; Chowell, Diego

2005-01-01

Tuberculosis is a public health problem in Mexico. From 1999 to 2002, we assessed retrospectively the epidemiological, clinical, and treatment characteristics of pulmonary tuberculosis in the hospitals of the Mexican Institute of Public Health in the state of Colima (Mexico). We included 184 cases diagnosed with pulmonary tuberculosis. A database containing demographic, epidemiological, and clinical information was constructed and analyzed. We estimate a median patient delay of 83 d and a mean treatment delay of 2.3 d. Of 14 cases suspected for multiresistance and microbiologically assayed, 5 were found to carry a multi-drug-resistant strain. We also found a significant association between a short patient delay and the presence of hemoptysis (p = 0.002) or dyspnea (p<0.001). 86 patients (46.8%) were sputum smear microscopy negative at the end of treatment and 40 (21.7%) completed treatment giving an overall success rate of 68.5%, which compares unfavorably with the World Health Organization target success rate of 85%. Five (2.7%) patients failed treatment, 10 (5.4%) died, 39 (21.2%) interrupted treatment, and 4 (2.2%) transferred to another reporting unit. A 2002 strategic change in drug distribution seemed to prove successful.

Hamstring Muscle Injuries, a Rehabilitation Protocol Purpose.

PubMed

Valle, Xavier; L Tol, Johannes; Hamilton, Bruce; Rodas, Gil; Malliaras, Peter; Malliaropoulos, Nikos; Rizo, Vicenc; Moreno, Marcel; Jardi, Jaume

2015-12-01

Hamstring acute muscle injuries are prevalent in several sports including AFL football (Australian Football League), sprinting and soccer, and are often associated with prolonged time away from sport. In response to this, research into prevention and management of hamstring injury has increased, but epidemiological data shows no decline in injury and re-injury rates, suggesting that rehabilitation programs and return to play (RTP) criteria have to be improved. There continues to be a lack of consensus regarding how to assess performance, recovery and readiness to RTP, following hamstring strain injury. The aim of this paper was to propose rehabilitation protocol for hamstring muscle injuries based on current basic science and research knowledge regarding injury demographics and management options. Criteria-based (subjective and objective) progression through the rehabilitation program will be outlined along with exercises for each phase, from initial injury to RTP.

Geometric design and mechanical behavior of a deployable cylinder with Miura origami

NASA Astrophysics Data System (ADS)

Cai, Jianguo; Deng, Xiaowei; Feng, Jian; Zhou, Ya

2015-12-01

The folding and deployment of a cylinder with Miura origami patterns are studied in this paper. First, the geometric formulation of the design problem is discussed. Then the loading case of the axial strains and corresponding external nodal loads applied on the vertices of the top polygon during the motion is investigated analytically. The influence of the angle between the diagonal and horizontal fold lines α and β and the number of Miura origami elements n on the dynamic behavior of the basic segment is also discussed. Then the dynamic behavior is analyzed using numerical simulations. Finally, the deployment process of a cylinder with multi-stories is discussed. The numerical results agree well with the analytical predictions. The results show that the range of motion, i.e. the maximal displacement of top nodes, will also increase with the increase of angles α and β. This cylinder, with a smaller n, may have a bistable behavior. When n is larger, the influence of n on the axial strains and external nodal loads is slight. The numerical results agree well with the analytical predictions. Moreover, the deployment of the cylinder with multi-stories is non-uniform, which deploys from the upper story to the lower story.

Random Amplified Polymorphic DNA PCR in the Teaching of Molecular Epidemiology

ERIC Educational Resources Information Center

Reinoso, Elina B.; Bettera, Susana G.

2016-01-01

In this article, we describe a basic practical laboratory designed for fifth-year undergraduate students of Microbiology as part of the Epidemiology course. This practice provides the students with the tools for molecular epidemiological analysis of pathogenic microorganisms using a rapid and simple PCR technique. The aim of this work was to assay…

Development and evaluation of a multi-locus sequence typing scheme for Mycoplasma synoviae.

PubMed

Dijkman, R; Feberwee, A; Landman, W J M

2016-08-01

Reproducible molecular Mycoplasma synoviae typing techniques with sufficient discriminatory power may help to expand knowledge on its epidemiology and contribute to the improvement of control and eradication programmes of this mycoplasma species. The present study describes the development and validation of a novel multi-locus sequence typing (MLST) scheme for M. synoviae. Thirteen M. synoviae isolates originating from different poultry categories, farms and lesions, were subjected to whole genome sequencing. Their sequences were compared to that of M. synoviae reference strain MS53. A high number of single nucleotide polymorphisms (SNPs) indicating considerable genetic diversity were identified. SNPs were present in over 40 putative target genes for MLST of which five target genes were selected (nanA, uvrA, lepA, ruvB and ugpA) for the MLST scheme. This scheme was evaluated analysing 209 M. synoviae samples from different countries, categories of poultry, farms and lesions. Eleven clonal clusters and 76 different sequence types (STs) were obtained. Clustering occurred following geographical origin, supporting the hypothesis of regional population evolution. M. synoviae samples obtained from epidemiologically linked outbreaks often harboured the same ST. In contrast, multiple M. synoviae lineages were found in samples originating from swollen joints or oviducts from hens that produce eggs with eggshell apex abnormalities indicating that further research is needed to identify the genetic factors of M. synoviae that may explain its variations in tissue tropism and disease inducing potential. Furthermore, MLST proved to have a higher discriminatory power compared to variable lipoprotein and haemagglutinin A typing, which generated 50 different genotypes on the same database.

Direct Detection and Differentiation of Pathogenic Leptospira Species Using a Multi-Gene Targeted Real Time PCR Approach

PubMed Central

Ferreira, Ana Sofia; Costa, Pedro; Rocha, Teresa; Amaro, Ana; Vieira, Maria Luísa; Ahmed, Ahmed; Thompson, Gertrude; Hartskeerl, Rudy A.; Inácio, João

2014-01-01

Leptospirosis is a growing public and veterinary health concern caused by pathogenic species of Leptospira. Rapid and reliable laboratory tests for the direct detection of leptospiral infections in animals are in high demand not only to improve diagnosis but also for understanding the epidemiology of the disease. In this work we describe a novel and simple TaqMan-based multi-gene targeted real-time PCR approach able to detect and differentiate Leptospira interrogans, L. kirschneri, L. borgpeteresenii and L. noguchii, which constitute the veterinary most relevant pathogenic species of Leptospira. The method uses sets of species-specific probes, and respective flanking primers, designed from ompL1 and secY gene sequences. To monitor the presence of inhibitors, a duplex amplification assay targeting both the mammal β-actin and the leptospiral lipL32 genes was implemented. The analytical sensitivity of all primer and probe sets was estimated to be <10 genome equivalents (GE) in the reaction mixture. Application of the amplification reactions on genomic DNA from a variety of pathogenic and non-pathogenic Leptospira strains and other non-related bacteria revealed a 100% analytical specificity. Additionally, pathogenic leptospires were successfully detected in five out of 29 tissue samples from animals (Mus spp., Rattus spp., Dolichotis patagonum and Sus domesticus). Two samples were infected with L. borgpetersenii, two with L. interrogans and one with L. kirschneri. The possibility to detect and identify these pathogenic agents to the species level in domestic and wildlife animals reinforces the diagnostic information and will enhance our understanding of the epidemiology of leptopirosis. PMID:25398140

Recent transmission of Mycobacterium tuberculosis in China: the implication of molecular epidemiology for tuberculosis control.

PubMed

Yang, Chongguang; Gao, Qian

2018-02-01

Tuberculosis (TB) has remained an ongoing concern in China. The national scale-up of the Directly Observed Treatment, Short Course (DOTS) program has accelerated the fight against TB in China. Nevertheless, many challenges still remain, including the spread of drug-resistant strains, high disease burden in rural areas, and enormous rural-to-urban migrations. Whether incident active TB represents recent transmission or endogenous reactivation has helped to prioritize the strategies for TB control. Evidence from molecular epidemiology studies has delineated the recent transmission of Mycobacterium tuberculosis (M. tuberculosis) strains in many settings. However, the transmission patterns of TB in most areas of China are still not clear. Studies carried out to date could not capture the real burden of recent transmission of the disease in China because of the retrospective study design, incomplete sampling, and use of low-resolution genotyping methods. We reviewed the implementations of molecular epidemiology of TB in China, the estimated disease burden due to recent transmission of M. tuberculosis strains, the primary transmission of drug-resistant TB, and the evaluation of a feasible genotyping method of M. tuberculosis strains in circulation.

Tick-Borne Transmission of Two Genetically Distinct Anaplasma marginale Strains following Superinfection of the Mammalian Reservoir Host

USDA-ARS?s Scientific Manuscript database

Strain superinfection affects the dynamics of epidemiological spread of pathogens through a host population. Superinfection has recently been shown to occur for genetically distinct strains of the tick-borne pathogen Anaplasma marginale that encode distinctly different surface protein variants. Supe...

Phage typing or CRISPR typing for epidemiological surveillance of Salmonella Typhimurium?

PubMed

Mohammed, Manal

2017-11-07

Salmonella Typhimurium is the most dominant Salmonella serovar around the world. It is associated with foodborne gastroenteritis outbreaks but has recently been associated with invasive illness and deaths. Characterization of S. Typhimurium is therefore very crucial for epidemiological surveillance. Phage typing has been used for decades for subtyping of S. Typhimurium to determine the epidemiological relation among isolates. Recent studies however have suggested that high throughput clustered regular interspaced short palindromic repeats (CRISPR) typing has the potential to replace phage typing. This study aimed to determine the efficacy of high-throughput CRISPR typing over conventional phage typing in epidemiological surveillance and outbreak investigation of S. Typhimurium. In silico analysis of whole genome sequences (WGS) of well-documented phage types of S. Typhimurium reveals the presence of different CRISPR type among strains belong to the same phage type. Furthermore, different phage types of S. Typhimurium share identical CRISPR type. Interestingly, identical spacers were detected among outbreak and non-outbreak associated DT8 strains of S. Typhimurium. Therefore, CRISPR typing is not useful for the epidemiological surveillance and outbreak investigation of S. Typhimurium and phage typing, until it is replaced by WGS, is still the gold standard method for epidemiological surveillance of S. Typhimurium.

Molecular epidemiology of hydropericardium syndrome outbreak-associated serotype 4 fowl adenovirus isolates in central China.

PubMed

Zhang, Teng; Jin, Qianyue; Ding, Peiyang; Wang, Yinbiao; Chai, Yongxiao; Li, Yafei; Liu, Xiao; Luo, Jun; Zhang, Gaiping

2016-11-18

In several parts of China, there have been a large number of hydropericardium syndrome (HPS) outbreaks caused by serotype 4 fowl adenovirus (FAdV-4) in broiler chickens since 2015. These outbreak-associated FAdV-4 strains were distinct from previous circulating strains which did not lead to severe HPS outbreaks. To better understand the molecular epidemiology of the currently circulating FAdV strains for effective diagnosis and treatment of HPS, we isolated 12 HPS outbreak-associated FAdV-4 strains from different regions in central China and investigated their molecular characteristics by performing phylogenetic analyses based on the hexon genes. Our results indicated the FAdV-4 strains in this study all belonged to serotype FAdV-4, species FAdV-C. And in comparison with ON1, KR5, MX-SHP95, PK-01, PJ-06 strains within the cluster where outbreak-associated FAdV-4 strains were located, the nucleotide sequence divergence were 1.31, 1.10, 1.42, 2.77 and 2.84%, respectively. Phylogenetic analyses revealed the hexon genes of the 12 outbreak-associated strains clustered to a relatively independent branch of the tree, and evolved from the same ancestor and we suggested that these outbreak-associated FAdV-4 strains originate from earlier strains in India.

Fluctuations in epidemic modeling - disease extinction and control

NASA Astrophysics Data System (ADS)

Schwartz, Ira

2009-03-01

The analysis of infectious disease fluctuations has recently seen an increasing rise in the use of new tools and models from stochastic dynamics and statistical physics. Examples arise in modeling fluctuations of multi-strain diseases, in modeling adaptive social behavior and its impact on disease fluctuations, and in the analysis of disease extinction in finite population models. Proper stochastic model reduction [1] allows one to predict unobserved fluctuations from observed data in multi-strain models [2]. Degree alteration and power law behavior is predicted in adaptive network epidemic models [3,4]. And extinction rates derived from large fluctuation theory exhibit scaling with respect to distance to the bifurcation point of disease onset with an unusual exponent [5]. In addition to outbreak prediction, another main goal of epidemic modeling is one of eliminating the disease to extinction through various control mechanisms, such as vaccine implementation or quarantine. In this talk, a description will be presented of the fluctuational behavior of several epidemic models and their extinction rates. A general framework and analysis of the effect of non-Gaussian control actuations which enhance the rate to disease extinction will be described. In particular, in it is shown that even in the presence of a small Poisson distributed vaccination program, there is an exponentially enhanced rate to disease extinction. These ideas may lead to improved methods of controlling disease where random vaccinations are prevalent. [4pt] Recent papers:[0pt] [1] E. Forgoston and I. B. Schwartz, ``Escape Rates in a Stochastic Environment with Multiple Scales,'' arXiv:0809.1345 2008.[0pt] [2] L. B. Shaw, L. Billings, I. B. Schwartz, ``Using dimension reduction to improve outbreak predictability of multi-strain diseases,'' J. Math. Bio. 55, 1 2007.[0pt] [3] L. B. Shaw and I. B. Schwartz, ``Fluctuating epidemics on adaptive networks,'' Physical Review E 77, 066101 2008.[0pt] [4] L. B. Shaw and I. B. Schwartz, ``Noise induced dynamics in adaptivenetworks with applications to epidemiology,'' arXiv:0807.3455 2008.[0pt] [5] M. I. Dykman, I. B. Schwartz, A. S. Landsman, ``Disease Extinction in the Presence of Random Vaccination,'' Phys. Rev. Letts. 101, 078101 2008.

Draft Genome Sequences of Two Mycobacterium bovis Strains Isolated from Beef Cattle in Paraguay

PubMed Central

Sanabria, Lidia; Lagrave, Lorena; Nishibe, Christiane; Ribas, Augusto C. A.; Zumárraga, Martín J.; Araújo, Flábio R.

2017-01-01

ABSTRACT This work reports the draft genome sequences of the Mycobacterium bovis strains M1009 and M1010, isolated from the lymph nodes of two infected cows on a beef farm in Paraguay. Comparative genomics between these strains and other regional strains may provide more insights regarding M. bovis epidemiology in South America. PMID:28705977

Molecular Epidemiology of Dengue Viruses Co-circulating in Upper Myanmar in 2006.

PubMed

Thant, Kyaw Zin; Tun, Mya Myat Ngwe; Parquet, Maria Del Carmen; Inoue, Shingo; Lwin, Yee Yee; Lin, Sanda; Aye, Kay Thi; Khin, Pe Thet; Myint, Tin; Htwe, Khin; Nabeshima, Takeshi; Morita, Kouichi

2015-03-01

To understand the molecular epidemiology of circulating dengue viruses (DENV) in Upper Myanmar, DENV isolation was attempted by inoculating the sera of a panel of 110 serum samples onto a C6/36 mosquito cell line. The samples were collected from dengue (DEN) patients admitted at Mandalay Children's Hospital in 2006. Infected culture fluids were subjected to a RT-PCR to detect the DENV genome. Three DENV strains were isolated. This was the first DENV isolation performed either in Mandalay or in Upper Myanmar. One strain belonged to DENV serotype-3 (DENV-3), and two other strains belonged to DENV serotype-4 (DEN-4). The sequence data for the envelope gene of these strains were used in a phylogenetic comparison of DENV-3 and DENV-4 from various countries. Phylogenetic analyses revealed that this DENV-3 strain was clustered within genotype II, and the two DENV-4 strains were clustered within genotype I in each serotype. The Myanmar strains were closely related to strains from the neighboring countries of Thailand and Bangladesh. These results are important for elucidating the trends of recent and future DEN outbreaks in Myanmar.

Genetics and epidemiology, congenital anomalies and cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Friedman, J.M.

1997-03-01

Many of the basic statistical methods used in epidemiology - regression, analysis of variance, and estimation of relative risk, for example - originally were developed for the genetic analysis of biometric data. The familiarity that many geneticists have with this methodology has helped geneticists to understand and accept genetic epidemiology as a scientific discipline. It worth noting, however, that most of the work in genetic epidemiology during the past decade has been devoted to linkage and other family studies, rather than to population-based investigations of the type that characterize much of mainstream epidemiology. 30 refs., 2 tabs.

Molecular Epidemiological Study of Nosocomial Enterobacter aerogenes Isolates in a Belgian Hospital

PubMed Central

Jalaluddin, Sheikh; Devaster, Jeanne-Marie; Scheen, Robert; Gerard, Michele; Butzler, Jean-Paul

1998-01-01

In 1995, the rate of isolation of Enterobacter aerogenes in the Saint-Pierre University Hospital in Brussels, Belgium, was higher than that in the preceding years. A total of 45 nosocomial E. aerogenes strains were collected from 33 patients of different units during that year, and they were isolated from 19 respiratory specimens, 13 pus specimens, 7 blood specimens, 4 urinary specimens, 1 catheter specimen, and 1 heparin vial. The strains were analyzed to determine their epidemiological relatedness and were characterized by their antibiotic resistance pattern determination, plasmid profiling, and genomic fingerprinting by macrorestriction analysis with pulsed-field gel electrophoresis (PFGE). The majority of the strains (82%) were multiply resistant to different commonly used antibiotics. Two major plasmid profiles were found: most strains (64%) harbored two plasmids of different sizes, whereas the others (20%) contained a single plasmid. PFGE with SpeI and/or XbaI restriction enzymes revealed that a single clone (80%) was responsible for causing infections or colonizations throughout the year, and this result was concordant with those obtained by plasmid profiling, with slight variations. By comparing the results of these three methods, PFGE and plasmid profiling were found to be the techniques best suited for investigating the epidemiological relatedness of E. aerogenes strains, and they are therefore proposed as useful tools for the investigation of nosocomial outbreaks caused by this organism. PMID:9650923

Public health surveillance of multidrug-resistant clones of Neisseria gonorrhoeae in Europe: a genomic survey.

PubMed

Harris, Simon R; Cole, Michelle J; Spiteri, Gianfranco; Sánchez-Busó, Leonor; Golparian, Daniel; Jacobsson, Susanne; Goater, Richard; Abudahab, Khalil; Yeats, Corin A; Bercot, Beatrice; Borrego, Maria José; Crowley, Brendan; Stefanelli, Paola; Tripodo, Francesco; Abad, Raquel; Aanensen, David M; Unemo, Magnus

2018-05-15

Traditional methods for molecular epidemiology of Neisseria gonorrhoeae are suboptimal. Whole-genome sequencing (WGS) offers ideal resolution to describe population dynamics and to predict and infer transmission of antimicrobial resistance, and can enhance infection control through linkage with epidemiological data. We used WGS, in conjunction with linked epidemiological and phenotypic data, to describe the gonococcal population in 20 European countries. We aimed to detail changes in phenotypic antimicrobial resistance levels (and the reasons for these changes) and strain distribution (with a focus on antimicrobial resistance strains in risk groups), and to predict antimicrobial resistance from WGS data. We carried out an observational study, in which we sequenced isolates taken from patients with gonorrhoea from the European Gonococcal Antimicrobial Surveillance Programme in 20 countries from September to November, 2013. We also developed a web platform that we used for automated antimicrobial resistance prediction, molecular typing (N gonorrhoeae multi-antigen sequence typing [NG-MAST] and multilocus sequence typing), and phylogenetic clustering in conjunction with epidemiological and phenotypic data. The multidrug-resistant NG-MAST genogroup G1407 was predominant and accounted for the most cephalosporin resistance, but the prevalence of this genogroup decreased from 248 (23%) of 1066 isolates in a previous study from 2009-10 to 174 (17%) of 1054 isolates in this survey in 2013. This genogroup previously showed an association with men who have sex with men, but changed to an association with heterosexual people (odds ratio=4·29). WGS provided substantially improved resolution and accuracy over NG-MAST and multilocus sequence typing, predicted antimicrobial resistance relatively well, and identified discrepant isolates, mixed infections or contaminants, and multidrug-resistant clades linked to risk groups. To our knowledge, we provide the first use of joint analysis of WGS and epidemiological data in an international programme for regional surveillance of sexually transmitted infections. WGS provided enhanced understanding of the distribution of antimicrobial resistance clones, including replacement with clones that were more susceptible to antimicrobials, in several risk groups nationally and regionally. We provide a framework for genomic surveillance of gonococci through standardised sampling, use of WGS, and a shared information architecture for interpretation and dissemination by use of open access software. The European Centre for Disease Prevention and Control, The Centre for Genomic Pathogen Surveillance, Örebro University Hospital, and Wellcome. Copyright © 2018 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.

Biological and Epidemiological Features of Antibiotic-Resistant Streptococcus pneumoniae in Pre- and Post-Conjugate Vaccine Eras: a United States Perspective

PubMed Central

Kim, Lindsay; McGee, Lesley; Tomczyk, Sara

2016-01-01

SUMMARY Streptococcus pneumoniae inflicts a huge disease burden as the leading cause of community-acquired pneumonia and meningitis. Soon after mainstream antibiotic usage, multiresistant pneumococcal clones emerged and disseminated worldwide. Resistant clones are generated through adaptation to antibiotic pressures imposed while naturally residing within the human upper respiratory tract. Here, a huge array of related commensal streptococcal strains transfers core genomic and accessory resistance determinants to the highly transformable pneumococcus. β-Lactam resistance is the hallmark of pneumococcal adaptability, requiring multiple independent recombination events that are traceable to nonpneumococcal origins and stably perpetuated in multiresistant clonal complexes. Pneumococcal strains with elevated MICs of β-lactams are most often resistant to additional antibiotics. Basic underlying mechanisms of most pneumococcal resistances have been identified, although new insights that increase our understanding are continually provided. Although all pneumococcal infections can be successfully treated with antibiotics, the available choices are limited for some strains. Invasive pneumococcal disease data compiled during 1998 to 2013 through the population-based Active Bacterial Core surveillance program (U.S. population base of 30,600,000) demonstrate that targeting prevalent capsular serotypes with conjugate vaccines (7-valent and 13-valent vaccines implemented in 2000 and 2010, respectively) is extremely effective in reducing resistant infections. Nonetheless, resistant non-vaccine-serotype clones continue to emerge and expand. PMID:27076637

Using an Epidemiological Approach to Examine Outcomes Affecting Young Children with Down Syndrome and Their Families

ERIC Educational Resources Information Center

Hodapp, Robert M.; Urbano, Richard C.; So, Stephanie A.

2006-01-01

In this paper, we utilise an approach drawn from the field of epidemiology to explore what is known and unknown about young children with Down syndrome and their families. After describing what we mean by an epidemiological approach, we review basic findings for children with intellectual disabilities, as well as challenges to performing such…

Energy harvesting for dielectric elastomer sensing

NASA Astrophysics Data System (ADS)

Anderson, Iain A.; Illenberger, Patrin; O'Brien, Ben M.

2016-04-01

Soft and stretchy dielectric elastomer (DE) sensors can measure large strains on robotic devices and people. DE strain measurement requires electric energy to run the sensors. Energy is also required for information processing and telemetering of data to phone or computer. Batteries are expensive and recharging is inconvenient. One solution is to harvest energy from the strains that the sensor is exposed to. For this to work the harvester must also be wearable, soft, unobtrusive and profitable from the energy perspective; with more energy harvested than used for strain measurement. A promising way forward is to use the DE sensor as its own energy harvester. Our study indicates that it is feasible for a basic DE sensor to provide its own power to drive its own sensing signal. However telemetry and computation that are additional to this will require substantially more power than the sensing circuit. A strategy would involve keeping the number of Bluetooth data chirps low during the entire period of energy harvesting and to limit transmission to a fraction of the total time spent harvesting energy. There is much still to do to balance the energy budget. This will be a challenge but when we succeed it will open the door to autonomous DE multi-sensor systems without the requirement for battery recharge.

Cancer Pharmacogenomics: Integrating Discoveries in Basic, Clinical and Population Sciences to Advance Predictive Cancer Care

Cancer.gov

Cancer Pharmacogenomics: Integrating Discoveries in Basic, Clinical and Population Sciences to Advance Predictive Cancer Care, a 2010 workshop sponsored by the Epidemiology and Genomics Research Program.

Improved understanding of factors driving methicillin-resistant Staphylococcus aureus epidemic waves

PubMed Central

Chatterjee, Som S; Otto, Michael

2013-01-01

Methicillin-resistant Staphylococcus aureus (MRSA) remains one of the most important causes of nosocomial infections worldwide. Since the global spread of MRSA in the 1960s, MRSA strains have evolved with increased pathogenic potential. Notably, some strains are now capable of causing persistent infections not only in hospitalized patients but also in healthy individuals in the community. Furthermore, MRSA is increasingly associated with infections among livestock-associated workers, primarily because of transmission from animals to humans. Moreover, many MRSA strains have gained resistance to most available antibiotics. In this review, we will present current knowledge on MRSA epidemiology and discuss new endeavors being undertaken to understand better the molecular and epidemiological underpinnings of MRSA outbreaks. PMID:23861600

Protection induced by a commercial bivalent vaccine against Foot-and-Mouth Disease 2010 field virus from Ecuador.

PubMed

Duque, Hernando; Naranjo, Jose; Carrillo, Consuelo; Burbano, Alexandra; Vargas, Javier; Pauszek, Lisa; Olesen, Ian; Sanchez-Vazquez, Manuel J; Cosivi, Ottorino; Allende, Rossana M

2016-07-29

Foot-and-Mouth Disease serotype O circulated endemically in Ecuador for many years, with an upsurge occurring in 2009. This manuscript describes retrospectively in vitro and in vivo laboratory studies to predict the field effectiveness of a commercial FMD vaccine to protect against the field strain, and explains the key actions and epidemiological strategies followed by the country to control the disease. The results established that the use of a good quality oil vaccine, manufactured with strains that were isolated long ago: O1 Campos Br/58 and A24 Cruzeiro Br/55; combined with the correct epidemiological strategies, are useful to control field strains when used in periodic biannual vaccination campaigns. Published by Elsevier Ltd.

Changing Pattern of Chlamydia trachomatis Strains in Lymphogranuloma Venereum Outbreak, France, 2010-2015.

PubMed

Peuchant, Olivia; Touati, Arabella; Sperandio, Clément; Hénin, Nadège; Laurier-Nadalié, Cécile; Bébéar, Cécile; de Barbeyrac, Bertille

2016-11-01

We describe a change in the molecular epidemiology of Chlamydia trachomatis strains involved in an outbreak of rectal lymphogranuloma venereum in France during January 2010-April 2015. Until 2012, the C. trachomatis L2b strain predominated; however, starting in 2013, most cases involved the L2 strain. We also identified 4 genetic L2b ompA variants.

Correlates of protection, antigen delivery and molecular epidemiology: basics for designing an HIV vaccine.

PubMed

Wagner, R; Shao, Y; Wolf, H

1999-03-26

Major obstacles in the development of HIV vaccines are the high variability of the virus and its complex interaction with the immune system. Recent studies demonstrated, that CTLs recognizing highly conserved epitopes in the group-specific antigen are capable of controlling HIV-replication in long-term nonprogressors. Necessary consequences for novel vaccine concepts are the presentation of a large repertoire of antigenic sites as well as the stimulation of different effectors of the immune system. Accordingly, different types of recombinant HIV-1 virus-like particles (VLPs) have been constructed stimulating the induction of neutralizing antibodies and HIV-specific CD8-positive CTL responses in preclinical studies. With respect to future vaccine trials, HIV vaccine formulations may need to be tailored to the local strains circulating within a geographical region. The expert group of the joint United Nations Programme on AIDS recently identified Yunnan, a southwestern province of China, as a region, in which the HIV epidemic is starting to gain speed, resembling to the situation in Thailand 10 years ago. A molecular clone of a representative virus strain is now available for the development of innovative antigen delivery systems aiming to be evaluated in future clinical vaccine trials throughout this area.

Chemometric analysis of attenuated total reflectance infrared spectra of Proteus mirabilis strains with defined structures of LPS.

PubMed

Zarnowiec, Paulina; Mizera, Andrzej; Chrapek, Magdalena; Urbaniak, Mariusz; Kaca, Wieslaw

2016-07-01

Proteus spp. strains are some of the most important pathogens associated with complicated urinary tract infections and bacteremia affecting patients with immunodeficiency and long-term urinary catheterization. For epidemiological purposes, various molecular typing methods have been developed for this pathogen. However, these methods are labor intensive and time consuming. We evaluated a new method of differentiation between strains. A collection of Proteus spp. strains was analyzed by attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy in the mid-infrared region. ATR FT-IR spectroscopy used in conjunction with a diamond ATR accessory directly produced the biochemical profile of the surface chemistry of bacteria. We conclude that a combination of ATR FT-IR spectroscopy and mathematical modeling provides a fast and reliable alternative for discrimination between Proteus isolates, contributing to epidemiological research. © The Author(s) 2016.

The Epidemiological Characteristics of Beijing Lineage Mycobacterium tuberculosis from a National Referral Center in China.

PubMed

Li, Xiao Ying; Li, Ying; Zhang, Yao; Kang, Wan Li; Zhao, Li Ping; Ding, Peng Ju; Dai, Wen Tao; Huang, Hai Rong; Huang, Yan Feng; Li, Wei Min

2015-07-01

Our study was to investigate the epidemiological characteristics of M.tuberculosis from a national tuberculosis referral center in China. All strains isolated from TB patients, were genotyped by the RD105 deletion, 8 and 51 SNP loci and VNTR. The high differentiation SNPs of modern Beijing strains were analyzed for protein function and structure. 413 M. tuberculosis were included. Of 379 Beijing lineage M. tuberculosis, 'modern' and 'ancient' strains respectively represented 85.5% (324/379) and 14.5% (55/379). Rv2494 (V48A) and Rv0245 (S103F) were confirmed as high differentiation SNPs associated with modern strains. In a word, Modern Beijing lineage M.tuberculosis was dominant and the structural models suggested that modern sub-lineage may more easily survive in 'extreme' host condition. Copyright © 2015 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Molecular epidemiology of eastern equine encephalitis Virus, New York

USGS Publications Warehouse

Young, David S.; Kramer, Laura D.; Maffei, Joseph G.; Dusek, Robert J.; Backenson, P. Bryon; Mores, Christopher N.; Bernard, Kristen A.; Ebel, Gregory D.

2008-01-01

Perpetuation, overwintering, and extinction of eastern equine encephalitis virus (EEEV) in northern foci are poorly understood. We therefore sought to describe the molecular epidemiology of EEEV in New York State during current and past epizootics. To determine whether EEEV overwinters, is periodically reintroduced, or both, we sequenced the E2 and partial NSP3 coding regions of 42 EEEV isolates from New York State and the Eastern Seaboard of the United States. Our phylogenetic analyses indicated that derived subclades tended to contain southern strains that had been isolated before genetically similar northern strains, suggesting southern to northern migration of EEEV along the Eastern Seaboard. Strong clustering among strains isolated during epizootics in New York from 2003–2005, as well as from 1974–1975, demonstrates that EEEV has overwintered in this focus. This study provides molecular evidence for the introduction of southern EEEV strains to New York, followed by local amplification, perpetuation, and overwintering.

Estimated effects of projected climate change on the basic reproductive number of the Lyme disease vector Ixodes scapularis.

PubMed

Ogden, Nicholas H; Radojevic, Milka; Wu, Xiaotian; Duvvuri, Venkata R; Leighton, Patrick A; Wu, Jianhong

2014-06-01

The extent to which climate change may affect human health by increasing risk from vector-borne diseases has been under considerable debate. We quantified potential effects of future climate change on the basic reproduction number (R0) of the tick vector of Lyme disease, Ixodes scapularis, and explored their importance for Lyme disease risk, and for vector-borne diseases in general. We applied observed temperature data for North America and projected temperatures using regional climate models to drive an I. scapularis population model to hindcast recent, and project future, effects of climate warming on R0. Modeled R0 increases were compared with R0 ranges for pathogens and parasites associated with variations in key ecological and epidemiological factors (obtained by literature review) to assess their epidemiological importance. R0 for I. scapularis in North America increased during the years 1971-2010 in spatio-temporal patterns consistent with observations. Increased temperatures due to projected climate change increased R0 by factors (2-5 times in Canada and 1.5-2 times in the United States), comparable to observed ranges of R0 for pathogens and parasites due to variations in strains, geographic locations, epidemics, host and vector densities, and control efforts. Climate warming may have co-driven the emergence of Lyme disease in northeastern North America, and in the future may drive substantial disease spread into new geographic regions and increase tick-borne disease risk where climate is currently suitable. Our findings highlight the potential for climate change to have profound effects on vectors and vector-borne diseases, and the need to refocus efforts to understand these effects.

Comparison of Epidemiological and Antibiotic Susceptibility Pattern of Metallo-Beta-Lactamase-Positive and Metallo-Beta-Lactamase-Negative Strains of Pseudomonas Aeruginosa

PubMed Central

Ranjan, Shikha; Banashankari, GS; Babu, PR Sreenivasa

2014-01-01

Background: The infections caused by metallo-beta-lactamases (MBLs) producing Pseudomonas aeruginosa are associated with higher rates of mortality, morbidity, and overall healthcare costs compared to non-MBL P. aeruginosa infections. Purpose: To compare the epidemiologic factors and antibiograms of MBL-positive and MBL-negative P. aeruginosa isolates in a tertiary care hospital. Methods: In an observational study, from January 2011 to December 2012, all non-duplicate P. aeruginosa isolates were subjected to an antimicrobial sensitivity test against 10 antibiotics of five different classes. All P. aeruginosa strains showing resistance to at least one of the carbapenems were subjected to the MBL-E test. Epidemiological features and antibiograms of MBL-positive and MBL-negative strains were compared and statistically analyzed. Results: Out of 350 isolates (total sample = 5330) of P. aeruginosa, MBL was detected in 58 isolates by the E-test, resulting in a prevalence of 16.57%. Resistance to most of the antibiotics was significantly higher in the MBL-positive strains with 100% resistance to ciprofloxacin, tobramycin, and meropenem, followed by imipenem (93.10%) and gentamicin (89.66%). The prevalence of multidrug-resistant and pandrug-resistant strains was significantly higher among the MBL group as compared to that in the non-MBL group ((55.17 vs. 7.88% (P < 0.0001) and 8.62 vs. 0.68% (P = 0.0006)), respectively. Conclusions: MBL-positive P. aeruginosa strains showed very high resistance to various antibiotics, as compared to the non-MBL strains. Increasing prevalence of MBL-producing isolates in hospital settings makes it important to perform routine detection of MBL-positive P. aeruginosa strains by in vitro testing before antibiotic use, for the purposes of infection prevention, and control, and for minimizing the adverse outcomes of infections with MBL-producing strains. PMID:25328336

Antibiotic resistance and molecular characterization of diarrheagenic Escherichia coli and non-typhoidal Salmonella strains isolated from infections in Southwest China.

PubMed

Zhang, Shun-Xian; Zhou, Yong-Ming; Tian, Li-Guang; Chen, Jia-Xu; Tinoco-Torres, Rita; Serrano, Emmanuel; Li, Shi-Zhu; Chen, Shao-Hong; Ai, Lin; Chen, Jun-Hu; Xia, Shang; Lu, Yan; Lv, Shan; Teng, Xue-Jiao; Xu, Wen; Gu, Wen-Peng; Gong, Si-Tang; Zhou, Xiao-Nong; Geng, Lan-Lan; Hu, Wei

2018-05-07

Bacterial diarrhea is one of the most common causes for medical consultations, mortality and morbidity in the world. Diarrheagenic Escherichia coli (DEC) and non-typhoidal Salmonella (NTS) are major intestinal pathogens in developing countries, and the indiscriminate use of antibiotics has greatly contributed to resistant strains. Hence, the aim of the present study is to identify the antimicrobial resistance patterns and the molecular characteristics of DEC and NTS in southwest, China. 1121 diarrheal patients and 319 non-diarrheal subjects across all age groups were recruited from four sentinel hospitals from June 2014 to July 2015 in Kunming City, Yunnan Province. Each stool specimen was collected to detect DEC and NTS with standard microbiological and molecular methods. Antimicrobial resistance testing was performed with the Kirby-Bauer disk diffusion method, and the standards for antimicrobial susceptibility testing complied with the Clinical and Laboratory Standards Institute (CLSI). Molecular characterization of strains was carried out using pulsed-field gel electrophoresis (PFGE). A structured questionnaire was used to record basic epidemiological data (e.g. sex, age, residence, season, etc.). Data were analyzed using Chi-square or Fisher's exact test. DEC was detected in 127 (11.33%) diarrhea cases and 9 (2.82%) non-diarrheal cases (χ 2  = 20.69, P < 0.001, OR = 4.36, 95% CI: 2.19-8.65), and the prevalence of NTS isolated from diarrhea cases was higher than that of non-diarrheal cases across all age groups (n = 42, 3.75%, n = 1, 0.31%, χ 2  = 10.10, P = 0.002, OR = 12.38, 95% CI: 1.70-90.29). The rates of resistance to ten antibiotics of DEC and NTS showed significant differences (χ 2  = 386.77, P < 0.001; χ 2  = 191.16, P < 0.001). The rates of resistance to Amoxicillin and Clavulafiate (AMC), Cephalothin (CEP), Gentamicin (GEN) and Sulfamethoxazole-Trimethoprim (SXT) of DEC isolated from diarrhea cases were higher than those of NTS isolated from diarrhea patients (37.01% vs 14.29%, χ 2  = 7.57, P = 0.006; 29.92% vs 11.90%, χ 2  = 5.40, P = 0.02; 37.01% vs 11.90%, χ 2  = 5.80, P = 0.016; 62.20% vs 26.19%, χ 2  = 16.44, P < 0.001; respectively). Ciprofloxacin (CIP) was the most sensitive antibiotic for DEC and NTS strains isolated from diarrhea cases. Resistance rates of DEC isolates from cases and controls to more than three kinds antimicrobials (multidrug resistance, MDR) showed no significant differences (81.10% vs 88.89%, P = 0.33). Pulsotype patterns of DEC strains were highly diverse; however, the pulsotype pattern of NTS strains was closely related to the serotype. The pattern of S. enteritidis was highly similar, but the S. enterica Typhimurium strain was discrete. Antibiotic resistance of Enterobacteriaceae is of great concern. The societal effects of antibiotic use justify strict monitoring to combat increases in antimicrobial resistance. Molecular epidemiology and systematic epidemiological investigation can provide accurate evidence for tracking the infection source.

Establishment of a national database to link epidemiological and molecular data from norovirus outbreaks in Ireland

PubMed Central

KELLY, S.; FOLEY, B.; DUNFORD, L.; COUGHLAN, S.; TUITE, G.; DUFFY, M.; MITCHELL, S.; SMYTH, B.; O'NEILL, H.; McKEOWN, P.; HALL, W.; LYNCH, M.

2008-01-01

SUMMARY A prospective study of norovirus outbreaks in Ireland was carried out over a 1-year period from 1 October 2004 to 30 September 2005. Epidemiological and molecular data on norovirus outbreaks in the Republic of Ireland (ROI) and Northern Ireland (NI) were collected and combined in real time in a common database. Most reported outbreaks occurred in hospitals and residential institutions and person-to-person spread was the predominant mode of transmission. The predominant circulating norovirus strain was the GII.4-2004 strain with a small number of outbreaks due to GII.2. This study represents the first time that enhanced epidemiological and virological data on norovirus outbreaks in Ireland have been described. The link established between the epidemiological and virological institutions during the course of this study has been continued and the data is being used as a source of data for the Foodborne Viruses in Europe Network (DIVINE-NET). PMID:18252027

Brain Tumor Epidemiology Consortium (BTEC)

Cancer.gov

The Brain Tumor Epidemiology Consortium is an open scientific forum organized to foster the development of multi-center, international and inter-disciplinary collaborations that will lead to a better understanding of the etiology, outcomes, and prevention of brain tumors.

A review on prevalence, control measure, and tolerance of Tanzania Shorthorn Zebu cattle to East Coast fever in Tanzania.

PubMed

Laisser, E L K; Chenyambuga, S W; Karimuribo, E D; Msalya, G; Kipanyula, M J; Mwilawa, A J; Mdegela, R H; Kusiluka, L J M

2017-04-01

In Tanzania, control of East Coast fever (ECF) has predominantly relied on tick control using acaricides and chemotherapy, little on ECF vaccination, and very little on dissemination regarding animal immunization. In this paper, the prevalence, control measure, and tolerance of Tanzania Shorthorn Zebu (TSHZ) cattle to ECF are reviewed. In addition, the opportunities available for reducing the use of acaricides for the benefit of the farmers in terms of reduction of costs of purchasing acaricides and environmental pollution are described. The tick distribution and epidemiological factors for ECF such as the agro-ecological zones (AEZ), livestock production systems (LPS), strain, and age of the animals are also described. These factors influence the epidemiology of ECF and the distribution of TSHZ strains in different geographic locations of Tanzania. We have further showed that there is a tendency of farmers to select among the strains of TSHZ for animals which can tolerate ticks and ECF and crossbreed them with their local strains with the aim of benefiting from the inherent characteristics of the most tolerant strains. Generally, many strains of TSHZ cattle are tolerant to tick infestation and ECF infection and can be bred to respond to the needs of the people. In this review paper, we recommend that in future, ECF epidemiological studies should account for factors such as livestock production system, agro-climate, breed of animal, tick control strategy, and the dynamic interactions between them. In conclusion, we have demonstrated that an integrated control method involving use of acaricides, immunization, and ECF-tolerant/-resistant animals is required.

Demystifying Concepts of Epidemic and Causal Association for Public Health Students--A Pedagogical Approach to Promote Critical and Analytical Thinking

ERIC Educational Resources Information Center

Patil, Rajan R.

2011-01-01

Epidemiology is a difficult but an important subject in public health curriculum. As teachers, we need to be very innovative in teaching the core concepts in epidemiology since it is basically a research oriented subject that calls for enormous application of logic and mathematical skills. Very often, complex epidemiological concepts need to be…

Cluster of cases of Salmonella enterica serotype Rissen infection in a general hospital, Italy, 2007.

PubMed

Boschi, T; Aquilini, D; Degl'Innocenti, R; Aleo, A; Romani, C; Nicoletti, P; Buonomini, M I; Marconi, P; Bilei, S; Mammina, C; Nastasi, A

2010-12-01

In 2007, three strains of Salmonella enterica serotype Rissen (S. Rissen) were isolated in the laboratory of diagnostic microbiology of the General Hospital of Prato, Tuscany, Italy, over a 1 month and half interval of time. The first isolate was recovered on January 26 from an outpatient with enteritis. Then, two strains were isolated on February 16 and March 11 respectively, from central venous catheters of patients who were being hospitalized in two departments of the Hospital. An epidemiologically linked cluster of cases of salmonellosis was suspected. The three strains were submitted to single enzyme-amplified fragment length polymorphism (SE-AFLP) and XbaI macrorestriction and pulsed-field gel electrophoresis (PFGE) that yielded undistinguishable profiles. Epidemiological investigations failed to identify a common source of infection within the Hospital. Moreover, the third patient had been exclusively total parenteral nutrition fed since his admission with a stomach cancer diagnosis. The first patient had a community-acquired infection, but the source of her illness was uncertain. Twenty-five further isolates identified in the years 2004-2007 in the same geographical area showed distinctly different PFGE and SE-AFLP patterns. The three patients seemed to represent a cluster of epidemiologically unrelated cases caused by a previously never recognized S. Rissen strain. Rapid subtyping of isolates is essential in the early investigation of potential outbreaks, but synthesis of conventional and molecular epidemiological investigation and availability of surveillance data is often critical to prevent the initiation of time-consuming, expensive and ineffective further investigations and control interventions. © 2009 Blackwell Verlag GmbH.

Hepatitis A virus: host interactions, molecular epidemiology and evolution.

PubMed

Vaughan, Gilberto; Goncalves Rossi, Livia Maria; Forbi, Joseph C; de Paula, Vanessa S; Purdy, Michael A; Xia, Guoliang; Khudyakov, Yury E

2014-01-01

Infection with hepatitis A virus (HAV) is the commonest viral cause of liver disease and presents an important public health problem worldwide. Several unique HAV properties and molecular mechanisms of its interaction with host were recently discovered and should aid in clarifying the pathogenesis of hepatitis A. Genetic characterization of HAV strains have resulted in the identification of different genotypes and subtypes, which exhibit a characteristic worldwide distribution. Shifts in HAV endemicity occurring in different parts of the world, introduction of genetically diverse strains from geographically distant regions, genotype displacement observed in some countries and population expansion detected in the last decades of the 20th century using phylogenetic analysis are important factors contributing to the complex dynamics of HAV infections worldwide. Strong selection pressures, some of which, like usage of deoptimized codons, are unique to HAV, limit genetic variability of the virus. Analysis of subgenomic regions has been proven useful for outbreak investigations. However, sharing short sequences among epidemiologically unrelated strains indicates that specific identification of HAV strains for molecular surveillance can be achieved only using whole-genome sequences. Here, we present up-to-date information on the HAV molecular epidemiology and evolution, and highlight the most relevant features of the HAV-host interactions. Published by Elsevier B.V.

78 FR 55752 - Center For Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-11

... Epidemiology Integrated Review Group, Behavioral Genetics and Epidemiology Study Section. Date: October 8, 2013... Committee: Oncology 1-Basic Translational Integrated Review Group, Cancer Genetics Study Section. Date... Biology Integrated Review Group, Molecular and Integrative Signal Transduction Study Section. Date...

Combined Genotypic, Phylogenetic, and Epidemiologic Analyses of Mycobacterium tuberculosis Genetic Diversity in the Rhône Alpes Region, France.

PubMed

Pichat, Catherine; Couvin, David; Carret, Gérard; Frédénucci, Isabelle; Jacomo, Véronique; Carricajo, Anne; Boisset, Sandrine; Dumitrescu, Oana; Flandrois, Jean-Pierre; Lina, Gérard; Rastogi, Nalin

2016-01-01

The present work relates to identification and a deep molecular characterization of circulating Mycobacterium tuberculosis complex (MTBC) strains in the Rhône-Alpes region, France from 2000 to 2010. It aimed to provide with a first snapshot of MTBC genetic diversity in conjunction with bacterial drug resistance, type of disease and available demographic and epidemiologic characteristics over an eleven-year period, in the south-east of France. Mycobacterium tuberculosis complex (MTBC) strains isolated in the Rhône-Alpes region, France (n = 2257, 1 isolate per patient) between 2000 and 2010 were analyzed by spoligotyping. MIRU-VNTR typing was applied on n = 1698 strains (with full results available for 974 strains). The data obtained were compared with the SITVIT2 database, followed by detailed genotyping, phylogenetic, and epidemiologic analyses in correlation with anonymized data on available demographic, and epidemiologic characteristics, and location of disease (pulmonary or extrapulmonary TB). The most predominant spoligotyping clusters were SIT53/T1 (n = 346, 15.3%) > SIT50/H3 (n = 166, 7.35%) > SIT42/LAM9 (n = 125, 5.5%) > SIT1/Beijing (n = 72, 3.2%) > SIT47/H1 (n = 71, 3.1%). Evolutionary-recent strains belonging to the Principal Genetic Group (PGG) 2/3, or Euro-American lineages (T, LAM, Haarlem, X, S) were predominant and represented 1768 or 78.33% of all isolates. For strains having drug resistance information (n = 1119), any drug resistance accounted for 14.83% cases vs. 1.52% for multidrug resistance (MDR); and was significantly more associated with age group 21-40 years (p-value<0.001). Extra-pulmonary TB was more common among female patients while pulmonary TB predominated among men (p-value<0.001; OR = 2.16 95%CI [1.69; 2.77]). Also, BOV and CAS lineages were significantly well represented in patients affected by extra-pulmonary TB (p-value<0.001). The origin was known for 927/2257 patients: 376 (40.6%) being French-born vs. 551 (59.4%) Foreign-born. French patients were significantly older (mean age: 58.42 yrs 95%CI [56.04; 60.80]) than Foreign-born patients (mean age: 42.38 yrs. 95%CI [40.75; 44.0]). The study underlined the importance of imported TB cases on the genetic diversity and epidemiologic characteristics of circulating MTBC strains in Rhône-Alpes region, France over a large time-period. It helps better understand intricate relationships between certain lineages and geographic origin of the patients, and pinpoints genotypic and phylogenetic specificities of prevailing MTBC strains. Lastly, it also demonstrated a slow decline in isolation of M. africanum lineage in this region between 2000 and 2010.

Molecular epidemiology of rotavirus gastroenteritis in Central Kenya before vaccine introduction, 2009-2014.

PubMed

Wandera, Ernest A; Mohammad, Shah; Komoto, Satoshi; Maeno, Yoshimasa; Nyangao, James; Ide, Tomihiko; Kathiiko, Cyrus; Odoyo, Erick; Tsuji, Takao; Taniguchi, Koki; Ichinose, Yoshio

2017-05-01

Between July 2009 and June 2014, a total of 1,546 fecal specimens were collected from children <5 years of age with acute gastroenteritis admitted to Kiambu County Hospital, Central Kenya. The specimens were screened for group A rotavirus (RVA) using ELISA, and RVA-positive specimens were subjected to semi-nested RT-PCR to determine the G and P genotypes. RVA was detected in 429/1,546 (27.5%) fecal specimens. RVA infections occurred in all age groups <59 months, with an early peak at 6-17 months. The infections persisted year-round with distinct seasonal peaks depending on the year. G1P[8] (28%) was the most predominant genotype, followed by G9P[8] (12%), G8P[4] (7%), G1P[4] (5%), G9P[4] (4%), and G12P[6] (3%). In the yearly change of G and P genotypes, a major shift from G9P[8] to G1P[8] was found in 2012. Phylogenetic analysis of the nucleotide sequences of the VP7 and VP4 genes of seven strains with unusual G8 or P[6] showed that the VP7 nucleotide sequences of G8 were clustered in lineage 6 in which African strains are included, and that there are at least two distinct VP4 nucleotide sequences of P[6] strains. These results represent basic data on RVA strains circulating in this region before vaccine introduction. J. Med. Virol. 89:809-817, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Multi-scale Modeling of the Impact Response of a Strain Rate Sensitive High-Manganese Austenitic Steel

NASA Astrophysics Data System (ADS)

Önal, Orkun; Ozmenci, Cemre; Canadinc, Demircan

2014-09-01

A multi-scale modeling approach was applied to predict the impact response of a strain rate sensitive high-manganese austenitic steel. The roles of texture, geometry and strain rate sensitivity were successfully taken into account all at once by coupling crystal plasticity and finite element (FE) analysis. Specifically, crystal plasticity was utilized to obtain the multi-axial flow rule at different strain rates based on the experimental deformation response under uniaxial tensile loading. The equivalent stress - equivalent strain response was then incorporated into the FE model for the sake of a more representative hardening rule under impact loading. The current results demonstrate that reliable predictions can be obtained by proper coupling of crystal plasticity and FE analysis even if the experimental flow rule of the material is acquired under uniaxial loading and at moderate strain rates that are significantly slower than those attained during impact loading. Furthermore, the current findings also demonstrate the need for an experiment-based multi-scale modeling approach for the sake of reliable predictions of the impact response.

Comparison and Evaluation of the Molecular Typing Methods for Toxigenic Vibrio cholerae in Southwest China.

PubMed

Liao, Feng; Mo, Zhishuo; Chen, Meiling; Pang, Bo; Fu, Xiaoqing; Xu, Wen; Jing, Huaiqi; Kan, Biao; Gu, Wenpeng

2018-01-01

Vibrio cholerae O1 strains taken from the repository of Yunnan province, southwest China, were abundant and special. We selected 70 typical toxigenic V. cholerae (69 O1 and one O139 serogroup strains) isolated from Yunnan province, performed the pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and MLST of virulence gene (V-MLST) methods, and evaluated the resolution abilities for typing methods. The ctxB subunit sequence analysis for all strains have shown that cholera between 1986 and 1995 was associated with mixed infections with El Tor and El Tor variants, while infections after 1996 were all caused by El Tor variant strains. Seventy V. cholerae obtained 50 PFGE patterns, with a high resolution. The strains could be divided into three groups with predominance of strains isolated during 1980s, 1990s, and 2000s, respectively, showing a good consistency with the epidemiological investigation. We also evaluated two MLST method for V. cholerae , one was used seven housekeeping genes ( adk , gyrB , metE , pntA , mdh , purM , and pyrC ), and all the isolates belonged to ST69; another was used nine housekeeping genes ( cat , chi , dnaE , gyrB , lap , pgm , recA , rstA , and gmd ). A total of seven sequence types (STs) were found by using this method for all the strains; among them, rstA gene had five alleles, recA and gmd have two alleles, and others had only one allele. The virulence gene sequence typing method ( ctxAB , tcpA , and toxR ) showed that 70 strains were divided into nine STs; among them, tcpA gene had six alleles, toxR had five alleles, while ctxAB was identical for all the strains. The latter two sequences based typing methods also had consistency with epidemiology of the strains. PFGE had a higher resolution ability compared with the sequence based typing method, and MLST used seven housekeeping genes showed the lower resolution power than nine housekeeping genes and virulence genes methods. These two sequence typing methods could distinguish some epidemiological special strains in local area.

Changing Pattern of Chlamydia trachomatis Strains in Lymphogranuloma Venereum Outbreak, France, 2010–2015

PubMed Central

Touati, Arabella; Sperandio, Clément; Hénin, Nadège; Laurier-Nadalié, Cécile; Bébéar, Cécile; de Barbeyrac, Bertille

2016-01-01

We describe a change in the molecular epidemiology of Chlamydia trachomatis strains involved in an outbreak of rectal lymphogranuloma venereum in France during January 2010–April 2015. Until 2012, the C. trachomatis L2b strain predominated; however, starting in 2013, most cases involved the L2 strain. We also identified 4 genetic L2b ompA variants. PMID:27767927

A RESTful application programming interface for the PubMLST molecular typing and genome databases

PubMed Central

Bray, James E.; Maiden, Martin C. J.

2017-01-01

Abstract Molecular typing is used to differentiate microorganisms at the subspecies or strain level for epidemiological investigations, infection control, public health and environmental sampling. DNA sequence-based typing methods require authoritative databases that link sequence variants to nomenclature in order to facilitate communication and comparison of identified types in national or global settings. The PubMLST website (https://pubmlst.org/) fulfils this role for over a hundred microorganisms for which it hosts curated molecular sequence typing data, providing sequence and allelic profile definitions for multi-locus sequence typing (MLST) and single-gene typing approaches. In recent years, these have expanded to cover the whole genome with schemes such as core genome MLST (cgMLST) and whole genome MLST (wgMLST) which catalogue the allelic diversity found in hundreds to thousands of genes. These approaches provide a common nomenclature for high-resolution strain characterization and comparison. Molecular typing information is linked to isolate provenance, phenotype, and increasingly genome assemblies, providing a resource for outbreak investigation and research in to population structure, gene association, global epidemiology and vaccine coverage. A Representational State Transfer (REST) Application Programming Interface (API) has been developed for the PubMLST website to make these large quantities of structured molecular typing and whole genome sequence data available for programmatic access by any third party application. The API is an integral component of the Bacterial Isolate Genome Sequence Database (BIGSdb) platform that is used to host PubMLST resources, and exposes all public data within the site. In addition to data browsing, searching and download, the API supports authentication and submission of new data to curator queues. Database URL: http://rest.pubmlst.org/ PMID:29220452

Characterization of antimicrobial resistance of Salmonella Newport isolated from animals, the environment, and animal food products in Canada

PubMed Central

Martin, Laura; Muckle, Anne; Archambault, Marie; McEwen, Scott; Weir, Emily

2006-01-01

Abstract Multi-drug-resistant (MDR) Salmonella enterica serovar Newport strains are increasingly isolated from animals and food products of animal origin and have caused septicemic illness in animals and humans. The purpose of this study was to determine the occurrence and the epidemiologic, phenotypic, and genotypic characteristics of S. Newport of animal origin that may infect humans, either via the food chain or directly. During the 1993–2002 period, the Office International des Épizooties Reference Laboratory for Salmonellosis in Guelph, Ontario, received 36 841 Salmonella strains for serotyping that had been isolated from animals, environmental sources, and food of animal origin in Canada. Of these, 119 (0.3%) were S. Newport. Before 2000, none of 49 S. Newport strains was resistant to more than 3 antimicrobials. In contrast, between January 2000 and December 2002, 35 of 70 isolates, primarily of bovine origin, were resistant to at least 11 antimicrobials, including the extended-spectrum cephalosporins. The blaCMY-2, flost, strA, strB, sulII, and tetA resistance genes were located on plasmids of 80 to 90 MDa that were self-transmissible in 25% of the strains. Conserved segments of the integron 1 gene were found on the large MDR-encoding plasmids in 3 of 35 strains additionally resistant to gentamicin and spectinomycin or to spectinomycin, sulfamethoxazole– trimethoprim, and trimethoprim. Resistance to kanamycin and neomycin was encoded by the aphA-1 gene, located on small plasmids (2.3 to 6 MDa). The increase in bovine-associated MDR S. Newport infections is cause for concern since it indicates an increased risk of human acquisition of the infection via the food chain. PMID:16639942

Genotyping of Mycobacterium leprae strains from a region of high endemic leprosy prevalence in India.

PubMed

Lavania, Mallika; Jadhav, Rupendra; Turankar, Ravindra P; Singh, Itu; Nigam, Astha; Sengupta, U

2015-12-01

Leprosy is still a major health problem in India which has the highest number of cases. Multiple locus variable number of tandem repeat analysis (MLVA) and single nucleotide polymorphism (SNP) have been proposed as tools of strain typing for tracking the transmission of leprosy. However, empirical data for a defined population from scale and duration were lacking for studying the transmission chain of leprosy. Seventy slit skin scrapings were collected from Purulia (West Bengal), Miraj (Maharashtra), Shahdara (Delhi), and Naini (UP) hospitals of The Leprosy Mission (TLM). SNP subtyping and MLVA on 10 VNTR loci were applied for the strain typing of Mycobacterium leprae. Along with the strain typing conventional epidemiological investigation was also performed to trace the transmission chain. In addition, phylogenetic analysis was done on variable number of tandem repeat (VNTR) data sets using sequence type analysis and recombinational tests (START) software. START software performs analyses to aid in the investigation of bacterial population structure using multilocus sequence data. These analyses include data summary, lineage assignment, and tests for recombination and selection. Diversity was observed in the cross-sectional survey of isolates obtained from 70 patients. Similarity in fingerprinting profiles observed in specimens of cases from the same family or neighborhood locations indicated a possible common source of infection. The data suggest that these VNTRs including subtyping of SNPs can be used to study the sources and transmission chain in leprosy, which could be very important in monitoring of the disease dynamics in high endemic foci. The present study strongly indicates that multi-case families might constitute epidemic foci and the main source of M. leprae in villages, causing the predominant strain or cluster infection leading to the spread of leprosy in the community. Copyright © 2015 Elsevier B.V. All rights reserved.

Hamstring Muscle Injuries, a Rehabilitation Protocol Purpose

PubMed Central

Valle, Xavier; L.Tol, Johannes; Hamilton, Bruce; Rodas, Gil; Malliaras, Peter; Malliaropoulos, Nikos; Rizo, Vicenc; Moreno, Marcel; Jardi, Jaume

2015-01-01

Context: Hamstring acute muscle injuries are prevalent in several sports including AFL football (Australian Football League), sprinting and soccer, and are often associated with prolonged time away from sport. Evidence Acquisition: In response to this, research into prevention and management of hamstring injury has increased, but epidemiological data shows no decline in injury and re-injury rates, suggesting that rehabilitation programs and return to play (RTP) criteria have to be improved. There continues to be a lack of consensus regarding how to assess performance, recovery and readiness to RTP, following hamstring strain injury. Results: The aim of this paper was to propose rehabilitation protocol for hamstring muscle injuries based on current basic science and research knowledge regarding injury demographics and management options. Conclusions: Criteria-based (subjective and objective) progression through the rehabilitation program will be outlined along with exercises for each phase, from initial injury to RTP. PMID:26715969

Molecular Typing of Borrelia burgdorferi

PubMed Central

Wang, Guiqing; Liveris, Dionysios; Mukherjee, Priyanka; Jungnick, Sabrina; Margos, Gabriele; Schwartz, Ira

2015-01-01

Borrelia burgdorferi sensu lato is a group of spirochetes belonging to the genus Borrelia in the family of Spirochaetaceae. The spirochete is transmitted between reservoirs and hosts by ticks of the family Ixodidae. Infection with B. burgdorferi in humans causes Lyme disease or Lyme borreliosis. Currently, 20 Lyme disease-associated Borrelia species and more than 20 relapsing fever-associated Borrelia species have been described. Identification and differentiation of different Borrelia species and strains is largely dependent on analyses of their genetic characteristics. A variety of molecular techniques have been described for Borrelia isolate speciation, molecular epidemiology, and pathogenicity studies. In this unit, we focus on three basic protocols, PCR-RFLP-based typing of the rrs-rrlA and rrfA-rrlB ribosomal spacer, ospC typing, and MLST. These protocols can be employed alone or in combination for characterization of B. burgdorferi isolates or directly on uncultivated organisms in ticks, mammalian host reservoirs, and human clinical specimens. PMID:25082003

Etiological agents causing leptospirosis in Sri Lanka: A review.

PubMed

Naotunna, Chamidri; Agampodi, Suneth Buddhika; Agampodi, Thilini Chanchala

2016-04-01

To systematically review the etiological agent causing human leptospirosis in Sri Lanka. Published articles on leptospirosis and Leptospira in Sri Lanka were all reviewed to determine serovar, strain and species level identification of Leptospira. After screening process, 74 full text articles/reports were reviewed and among of them, 12 published papers describing isolation of Leptospira from Sri Lankan patients/animals, 5 molecular epidemiology papers on newer typing methods citing Sri Lanka isolates, with a descriptions of the isolates and 6 published papers reporting PCR based species level identification were identified. Published literature showed that more than 40 strains classified under at least 20 serovars and 10 serogroups have been isolated from Sri Lanka. These isolates belong to four species, namely, Leptospira interrogans, Leptospira kirschneri, Leptospira borgpetersenii, and Leptospira santarosai. In addition, recent studies on direct patient samples without culture and isolation showed Leptospira from Leptospira weilli is also circulating in Sri Lanka. Multi locus sequence typing showed 13 genotypes of Leptospira from Sri Lankan isolates. This review shows the diversity of Leptospira in Sri Lanka, but culture isolation data has not been published in Sri Lanka during last 30 years. Copyright © 2016 Hainan Medical College. Production and hosting by Elsevier B.V. All rights reserved.

Taxonomic evaluation of putative Streptomyces scabiei strains held in the ARS Culture Collection (NRRL) using multi-locus sequence analysis.

PubMed

Labeda, David P

2016-03-01

Multi-locus sequence analysis has been demonstrated to be a useful tool for identification of Streptomyces species and was previously applied to phylogenetically differentiate the type strains of species pathogenic on potatoes (Solanum tuberosum L.). The ARS Culture Collection (NRRL) contains 43 strains identified as Streptomyces scabiei deposited at various times since the 1950s and these were subjected to multi-locus sequence analysis utilising partial sequences of the house-keeping genes atpD, gyrB, recA, rpoB and trpB. Phylogenetic analyses confirmed the identity of 17 of these strains as Streptomyces scabiei, 9 of the strains as the potato-pathogenic species Streptomyces europaeiscabiei and 6 strains as potentially new phytopathogenic species. Of the 16 other strains, 12 were identified as members of previously described non-pathogenic Streptomyces species while the remaining 4 strains may represent heretofore unrecognised non-pathogenic species. This study demonstrated the value of this technique for the relatively rapid, simple and sensitive molecular identification of Streptomyces strains held in culture collections.

Epidemiology, pathophysiology, and the future of ocular toxoplasmosis.

PubMed

Kijlstra, Aize; Petersen, Eskild

2014-04-01

Despite large advances in the field of ocular toxoplasmosis, large gaps still exist in our knowledge concerning the epidemiology and pathophysiology of this potentially blinding infectious disease. Although ocular toxoplasmosis is considered to have a high health burden, still little is known about its exact prevalence and how it affects the quality of life. The epidemiology of toxoplasmosis depends on local habits throughout the globe, and changes are likely in view of increased meat consumption in developing countries and demands for higher animal welfare in the Western world. Water is increasingly seen as an important risk factor and more studies are needed to quantitate and control the role of water exposure (drinking, swimming). Tools are now becoming available to study both the human host as well as parasite genetic factors in the development of ocular toxoplasmosis. Further research on the role of Toxoplasma strains as well as basic studies on parasite virulence is needed to explain why Toxoplasma associated eye disease is so severe in some countries, such as Brazil. Although genetic analysis of the parasite represents the gold standard, further developments in serotyping using peptide arrays may offer practical solutions to study the role of parasite strains in the pathogenesis of Toxoplasma retinochoroiditis. More research is needed concerning the pathways whereby the parasite can infect the retina. Once in the retina further tissue damage may be due to parasite virulence factors or could be caused by an aberrant host immune response. Local intraocular immune responses are nowadays used for diagnostic procedures. Future developments may include the use of Raman technology or the direct visualization of a Toxoplasma cyst by optical coherence tomography (OCT). With the availability of ocular fluid specimens obtained for diagnostic purposes and the development of advanced proteomic techniques, a biomarker fingerprint that is unique for an eye with toxoplasmosis may become available. It is hoped that such a biomarker analysis may also be able to distinguish between acquired versus congenital disease. Recently developed mouse models of congenital ocular toxoplasmosis are extremely promising with regard to disease pathogenesis, diagnosis, and treatment.

Study on stress-strain response of multi-phase TRIP steel under cyclic loading

NASA Astrophysics Data System (ADS)

Dan, W. J.; Hu, Z. G.; Zhang, W. G.; Li, S. H.; Lin, Z. Q.

2013-12-01

The stress-strain response of multi-phase TRIP590 sheet steel is studied in cyclic loading condition at room temperature based on a cyclic phase transformation model and a multi-phase mixed kinematic hardening model. The cyclic martensite transformation model is proposed based on the shear-band intersection, where the repeat number, strain amplitude and cyclic frequency are used to control the phase transformation process. The multi-phase mixed kinematic hardening model is developed based on the non-linear kinematic hardening rule of per-phase. The parameters of transformation model are identified with the relationship between the austenite volume fraction and the repeat number. The parameters in Kinematic hardening model are confirmed by the experimental hysteresis loops in different strain amplitude conditions. The responses of hysteresis loop and stress amplitude are evaluated by tension-compression data.

Novel Reassortant H3N2 Avian Influenza Virus Isolated from Domestic Ducks in Eastern China in 2016.

PubMed

Sun, Wenqiang; Li, Jiaxin; Hu, Jiao; Jiang, Daxiu; Ge, Zhichuang; Xing, Chaonan; Wang, Xiaoquan; Gu, Min; Liu, Xiaowen; Hu, Shunlin; Liu, Xiufan

2017-11-30

H3 subtype avian influenza virus (AIV) poses a great threat to public health, and so investigating its epidemiology is of great importance. A novel reassortant H3N2 AIV strain was isolated from a live poultry market in eastern China. The strain's genes originated from H1N1, H3, and H7 AIVs. Thus, the genome information of the H3N2 isolate will help to investigate further the epidemiology of H3 subtype AIVs in China. Copyright © 2017 Sun et al.

Clostridium difficile infection: Early history, diagnosis and molecular strain typing methods.

PubMed

Rodriguez, C; Van Broeck, J; Taminiau, B; Delmée, M; Daube, G

2016-08-01

Recognised as the leading cause of nosocomial antibiotic-associated diarrhoea, the incidence of Clostridium difficile infection (CDI) remains high despite efforts to improve prevention and reduce the spread of the bacterium in healthcare settings. In the last decade, many studies have focused on the epidemiology and rapid diagnosis of CDI. In addition, different typing methods have been developed for epidemiological studies. This review explores the history of C. difficile and the current scope of the infection. The variety of available laboratory tests for CDI diagnosis and strain typing methods are also examined. Copyright © 2016 Elsevier Ltd. All rights reserved.

Circular epidemiology.

PubMed

Kuller, L H

1999-11-01

Circular epidemiology can be defined as the continuation of specific types of epidemiologic studies beyond the point of reasonable doubt of the true existence of an important association or the absence of such an association. Circular epidemiology is an extreme example of studies of the consistency of associations. A basic problem for epidemiology is the lack of a systematic approach to acquiring new knowledge to reach a goal of improving public health and preventive medicine. For epidemiologists, research support unfortunately is biased toward the continued study of already proven hypotheses. Circular epidemiology, however, freezes at one point in the evolution of epidemiologic studies, failing to move from descriptive to analytical case-control and longitudinal studies, for example, to experimental, clinical trials. Good epidemiology journals are filled with very well-conducted epidemiologic studies that primarily repeat the obvious or are variations on the theme.

Chimera states in multi-strain epidemic models with temporary immunity

NASA Astrophysics Data System (ADS)

Bauer, Larissa; Bassett, Jason; Hövel, Philipp; Kyrychko, Yuliya N.; Blyuss, Konstantin B.

2017-11-01

We investigate a time-delayed epidemic model for multi-strain diseases with temporary immunity. In the absence of cross-immunity between strains, dynamics of each individual strain exhibit emergence and annihilation of limit cycles due to a Hopf bifurcation of the endemic equilibrium, and a saddle-node bifurcation of limit cycles depending on the time delay associated with duration of temporary immunity. Effects of all-to-all and non-local coupling topologies are systematically investigated by means of numerical simulations, and they suggest that cross-immunity is able to induce a diverse range of complex dynamical behaviors and synchronization patterns, including discrete traveling waves, solitary states, and amplitude chimeras. Interestingly, chimera states are observed for narrower cross-immunity kernels, which can have profound implications for understanding the dynamics of multi-strain diseases.

Comparative typing analyses of clinical and environmental strains of the Cryptococcus neoformans/Cryptococcus gattii species complex from Ivory Coast.

PubMed

Kassi, Fulgence K; Bellet, Virginie; Drakulovski, Pascal; Krasteva, Donika; Roger, Frédéric; Valérie, Bedia-Tanoh A; Aboubakar, Touré; Doumbia, Adama; Kouakou, Gisèle A; Delaporte, Eric; Reynes, Jacques; Yavo, William; Menan, Hervé I E; Bertout, Sebastien

2018-01-01

The aim of this study was to assess the biotope of the Cryptococcus neoformans/Cryptococcus gattii species complex from Ivory Coast, and clarify the possible epidemiological relationship between environmental and clinical strains. Samples from Eucalyptus camaldulensis (n=136), Mangifera indica (n=13) and pigeon droppings (n=518) were collected from different sites close to the living environment of Ivorian HIV patients with cryptococcosis (n=10, 50 clinical strains). Clinical and environmental strains were characterized by molecular serotyping and genotyping [RFLP analysis of the URA5 gene, (GACA)4, (GTG)5 and M13 PCR fingerprinting] and compared.Results/Key findings. Environmental strains were recovered only from the pigeon droppings. In vitro susceptibility profiles showed that all strains were susceptible to fluconazole, flucytosine and amphotericin B. All environmental strains consisted of C. neoformans (A, AFLP1/VNI), whereas clinical strains included C. neoformans (A, AFLP1/VNI), C. neoformans x Cryptococcus deneoformans hybrids (AD, AFLP3/VNIII) and Cryptococcus deuterogattii (B, AFLP6/VGII). Two patients were co-infected with both C. neoformans and C. neoformans x C. deneoformans hybrids. We noticed a low genetic diversity among the environmental samples compared to the high diversity of the clinical samples. Some clinical strains were genetically more similar to environmental strains than to other clinical strains, including those from the same patient. These results provide new information on the ecology and epidemiology of the C. neoformans/C. gattii species complex in Ivory Coast.

Multi-Virulence-Locus Sequence Typing of Staphylococcus lugdunensis Generates Results Consistent with a Clonal Population Structure and Is Reliable for Epidemiological Typing

PubMed Central

Didi, Jennifer; Lemée, Ludovic; Gibert, Laure; Pons, Jean-Louis

2014-01-01

Staphylococcus lugdunensis is an emergent virulent coagulase-negative staphylococcus responsible for severe infections similar to those caused by Staphylococcus aureus. To understand its potentially pathogenic capacity and have further detailed knowledge of the molecular traits of this organism, 93 isolates from various geographic origins were analyzed by multi-virulence-locus sequence typing (MVLST), targeting seven known or putative virulence-associated loci (atlLR2, atlLR3, hlb, isdJ, SLUG_09050, SLUG_16930, and vwbl). The polymorphisms of the putative virulence-associated loci were moderate and comparable to those of the housekeeping genes analyzed by multilocus sequence typing (MLST). However, the MVLST scheme generated 43 virulence types (VTs) compared to 20 sequence types (STs) based on MLST, indicating that MVLST was significantly more discriminating (Simpson's index [D], 0.943). No hypervirulent lineage or cluster specific to carriage strains was defined. The results of multilocus sequence analysis of known and putative virulence-associated loci are consistent with a clonal population structure for S. lugdunensis, suggesting a coevolution of these genes with housekeeping genes. Indeed, the nonsynonymous to synonymous evolutionary substitutions (dN/dS) ratio, the Tajima's D test, and Single-likelihood ancestor counting (SLAC) analysis suggest that all virulence-associated loci were under negative selection, even atlLR2 (AtlL protein) and SLUG_16930 (FbpA homologue), for which the dN/dS ratios were higher. In addition, this analysis of virulence-associated loci allowed us to propose a trilocus sequence typing scheme based on the intragenic regions of atlLR3, isdJ, and SLUG_16930, which is more discriminant than MLST for studying short-term epidemiology and further characterizing the lineages of the rare but highly pathogenic S. lugdunensis. PMID:25078912

Presence, distribution and molecular epidemiology of multi-drug-resistant Gram-negative bacilli from medical personnel of intensive care units in Tianjin, China, 2007-2015.

PubMed

Liu, H; Fei, C N; Zhang, Y; Liu, G W; Liu, J; Dong, J

2017-06-01

Multi-drug-resistant Gram-negative bacteria (MDRGNB) have become an important cause of nosocomial infection in intensive care units (ICUs). To investigate the molecular epidemiology of MDRGNB isolated from medical personnel (MP) and non-medical personnel (NMP) at 69 ICUs in Tianjin, China. From April 2007 to October 2015, 2636 nasal and hand swab samples from 1185 MP and 133 NMP were cultured for GNB (including MDRGNB), meticillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). The susceptibilities of GNB to 14 antimicrobial agents were determined, and 80 MDRGNB were characterized using pulsed-field gel electrophoresis (PFGE) and dendrogram analysis. In total, 301 GNB were identified in 269 MP, including 109 MDRGNB isolates in 104 MP. Forty-two GNB were isolated from 39 NMP, which included 20 NMP with MDRGNB. Overall, 8.8% of MP were colonized with MDRGNB, which greatly exceeded colonization rates with MRSA (0.9%) and VRE (0.1%). Three pairs of Klebsiella pneumoniae and one pair of Enterobacter aerogenes were indistinguishable from each other, but the majority of isolate tests had distinct PFGE profiles. The prevalence of MDRGNB was high among ICU MP in Tianjin, and greatly exceeded that of VRE and MRSA. There was no difference in the rates of nasal carriage of MDRGNB between MP and NMP, but NMP were significantly more likely to have hand colonization with MDRGNB. PFGE profiles showed that there was only limited sharing of strains of MDR E. aerogenes and K. pneumoniae between personnel. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Differentiation and Gene Flow among European Populations of Leishmania infantum MON-1

PubMed Central

Kuhls, Katrin; Chicharro, Carmen; Cañavate, Carmen; Cortes, Sofia; Campino, Lenea; Haralambous, Christos; Soteriadou, Ketty; Pratlong, Francine; Dedet, Jean-Pierre; Mauricio, Isabel; Miles, Michael; Schaar, Matthias; Ochsenreither, Sebastian; Radtke, Oliver A.; Schönian, Gabriele

2008-01-01

Background Leishmania infantum is the causative agent of visceral and cutaneous leishmaniasis in the Mediterranean region, South America, and China. MON-1 L. infantum is the predominating zymodeme in all endemic regions, both in humans and dogs, the reservoir host. In order to answer important epidemiological questions it is essential to discriminate strains of MON-1. Methodology/Principal Findings We have used a set of 14 microsatellite markers to analyse 141 strains of L. infantum mainly from Spain, Portugal, and Greece of which 107 strains were typed by MLEE as MON-1. The highly variable microsatellites have the potential to discriminate MON-1 strains from other L. infantum zymodemes and even within MON-1 strains. Model- and distance-based analysis detected a considerable amount of structure within European L. infantum. Two major monophyletic groups—MON-1 and non-MON-1—could be distinguished, with non-MON-1 being more polymorphic. Strains of MON-98, 77, and 108 were always part of the MON-1 group. Among MON-1, three geographically determined and genetically differentiated populations could be identified: (1) Greece; (2) Spain islands–Majorca/Ibiza; (3) mainland Portugal/Spain. All four populations showed a predominantly clonal structure; however, there are indications of occasional recombination events and gene flow even between MON-1 and non-MON-1. Sand fly vectors seem to play an important role in sustaining genetic diversity. No correlation was observed between Leishmania genotypes, host specificity, and clinical manifestation. In the case of relapse/re-infection, only re-infections by a strain with a different MLMT profile can be unequivocally identified, since not all strains have individual MLMT profiles. Conclusion In the present study for the first time several key epidemiological questions could be addressed for the MON-1 zymodeme, because of the high discriminatory power of microsatellite markers, thus creating a basis for further epidemiological investigations. PMID:18612461

Molecular epidemiology of Vibrio cholerae in Hong Kong.

PubMed Central

Yam, W C; Lung, M L; Ng, K Y; Ng, M H

1989-01-01

We studied restriction fragment length polymorphism of the enterotoxin genes of isolates of Vibrio cholerae El Tor, indistinguishable by bacteriophage typing, which were collected in Hong Kong since 1978. Using this approach, we could distinguish indigenous and exogenous strains obtained from different sources and epidemiological settings. Images PMID:2570082

Evolutionary history of Leishmania killicki (synonymous Leishmania tropica) and taxonomic implications.

PubMed

Chaara, Dhekra; Ravel, Christophe; Bañuls, Anne- Laure; Haouas, Najoua; Lami, Patrick; Talignani, Loïc; El Baidouri, Fouad; Jaouadi, Kaouther; Harrat, Zoubir; Dedet, Jean-Pierre; Babba, Hamouda; Pratlong, Francine

2015-04-01

The taxonomic status of Leishmania (L.) killicki, a parasite that causes chronic cutaneous leishmaniasis, is not well defined yet. Indeed, some researchers suggested that this taxon could be included in the L. tropica complex, whereas others considered it as a distinct phylogenetic complex. To try to solve this taxonomic issue we carried out a detailed study on the evolutionary history of L. killicki relative to L. tropica. Thirty-five L. killicki and 25 L. tropica strains isolated from humans and originating from several countries were characterized using the MultiLocus Enzyme Electrophoresis (MLEE) and the MultiLocus Sequence Typing (MLST) approaches. The results of the genetic and phylogenetic analyses strongly support the hypothesis that L. killicki belongs to the L. tropica complex. Our data suggest that L. killicki emerged from a single founder event and that it evolved independently from L. tropica. However, they do not validate the hypothesis that L. killicki is a distinct complex. Therefore, we suggest naming this taxon L. killicki (synonymous L. tropica) until further epidemiological and phylogenetic studies justify the L. killicki denomination. This study provides taxonomic and phylogenetic information on L. killicki and improves our knowledge on the evolutionary history of this taxon.

Modeling influenza-like illnesses through composite compartmental models

NASA Astrophysics Data System (ADS)

Levy, Nir; , Michael, Iv; Yom-Tov, Elad

2018-03-01

Epidemiological models for the spread of pathogens in a population are usually only able to describe a single pathogen. This makes their application unrealistic in cases where multiple pathogens with similar symptoms are spreading concurrently within the same population. Here we describe a method which makes possible the application of multiple single-strain models under minimal conditions. As such, our method provides a bridge between theoretical models of epidemiology and data-driven approaches for modeling of influenza and other similar viruses. Our model extends the Susceptible-Infected-Recovered model to higher dimensions, allowing the modeling of a population infected by multiple viruses. We further provide a method, based on an overcomplete dictionary of feasible realizations of SIR solutions, to blindly partition the time series representing the number of infected people in a population into individual components, each representing the effect of a single pathogen. We demonstrate the applicability of our proposed method on five years of seasonal influenza-like illness (ILI) rates, estimated from Twitter data. We demonstrate that our method describes, on average, 44% of the variance in the ILI time series. The individual infectious components derived from our model are matched to known viral profiles in the populations, which we demonstrate matches that of independently collected epidemiological data. We further show that the basic reproductive numbers (R 0) of the matched components are in range known for these pathogens. Our results suggest that the proposed method can be applied to other pathogens and geographies, providing a simple method for estimating the parameters of epidemics in a population.

Unusual Enhancement in Intrinsic Thermal Conductivity of Multilayer Graphene by Tensile Strains

DOE PAGES

Kuang, Youdi; Lindsay, Lucas R.; Huang, Baoling

2015-01-01

High basal plane thermal conductivity k of multi-layer graphene makes it promising for thermal management applications. Here we examine the effects of tensile strain on thermal transport in this system. Using a first principles Boltzmann-Peierls equation for phonon transport approach, we calculate the room-temperature in-plane lattice k of multi-layer graphene (up to four layers) and graphite under different isotropic tensile strains. The calculated in-plane k of graphite, finite mono-layer graphene and 3-layer graphene agree well with previous experiments. The dimensional transitions of the intrinsic k and the extent of the diffusive transport regime from mono-layer graphene to graphite are presented.more » We find a peak enhancement of intrinsic k for multi-layer graphene and graphite with increasing strain and the largest enhancement amplitude is about 40%. In contrast the calculated intrinsic k with tensile strain decreases for diamond and diverges for graphene, we show that the competition between the decreased mode heat capacities and the increased lifetimes of flexural phonons with increasing strain contribute to this k behavior. Similar k behavior is observed for 2-layer hexagonal boron nitride systems, suggesting that it is an inherent thermal transport property in multi-layer systems assembled of purely two dimensional atomic layers. This study provides insights into engineering k of multi-layer graphene and boron nitride by strain and into the nature of thermal transport in quasi-two-dimensional and highly anisotropic systems.« less

Hospital costs of nosocomial multi-drug resistant Pseudomonas aeruginosa acquisition

PubMed Central

2012-01-01

Background We aimed to assess the hospital economic costs of nosocomial multi-drug resistant Pseudomonas aeruginosa acquisition. Methods A retrospective study of all hospital admissions between January 1, 2005, and December 31, 2006 was carried out in a 420-bed, urban, tertiary-care teaching hospital in Barcelona (Spain). All patients with a first positive clinical culture for P. aeruginosa more than 48 h after admission were included. Patient and hospitalization characteristics were collected from hospital and microbiology laboratory computerized records. According to antibiotic susceptibility, isolates were classified as non-resistant, resistant and multi-drug resistant. Cost estimation was based on a full-costing cost accounting system and on the criteria of clinical Activity-Based Costing methods. Multivariate analyses were performed using generalized linear models of log-transformed costs. Results Cost estimations were available for 402 nosocomial incident P. aeruginosa positive cultures. Their distribution by antibiotic susceptibility pattern was 37.1% non-resistant, 29.6% resistant and 33.3% multi-drug resistant. The total mean economic cost per admission of patients with multi-drug resistant P. aeruginosa strains was higher than that for non-resistant strains (15,265 vs. 4,933 Euros). In multivariate analysis, resistant and multi-drug resistant strains were independently predictive of an increased hospital total cost in compared with non-resistant strains (the incremental increase in total hospital cost was more than 1.37-fold and 1.77-fold that for non-resistant strains, respectively). Conclusions P. aeruginosa multi-drug resistance independently predicted higher hospital costs with a more than 70% increase per admission compared with non-resistant strains. Prevention of the nosocomial emergence and spread of antimicrobial resistant microorganisms is essential to limit the strong economic impact. PMID:22621745

Hospital costs of nosocomial multi-drug resistant Pseudomonas aeruginosa acquisition.

PubMed

Morales, Eva; Cots, Francesc; Sala, Maria; Comas, Mercè; Belvis, Francesc; Riu, Marta; Salvadó, Margarita; Grau, Santiago; Horcajada, Juan P; Montero, Maria Milagro; Castells, Xavier

2012-05-23

We aimed to assess the hospital economic costs of nosocomial multi-drug resistant Pseudomonas aeruginosa acquisition. A retrospective study of all hospital admissions between January 1, 2005, and December 31, 2006 was carried out in a 420-bed, urban, tertiary-care teaching hospital in Barcelona (Spain). All patients with a first positive clinical culture for P. aeruginosa more than 48 h after admission were included. Patient and hospitalization characteristics were collected from hospital and microbiology laboratory computerized records. According to antibiotic susceptibility, isolates were classified as non-resistant, resistant and multi-drug resistant. Cost estimation was based on a full-costing cost accounting system and on the criteria of clinical Activity-Based Costing methods. Multivariate analyses were performed using generalized linear models of log-transformed costs. Cost estimations were available for 402 nosocomial incident P. aeruginosa positive cultures. Their distribution by antibiotic susceptibility pattern was 37.1% non-resistant, 29.6% resistant and 33.3% multi-drug resistant. The total mean economic cost per admission of patients with multi-drug resistant P. aeruginosa strains was higher than that for non-resistant strains (15,265 vs. 4,933 Euros). In multivariate analysis, resistant and multi-drug resistant strains were independently predictive of an increased hospital total cost in compared with non-resistant strains (the incremental increase in total hospital cost was more than 1.37-fold and 1.77-fold that for non-resistant strains, respectively). P. aeruginosa multi-drug resistance independently predicted higher hospital costs with a more than 70% increase per admission compared with non-resistant strains. Prevention of the nosocomial emergence and spread of antimicrobial resistant microorganisms is essential to limit the strong economic impact.

Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar III Strain PH-97028 (=CIP 109753).

PubMed

Criscuolo, Alexis; Chesneau, Olivier; Clermont, Dominique; Bizet, Chantal

2018-04-05

Flavobacterium columnare strain PH-97028 (=CIP 109753) is a genomovar III reference strain that was isolated from a diseased Ayu fish in Japan. We report here the analysis of the first available genomovar III sequence of this species to aid in identification, epidemiological tracking, and virulence studies. Copyright © 2018 Criscuolo et al.

Fruiting Body Formation of Cordyceps militaris from Multi-Ascospore Isolates and Their Single Ascospore Progeny Strains

PubMed Central

Shrestha, Bhushan; Han, Sang-Kuk; Sung, Jae-Mo

2012-01-01

Interest in commercial cultivation and product development of Cordyceps species has shown a recent increase. Due to its biochemical and pharmacological effects, Cordyceps militaris, commonly known as orange caterpillar fungus, is being investigated with great interest. Cultivation of C. militaris has been practiced on a large scale in order to fulfill a demand for scientific investigation and product development. Isolates of C. militaris can be easily established from both spores and tissue. For isolation of spores, ascospores released from mature stromata are trapped in sterile medium. Multi-ascospore isolates, as well as combinations of single ascospore strains, are used for production of fruiting bodies. Progeny ascospore strains can be isolated from artificial fruiting bodies, thus, the cycle of fruiting body production can be continued for a long period of time. In this study, we examined fruiting body production from multi-ascospore isolates and their progeny strains for three generations. F1 progeny strains generally produced a larger number of fruiting bodies, compared with their mother multi-ascospore isolates; however, F2 and F3 progeny strains produced fewer fruiting bodies. Optimum preservation conditions could help to increase the vitality of the progeny strains. In order to retain the fruiting ability of the strains, further testing of various methods of preservation and different methods for isolation should be performed. PMID:22870051

Epidemiological Investigation of Vaginal Saccharomyces cerevisiae Isolates by a Genotypic Method

PubMed Central

McCullough, Michael J.; Clemons, Karl V.; Farina, Claudio; McCusker, John H.; Stevens, David A.

1998-01-01

Saccharomyces cerevisiae is a ubiquitous, ascomycetous yeast, and vaginitis caused by this organism has been reported only very rarely. The aim of the present investigation was to assess the epidemiological relatedness of a group of vaginal and commercial S. cerevisiae isolates by a previously reported genetic typing method, which divided the isolates into two broad groups with numerous subtypes. Nineteen S. cerevisiae isolates obtained from patients suffering from vaginitis and four isolates from commercial products in the same city were analyzed. The cellular DNA from each isolate was digested with the restriction endonuclease EcoRI, and restriction fragment length polymorphisms were generated by horizontal gel electrophoresis. The results showed that although vaginal isolates did not cluster in any particular genetic subtype, multiple patients were infected with indistinguishable strains (there were nine distinct strains among 23 isolates). For two of three patients, all three with two episodes of S. cerevisiae vaginitis, different strains were isolated during the recurrence of this disease. Three other patients with indistinguishable isolates were epidemiologically related in that two were practitioners in the same clinic and the third was a patient at this clinic. We also found that one commercial strain was indistinguishable from the strain isolated from three different women at the time that they were suffering from vaginitis. The findings of the present study suggest that some S. cerevisiae strains may possess properties permitting persistence in the human host. Furthermore, person-to-person contact and the proliferation of the use of S. cerevisiae as a health-food product, in home baking, and in home brewing may be a contributing factor in human colonization and infection with this organism. PMID:9466776

Changing epidemiology of rotavirus G-types circulating in Hong Kong, China.

PubMed

Lo, Janice Yee Chi; Szeto, Kai Cheung; Tsang, Dominic Ngai Chong; Leung, Kwok Hung; Lim, Wilina Wei Ling

2005-01-01

Group A rotaviruses are the most common cause of severe diarrhoeal disease in young children worldwide. The development of a vaccine is advocated by the World Health Organization. Obtaining local baseline information regarding rotavirus strain variation is important to ensure matching of circulating and vaccine strains. The current study was undertaken to determine the epidemiology of rotavirus G-types in Hong Kong in anticipation of a vaccination program. From 2001 to 2002 over a period of one year, diarrhoeal stool specimens known to be positive for rotavirus were subjected to G-typing by reverse transcriptase-polymerase chain reaction using nested type-specific primers. Rotavirus G-type distribution was correlated with patient demographics. Among 747 rotavirus positive stool specimens, 723 strains could be G-typed as G1 (302, 40.4%), G2 (128, 17.1%), G3 (231, 30.9%), G4 (24, 3.2%), and G9 (38, 5.1%). G1 strains were found predominantly in those 5 years old or younger (P < 0.0001), while G2 strains were more prevalent among those over 5 years of age (P < 0.001). When compared with similar studies in 1983 to 1984 and 1999 to 2000, there were significant changes in the prevalence of various G-types, with consistent detection of G9 strains in the current study. It is concluded that rotavirus G-type distribution in Hong Kong has varied with time. Continuous monitoring of the epidemiology of rotavirus is important, especially in anticipation of the introduction of a vaccine, in order to document its impact and to ensure its continued effectiveness. Copyright 2005 Wiley-Liss, Inc.

Avian influenza A (H7N9) virus infection in humans: epidemiology, evolution, and pathogenesis.

PubMed

Husain, Matloob

2014-12-01

New human influenza A virus strains regularly emerge causing seasonal epidemics and occasional pandemics. Lately, several zoonotic avian influenza A strains have been reported to directly infect humans. In early 2013, a novel avian influenza A virus (H7N9) strain was discovered in China to cause severe respiratory disease in humans. Since then, over 450 human cases of H7N9 infection have been discovered and 165 of them have died. Multiple epidemiological, phylogenetic, in vivo, and in vitro studies have been done to determine the origin and pathogenesis of novel H7N9 strain. This article reviews the literature related to the epidemiology, evolution, and pathogenesis of the H7N9 strain since its discovery in February 2013 till August 2014. The data available so far indicate that H7N9 was originated by a two-step reassortment process in birds and transmitted to humans through direct contact with live-bird markets. H7N9 is a low-pathogenic avian virus and contains several molecular signatures for adaptation in mammals. The severity of the respiratory disease caused by novel H7N9 virus in humans can be partly attributed to the age, sex, and underlying medical conditions of the patients. A universal influenza vaccine is not available, though several strain-specific H7N9 candidate vaccine viruses have been developed. Further, novel H7N9 virus is resistant to antiviral drug amantadine and some H7N9 isolates have acquired the resistance to neuraminidase-inhibitors. Therefore, constant surveillance and prompt control measures combined with novel research approaches to develop alternative and effective anti-influenza strategies are needed to overcome influenza A virus. Copyright © 2014 Elsevier B.V. All rights reserved.

Haemophilus ducreyi Cutaneous Ulcer Strains Diverged from Both Class I and Class II Genital Ulcer Strains: Implications for Epidemiological Studies.

PubMed

Gangaiah, Dharanesh; Spinola, Stanley M

2016-12-01

Haemophilus ducreyi has emerged as a major cause of cutaneous ulcers (CU) in yaws-endemic regions of the tropics in the South Pacific, South East Asia and Africa. H. ducreyi was once thought only to cause the genital ulcer (GU) disease chancroid; GU strains belong to 2 distinct classes, class I and class II. Using whole-genome sequencing of 4 CU strains from Samoa, 1 from Vanuatu and 1 from Papua New Guinea, we showed that CU strains diverged from the class I strain 35000HP and that one CU strain expressed β-lactamase. Recently, the Center for Disease Control and Prevention released the genomes of 11 additional CU strains from Vanuatu and Ghana; however, the evolutionary relationship of these CU strains to previously-characterized CU and GU strains is unknown. We performed phylogenetic analysis of 17 CU and 10 GU strains. Class I and class II GU strains formed two distinct clades. The class I strains formed two subclades, one containing 35000HP and HD183 and the other containing the remainder of the class I strains. Twelve of the CU strains formed a subclone under the class I 35000HP subclade, while 2 CU strains formed a subclone under the other class I subclade. Unexpectedly, 3 of the CU strains formed a subclone under the class II clade. Phylogenetic analysis of dsrA-hgbA-ncaA sequences yielded a tree similar to that of whole-genome phylogenetic tree. CU strains diverged from multiple lineages within both class I and class II GU strains. Multilocus sequence typing of dsrA-hgbA-ncaA could be reliably used for epidemiological investigation of CU and GU strains. As class II strains grow relatively poorly and are relatively more susceptible to vancomycin than class I strains, these findings have implications for methods to recover CU strains. Comparison of contemporary CU and GU isolates would help clarify the relationship between these entities.

Stability analysis of multi-group deterministic and stochastic epidemic models with vaccination rate

NASA Astrophysics Data System (ADS)

Wang, Zhi-Gang; Gao, Rui-Mei; Fan, Xiao-Ming; Han, Qi-Xing

2014-09-01

We discuss in this paper a deterministic multi-group MSIR epidemic model with a vaccination rate, the basic reproduction number ℛ0, a key parameter in epidemiology, is a threshold which determines the persistence or extinction of the disease. By using Lyapunov function techniques, we show if ℛ0 is greater than 1 and the deterministic model obeys some conditions, then the disease will prevail, the infective persists and the endemic state is asymptotically stable in a feasible region. If ℛ0 is less than or equal to 1, then the infective disappear so the disease dies out. In addition, stochastic noises around the endemic equilibrium will be added to the deterministic MSIR model in order that the deterministic model is extended to a system of stochastic ordinary differential equations. In the stochastic version, we carry out a detailed analysis on the asymptotic behavior of the stochastic model. In addition, regarding the value of ℛ0, when the stochastic system obeys some conditions and ℛ0 is greater than 1, we deduce the stochastic system is stochastically asymptotically stable. Finally, the deterministic and stochastic model dynamics are illustrated through computer simulations.

Modelling Marek's Disease Virus (MDV) infection: parameter estimates for mortality rate and infectiousness

PubMed Central

2011-01-01

Background Marek's disease virus (MDV) is an economically important oncogenic herpesvirus of poultry. Since the 1960s, increasingly virulent strains have caused continued poultry industry production losses worldwide. To understand the mechanisms of this virulence evolution and to evaluate the epidemiological consequences of putative control strategies, it is imperative to understand how virulence is defined and how this correlates with host mortality and infectiousness during MDV infection. We present a mathematical approach to quantify key epidemiological parameters. Host lifespan, virus latent periods and host viral shedding rates were estimated for unvaccinated and vaccinated birds, infected with one of three MDV strains. The strains had previously been pathotyped to assign virulence scores according to pathogenicity of strains in hosts. Results Our analyses show that strains of higher virulence have a higher viral shedding rate, and more rapidly kill hosts. Vaccination enhances host life expectancy but does not significantly reduce the shedding rate of the virus. While the primary latent period of the virus does not vary with challenge strain nor vaccine treatment of host, the time until the maximum viral shedding rate is increased with vaccination. Conclusions Our approach provides the tools necessary for a formal analysis of the evolution of virulence in MDV, and potentially simpler and cheaper approaches to comparing the virulence of MDV strains. PMID:22078942

Pharmacokinetic-Pharmacodynamic Model To Evaluate Intramuscular Tetracycline Treatment Protocols To Prevent Antimicrobial Resistance in Pigs

PubMed Central

Ahmad, Amais; Græsbøll, Kaare; Christiansen, Lasse Engbo; Toft, Nils; Matthews, Louise

2014-01-01

High instances of antimicrobial resistance are linked to both routine and excessive antimicrobial use, but excessive or inappropriate use represents an unnecessary risk. The competitive growth advantages of resistant bacteria may be amplified by the strain dynamics; in particular, the extent to which resistant strains outcompete susceptible strains under antimicrobial pressure may depend not only on the antimicrobial treatment strategies but also on the epidemiological parameters, such as the composition of the bacterial strains in a pig. This study evaluated how variation in the dosing protocol for intramuscular administration of tetracycline and the composition of bacterial strains in a pig affect the level of resistance in the intestine of a pig. Predictions were generated by a mathematical model of competitive growth of Escherichia coli strains in pigs under specified plasma concentration profiles of tetracycline. All dosing regimens result in a clear growth advantage for resistant strains. Short treatment duration was found to be preferable, since it allowed less time for resistant strains to outcompete the susceptible ones. Dosing frequency appeared to be ineffective at reducing the resistance levels. The number of competing strains had no apparent effect on the resistance level during treatment, but possession of fewer strains reduced the time to reach equilibrium after the end of treatment. To sum up, epidemiological parameters may have more profound influence on growth dynamics than dosing regimens and should be considered when designing improved treatment protocols. PMID:25547361

["Group" and organization: a dimension of collaboration of anthropology and epidemiology].

PubMed

Song, Lei-ming; Wang, Ning

2012-04-01

"Group" is a key concept in epidemiological research and "organization" is a core concept in anthropology. Group takes focus on the specific characteristics of the subjects, while organization takes focus on the relationship between the objects. For the characteristics and relationship of the objects that interacting with each other, the two concepts could be complementary in specific studies, and this will be the basic dimension of Interdisciplinary collaboration of anthropology and epidemiology.

Genotyping of Mycobacterium tuberculosis with additional markers enhances accuracy in epidemiological studies.

PubMed Central

Warren, R; Richardson, M; Sampson, S; Hauman, J H; Beyers, N; Donald, P R; van Helden, P D

1996-01-01

Two highly polymorphic Mycobacterium tuberculosis genomic domains, characterized by hybridization to the oligonucleotide (GTG)5, were identified as potential DNA fingerprinting probes. These domains were cloned [pMTB484(1) and pMTB484(2K4), respectively] and shown to be useful for genotype analysis by Southern blotting. These probes were used to genotype geographically linked strains of M. tuberculosis previously shown to have identical IS6110 fingerprints. Subsequent DNA fingerprints generated with MTB484(1) and MTB484(2K4) showed a high degree of polymorphism, allowing subclassification of IS6110-defined clusters into composites of smaller clusters and unique strains. Correlation of the molecular data with patient interviews and clinical records confirmed the sensitivity of these probes, as contacts were established only within subclusters. These findings demonstrate the requirement for multiple probes to accurately classify M. tuberculosis strains, even those with high copy numbers of IS6110. The enhanced accuracy of strain typing should, in turn, further our understanding of the epidemiology of tuberculosis. PMID:8862588

Influence of vectors' risk-spreading strategies and environmental stochasticity on the epidemiology and evolution of vector-borne diseases: the example of Chagas' disease.

PubMed

Pelosse, Perrine; Kribs-Zaleta, Christopher M; Ginoux, Marine; Rabinovich, Jorge E; Gourbière, Sébastien; Menu, Frédéric

2013-01-01

Insects are known to display strategies that spread the risk of encountering unfavorable conditions, thereby decreasing the extinction probability of genetic lineages in unpredictable environments. To what extent these strategies influence the epidemiology and evolution of vector-borne diseases in stochastic environments is largely unknown. In triatomines, the vectors of the parasite Trypanosoma cruzi, the etiological agent of Chagas' disease, juvenile development time varies between individuals and such variation most likely decreases the extinction risk of vector populations in stochastic environments. We developed a simplified multi-stage vector-borne SI epidemiological model to investigate how vector risk-spreading strategies and environmental stochasticity influence the prevalence and evolution of a parasite. This model is based on available knowledge on triatomine biodemography, but its conceptual outcomes apply, to a certain extent, to other vector-borne diseases. Model comparisons between deterministic and stochastic settings led to the conclusion that environmental stochasticity, vector risk-spreading strategies (in particular an increase in the length and variability of development time) and their interaction have drastic consequences on vector population dynamics, disease prevalence, and the relative short-term evolution of parasite virulence. Our work shows that stochastic environments and associated risk-spreading strategies can increase the prevalence of vector-borne diseases and favor the invasion of more virulent parasite strains on relatively short evolutionary timescales. This study raises new questions and challenges in a context of increasingly unpredictable environmental variations as a result of global climate change and human interventions such as habitat destruction or vector control.

Influence of Vectors’ Risk-Spreading Strategies and Environmental Stochasticity on the Epidemiology and Evolution of Vector-Borne Diseases: The Example of Chagas’ Disease

PubMed Central

Pelosse, Perrine; Kribs-Zaleta, Christopher M.; Ginoux, Marine; Rabinovich, Jorge E.; Gourbière, Sébastien; Menu, Frédéric

2013-01-01

Insects are known to display strategies that spread the risk of encountering unfavorable conditions, thereby decreasing the extinction probability of genetic lineages in unpredictable environments. To what extent these strategies influence the epidemiology and evolution of vector-borne diseases in stochastic environments is largely unknown. In triatomines, the vectors of the parasite Trypanosoma cruzi, the etiological agent of Chagas’ disease, juvenile development time varies between individuals and such variation most likely decreases the extinction risk of vector populations in stochastic environments. We developed a simplified multi-stage vector-borne SI epidemiological model to investigate how vector risk-spreading strategies and environmental stochasticity influence the prevalence and evolution of a parasite. This model is based on available knowledge on triatomine biodemography, but its conceptual outcomes apply, to a certain extent, to other vector-borne diseases. Model comparisons between deterministic and stochastic settings led to the conclusion that environmental stochasticity, vector risk-spreading strategies (in particular an increase in the length and variability of development time) and their interaction have drastic consequences on vector population dynamics, disease prevalence, and the relative short-term evolution of parasite virulence. Our work shows that stochastic environments and associated risk-spreading strategies can increase the prevalence of vector-borne diseases and favor the invasion of more virulent parasite strains on relatively short evolutionary timescales. This study raises new questions and challenges in a context of increasingly unpredictable environmental variations as a result of global climate change and human interventions such as habitat destruction or vector control. PMID:23951018

Ribotyping for differentiating Flavobacterium meningosepticum isolates from clinical and environmental sources.

PubMed Central

Colding, H; Bangsborg, J; Fiehn, N E; Bennekov, T; Bruun, B

1994-01-01

On the basis of DNA-DNA hybridization data, two main genomic relatedness groups (I and II) have been reported for a geographically varied collection of 52 strains of Flavobacterium meningosepticum. Herein, we have shown that genomic group II can be further divided into four subgroups (II:1 to II:4). To examine the taxonomic relevance of the ribosomal patterns of the 52 F. meningosepticum strains, the patterns were compared with existing DNA-DNA hybridization data with restriction enzymes PstI and HindIII. Ribotyping of the 52 F. meningosepticum strains showed banding patterns that could identify them correctly to one of the five genomic groups or subgroups. To assess the value of ribotyping for the interpretation of epidemiological data, the discriminatory power of the method was investigated for the 52 F. meningosepticum strains. With one to four restriction enzymes (PstI, HindIII, ClaI, EcoRI), a discriminatory index of 0.95 to 0.97 was found. The value of ribotyping in an epidemiological setting was assessed for three clinical isolates of F. meningosepticum from an outbreak of meningitis and bacteremia in the neonatal intensive care unit, Rigshospitalet, Copenhagen, Denmark. The three clinical isolates were shown to belong to the same ribotype, characteristic of genomic subgroup II:1. This ribotyping method will prove to be a useful tool for epidemiological studies concerning F. meningosepticum in the future. Images PMID:8150962

Molecular Epidemiology of Staphylococcus aureus Colonization in 2 Long-Term Care Facilities

PubMed Central

Mody, Lona; Flannery, Erica; Bielaczyc, Andrew; Bradley, Suzanne F.

2012-01-01

Persistent colonization with Staphylococcus aureus was assessed in 22 nursing home residents. Eighteen residents (82%) remained colonized with the same strain found at baseline; 6 (33%) of 18 residents transiently acquired a new strain. Four residents (18%) acquired a new persistent strain. Residents colonized with methicillin-resistant S. aureus were more likely to acquire a new strain (67%) than were residents colonized with methicillin-susceptible S. aureus (20%) (P =.04). PMID:16465644

Experimental evolution in silico: a custom-designed mathematical model for virulence evolution of Bacillus thuringiensis.

PubMed

Strauß, Jakob Friedrich; Crain, Philip; Schulenburg, Hinrich; Telschow, Arndt

2016-08-01

Most mathematical models on the evolution of virulence are based on epidemiological models that assume parasite transmission follows the mass action principle. In experimental evolution, however, mass action is often violated due to controlled infection protocols. This "theory-experiment mismatch" raises the question whether there is a need for new mathematical models to accommodate the particular characteristics of experimental evolution. Here, we explore the experimental evolution model system of Bacillus thuringiensis as a parasite and Caenorhabditis elegans as a host. Recent experimental studies with strict control of parasite transmission revealed that one-sided adaptation of B. thuringiensis with non-evolving hosts selects for intermediate or no virulence, sometimes coupled with parasite extinction. In contrast, host-parasite coevolution selects for high virulence and for hosts with strong resistance against B. thuringiensis. In order to explain the empirical results, we propose a new mathematical model that mimics the basic experimental set-up. The key assumptions are: (i) controlled parasite transmission (no mass action), (ii) discrete host generations, and (iii) context-dependent cost of toxin production. Our model analysis revealed the same basic trends as found in the experiments. Especially, we could show that resistant hosts select for highly virulent bacterial strains. Moreover, we found (i) that the evolved level of virulence is independent of the initial level of virulence, and (ii) that the average amount of bacteria ingested significantly affects the evolution of virulence with fewer bacteria ingested selecting for highly virulent strains. These predictions can be tested in future experiments. This study highlights the usefulness of custom-designed mathematical models in the analysis and interpretation of empirical results from experimental evolution. Copyright © 2016 The Authors. Published by Elsevier GmbH.. All rights reserved.

Epidemiological survey of Streptococcus mutans among Japanese children. Identification and serological typing of the isolated strains.

PubMed

Hamada, S; Masuda, N; Ooshima, T; Sobue, S; Kotani, S

1976-02-01

An epidemiological investigation was carried out to identify and determine the serotypes of Streptococcus mutans from carious lesions of young Japanese children. For this purpose, a direct fluorescent antibody technique was mainly used. Fluorescein isothiocyanate-conjugated antibodies were prepared for the five known serotypes of S. mutans. Cross reactions and nonspecific reactions were eliminated by adsorption, counterstaining, or DEAE-cellulosecolumn chromatography. Agar-gel immunodiffusion was used to distinguish between serotypes a and d. The epidemiological survey suggested that serotype c strains were most prevalent in dental plaques of Japanese children. The d and e serotypes were rare and serotypes a and b were not detected. It was also noted that more than one serotype of S. mutans could be found in the same locus of a carious lesion and that there might be no relationship between the degree of caries and the causative serotype(s) of S. mutans.

Development of Pollution Prevention Technologies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polle, Juergen; Sanchez-Delgado, Roberto

2013-12-30

This project investigated technologies that may reduce environmental pollution. This was a basic research/educational project addressing two major areas: A. In the algae research project, newly isolated strains of microalgae were investigated for feedstock production to address the production of renewable fuels. An existing collection of microalgae was screened for lipid composition to determine strains with superior composition of biofuel molecules. As many microalgae store triacylglycerides in so-called oil bodies, selected candidate strains identified from the first screen that accumulate oil bodies were selected for further biochemical analysis, because almost nothing was known about the biochemistry of these oil bodies.more » Understanding sequestration of triacylglycerides in intracellular storage compartments is essential to developing better strains for achieving high oil productivities by microalgae. At the onset of the project there was almost no information available on how to obtain detailed profiles of lipids from strains of microalgae. Our research developed analytical methods to determine the lipid profiles of novel microalgal strains. The project was embedded into other ongoing microalgal projects in the Polle laboratory. The project benefited the public, because students were trained in cell cultivation and in the operation of state-of-the-art analytical equipment. In addition, students at Brooklyn College were introduced into the concept of a systems biology approach to study algal biofuels production. B. A series of new nanostructured catalysts were synthesized, and characterized by a variety of physical and chemical methods. Our catalyst design leads to active nanostructures comprising small metal particles in intimate contact with strongly basic sites provided by the supports, which include poly(4-vinylpyridine), magnesium oxide, functionalized multi-walled carbon nanotubes, and graphene oxide. The new materials display a good potential as catalysts for reactions of relevance to the manufacture of cleaner fossil fuels and biodiesel, and to hydrogen storage in organic liquids. Specifically the catalysts are highly active in the hydrogenation of aromatic and heteroaromatic components of fossil fuels, the reduction of unsaturated C=C bonds in biodiesel, and the dehydrogenation of nitrogen heterocycles. In the course of our studies we identified a novel dual-site substrate-dependent hydrogenation mechanism that explains the activity and selectivity data obtained and the resistance of the new catalysts to poisoning. These results represent an important advance in basic catalytic science, regarding design and synthesis and reaction mechanisms. Additionally, this project allowed the enhancement of the laboratory facilities in the Chemistry Department of Brooklyn College for catalysis and energy research, and served as an excellent vehicle for the training of several young researchers at the undergraduate, graduate and postdoctoral level, to join the national scientific workforce.« less

Constitutive relations describing creep deformation for multi-axial time-dependent stress states

NASA Astrophysics Data System (ADS)

McCartney, L. N.

1981-02-01

A THEORY of primary and secondary creep deformation in metals is presented, which is based upon the concept of tensor internal state variables and the principles of continuum mechanics and thermodynamics. The theory is able to account for both multi-axial and time-dependent stress and strain states. The wellknown concepts of elastic, anelastic and plastic strains follow naturally from the theory. Homogeneous stress states are considered in detail and a simplified theory is derived by linearizing with respect to the internal state variables. It is demonstrated that the model can be developed in such a way that multi-axial constant-stress creep data can be presented as a single relationship between an equivalent stress and an equivalent strain. It is shown how the theory may be used to describe the multi-axial deformation of metals which are subjected to constant stress states. The multi-axial strain response to a general cyclic stress state is calculated. For uni-axial stress states, square-wave loading and a thermal fatigue stress cycle are analysed.

Rapid genotyping of Legionella pneumophila serogroup 1 strains by a novel DNA microarray-based assay during the outbreak investigation in Warstein, Germany 2013.

PubMed

Petzold, Markus; Ehricht, Ralf; Slickers, Peter; Pleischl, Stefan; Brockmann, Ansgar; Exner, Martin; Monecke, Stefan; Lück, Christian

2017-06-01

Between 1 August and 6 September 2013, an outbreak of Legionnaires' disease (LD) with 78 cases confirmed by positive urinary antigen tests occurred in Warstein, North Rhine-Westphalia, Germany. Legionella (L.) pneumophila, serogroup (Sg) 1, monoclonal antibody (mAb) subgroup Knoxville, sequence type (ST) 345, was identified as the epidemic strain. This strain was isolated from seven patients. To detect the source of the infection, epidemiological typing of clinical and environmental strains was performed in two consecutive steps. First, strains were typed by monoclonal antibodies. Indistinguishable strains were further subtyped by sequence-based typing (SBT) which is the internationally recognized standard method for epidemiological genotyping of L. pneumophila. In an early stage of the outbreak investigation, many environmental isolates were found to belong to the mAb subgroup Knoxville, but to two different STs, namely to ST 345, the epidemic strain, and to ST 600. A majority of environmental isolates belonged to ST 600 whereas the epidemic ST 345 strain was less common in environmental samples. To rapidly distinguish both Knoxville strains, we applied a novel typing method based on DNA-hybridization on glass chips. The new assay can easily and rapidly discriminate L. pneumophila Sg 1 strains. Thus, we were able to quickly identify the sources harboring the epidemic strain, i.e., two cooling towers of different companies, the waste water treatment plants (WWTP) of the city and one company as well as water samples of the river Wester and its branches. Copyright © 2016 Elsevier GmbH. All rights reserved.

New insight into the epidemiology of rabbit hemorrhagic disease viruses in Portugal: retrospective study reveals the circulation of genogroup 5 (G5) in Azores and discloses the circulation of G1 and G6 strains in mainland until 2008.

PubMed

Duarte, Margarida Dias; Henriques, Ana Margarida; Barros, Sílvia; Luís, Tiago; Fagulha, Teresa; Ramos, Fernanda; Fevereiro, Miguel

2014-10-01

The genetic relationships between 10 rabbit hemorrhagic disease strains collected in Portugal between 2006 and 2013, originated in the mainland and Azorean islands, were investigated based on the vp60 gene variability. A genetic diversity ranging from 2% to 13% was determined among the 10-vp60 complete sequences revealing a significant level of genetic heterogeneity between same strains. Phylogenetic Bayesian analysis showed that the Portuguese RHDV strains fell within different genogroups, namely G1, G5 and G6. Interestingly, all strains obtained from Azores, where RHDV was first detected in 1988, belong to G5 genogroup. G5 strains, that were not identified in the continent so far, seem to be the dominant group in these Atlantic islands. G1-related strains belonging to the Iberian group 3 (n=3) and G6 (RHDVa) strains (n=2) were identified among the samples originated in mainland which were collected between 2006 and 2008. Although the presence of G1 and G6 in Portugal had been shown before, our data refines the time of circulation of these strains until at least 2008. In summary, this study revises the epidemiological information of RHDV in Portugal since it reports for the first time the presence of G5 strains in Azores and demonstrates the circulation of G1 and G6 strains in mainland Portugal until the late 2000s. Copyright © 2014 Elsevier B.V. All rights reserved.

Molecular epidemiology of yellow fever in Bolivia from 1999 to 2008.

PubMed

Baronti, Cécile; Goitia, Norma Janeth Velasquez; Cook, Shelley; Roca, Yelin; Revollo, Jimmy; Flores, Jorge Vargas; de Lamballerie, Xavier

2011-03-01

Yellow fever (YF) is a serious public health problem in Bolivia since at least the 19th century. Surprisingly, very limited information has been made available to date regarding the genetic characterisation and epidemiology of Bolivian YF virus (YFV) strains. Here, we conducted the genetic characterization of 12 human isolates of YFV collected in Bolivia between 1999 and 2008, by sequencing and analysis of two regions of the viral genome: a fragment encoding structural proteins "PrM" (premembrane and envelope) and a distal region "EMF," spanning the end of the virus genome. Our study reveals a high genetic diversity of YFV strains circulating in Bolivia during the last decade: we identified not only "Peruvian-like" genotype II viruses (related to previously characterized Bolivian strains), but also, for the fist time, "Brazilian-like" genotype I viruses. During the complete period of the study, only cases of "jungle" YF were detected (i.e., circulation of YFV via a sylvatic cycle) with no cluster of urban cases. However, the very significant spread of the Aedes aegypti mosquito across Bolivian cities threatens the country with the reappearance of an urban YFV transmission cycle and thus is required a sustained epidemiological surveillance.

Characterization of Carbapenem-Resistant Enterobacteriaceae with High Rate of Autochthonous Transmission in the Arabian Peninsula

PubMed Central

Sonnevend, Ágnes; Ghazawi, Akela A.; Hashmey, Rayhan; Jamal, Wafaa; Rotimi, Vincent O.; Shibl, Atef M.; Al-Jardani, Amina; Al-Abri, Seif S.; Tariq, Waheed U. Z.; Weber, Stefan; Pál, Tibor

2015-01-01

To establish the role of local transmission versus possible pathogen import due to previous foreign exposure in infections caused by carbapenem non-susceptible Enterobacteriaceae in the Arabian Peninsula, 200 independent isolates collected in 16 hospitals of Saudi Arabia, Kuwait, Oman and the United Arab Emirates were studied. All strains were multidrug resistant; 42.5% of them also qualified as extremely drug resistant. The frequency of various carbapenemases varied according to the participating countries, but in the collection, as a whole, bla NDM-1 was the most frequently encountered carbapenemase gene (46.5%) followed by bla OXA-48-like gene (32.5%). A comparatively high rate (8.9%) of multi-clonal strains carrying both bla NDM and bla OXA-48-like genes in the United Arab Emirates, representing the most resistant subgroup, was encountered. No KPC-expressing isolates were detected. Three major clones of bla NDM-1 carrying Klebsiella pneumoniae of ST152 (n = 22, Saudi Arabia), ST14 (n = 7, United Arab Emirates) and ST147 types (n = 9, Oman) were identified, the latter two clones carrying similar, but not identical HI1b incompatibility type plasmids of >170kb. While from 78.6% of the cases with documented foreign hospitalization bla NDM positive strains were isolated, these strains formed only 25.6% of all the isolates expressing this enzyme. In fact, 56.8% of the NDM, 75.7% of OXA-48-like and 90.9% of VIM positive strains were recovered from patients without documented foreign exposure, neither in the form of travel or prior hospitalization abroad, suggesting a high rate of autochthonous infections. This, considering the extensive links of these countries to the rest of the world, predicts that trends in the local epidemiology of carbapenem resistant strains may increasingly affect the spread of these pathogens on the global scale. These results call for improved surveillance of carbapenem resistant Enterobacteriaceae in the countries of the Arabian Peninsula. PMID:26110660

Wound infections with multi-drug resistant bacteria.

PubMed

Pîrvănescu, H; Bălăşoiu, M; Ciurea, M E; Bălăşoiu, A T; Mănescu, R

2014-01-01

Wound infections remain a public health problem, despite the progress made on improving surgical techniques and antibiotic prophylaxis application. Misuse of antibiotics to prevent bacterial infections leads to increased bacterial resistance and their dissemination. The study refers to 470 samples taken from wound infections of which only multi-drug resistant strains were selected for study, using two special culture mediums (Metistaph-2 for methicillin-resistant staphylococci and ESBLs-Agar for extended-spectrum betalactamases secreting bacteria). Sensitivity of these strains was tested using the diffusion method. Of all studied samples, a rate of 27.6 bacterial strains showed multi-drug resistance. Among them stood primarily Staphylococcus aureus; both MRSA strains and ESBL Gram negative bacteria studied showed high resistance to aminoglycosides, quinolones, third generation cephalosporins and low to fourth generation cephalosporins. No vancomycin resitant nor vancomycin-intermediate Staphylococcus aureus strains were isolated. Knowing the antibiotic resistance is very useful in antibiotic "cycling"application, avoiding this way the emergence of increased resistant strains. Celsius.

Epidemiology of Quadriceps Strains in National Collegiate Athletic Association Athletes, 2009–2010 Through 2014–2015

PubMed Central

Eckard, Timothy G.; Kerr, Zachary Y.; Padua, Darin A.; Djoko, Aristarque; Dompier, Thomas P.

2017-01-01

Context:  Few researchers have examined the rates and patterns of quadriceps strains in student-athletes in the National Collegiate Athletic Association (NCAA). Objective:  To describe the epidemiology of quadriceps strains in 25 NCAA sports during the 2009–2010 through 2014–2015 academic years. Design:  Descriptive epidemiology study. Setting:  Convenience sample of NCAA programs from 25 sports during the 2009–2010 through 2014–2015 academic years. Patients or Other Particpants:  Collegiate student-athletes participating in men's and women's NCAA athletics during the 2009–2010 through 2014–2015 academic years. Main Outcome Measure(s):  Aggregate quadriceps strain injury and exposure data from the NCAA Injury Surveillance Program during the 2009–2010 through 2014–2015 academic years were analyzed. Quadriceps strain injury rates and injury rate ratios (IRRs) were reported with 95% confidence intervals (CIs). Results:  Overall, 517 quadriceps strains were reported, resulting in an injury rate of 1.07/10 000 athlete-exposures (AEs). The sports with the highest overall quadriceps strain rates were women's soccer (5.61/10 000 AEs), men's soccer (2.52/10 000 AEs), women's indoor track (2.24/10 000 AEs), and women's softball (2.15/10 000 AEs). Across sex-comparable sports, women had a higher rate of quadriceps strains than men overall (1.97 versus 0.65/10 000 AEs; IRR = 3.03; 95% CI = 2.45, 3.76). The majority of quadriceps strains were sustained during practice (77.8%). However, the quadriceps strain rate was higher during competition than during practice (1.29 versus 1.02/10 000 AEs; IRR = 1.27; 95% CI = 1.03, 1.56). Most quadriceps strains occurred in the preseason (57.8%), and rates were higher during the preseason compared with the regular season (2.29 versus 0.63/10 000 AEs; IRR = 3.60; 95% CI = 3.02, 4.30). Common injury mechanisms were noncontact (63.2%) and overuse (21.9%). Most quadriceps strains restricted participation by less than 1 week (79.3%). Conclusions:  Across 25 sports, higher quadriceps strain rates were found in women versus men, in competitions versus practices, and in the preseason versus the regular season. Most quadriceps strains were minor in severity, although further surveillance is needed to better examine the risk factors associated with incidence and severity. PMID:28383282

Epidemiology of Brucellosis and Genetic Diversity of Brucella abortus in Kazakhstan

PubMed Central

Shevtsova, Elena; Shevtsov, Alexandr; Mukanov, Kasim; Filipenko, Maxim; Kamalova, Dinara; Sytnik, Igor; Syzdykov, Marat; Kuznetsov, Andrey; Akhmetova, Assel; Zharova, Mira; Karibaev, Talgat; Tarlykov, Pavel; Ramanculov, Erlan

2016-01-01

Brucellosis is a major zoonotic infection in Kazakhstan. However, there is limited data on its incidence in humans and animals, and the genetic diversity of prevalent strains is virtually unstudied. Additionally, there is no detailed overview of Kazakhstan brucellosis control and eradication programs. Here, we analyzed brucellosis epidemiological data, and assessed the effectiveness of eradication strategies employed over the past 70 years to counteract this infection. We also conducted multiple loci variable-number tandem repeat analysis (MLVA) of Brucella abortus strains found in Kazakhstan. We analyzed official data on the incidence of animal brucellosis in Kazakhstan. The records span more than 70 years of anti-brucellosis campaigns, and contain a brief description of the applied control strategies, their effectiveness, and their impact on the incidence in humans. The MLVA-16 method was used to type 94 strains of B. abortus and serial passages of B. abortus 82, a strain used in vaccines. MLVA-8 and MLVA-11 analyses clustered strains into a total of four and seven genotypes, respectively; it is the first time that four of these genotypes have been described. MLVA-16 analysis divided strains into 28 distinct genotypes having genetic similarity coefficient that varies from 60 to100% and a Hunter & Gaston diversity index of 0.871. MST analysis reconstruction revealed clustering into "Kazakhstani-Chinese (Central Asian)", "European" and "American" lines. Detection of multiple genotypes in a single outbreak confirms that poorly controlled trade of livestock plays a crucial role in the spread of infection. Notably, the MLVA-16 profile of the B. abortus 82 strain was unique and did not change during 33 serial passages. MLVA genotyping may thus be useful for epidemiological monitoring of brucellosis, and for tracking the source(s) of infection. We suggest that countrywide application of MLVA genotyping would improve the control of brucellosis in Kazakhstan. PMID:27907105

Epidemiology of Brucellosis and Genetic Diversity of Brucella abortus in Kazakhstan.

PubMed

Shevtsova, Elena; Shevtsov, Alexandr; Mukanov, Kasim; Filipenko, Maxim; Kamalova, Dinara; Sytnik, Igor; Syzdykov, Marat; Kuznetsov, Andrey; Akhmetova, Assel; Zharova, Mira; Karibaev, Talgat; Tarlykov, Pavel; Ramanculov, Erlan

2016-01-01

Brucellosis is a major zoonotic infection in Kazakhstan. However, there is limited data on its incidence in humans and animals, and the genetic diversity of prevalent strains is virtually unstudied. Additionally, there is no detailed overview of Kazakhstan brucellosis control and eradication programs. Here, we analyzed brucellosis epidemiological data, and assessed the effectiveness of eradication strategies employed over the past 70 years to counteract this infection. We also conducted multiple loci variable-number tandem repeat analysis (MLVA) of Brucella abortus strains found in Kazakhstan. We analyzed official data on the incidence of animal brucellosis in Kazakhstan. The records span more than 70 years of anti-brucellosis campaigns, and contain a brief description of the applied control strategies, their effectiveness, and their impact on the incidence in humans. The MLVA-16 method was used to type 94 strains of B. abortus and serial passages of B. abortus 82, a strain used in vaccines. MLVA-8 and MLVA-11 analyses clustered strains into a total of four and seven genotypes, respectively; it is the first time that four of these genotypes have been described. MLVA-16 analysis divided strains into 28 distinct genotypes having genetic similarity coefficient that varies from 60 to100% and a Hunter & Gaston diversity index of 0.871. MST analysis reconstruction revealed clustering into "Kazakhstani-Chinese (Central Asian)", "European" and "American" lines. Detection of multiple genotypes in a single outbreak confirms that poorly controlled trade of livestock plays a crucial role in the spread of infection. Notably, the MLVA-16 profile of the B. abortus 82 strain was unique and did not change during 33 serial passages. MLVA genotyping may thus be useful for epidemiological monitoring of brucellosis, and for tracking the source(s) of infection. We suggest that countrywide application of MLVA genotyping would improve the control of brucellosis in Kazakhstan.

Genomics, evolution, and molecular epidemiology of the Streptococcus bovis/Streptococcus equinus complex (SBSEC).

PubMed

Jans, Christoph; Meile, Leo; Lacroix, Christophe; Stevens, Marc J A

2015-07-01

The Streptococcus bovis/Streptococcus equinus complex (SBSEC) is a group of human and animal derived streptococci that are commensals (rumen and gastrointestinal tract), opportunistic pathogens or food fermentation associates. The classification of SBSEC has undergone massive changes and currently comprises 7 (sub)species grouped into four branches based on sequences identities: the Streptococcus gallolyticus, the Streptococcus equinus, the Streptococcus infantarius and the Streptococcus alactolyticus branch. In animals, SBSEC are causative agents for ruminal acidosis, potentially laminitis and infective endocarditis (IE). In humans, a strong association was established between bacteraemia, IE and colorectal cancer. Especially the SBSEC-species S. gallolyticus subsp. gallolyticus is an emerging pathogen for IE and prosthetic joint infections. S. gallolyticus subsp. pasteurianus and the S. infantarius branch are further associated with biliary and urinary tract infections. Knowledge on pathogenic mechanisms is so far limited to colonization factors such as pili and biofilm formation. Certain strain variants of S. gallolyticus subsp. macedonicus and S. infantarius subsp. infantarius are associated with traditional dairy and plant-based food fermentations and display traits suggesting safety. However, due to their close relationship to virulent strains, their use in food fermentation has to be critically assessed. Additionally, implementing accurate and up-to-date taxonomy is critical to enable appropriate treatment of patients and risk assessment of species and strains via recently developed multilocus sequence typing schemes to enable comparative global epidemiology. Comparative genomics revealed that SBSEC strains harbour genomics islands (GI) that seem acquired from other streptococci by horizontal gene transfer. In case of virulent strains these GI frequently encode putative virulence factors, in strains from food fermentation the GI encode functions that are pivotal for strain performance during fermentation. Comparative genomics is a powerful tool to identify acquired pathogenic functions, but there is still an urgent need for more physiological and epidemiological data to understand SBSEC-specific traits. Copyright © 2014 Elsevier B.V. All rights reserved.

[Epidemiology, clinical and microbiological characteristics of invasive streptococcal infections in Turkey, 2010-2011].

PubMed

Topkaya, Aynur Eren; Balıkcı, Ahmet; Aydın, Faruk; Hasçelik, Gülşen; Kayman, Tuba; Kesli, Recep; Aydemir, Söhret; Akyar, Işın; Gökalp, Aslı; Dündar, Günnur; Gürler, Nezahat; Perçin, Duygu; Fındık, Duygu; Avunduk, Haluk; Bayraktar, Banu

2014-01-01

A one-year active surveillance study was conducted to investigate the epidemiological and microbiological characteristics of invasive group A streptococci (GAS) infections in Turkey and to provide data for the establishment of national preventive strategies related to invasive GAS infections. A total of 46 clinical microbiology laboratories from 12 different regions of Turkey (Istanbul; Eastern and Western Marmara; Eastern and Western Blacksea; Aegean; Mediterranean; Western, Central, Northeastern, Middle-eastern and Southeastern Anatolia) participated in the study. Accordingly, GAS strains isolated from sterile body sites (blood, cerebrospinal, synovial, pleural, peritoneal, pericardial fluids) in the study centers between June 2010-June 2011, were sent to Maltepe University Hospital Clinical Microbiology Laboratory for microbiological confirmation and further analysis. The isolates were identified by conventional methods, and for serotyping, opacity factor (OF) and T protein types were investigated. For genotyping GAS lysate preparation, emm gene amplification and sequencing were performed by using the protocols recommended by Centers for Disease Control and Prevention. A total of 65 invasive GAS strains were isolated in 15 of the participant centers, during the study period. The rate of invasive GAS isolation exhibited regional variation, with the highest rates in the Eastern Blacksea (Trabzon, n= 19), followed by Istanbul (n= 17) and Western Anatolia (Ankara, Konya, n= 14). Of the patients with invasive GAS infection 33 were female, 32 were male, with the age range of 0-89 years. GAS strains were most commonly isolated from soft tissue specimens (n= 18), followed by abscess material (n= 10), sterile body fluids (n= 8) and blood (n= 7) samples. Serotyping revealed that 55% (36/65) of the strains were OF positive, and the majority of T protein was polygroup T (n= 20), followed by U (n= 14), B (n= 5), X (n= 3) and Y (n= 2). T protein was not detected in 22 isolates. The strains were found to have 17 different emm types;emm1 (n= 13), emm4 (n= 6), emm6 (n= 6), emm12 (n= 6), emm24 (n= 4), emm14 (n= 3) and emm28 (n= 3). Nine of the strains could not be typed by sequencing. The correlation between emm typing and serotyping was detected as 58%. It was observed that 26-valent vaccines included 70.5% of the invasive GAS strains included in this study. Our study provided initial data concerning the epidemiological properties of invasive GAS infections and characterization of GAS strains in Turkey. The incidence of invasive GAS infections is low in our country. Although immunization programme by 26-valent GAS vaccine is not currently an urgent public health issue for our country, the results of this study indicated that emm types 4 and 24 should better be included in such a vaccine to be used in Turkey. Additionally, since epidemiological features of GAS infections and the microbiological characteristics of the strains can vary by time, for the diagnosis of invasive streptococcal infections and to take the necessary preventive measures, epidemiological studies should be conducted repeatedly.

Strain and Torsion Quantification in Mouse Hearts under Dobutamine Stimulation using 2D Multi-Phase MR DENSE

PubMed Central

Zhong, Jia; Yu, Xin

2010-01-01

In the current study, a 2D multi-phase MR displacement encoding with stimulated echoes (DENSE) imaging and analysis method was developed for direct quantification of Lagrangian strain in the mouse heart. Using the proposed method, less than 10 ms temporal resolution and 0.56 mm in-plane resolution were achieved. A validation study that compared strain calculation by DENSE and by MR tagging showed high correlation between the two methods (R2 > 0.80). Regional ventricular wall strain and twist were characterized in mouse hearts at baseline and under dobutamine stimulation. Dobutamine stimulation induced significant increase in radial and circumferential strains and torsion at peak-systole. A rapid untwisting was also observed during early diastole. This work demonstrates the capability of characterizing cardiac functional response to dobutamine stimulation in the mouse heart using 2D multi-phase MR DENSE. PMID:20740659

The Role of School Culture and Basic Psychological Needs on Iranian Adolescents' Academic Alienation: A Multi-Level Examination

ERIC Educational Resources Information Center

Mahmoudi, Hojjat; Brown, Monica R.; Amani Saribagloo, Javad; Dadashzadeh, Shiva

2018-01-01

This aim of this current research was a multi-level analysis of the relationship between school culture, basic psychological needs, and adolescents' academic alienation. One thousand twenty-nine (N = 1,029) high school students from Qom City were randomly selected through a multi-phase cluster sampling method and answered questions regarding…

SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel

PubMed Central

Chen, Bowang; Wilkening, Stefan; Drechsel, Marion; Hemminki, Kari

2009-01-01

Background Single nucleotide polymorphism (SNP) genotyping is a major activity in biomedical research. Scientists prefer to have a facile access to the results which may require conversions between data formats. First hand SNP data is often entered in or saved in the MS-Excel format, but this software lacks genetic and epidemiological related functions. A general tool to do basic genetic and epidemiological analysis and data conversion for MS-Excel is needed. Findings The SNP_tools package is prepared as an add-in for MS-Excel. The code is written in Visual Basic for Application, embedded in the Microsoft Office package. This add-in is an easy to use tool for users with basic computer knowledge (and requirements for basic statistical analysis). Conclusion Our implementation for Microsoft Excel 2000-2007 in Microsoft Windows 2000, XP, Vista and Windows 7 beta can handle files in different formats and converts them into other formats. It is a free software. PMID:19852806

SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel.

PubMed

Chen, Bowang; Wilkening, Stefan; Drechsel, Marion; Hemminki, Kari

2009-10-23

Single nucleotide polymorphism (SNP) genotyping is a major activity in biomedical research. Scientists prefer to have a facile access to the results which may require conversions between data formats. First hand SNP data is often entered in or saved in the MS-Excel format, but this software lacks genetic and epidemiological related functions. A general tool to do basic genetic and epidemiological analysis and data conversion for MS-Excel is needed. The SNP_tools package is prepared as an add-in for MS-Excel. The code is written in Visual Basic for Application, embedded in the Microsoft Office package. This add-in is an easy to use tool for users with basic computer knowledge (and requirements for basic statistical analysis). Our implementation for Microsoft Excel 2000-2007 in Microsoft Windows 2000, XP, Vista and Windows 7 beta can handle files in different formats and converts them into other formats. It is a free software.

An Assessment of Physician Knowledge of Epidemiology and Biostatistics.

ERIC Educational Resources Information Center

Weiss, Scott T.; Samet, Jonathan M.

1980-01-01

A study designed to assess knowledge of biostatistics and epidemiology relevant to medical literature and administered to internists and medical house staff at a teaching hospital is assessed. The results of the study suggest that knowledge of basic biostatistics and of study design is important for reading medical literature. (Author/MLW)

Methicillin-resistant Staphylococcus aureus in public transportation vehicles (buses): another piece to the epidemiologic puzzle.

PubMed

Lutz, Jonathan K; van Balen, Joany; Crawford, John Mac; Wilkins, John R; Lee, Jiyoung; Nava-Hoet, Rocio C; Hoet, Armando E

2014-12-01

Little is known about the occurrence and epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in public transportation in the United States. This research sought to determine the background prevalence and phenotypic and genotypic characteristics of MRSA strains circulating on buses from a large, metropolitan transportation agency. Electrostatic wipes were used to collect 237 surface samples from 40 buses randomly selected from July-October 2010. Six samples were collected from each bus immediately postservice and before any cleaning and disinfection. Positive isolates were analyzed for antibiotic resistance, staphylococcal cassette chromosome mec (SCCmec) type, and pulsed-field gel electrophoresis; and potential epidemiologic factors were examined. Of the buses, 68% (27/40) were contaminated with S aureus, and 63% (25/40) were contaminated with MRSA. Seats and seat rails were the surfaces most frequently contaminated, followed by the back door and stanchions. Most (62.9%) of the MRSA isolates were classified as community-associated MRSA clones (SCCmec type IV), and 22.9% were health care-associated MRSA clones (SCCmec type II). Of the MRSA strains, 65% (5/20) were multidrug resistant. MRSA was frequently isolated from commonly touched surfaces in buses serving both hospital and community routes. Phenotypic and genotypic analysis demonstrated that buses may be effective mixing vessels for MRSA strains of both community and health care-associated origin. Copyright © 2014 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Molecular subtyping of Clostridium perfringens by pulsed-field gel electrophoresis to facilitate food-borne-disease outbreak investigations.

PubMed

Maslanka, S E; Kerr, J G; Williams, G; Barbaree, J M; Carson, L A; Miller, J M; Swaminathan, B

1999-07-01

Clostridium perfringens is a common cause of food-borne illness. The illness is characterized by profuse diarrhea and acute abdominal pain. Since the illness is usually self-limiting, many cases are undiagnosed and/or not reported. Investigations are often pursued after an outbreak involving large numbers of people in institutions, at restaurants, or at catered meals. Serotyping has been used in the past to assist epidemiologic investigations of C. perfringens outbreaks. However, serotyping reagents are not widely available, and many isolates are often untypeable with existing reagents. We developed a pulsed-field gel electrophoresis (PFGE) method for molecular subtyping of C. perfringens isolates to aid in epidemiologic investigations of food-borne outbreaks. Six restriction endonucleases (SmaI, ApaI, FspI, MluI, KspI, and XbaI) were evaluated with a select panel of C. perfringens strains. SmaI was chosen for further studies because it produced 11 to 13 well-distributed bands of 40 to approximately 1,100 kb which provided good discrimination between isolates. Seventeen distinct patterns were obtained with 62 isolates from seven outbreak investigations or control strains. In general, multiple isolates from a single individual had indistinguishable PFGE patterns. Epidemiologically unrelated isolates (outbreak or control strains) had unique patterns; isolates from different individuals within an outbreak had similar, if not identical, patterns. PFGE identifies clonal relationships of isolates which will assist epidemiologic investigations of food-borne-disease outbreaks caused by C. perfringens.

Genome analysis of Mycoplasma synoviae strain MS-H, the most common M. synoviae strain with a worldwide distribution.

PubMed

Zhu, Ling; Shahid, Muhammad A; Markham, John; Browning, Glenn F; Noormohammadi, Amir H; Marenda, Marc S

2018-02-02

The bacterial pathogen Mycoplasma synoviae can cause subclinical respiratory disease, synovitis, airsacculitis and reproductive tract disease in poultry and is a major cause of economic loss worldwide. The M. synoviae strain MS-H was developed by chemical mutagenesis of an Australian isolate and has been used as a live attenuated vaccine in many countries over the past two decades. As a result it may now be the most prevalent strain of M. synoviae globally. Differentiation of the MS-H vaccine from local field strains is important for epidemiological investigations and is often required for registration of the vaccine. The complete genomic sequence of the MS-H strain was determined using a combination of Illumina and Nanopore methods and compared to WVU-1853, the M. synoviae type strain isolated in the USA 30 years before the parent strain of MS-H, and MS53, a more recent isolate from Brazil. The vaccine strain genome had a slightly larger number of pseudogenes than the two other strains and contained a unique 55 kb chromosomal inversion partially affecting a putative genomic island. Variations in gene content were also noted, including a deoxyribose-phosphate aldolase (deoC) fragment and an ATP-dependent DNA helicase gene found only in MS-H. Some of these sequences may have been acquired horizontally from other avian mycoplasma species. MS-H was somewhat more similar to WVU-1853 than to MS53. The genome sequence of MS-H will enable identification of vaccine-specific genetic markers for use as diagnostic and epidemiological tools to better control M. synoviae.

A Proof-of-Concept Approach for Quantifying Multi-Pollutant Health Impacts Using the Open-Source BenMAP-CE Software Program

EPA Science Inventory

Background Air pollution risk assessments often employ effect coefficients from epidemiologic studies to quantify the public health impact of changes in air quality. Partly due to data and methodological limitations, epidemiologic studies have traditionally characterized the heal...

THE NATIONAL EPIDEMIOLOGICAL AND ENVIRONMENTAL ASSESSMENT OF RECREATIONAL WATERS: RESULTS FROM THE FIRST SUMMER OF FULL-SCALE STUDIES

EPA Science Inventory

Introduction

The National Epidemiological and Environmental Assessment of Recreational Waters (NEEAR) is a multi-year study of recreational water conducted by the United States Environmental Protection Agency and the Centers for Disease Control and Prevention (CDC), design...

THE NATIONAL EPIDEMIOLOGICAL AND ENVIRONMENTAL ASSESSMENT OF RECREATIONAL WATERS: RESULTS FROM THE FIRST SUMMER FULL-SCALE STUDIES

EPA Science Inventory

Introduction

The National Epidemiological and Environmental Assessment of Recreational Waters (NEEAR) is a multi-year study of recreational water conducted by the United States Environmental Protection Agency and the Centers for Disease Control and Prevention (CDC), design...

The use of (GTG)5 oligonucleotide as an RAPD primer to type Campylobacter concisus.

PubMed

Matsheka, M I; Lastovica, A J; Zappe, H; Elisha, B G

2006-06-01

DNA fingerprinting using (GTG)(5) oligonucleotide as a primer in a random amplified polymorphic DNA (RAPD) assay was assessed by typing isolates of Campylobacter concisus strains, collected over a period of 8 years. RAPD analysis using the (GTG)(5) oligonucleotide as a primer was used to type 100 isolates of C. concisus comprising mostly isolates from children with diarrhoea. Using this method, 86% of the isolates were found to be genotypically diverse. Of these heterogeneous isolates, 25 of the strains were also shown to be genetically distinct in a previous study using pulsed field gel electrophoresis. The remaining isolates (14) could be classified into five profile groups based on the DNA fingerprinting patterns. The assay successfully identified epidemiologically linked strains from the unrelated genetically diverse pool of strains. Laboratory RADP typing using the (GTG)(5) primer proved to be useful in distinguishing related strains of C. concisus from a large pool of unrelated strains of this organism. RAPD typing using (GTG)(5) is a simple method that could be used to investigate the epidemiology of C. concisus. The results suggest that homologous lineages of C. concisus may exist within an otherwise heterogeneous species complex. However, these data need to be confirmed using a more robust typing method.

Development of a multi-cycle shear-compression testing for the modeling of severe plastic deformation

NASA Astrophysics Data System (ADS)

Pesin, A.; Pustovoytov, D.; Lokotunina, N.

2017-12-01

The mechanism of severe plastic deformation comes from very significant shear strain. Shear-compression testing of materials is complicated by the fact that a state of large equivalent strain with dominant shear strain is not easily achievable. This paper presents the novel technique of laboratory simulation of severe plastic deformation by multi-cycle shear-compression testing at room temperature with equivalent strain e=1…5. The specimen consisted of a parallelepiped having an inclined gauge section created by two diametrically opposed semi-circular slots which were machined at 45°. Height of the specimen was 50 mm, section dimensions were 25×25 mm, gauge thickness was 5.0 mm and gauge width was 6.0 mm. The specimen provided dominant shear strain in an inclined gauge-section. The level of shear strain and equivalent strain was controlled through adjustment of the height reduction of the specimen, load application direction and number of cycles of shear-compression. Aluminium alloy Al-6.2Mg-0.7Mn was used as a material for specimen. FE simulation and analysis of the stress-strain state were performed. The microstructure of the specimen after multi-cycle shear-compression testing with equivalent strain e=1…5 was examined by optical and scanning electron microscope.

Molecular epidemiology of the rabies virus in Slovenia 1994-2010.

PubMed

Rihtarič, D; Hostnik, P; Grom, J; Toplak, I

2011-08-26

A molecular epidemiology study was performed on a selection of 30 rabies-positive brain samples collected between 1994 and 2010 in Slovenia and originating from the red fox (n=19), badger (n=3), cattle (n=3), dog (n=2), cat (n=1), marten (n=1) and horse (n=1). Based on the comparison of 1092 and 672 nucleotide sequences of nucleoprotein (N) and partial glycoprotein (G) gene regions, a low genetic diversity of the circulating strains was detected, but both phylogenetic trees were consistent with the topology where partial nucleoprotein or glycoprotein genes were used. A high sequence identity in the N and G gene to rabies virus isolates from neighbouring countries was found. The Slovenian strains were clearly different from the vaccine strains SAD B19 and SAD Bern, which have been used in Slovenia since 1988. Copyright © 2011 Elsevier B.V. All rights reserved.

Wound and soft tissue infections of Serratia marcescens in patients receiving wound care: A health care-associated outbreak.

PubMed

Us, Ebru; Kutlu, Huseyin H; Tekeli, Alper; Ocal, Duygu; Cirpan, Sevilay; Memikoglu, Kemal O

2017-04-01

We described a health care-associated Serratia marcescens outbreak of wound and soft tissue infection lasting approximately 11 months at Ankara University Ibni Sina Hospital. After identification of S marcescens strains from the clinical and environmental samples, and their susceptibility testing to antimicrobial agents, pulsed-field gel electrophoresis (PFGE) was performed to detect molecular epidemiologic relationships among these isolates. The strains which were isolated from the saline bottles used for wound cleansing in the wound care unit were found to be 100% interrelated by PFGE to the strains from the samples of the outbreak patients. Reuse of the emptied bottles has no longer been allowed since the outbreak occurred. Besides, more efficient and frequent infection control training for hospital staff has been conducted. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Bloodstream infections caused by multi-drug resistant Proteus mirabilis: Epidemiology, risk factors and impact of multi-drug resistance.

PubMed

Korytny, Alexander; Riesenberg, Klaris; Saidel-Odes, Lisa; Schlaeffer, Fransisc; Borer, Abraham

2016-01-01

The prevalence of antimicrobial co-resistance among ESBL-producing Enterobactereaceae is extremely high in Israel. Multidrug-resistant Proteus mirabilis strains (MDR-PM), resistant to almost all antibiotic classes have been described. The aim was to determine the risk factors for bloodstream infections caused by MDR-PM and clinical outcomes. A retrospective case-control study. Adult patients with PM bacteremia during 7 years were identified retrospectively and their files reviewed for demographics, underlying diseases, Charlson Comorbidity Index, treatment and outcome. One hundred and eighty patients with PM-bloodstream infection (BSI) were included; 90 cases with MDR-PM and 90 controls with sensitive PM (S-PM). Compared to controls, cases more frequently were from nursing homes, had recurrent hospital admissions in the past year and received antibiotic therapy in the previous 3 months, were bedridden and suffered from peripheral vascular disease and peptic ulcer disease (p < 0.001). Two-thirds of the MDR-PM isolates were ESBL-producers vs 4.4% of S-PM isolates (p < 0.001, OR = 47.6, 95% CI = 15.9-142.6). In-hospital crude mortality rate of patients with MDR-PM BSI was 37.7% vs 23.3% in those with S-PM BSI (p = 0.0359, OR = 2, 95% CI = 1.4-3.81). PM bacteremia in elderly and functionally-dependent patients is likely to be caused by nearly pan-resistant PM strains in the institution; 51.8% of the patients received inappropriate empiric antibiotic treatment. The crude mortality rate of patients with MDR-PM BSI was significantly higher than that of patients with S-PM BSI.

Constructing Rigorous and Broad Biosurveillance Networks for Detecting Emerging Zoonotic Outbreaks

PubMed Central

Brown, Mac; Moore, Leslie; McMahon, Benjamin; Powell, Dennis; LaBute, Montiago; Hyman, James M.; Rivas, Ariel; Jankowski, Mark; Berendzen, Joel; Loeppky, Jason; Manore, Carrie; Fair, Jeanne

2015-01-01

Determining optimal surveillance networks for an emerging pathogen is difficult since it is not known beforehand what the characteristics of a pathogen will be or where it will emerge. The resources for surveillance of infectious diseases in animals and wildlife are often limited and mathematical modeling can play a supporting role in examining a wide range of scenarios of pathogen spread. We demonstrate how a hierarchy of mathematical and statistical tools can be used in surveillance planning help guide successful surveillance and mitigation policies for a wide range of zoonotic pathogens. The model forecasts can help clarify the complexities of potential scenarios, and optimize biosurveillance programs for rapidly detecting infectious diseases. Using the highly pathogenic zoonotic H5N1 avian influenza 2006-2007 epidemic in Nigeria as an example, we determined the risk for infection for localized areas in an outbreak and designed biosurveillance stations that are effective for different pathogen strains and a range of possible outbreak locations. We created a general multi-scale, multi-host stochastic SEIR epidemiological network model, with both short and long-range movement, to simulate the spread of an infectious disease through Nigerian human, poultry, backyard duck, and wild bird populations. We chose parameter ranges specific to avian influenza (but not to a particular strain) and used a Latin hypercube sample experimental design to investigate epidemic predictions in a thousand simulations. We ranked the risk of local regions by the number of times they became infected in the ensemble of simulations. These spatial statistics were then complied into a potential risk map of infection. Finally, we validated the results with a known outbreak, using spatial analysis of all the simulation runs to show the progression matched closely with the observed location of the farms infected in the 2006-2007 epidemic. PMID:25946164

Epidemiological investigation of nosocomial outbreak of staphylococcal skin diseases in neonatal ward.

PubMed

Kurlenda, J; Grinholc, M; Krzysztoń-Russjan, J; Wiśniewska, K

2009-05-01

During a 1-month period, eight neonates developed staphylococcal skin disease diagnosed as a bullous impetigo in the maternity unit of the Provincial Hospital in Gdansk. An epidemiological investigation based on phenotyping and genotyping methods was performed. All neonates involved in the outbreak, their mothers and 15 staff members were screened for carriage of Staphylococcus aureus by nasal swabs. Isolated strains were compared with strains cultured from affected skin and purulent conjunctiva of infected newborns. Isolates were analyzed for the presence of the etA and etB genes using polymerase chain reaction and genotyped by pulsed-field gel electrophoresis (PFGE) and coa gene polymorphism. The analyzed S. aureus strains were methicillin-sensitive and could be divided into two groups according to antibiotyping, phage typing, coa polymorphism and PFGE pattern. The first group consisted of etA and etB negative strains, and the second one involved only the etB positive ones. Our results have shown that there were two different clusters of infection caused by two populations of S. aureus strains. Among the 15 medical staff members screened we have found seven carriers. However, phage typing revealed that distinct strains unrelated to the outbreak isolates were carried. Although we have not been able to establish the source of bacteria involved in the outbreak, our results suggest that for both groups, mothers could be the source of the infecting strains.

Transmission of tuberculosis in the prison of Antananarivo (Madagascar).

PubMed

Rasolofo-Razanamparany, V; Ménard, D; Ratsitorahina, M; Aurégan, G; Gicquel, B; Chanteau, S

2000-11-01

The prevalence of tuberculosis in the Antananarivo prison is 16 times higher than that in the general population of Madagascar. We compared the clustering of Mycobacterium tuberculosis strains within and outside the prison and studied the transmission of strains in the prison. M. tuberculosis strains isolated in 1994 to 1995 from 146 prisoners and from 260 nonprisoner patients from Antananarivo were typed using the genetic markers IS6110 and direct repeat. We compared the strains isolated from prisoners and nonprisoners and found that the clustering rate was higher within (58.9%) than outside the prison (40%) suggesting that the transmission rate was higher in prison. Of the 146 incarcerated patients, 82 were grouped into 22 clusters. We checked for possible tuberculosis transmission between prisoners with identical strains by epidemiological investigation of the various prison clusters. We found that 9.5% of the incarcerated patients could have been sources of infection and that only 15.1% could have been infected in the prison. One hundred and twenty-seven prison patients were new cases. Epidemiological data suggested that 37% of them resulted from a reactivation of an old infection, due to poor living conditions or recent transmission from an index case outside the prison.

[Biological markers in epidemiology: concepts, applications, perspectives (part I)].

PubMed

Hoffmann, W; Latza, U; Ahrens, W; Greiser, K H; Kroke, A; Nieters, A; Schulze, M B; Steiner, M; Terschüren, C; Wjst, M

2002-02-01

The inclusion of biomarkers in epidemiological research provides new possibilities for exposure assessment and the study of early structural or functional changes and pre-clinical stages of diseases. At the same time issues of validity, reliability, and quality control as well as logistics require special attention. Usually epidemiological studies become more expensive with regard to time and cost. Interdisciplinary collaboration between epidemiology, basic research, and laboratory research is crucial. A prerequisite for this collaboration are agreements on definitions, methods and procedures. The definition of "biomarker" and a description of previous uses of biomarkers in epidemiological studies are presented in the first part of this paper. The second part addresses genetic markers and markers of individual sensitivity and susceptibility. We will end with a discussion about the possible future of biomarkers in epidemiology.

3D Finite Element Analysis of Particle-Reinforced Aluminum

NASA Technical Reports Server (NTRS)

Shen, H.; Lissenden, C. J.

2002-01-01

Deformation in particle-reinforced aluminum has been simulated using three distinct types of finite element model: a three-dimensional repeating unit cell, a three-dimensional multi-particle model, and two-dimensional multi-particle models. The repeating unit cell model represents a fictitious periodic cubic array of particles. The 3D multi-particle (3D-MP) model represents randomly placed and oriented particles. The 2D generalized plane strain multi-particle models were obtained from planar sections through the 3D-MP model. These models were used to study the tensile macroscopic stress-strain response and the associated stress and strain distributions in an elastoplastic matrix. The results indicate that the 2D model having a particle area fraction equal to the particle representative volume fraction of the 3D models predicted the same macroscopic stress-strain response as the 3D models. However, there are fluctuations in the particle area fraction in a representative volume element. As expected, predictions from 2D models having different particle area fractions do not agree with predictions from 3D models. More importantly, it was found that the microscopic stress and strain distributions from the 2D models do not agree with those from the 3D-MP model. Specifically, the plastic strain distribution predicted by the 2D model is banded along lines inclined at 45 deg from the loading axis while the 3D model prediction is not. Additionally, the triaxial stress and maximum principal stress distributions predicted by 2D and 3D models do not agree. Thus, it appears necessary to use a multi-particle 3D model to accurately predict material responses that depend on local effects, such as strain-to-failure, fracture toughness, and fatigue life.

The 'PhenoBox', a flexible, automated, open-source plant phenotyping solution.

PubMed

Czedik-Eysenberg, Angelika; Seitner, Sebastian; Güldener, Ulrich; Koemeda, Stefanie; Jez, Jakub; Colombini, Martin; Djamei, Armin

2018-04-05

There is a need for flexible and affordable plant phenotyping solutions for basic research and plant breeding. We demonstrate our open source plant imaging and processing solution ('PhenoBox'/'PhenoPipe') and provide construction plans, source code and documentation to rebuild the system. Use of the PhenoBox is exemplified by studying infection of the model grass Brachypodium distachyon by the head smut fungus Ustilago bromivora, comparing phenotypic responses of maize to infection with a solopathogenic Ustilago maydis (corn smut) strain and effector deletion strains, and studying salt stress response in Nicotiana benthamiana. In U. bromivora-infected grass, phenotypic differences between infected and uninfected plants were detectable weeks before qualitative head smut symptoms. Based on this, we could predict the infection outcome for individual plants with high accuracy. Using a PhenoPipe module for calculation of multi-dimensional distances from phenotyping data, we observe a time after infection-dependent impact of U. maydis effector deletion strains on phenotypic response in maize. The PhenoBox/PhenoPipe system is able to detect established salt stress responses in N. benthamiana. We have developed an affordable, automated, open source imaging and data processing solution that can be adapted to various phenotyping applications in plant biology and beyond. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Predicting cell viability within tissue scaffolds under equiaxial strain: multi-scale finite element model of collagen-cardiomyocytes constructs.

PubMed

Elsaadany, Mostafa; Yan, Karen Chang; Yildirim-Ayan, Eda

2017-06-01

Successful tissue engineering and regenerative therapy necessitate having extensive knowledge about mechanical milieu in engineered tissues and the resident cells. In this study, we have merged two powerful analysis tools, namely finite element analysis and stochastic analysis, to understand the mechanical strain within the tissue scaffold and residing cells and to predict the cell viability upon applying mechanical strains. A continuum-based multi-length scale finite element model (FEM) was created to simulate the physiologically relevant equiaxial strain exposure on cell-embedded tissue scaffold and to calculate strain transferred to the tissue scaffold (macro-scale) and residing cells (micro-scale) upon various equiaxial strains. The data from FEM were used to predict cell viability under various equiaxial strain magnitudes using stochastic damage criterion analysis. The model validation was conducted through mechanically straining the cardiomyocyte-encapsulated collagen constructs using a custom-built mechanical loading platform (EQUicycler). FEM quantified the strain gradients over the radial and longitudinal direction of the scaffolds and the cells residing in different areas of interest. With the use of the experimental viability data, stochastic damage criterion, and the average cellular strains obtained from multi-length scale models, cellular viability was predicted and successfully validated. This methodology can provide a great tool to characterize the mechanical stimulation of bioreactors used in tissue engineering applications in providing quantification of mechanical strain and predicting cellular viability variations due to applied mechanical strain.

Oligonucleotide (GTG)5 as an epidemiological tool in the study of nontuberculous mycobacteria.

PubMed Central

Cilliers, F J; Warren, R M; Hauman, J H; Wiid, I J; van Helden, P D

1997-01-01

Analysis of restriction fragment length polymorphisms in the genome of Mycobacterium tuberculosis (DNA fingerprinting) has proved to be a useful epidemiological tool in the study of tuberculosis within populations or communities. However, to date, no similar method has been developed to study the epidemiology of nontuberculous mycobacteria (NTM). In this communication, we report that a simple oligonucleotide repeat, (GTG)5, can be used to accurately genotype all species and strains of NTM tested. We suggest that this technology is an easily applied and accurate tool which can be used for the study of the epidemiology of NTM. PMID:9163479

Outbreak of Acinetobacter baumannii in a neonatal intensive care unit: antimicrobial susceptibility and genotyping analysis.

PubMed

Touati, Arabella; Achour, Wafa; Cherif, Ahmed; Hmida, Hayet Ben; Afif, Firas Bou; Jabnoun, Sami; Khrouf, Naima; Hassen, Assia Ben

2009-06-01

We describe an outbreak of nosocomial respiratory infection caused by multi-drug resistant Acinetobacter baumannii in a neonatal intensive care unit (NICU) in Tunis and our investigation to determine the source. Between May 2006 and February 2007, 31 infants hospitalized in the NICU of the Centre of Maternity and Neonatology of La Rabta in Tunis developed A. baumannii pneumonia. A case (infected infant) was defined as any patient hospitalized in the NICU during the outbreak period, with clinical signs of pneumonia and isolation of A. baumannii from tracheal aspirate. Ten rectal swabs and 98 environmental specimens were collected for the epidemiological investigation. Thirty-nine A. baumannii isolates were collected: 31 clinical strains from tracheal aspirates (>10(3) colony-forming units [CFU]/mL), 3 environmental strains from incubators, and 5 from rectal swab. For the genotyping method, we used pulsed-field gel electrophoresis using ApaI restriction endonuclease. Thirty-one neonates developed multiple drug-resistant A. baumannii-associated pneumonia with 10 deaths due to A. baumannii infection, 48.4% had very low birth weight (

Coagulase-positive Staphylococcus isolated from wildlife: Identification, molecular characterization and evaluation of resistance profiles with focus on a methicillin-resistant strain.

PubMed

Nowakiewicz, Aneta; Ziółkowska, Grażyna; Zięba, Przemysław; Gnat, Sebastian; Wojtanowicz-Markiewicz, Katarzyna; Trościańczyk, Aleksandra

2016-02-01

The aim of the study was molecular analysis of coagulase-positive isolates of Staphylococcus bacteria obtained from wild animals and evaluation of their resistance to antimicrobial agents. A total of 76 rectal swabs were taken from wild animals. The species of the Staphylococcus isolates was determined by MALDI TOF MS, susceptibility to antimicrobials was evaluated by phenotypic and molecular methods, epidemiological analysis (ADSRRS-fingerprinting) was also carried out. MRSA isolate was typed by MLST and spa-typing. The animals tested, were carriers (n=38) of coagulase-positive Staphylococcus (S. aureus, S. pseudintermedius and S. delphini B). Analyzed isolates were resistant to 1 or 2 antimicrobials, which was confirmed by the presence of genes (blaZ, ermA, ermB, msrA, tetK and tetM). A multi-drug resistant and methicillin-resistant isolate of S. aureus was obtained as well (MRSA, ST8, t1635, PVL-positive and ACME-negative). The ADSRRS-fingerprinting method enabled interspecific and intraspecific differentiation of coagulase-positive Staphylococcus isolates, revealing a certain degree of correlation between the species of the isolate, and the degree of similarity between the isolates. The presence of resistance genes in 13% (5/38) of the isolates obtained from wild animals, including one methicillin-resistant isolate, is relatively small in comparison to the degree of colonization by resistant strains in humans, livestock or pets. Nevertheless, due to the possibility of contact between wild animals, domestic animals and humans, transmission of resistant strains is possible, as suggested by our isolation of a MRSA strain typed as ST8 and specific spa type t1635, which had previously been isolated exclusively from humans. Copyright © 2015 Elsevier Ltd. All rights reserved.

Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks.

PubMed

Rusconi, Brigida; Sanjar, Fatemeh; Koenig, Sara S K; Mammel, Mark K; Tarr, Phillip I; Eppinger, Mark

2016-01-01

Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and long-term evolution and can complement currently employed typing schemes for outbreak ex- and inclusion, diagnostics, surveillance, and forensic studies.

Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks

PubMed Central

Rusconi, Brigida; Sanjar, Fatemeh; Koenig, Sara S. K.; Mammel, Mark K.; Tarr, Phillip I.; Eppinger, Mark

2016-01-01

Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and long-term evolution and can complement currently employed typing schemes for outbreak ex- and inclusion, diagnostics, surveillance, and forensic studies. PMID:27446025

Genetic diversity of Vibrio parahaemolyticus strains isolated from farmed Pacific white shrimp and ambient pond water affected by acute hepatopancreatic necrosis disease outbreak in Thailand.

PubMed

Chonsin, Kaknokrat; Matsuda, Shigeaki; Theethakaew, Chonchanok; Kodama, Toshio; Junjhon, Jiraphan; Suzuki, Yasuhiko; Suthienkul, Orasa; Iida, Tetsuya

2016-01-01

Acute hepatopancreatic necrosis disease (AHPND) is an emerging shrimp disease that causes massive die-offs in farmed shrimps. Recent outbreaks of AHPND in Asia have been causing great losses for shrimp culture and have become a serious socioeconomic problem. The causative agent of AHPND is Vibrio parahaemolyticus, which is typically known to cause food-borne gastroenteritis in humans. However, there have been few reports of the epidemiology of V. parahaemolyticus AHPND strains, and the genetic relationship among AHPND strains is unclear. Here, we report the genetic characterization of V. parahaemolyticus strains isolated from AHPND outbreaks in Thailand. We found eight isolates from AHPND-suspected shrimps and pond water that were positive for AHPND markers AP1 and AP2. PCR analysis confirmed that none of these eight AP-positive AHPND strains possesses the genes for the conventional virulence factors affecting to humans, such as thermostable direct hemolysin (TDH), TDH-related hemolysin (TRH) and type III secretion system 2. Phylogenetic analysis by multilocus sequence typing showed that the AHPND strains are genetically diverse, suggesting that AHPND strains were not derived from a single genetic lineage. Our study represents the first report of molecular epidemiology of AHPND-causing V. parahaemolyticus strains using multilocus sequence typing, and provides an insight into their evolutionary mechanisms. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Population-based epidemiological study of infections caused by carbapenem-resistant Pseudomonas aeruginosa in the Calgary Health Region: importance of metallo-beta-lactamase (MBL)-producing strains.

PubMed

Laupland, Kevin B; Parkins, Michael D; Church, Deirdre L; Gregson, Daniel B; Louie, Thomas J; Conly, John M; Elsayed, Sameer; Pitout, Johann D D

2005-11-01

A study was conducted in the Calgary Health Region between May 2002 and April 2004 to define the population-based epidemiological characteristics of infections caused by imipenem-resistant Pseudomonas aeruginosa and to explore the clinical outcomes due to metallo- beta -lactamase (MBL)-producing and non-MBL-producing strains. Detailed clinical information was obtained by chart review, and phenotypic and molecular characterizations were performed using the MBL E-test, polymerase chain reaction with sequencing, and pulsed-field gel electrophoresis. A total of 228 patients with infections caused by imipenem-resistant P. aeruginosa were identified (annual incidence, 10.5 cases/100,000 population), with the highest incidence rate in those >or=75 years old. MBL-producing strains (98/228) were associated with higher rates of multidrug resistance and bacteremia. Ninety MBL-producing strains also produced VIM-2, 4 produced IMP-7, and 4 were unclassified. A cluster of VIM-2-producing strains was responsible for a nosocomial outbreak during 2003. The case-fatality rate was significantly higher for infections caused by MBL-producing strains than for those caused by non-MBL-producing strains (25% vs. 13%; relative risk, 1.98 [95% confidence interval, 1.00-3.90]; P=.05). MBL-producing P. aeruginosa strains were associated with a higher case-fatality rate and invasive disease. Our study highlights the potential importance of molecular laboratory techniques in infection control and patient care.

Analysis of clinical and food-borne isolates of Listeria monocytogenes in the United States by multilocus enzyme electrophoresis and application of the method to epidemiologic investigations.

PubMed Central

Bibb, W F; Gellin, B G; Weaver, R; Schwartz, B; Plikaytis, B D; Reeves, M W; Pinner, R W; Broome, C V

1990-01-01

To investigate the microbiology and epidemiology of the 1,700 sporadic cases of listeriosis that occur annually in the United States, we developed a multilocus enzyme electrophoresis (MEE) typing system for Listeria monocytogenes. We studied 390 isolates by MEE. Eighty-two electrophoretic types (ETs) were defined. Two distinct clusters of ETs, ET group A (ETGA) and ET group B (ETGB), separated at a genetic distance of 0.440, were identified. Strains of ETGB were associated with perinatal listeriosis (P = 0.03). All strains of H antigen type a were in ETGA, while all strains of H antigen type b were in ETGB. Among 328 clinical isolates from cases of literiosis, 55 ETs of L. monocytogenes were defined. Thirty-four ETs were identified among 62 isolates from food products. The mean number of strains per ET (5.2) was significantly higher among clinical isolates than among food-borne isolates. Examination of isolates from outbreaks further documented the link between cases and contaminated food products. In one investigation, we found 11 different ETs, ruling out a single common source as a cause of that outbreak. By examining a large number of isolates collected over a specified time in diverse geographic locations in the United States, we have begun to establish a baseline for the study of the epidemiology of listeriosis by MEE. PMID:2117880

New Multilocus Variable-Number Tandem-Repeat Analysis Tool for Surveillance and Local Epidemiology of Bacterial Leaf Blight and Bacterial Leaf Streak of Rice Caused by Xanthomonas oryzae

PubMed Central

Poulin, L.; Grygiel, P.; Magne, M.; Rodriguez-R, L. M.; Forero Serna, N.; Zhao, S.; El Rafii, M.; Dao, S.; Tekete, C.; Wonni, I.; Koita, O.; Pruvost, O.; Verdier, V.; Vernière, C.

2014-01-01

Multilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars of Xanthomonas oryzae can cause significant crop losses in tropical and temperate rice-growing countries. Bacterial leaf streak is caused by X. oryzae pv. oryzicola, and bacterial leaf blight is caused by X. oryzae pv. oryzae. For the latter, two genetic lineages have been described in the literature. We developed a universal MLVA typing tool both for the identification of the three X. oryzae genetic lineages and for epidemiological analyses. Sixteen candidate variable-number tandem-repeat (VNTR) loci were selected according to their presence and polymorphism in 10 draft or complete genome sequences of the three X. oryzae lineages and by VNTR sequencing of a subset of loci of interest in 20 strains per lineage. The MLVA-16 scheme was then applied to 338 strains of X. oryzae representing different pathovars and geographical locations. Linkage disequilibrium between MLVA loci was calculated by index association on different scales, and the 16 loci showed linear Mantel correlation with MLSA data on 56 X. oryzae strains, suggesting that they provide a good phylogenetic signal. Furthermore, analyses of sets of strains for different lineages indicated the possibility of using the scheme for deeper epidemiological investigation on small spatial scales. PMID:25398857

Haemophilus ducreyi Cutaneous Ulcer Strains Diverged from Both Class I and Class II Genital Ulcer Strains: Implications for Epidemiological Studies

PubMed Central

Gangaiah, Dharanesh

2016-01-01

Background Haemophilus ducreyi has emerged as a major cause of cutaneous ulcers (CU) in yaws-endemic regions of the tropics in the South Pacific, South East Asia and Africa. H. ducreyi was once thought only to cause the genital ulcer (GU) disease chancroid; GU strains belong to 2 distinct classes, class I and class II. Using whole-genome sequencing of 4 CU strains from Samoa, 1 from Vanuatu and 1 from Papua New Guinea, we showed that CU strains diverged from the class I strain 35000HP and that one CU strain expressed β-lactamase. Recently, the Center for Disease Control and Prevention released the genomes of 11 additional CU strains from Vanuatu and Ghana; however, the evolutionary relationship of these CU strains to previously-characterized CU and GU strains is unknown. Methodology/Principal Findings We performed phylogenetic analysis of 17 CU and 10 GU strains. Class I and class II GU strains formed two distinct clades. The class I strains formed two subclades, one containing 35000HP and HD183 and the other containing the remainder of the class I strains. Twelve of the CU strains formed a subclone under the class I 35000HP subclade, while 2 CU strains formed a subclone under the other class I subclade. Unexpectedly, 3 of the CU strains formed a subclone under the class II clade. Phylogenetic analysis of dsrA-hgbA-ncaA sequences yielded a tree similar to that of whole-genome phylogenetic tree. Conclusions/Significance CU strains diverged from multiple lineages within both class I and class II GU strains. Multilocus sequence typing of dsrA-hgbA-ncaA could be reliably used for epidemiological investigation of CU and GU strains. As class II strains grow relatively poorly and are relatively more susceptible to vancomycin than class I strains, these findings have implications for methods to recover CU strains. Comparison of contemporary CU and GU isolates would help clarify the relationship between these entities. PMID:28027326

Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in Thailand.

PubMed

Siriphap, Achiraya; Leekitcharoenphon, Pimlapas; Kaas, Rolf S; Theethakaew, Chonchanok; Aarestrup, Frank M; Sutheinkul, Orasa; Hendriksen, Rene S

2017-01-01

Cholera is still an important public health problem in several countries, including Thailand. In this study, a collection of clinical and environmental V. cholerae serogroup O1, O139, and non-O1/non-O139 strains originating from Thailand (1983 to 2013) was characterized to determine phenotypic and genotypic traits and to investigate the genetic relatedness. Using a combination of conventional methods and whole genome sequencing (WGS), 78 V. cholerae strains were identified. WGS was used to determine the serogroup, biotype, virulence, mobile genetic elements, and antimicrobial resistance genes using online bioinformatics tools. In addition, phenotypic antimicrobial resistance was determined by the minimal inhibitory concentration (MIC) test. The 78 V. cholerae strains belonged to the following serogroups O1: (n = 44), O139 (n = 16) and non-O1/non-O139 (n = 18). Interestingly, we found that the typical El Tor O1 strains were the major cause of clinical cholera during 1983-2000 with two Classical O1 strains detected in 2000. In 2004-2010, the El Tor variant strains revealed genotypes of the Classical biotype possessing either only ctxB or both ctxB and rstR while they harbored tcpA of the El Tor biotype. Thirty O1 and eleven O139 clinical strains carried CTXϕ (Cholera toxin) and tcpA as well four different pathogenic islands (PAIs). Beside non-O1/non-O139, the O1 environmental strains also presented chxA and Type Three Secretion System (TTSS). The in silico MultiLocus Sequence Typing (MLST) discriminated the O1 and O139 clinical strains from other serogroups and environmental strains. ST69 was dominant in the clinical strains belonging to the 7th pandemic clone. Non-O1/non-O139 and environmental strains showed various novel STs indicating genetic variation. Multidrug-resistant (MDR) strains were observed and conferred resistance to ampicillin, azithromycin, nalidixic acid, sulfamethoxazole, tetracycline, and trimethoprim and harboured variants of the SXT elements. For the first time since 1986, the presence of V. cholerae O1 Classical was reported causing cholera outbreaks in Thailand. In addition, we found that V. cholerae O1 El Tor variant and O139 were pre-dominating the pathogenic strains in Thailand. Using WGS and bioinformatic tools to analyze both historical and contemporary V. cholerae circulating in Thailand provided a more detailed understanding of the V. cholerae epidemiology, which ultimately could be applied for control measures and management of cholera in Thailand.

Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in Thailand

PubMed Central

Siriphap, Achiraya; Leekitcharoenphon, Pimlapas; Kaas, Rolf S.; Theethakaew, Chonchanok; Aarestrup, Frank M.; Sutheinkul, Orasa; Hendriksen, Rene S.

2017-01-01

Cholera is still an important public health problem in several countries, including Thailand. In this study, a collection of clinical and environmental V. cholerae serogroup O1, O139, and non-O1/non-O139 strains originating from Thailand (1983 to 2013) was characterized to determine phenotypic and genotypic traits and to investigate the genetic relatedness. Using a combination of conventional methods and whole genome sequencing (WGS), 78 V. cholerae strains were identified. WGS was used to determine the serogroup, biotype, virulence, mobile genetic elements, and antimicrobial resistance genes using online bioinformatics tools. In addition, phenotypic antimicrobial resistance was determined by the minimal inhibitory concentration (MIC) test. The 78 V. cholerae strains belonged to the following serogroups O1: (n = 44), O139 (n = 16) and non-O1/non-O139 (n = 18). Interestingly, we found that the typical El Tor O1 strains were the major cause of clinical cholera during 1983–2000 with two Classical O1 strains detected in 2000. In 2004–2010, the El Tor variant strains revealed genotypes of the Classical biotype possessing either only ctxB or both ctxB and rstR while they harbored tcpA of the El Tor biotype. Thirty O1 and eleven O139 clinical strains carried CTXϕ (Cholera toxin) and tcpA as well four different pathogenic islands (PAIs). Beside non-O1/non-O139, the O1 environmental strains also presented chxA and Type Three Secretion System (TTSS). The in silico MultiLocus Sequence Typing (MLST) discriminated the O1 and O139 clinical strains from other serogroups and environmental strains. ST69 was dominant in the clinical strains belonging to the 7th pandemic clone. Non-O1/non-O139 and environmental strains showed various novel STs indicating genetic variation. Multidrug-resistant (MDR) strains were observed and conferred resistance to ampicillin, azithromycin, nalidixic acid, sulfamethoxazole, tetracycline, and trimethoprim and harboured variants of the SXT elements. For the first time since 1986, the presence of V. cholerae O1 Classical was reported causing cholera outbreaks in Thailand. In addition, we found that V. cholerae O1 El Tor variant and O139 were pre-dominating the pathogenic strains in Thailand. Using WGS and bioinformatic tools to analyze both historical and contemporary V. cholerae circulating in Thailand provided a more detailed understanding of the V. cholerae epidemiology, which ultimately could be applied for control measures and management of cholera in Thailand. PMID:28103259

Epidemiological typing of Enterobacter aerogenes.

PubMed Central

Gaston, M A; Strickland, M A; Ayling-Smith, B A; Pitt, T L

1989-01-01

The applicability of Enterobacter cloacae and Klebsiella typing reagents for classifying clinical strains of Enterobacter aerogenes was evaluated. Of 75 strains, none were agglutinated by E. cloacae O antisera or were sensitive to E. cloacae bacteriophages. In contrast, 70 strains reacted with Klebsiella capsular antisera. Two-thirds of the strains were lysed by Klebsiella typing phages. A set of five E. aerogenes bacteriocin producers classified 92% of strains into 15 sensitivity types. In conclusion, E. aerogenes may be typed with Klebsiella reagents, and the simple bacteriocin test provides further discrimination between strains. The limited number of capsular antigens in the species and their apparent similarity to Klebsiella capsular antigens warrant further investigation. PMID:2715326

A surveillance network for meningococcal disease in Europe.

PubMed

Trotter, Caroline L; Chandra, Manosree; Cano, Rosa; Larrauri, Amparo; Ramsay, Mary E; Brehony, Carina; Jolley, Keith A; Maiden, Martin C J; Heuberger, Sigrid; Frosch, Matthias

2007-01-01

Between 1999 and 2004, the European Union Invasive Bacterial Infections Surveillance Network (EU-IBIS) received c. 50,000 reports of meningococcal disease from 27 participating countries. Analysis has demonstrated a major decline in the incidence of invasive disease in those countries that have introduced routine vaccination against serogroup C infection. The establishment of rapid reporting of W135 and B2a/B2b strains has been able to provide early reassurance that these strains are not emerging as major public health problems in Europe. Between September 2001 and February 2005, the EU-MenNet project offered further opportunities for enhancing this data resource. Collaborative projects included: improving the EU-IBIS website; reviewing case ascertainment in Europe; reviewing cost-effectiveness studies for meningococcal serogroup C conjugate (MCC) vaccination; international comparisons of MCC vaccine efficacy; and mathematical modelling studies. In addition, linking of data from the European Meningococcal Multi-locus Sequence Type Centre to epidemiological data was performed. Particular clonal complexes were found to be preferentially associated with certain serogroups. Case fatality was also found to vary with clonal complex, suggesting that genotype can be a marker for hypervirulence. The importance of close collaboration between networks of epidemiologists, microbiologists, and the wider scientific and public health community is demonstrated.

Molecular epidemiology of an outbreak of Legionnaires' disease associated with a cooling tower in Genova-Sestri Ponente, Italy.

PubMed

Castellani Pastoris, M; Ciceroni, L; Lo Monaco, R; Goldoni, P; Mentore, B; Flego, G; Cattani, L; Ciarrocchi, S; Pinto, A; Visca, P

1997-12-01

Fatty acid profile analysis, monoclonal antibody (MAb) subtyping, pulsed-field gel electrophoresis (PFGE), arbitrarily primed polymerase chain reaction (AP-PCR), and ribotyping were used to compare clinical and environmental Legionella pneumophila serogroup 1 isolates from an outbreak of Legionnaires' disease presumptively associated with cooling towers. According to the Oxford subtyping scheme, the MAb subtype of patients' isolates and of two strains originating from a cooling tower was Pontiac, whereas the other isolates were subtype Olda. The strains showed no intrinsic strain-to-strain difference in fatty acid profiles, and ribotyping and length polymorphism of the 16S-23S rDNA intervening regions failed to reveal any differences between the isolates. Conversely, PFGE and AP-PCR appeared to be more discriminatory, as the same genomic profile was found for the clinical and some environmental strains. Meteorologic and epidemiological data and the results of molecular analysis of the Legionella pneumophila serogroup 1 isolates support the hypothesis that the infection was transmitted from one of the cooling towers to the indoor environment of the same building, to homes in proximity that had open windows, and to the streets. In fact, the outbreak diminished and later ended after a part in the tower was replaced. This investigation demonstrates the utility of combined molecular methods (i.e., phenotypic and genomic typing) in comparing epidemiologically linked clinical and environmental isolates. Finally, the outbreak confirms the risk of Legionnaires' disease posed by cooling towers, mainly when atmospheric thermal and humidity inversions occur. This finding emphasizes the need to determine whether the source of infection is in the living or working environment or somewhere else.

Molecular Strain Typing of Clinical Isolates, Trichophyton rubrum using Non Transcribed Spacer (NTS) Region as a Molecular Marker

PubMed Central

Ramaraj, Vijayakumar; Vijayaraman, Rajyoganandh S; Elavarashi, Elangovan; Rangarajan, Sudha

2017-01-01

Introduction Dermatophytes are a group of fungi which infect keratinized tissues and causes superficial mycoses in humans and animals. The group comprises of three major genera, Trichophyton, Microsporum and Epidermophyton. Among them Trichophyton rubrum is a predominant anthropophilic fungi which causes chronic infections. Although, the infection is superficial and treatable, reinfection/coinfection causes inflation in the treatment cost. Identifying the source and mode of transmission is essential to prevent its transmission. Accurate discrimination is required to understand the clinical (relapse or reinfection) and epidemiological implications of the genetic heterogeneity of this species. Polymorphism in the Non Transcribed Spacer (NTS) region of ribosomal DNA (rDNA) clusters renders an effective way to discriminate strains among T. rubrum. Aim To carry out the strain typing of the clinical isolates, Trichophyton rubrum using NTS as a molecular marker. Materials and Methods Seventy T.rubrum clinical isolates obtained from April-2011-March 2013, from Sri Ramachandra Medical Centre, Chennai, Tamil Nadu, India, were identified by conventional phenotypic methods and included in this prospective study. The isolates were then subjected to Polymerase Chain Reaction (PCR) targeting two subrepeat elements (SREs), TRS-1 and TRS-2 of the NTS region. Results Strain-specific polymorphism was observed in both subrepeat loci. Total, nine different strains were obtained on combining both TRS-1 and TRS-2, SREs. Conclusion The outcome has given a strong representation for using NTS region amplification in discriminating the T. rubrum clinical isolates. The method can be adapted as a tool for conducting epidemiology and population based study in T. rubrum infections. This will help in future exploration of the epidemiology of T. rubrum. PMID:28658757

Molecular Strain Typing of Clinical Isolates, Trichophyton rubrum using Non Transcribed Spacer (NTS) Region as a Molecular Marker.

PubMed

Ramaraj, Vijayakumar; Vijayaraman, Rajyoganandh S; Elavarashi, Elangovan; Rangarajan, Sudha; Kindo, Anupma Jyoti

2017-05-01

Dermatophytes are a group of fungi which infect keratinized tissues and causes superficial mycoses in humans and animals. The group comprises of three major genera, Trichophyton , Microsporum and Epidermophyton . Among them Trichophyton rubrum is a predominant anthropophilic fungi which causes chronic infections. Although, the infection is superficial and treatable, reinfection/coinfection causes inflation in the treatment cost. Identifying the source and mode of transmission is essential to prevent its transmission. Accurate discrimination is required to understand the clinical (relapse or reinfection) and epidemiological implications of the genetic heterogeneity of this species. Polymorphism in the Non Transcribed Spacer (NTS) region of ribosomal DNA (rDNA) clusters renders an effective way to discriminate strains among T. rubrum . To carry out the strain typing of the clinical isolates, Trichophyton rubrum using NTS as a molecular marker. Seventy T.rubrum clinical isolates obtained from April-2011-March 2013, from Sri Ramachandra Medical Centre, Chennai, Tamil Nadu, India, were identified by conventional phenotypic methods and included in this prospective study. The isolates were then subjected to Polymerase Chain Reaction (PCR) targeting two subrepeat elements (SREs), TRS-1 and TRS-2 of the NTS region. Strain-specific polymorphism was observed in both subrepeat loci. Total, nine different strains were obtained on combining both TRS-1 and TRS-2, SREs. The outcome has given a strong representation for using NTS region amplification in discriminating the T. rubrum clinical isolates. The method can be adapted as a tool for conducting epidemiology and population based study in T. rubrum infections. This will help in future exploration of the epidemiology of T. rubrum .

Emergence of clusters of CRF02_AG and B human immunodeficiency viral strains among men having sex with men exhibiting HIV primary infection in southeastern France.

PubMed

Tamalet, Catherine; Ravaux, Isabelle; Moreau, Jacques; Brégigeon, Sylvie; Tourres, Christian; Richet, Hervé; Abat, Cedric; Colson, Philippe

2015-08-01

The number of new HIV diagnoses is increasing in the western world and transmission clusters have been recently identified among men having sex with men despite Highly Active Antiretroviral Therapy efficacy. The objective of this study was to assess temporal trends, epidemiological, clinical and virological characteristics of primary HIV infections. A retrospective analysis of 79 patients presenting primary HIV infections from 2005 to 2012 was performed in Marseille University Hospitals, southeastern France. Clinical, epidemiological and immunovirological data including phylogeny based on the polymerase gene were collected. 65 males and 14 females were enrolled. The main transmission route was homosexual contact (60.8%). Patients were mostly infected with subtype B (73.4%) and CRF02_AG (21.5%) HIV-1 strains. An increase in the annual number of HIV seroconversions among new HIV diagnoses from 5% in 2005 to 11.2% in 2012 (P = 0.06) and of the proportion of CRF02_AG HIV strains among primary HIV infections in 2011-2012 as compared to 2005-2010 (P = 0.055) was observed. Phylogenetic analysis revealed four transmission clusters including three transmission clusters among men having sex with men: two large clusters of nine CRF02_AG, six B HIV strains; and one small cluster of three B HIV strains. Clusters involved more frequently men (P = 0.01) belonging to caucasian ethicity (P = 0.05), with a higher HIV RNA load at inclusion (P = 0.03). These data highlight the importance of improving epidemiological surveillance and of implementing suitable prevention strategies to control the spread of HIV transmission among men having sex with men. © 2015 Wiley Periodicals, Inc.

Multi-target parallel processing approach for gene-to-structure determination of the influenza polymerase PB2 subunit.

PubMed

Armour, Brianna L; Barnes, Steve R; Moen, Spencer O; Smith, Eric; Raymond, Amy C; Fairman, James W; Stewart, Lance J; Staker, Bart L; Begley, Darren W; Edwards, Thomas E; Lorimer, Donald D

2013-06-28

Pandemic outbreaks of highly virulent influenza strains can cause widespread morbidity and mortality in human populations worldwide. In the United States alone, an average of 41,400 deaths and 1.86 million hospitalizations are caused by influenza virus infection each year (1). Point mutations in the polymerase basic protein 2 subunit (PB2) have been linked to the adaptation of the viral infection in humans (2). Findings from such studies have revealed the biological significance of PB2 as a virulence factor, thus highlighting its potential as an antiviral drug target. The structural genomics program put forth by the National Institute of Allergy and Infectious Disease (NIAID) provides funding to Emerald Bio and three other Pacific Northwest institutions that together make up the Seattle Structural Genomics Center for Infectious Disease (SSGCID). The SSGCID is dedicated to providing the scientific community with three-dimensional protein structures of NIAID category A-C pathogens. Making such structural information available to the scientific community serves to accelerate structure-based drug design. Structure-based drug design plays an important role in drug development. Pursuing multiple targets in parallel greatly increases the chance of success for new lead discovery by targeting a pathway or an entire protein family. Emerald Bio has developed a high-throughput, multi-target parallel processing pipeline (MTPP) for gene-to-structure determination to support the consortium. Here we describe the protocols used to determine the structure of the PB2 subunit from four different influenza A strains.

An untypeable Shigella flexneri strain associated with an outbreak in California.

PubMed

Trevejo, R T; Abbott, S L; Wolfe, M I; Meshulam, J; Yong, D; Flores, G R

1999-07-01

Eleven Shigella flexneri (group B) isolates were recovered from epidemiologically linked patrons and food handlers from a restaurant-associated outbreak of shigellosis. Six isolates available for pulsed-field gel electrophoresis were identical. All strains agglutinated in group B and subgroup factor 6 sera but not in group 1 through group 6 sera.

Molecular typing of Salmonella enterica serovar typhi.

PubMed Central

Navarro, F; Llovet, T; Echeita, M A; Coll, P; Aladueña, A; Usera, M A; Prats, G

1996-01-01

The efficiencies of different tests for epidemiological markers--phage typing, ribotyping, IS200 typing, and pulsed-field gel electrophoresis (PFGE)--were evaluated for strains from sporadic cases of typhoid fever and a well-defined outbreak. Ribotyping and PFGE proved to be the most discriminating. Both detected two different patterns among outbreak-associated strains. PMID:8897193

[The role of wild murine rodents in the selection of different strains of tick-borne encephalitis and Powassan viruses].

PubMed

Leonova, G N; Krugliak, S P; Lozovskaia, S A; Rybachuk, V N

1987-01-01

The study demonstrated the role of wild murine rodents in selection of different strains of tick-borne encephalitis and Powassan viruses, determined their ecological characteristics reflected in the epidemiological features of tick-borne encephalitis and Powassan encephalitis in southern Far East.

Molecular Epidemiology of Autochthonous Dengue Virus Strains Circulating in Mexico ▿

PubMed Central

Rivera-Osorio, Pilar; Vaughan, Gilberto; Ramírez-González, Jose Ernesto; Fonseca-Coronado, Salvador; Ruíz-Tovar, Karina; Cruz-Rivera, Mayra Yolanda; Ruíz-Pacheco, Juan Alberto; Vázquez-Pichardo, Mauricio; Carpio-Pedroza, Juan Carlos; Cázares, Fernando; Escobar-Gutiérrez, Alejandro

2011-01-01

Dengue virus (DENV) is the most important arthropod-borne viral infection in humans. Here, the genetic relatedness among autochthonous DENV Mexican isolates was assessed. Phylogenetic and median-joining network analyses showed that viral strains recovered from different geographic locations are genetically related and relatively homogeneous, exhibiting limited nucleotide diversity. PMID:21775538

[Molecular epidemiological characteristics of HIV-1 strains isolated from newly diagnosed MSM subjects (2006-2010) in Beijing, China].

PubMed

Ye, Jing-Rong; Zang, Wan-Chun; Su, Xue-Li; Lu, Hong-Yan; Hao, Ming-Qiang; Xin, Ruo-Lei; Chen, Guo-Min; He, Xiong; Zeng, Yi

2014-03-01

This study aims to analyze the molecular epidemiological characteristics of HIV-1 strains prevailing among men who have sex with men (MSM) in Beijing, China. The pol gene fragments from 250 newly diagnosed HIV-1-infected MSM individuals during 2006-2010 in Beijing were amplified by RT-nested PCR, sequenced, and phylogenetically analyzed. HIV-1 pol gene from 189 individuals were amplified and analyzed; 81 (42. 9%), 3 (1. 6%), 2 (1.0%), 88 (46. 6%), and 15 (7.9%) individuals were infected with HIV-1 subtypes B, B', C, CRF01_AE, and CRF07_BC, respectively. The subtypes B and CRF01_AE could both be grouped into two clusters, and CRFO7_BC strains shared high homology and were presumed to originate from a common ancestor. The HIV-1 circulating in MSM in Beijing had a lower genetic diversity than in heterosexuals. The HIV-1 epidemic (2006-2010) in MSM in Beijing was actually a rapid spread of HIV-1 CRF01 AE and B, or rather native strains of the two viruses.

Influenza virus surveillance, vaccine strain selection, and manufacture.

PubMed

Stöhr, Klaus; Bucher, Doris; Colgate, Tony; Wood, John

2012-01-01

As outlined in other chapters, the influenza virus, existing laboratory diagnostic abilities, and disease epidemiology have several peculiarities that impact on the timing and processes for the annual production of influenza vaccines. The chapter provides an overview on the key biological and other factors that influence vaccine production. They are the reason for an "annual circle race" beginning with global influenza surveillance during the influenza season in a given year to the eventual supply of vaccines 12 months later in time before the next seasonal outbreak and so on. As influenza vaccines are needed for the Northern and Southern Hemisphere outbreaks in fall and spring, respectively, global surveillance and vaccine production has become a year round business. Its highlights are the WHO recommendations on vaccine strains in February and September and the eventual delivery of vaccine doses in time before the coming influenza season. In between continues vaccine strain and epidemiological surveillance, preparation of new high growth reassortments, vaccine seed strain preparation and development of standardizing reagents, vaccine bulk production, fill-finishing and vaccine release, and in some regions, clinical trials for regulatory approval.

Characterization of Haemophilus parasuis isolated from Brazilian swine through serotyping, AFLP and PFGE.

PubMed

Castilla, Karina Salvagni; de Gobbi, Débora Dirani Sena; Moreno, Luisa Zanolli; Paixão, Renata; Coutinho, Tania Alen; dos Santos, José Lúcio; Moreno, Andrea Micke

2012-06-01

Haemophilus parasuis infection in pigs is characterized by fibrinous polyserositis, arthritis and meningitis. Despite the fact that traditional diagnosis is based on herd history, clinical signs, bacterial isolation and serotyping, molecular-based methods are alternatives for species-specific tests and epidemiological studies. The aim of this study was to characterize H. parasuis field strains from different states of Brazil, employing serotyping and genotyping methods. Serotyping revealed that serovar 4 was the most prevalent (26.1%), followed by serovars 5 (17.4%), 14 (8.7%), 13 (4.4%) and 2 (4.4%), whereas 39% of the strains were considered as untypeable. AFLP with a single enzyme and PFGE were able to type all isolates tested, generating 34 and 20 different profiles, respectively, including untypeable strains. Besides the slightly higher discrimination index presented by AFLP, PFGE with Not I restriction enzyme showed a better correlation with epidemiological data, grouping strains of the same serovar, animal or farm origin. The results indicated AFLP and PFGE as valuable tools for typing H. parasuis isolates collected in Brazil. Copyright © 2011 Elsevier Ltd. All rights reserved.

[Establishment and application of mechanical strain loading system of multi-channel cells].

PubMed

Li, Yongming; Wang, Hua; Zhang, Xiaodong; Tang, Lin

2012-02-01

Based on single-chip microcomputer, we have established a mechanical strain loading system with multi-channel to study the biological behavior of cultured cells in vitro under mechanical strain. We developed a multi-channel cell strain loading device controlled by single-chip microcomputer. We controlled the vacuum pump with vacuum chamber to make negative pressure changing periodically in the vacuum chamber. The tested cells were seeded on the surface of an elastic membrane mounted on the vacuum chamber, and could be strained or relaxed by cyclic pressure. Since the cells are attached to the surface of the membrane, they presumably experience the same deformation as that was applied to the membrane. The system was easy to carry and to operate, with deformation rate (1%-21%) and frequency (0-0. 5Hz) which could be adjusted correctly according to experimental requirement, and could compare different deformation rate of three channels at the same time. The system ran stably and completely achieved design aims, and provided a method to study the biological behavior of cultured cells attached to the surface of the elastic membrane under mechanical strain in vitro.

Subtyping of the Legionella pneumophila "Ulm" outbreak strain using the CRISPR-Cas system.

PubMed

Lück, Christian; Brzuszkiewicz, Elzbieta; Rydzewski, Kerstin; Koshkolda, Tetyana; Sarnow, Katharina; Essig, Andreas; Heuner, Klaus

2015-12-01

In 2009/2010 an outbreak of Legionnaires' disease with 64 cases including four fatalities took place in the city of Ulm/Neu-Ulm in Germany. L. pneumophila serogroup 1, mAb type Knoxville, sequence type (ST) 62 was identified as the epidemic strain. This strain was isolated from eight patients and from a cooling tower in the city of Ulm. Based on whole genome sequencing data from one patient strain, we identified an Lvh type IV secretion system containing a CRISPR-Cas system. The CRISPR sequence contains 38 spacer DNA sequences. We used these variable DNA spacers to further subtype the outbreak strain as well as six epidemiologically unrelated strains of CRISPR-Cas positive ST62 strains isolated at various regions in Germany. The first 12 spacer DNAs of eight patient isolates and three environmental isolates from the suspected source of infection were analyzed and found to be identical. Spacer DNAs were identified in further six epidemiologically unrelated patient isolates of L. pneumophila of ST62 in addition to the 12 "core" spacers. The presence of new spacer DNAs at the 5' site downstream of the first repeat indicates that these CRISPR-Cas systems seem to be functional. PCR analysis revealed that not all L. pneumophila sg1 ST62 strains investigated exhibited a CRISPR-Cas system. In addition, we could demonstrate that the CRISPR-Cas system is localized on a genomic island (LpuGI-Lvh) which can be excised from the chromosome and therefore may be transferable horizontally to other L. pneumophila strains. Copyright © 2015 Elsevier GmbH. All rights reserved.

Laterality defects in the national birth defects prevention study 1998-2007 birth prevalence and descriptive epidemiology

USDA-ARS?s Scientific Manuscript database

Little is known epidemiologically about laterality defects. Using data from the National Birth Defects Prevention Study (NBDPS), a large multi-site case-control study of birth defects, we analyzed prevalence and selected characteristics in children born with laterality defects born from 1998 to 2007...

Divorce Workshops: An Opportunity for Preventive Education & Epidemiological Research.

ERIC Educational Resources Information Center

Kalafat, John; And Others

This paper describes the program and research related to the "Making It" series of 18 multi-media divorce workshops co-sponsored by a community mental health center (CMHC) and a chapter of Parents without Partners (PWP). An introductory section discusses the rationale for larger scale community intervention and epidemiological research. The…

Combining Mass Spectrometry and Toxicology for a Multi-Country European Epidemiologic Study on Drinking Water Disinfection By-Products.

EPA Science Inventory

The HiWATE (Health Impacts of long-term exposure to disinfection by-products in drinking WATEr) project is the first systematic analysis that combines the epidemiology on adverse pregnancy outcomes with analytical chemistry and analytical biology in the European Union. This study...

Combining Mass Spectrometry and Toxicology for a Multi-Country European Epidemiologic Study on Drinking Water Disinfection By-Products

EPA Science Inventory

The HiWATE (Health Impacts of long-term exposure to disinfection by-products in drinking WATEr) project is the first systematic analysis that combines the epidemiology on adverse pregnancy outcomes with analytical chemistry and analytical biology in the European Union. This study...

[Training programs for staff at local Infectious Disease Surveillance Centers: the needs and usefulness].

PubMed

Suzuki, Tomoyuki; Kamiya, Nobuyuki; Yahata, Yuichiro; Ozeki, Yukie; Kishimoto, Tsuyoshi; Nadaoka, Yoko; Nakanishi, Yoshiko; Yoshimura, Takesumi; Shimada, Tomoe; Tada, Yuki; Shirabe, Komei; Kozawa, Kunihisa

2013-03-01

The objective of this study was to assess the need for and usefulness of training programs for Local Infectious Disease Surveillance Center (LIDSC) staff. A structured questionnaire survey was conducted to assess the needs and usefulness of training programs. The subjects of the survey were participants of a workshop held after an annual conference for the LIDSC staff. Data on demographic information, the necessity of training programs for LIDSC staff, the themes and contents of the training program, self-assessment of knowledge on epidemiology and statistics were covered by the questionnaire. A total of 55 local government officials responded to the questionnaire (response rate: 100%). Among these, 95% of participants believed that the training program for the LIDSC staff was necessary. Basic statistical analysis (85%), descriptive epidemiology (65%), outline of epidemiology (60%), interpretation of surveillance data (65%), background and objectives of national infectious disease surveillance in Japan (60%), methods of field epidemiology (60%), and methods of analysis data (51%) were selected by over half of the respondents as suitable themes for training programs. A total of 34 LIDSC staff answered the self-assessment question on knowledge of epidemiology. A majority of respondents selected "a little" or "none" for all questions about knowledge. Only a few respondents had received education in epidemiology. The results of this study indicate that LIDSC staff have basic demands for fundamental and specialized education to improve their work. Considering the current situation regarding the capacity of LIDSC staff, these training programs should be started immediately.

Molecular Epidemiology of Yellow Fever in Bolivia from 1999 to 2008

PubMed Central

Baronti, Cécile; Goitia, Norma Janeth Velasquez; Cook, Shelley; Roca, Yelin; Revollo, Jimmy; Flores, Jorge Vargas

2011-01-01

Abstract Yellow fever (YF) is a serious public health problem in Bolivia since at least the 19th century. Surprisingly, very limited information has been made available to date regarding the genetic characterisation and epidemiology of Bolivian YF virus (YFV) strains. Here, we conducted the genetic characterization of 12 human isolates of YFV collected in Bolivia between 1999 and 2008, by sequencing and analysis of two regions of the viral genome: a fragment encoding structural proteins “PrM” (premembrane and envelope) and a distal region “EMF,” spanning the end of the virus genome. Our study reveals a high genetic diversity of YFV strains circulating in Bolivia during the last decade: we identified not only “Peruvian-like” genotype II viruses (related to previously characterized Bolivian strains), but also, for the fist time, “Brazilian-like” genotype I viruses. During the complete period of the study, only cases of “jungle” YF were detected (i.e., circulation of YFV via a sylvatic cycle) with no cluster of urban cases. However, the very significant spread of the Aedes aegypti mosquito across Bolivian cities threatens the country with the reappearance of an urban YFV transmission cycle and thus is required a sustained epidemiological surveillance. PMID:20925524

Molecular Epidemiology of Leptospira Serogroup Pomona Infections Among Wild and Domestic Animals in Spain.

PubMed

Arent, Z J; Gilmore, C; San-Miguel Ayanz, J M; Neyra, L Quevedo; García-Peña, F J

2017-03-01

Strains of Leptospira serogroup Pomona are known to cause widespread animal infections in many parts of the world. Forty-three isolates retrieved from domestic animals and wild small mammals suggest that serogroup Pomona is epidemiologically relevant in Spain. This is supported by the high prevalence of serovar Pomona antibodies in livestock and wild animals. In this study, the strains were serologically and genetically characterized in an attempt to elucidate their epidemiology. Serological typing was based on the microscopic agglutination test but molecular typing involved species-specific polymerase chain reaction, restriction endonuclease analysis, and multiple-locus variable-number tandem repeat analysis. The study revealed that the infections are caused by two serovars, namely Pomona and Mozdok. Serovar Pomona was derived only from farm animals and may be adapted to pigs, which are recognized as the maintenance host. The results demonstrated that serovar Pomona is genetically heterogeneous and three different types were recognized. This heterogeneity was correlated with different geographical distributions of the isolates. All strains derived from small wild mammals were identified as serovar Mozdok. Some isolates of this serovar retrieved from cattle confirm that this serovar may also be the cause of infections in food-producing animals for which these wild species may be source of infection.

The Forest behind the Tree: Phylogenetic Exploration of a Dominant Mycobacterium tuberculosis Strain Lineage from a High Tuberculosis Burden Country

PubMed Central

Cardoso Oelemann, Maranibia; Gomes, Harrison M.; Willery, Eve; Possuelo, Lia; Batista Lima, Karla Valéria; Allix-Béguec, Caroline; Locht, Camille; Goguet de la Salmonière, Yves-Olivier L.; Gutierrez, Maria Cristina; Suffys, Philip; Supply, Philip

2011-01-01

Background Genotyping of Mycobacterium tuberculosis isolates is a powerful tool for epidemiological control of tuberculosis (TB) and phylogenetic exploration of the pathogen. Standardized PCR-based typing, based on 15 to 24 mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) loci combined with spoligotyping, has been shown to have adequate resolution power for tracing TB transmission and to be useful for predicting diverse strain lineages in European settings. Its informative value needs to be tested in high TB-burden countries, where the use of genotyping is often complicated by dominance of geographically specific, genetically homogeneous strain lineages. Methodology/Principal Findings We tested this genotyping system for molecular epidemiological analysis of 369 M. tuberculosis isolates from 3 regions of Brazil, a high TB-burden country. Deligotyping, targeting 43 large sequence polymorphisms (LSPs), and the MIRU-VNTRplus identification database were used to assess phylogenetic predictions. High congruence between the different typing results consistently revealed the countrywide supremacy of the Latin-American-Mediterranean (LAM) lineage, comprised of three main branches. In addition to an already known RDRio branch, at least one other branch characterized by a phylogenetically informative LAM3 spoligo-signature seems to be globally distributed beyond Brazil. Nevertheless, by distinguishing 321 genotypes in this strain population, combined MIRU-VNTR typing and spoligotyping demonstrated the presence of multiple distinct clones. The use of 15 to 24 loci discriminated 21 to 25% more strains within the LAM lineage, compared to a restricted lineage-specific locus set suggested to be used after SNP analysis. Noteworthy, 23 of the 28 molecular clusters identified were exclusively composed of patient isolates from a same region, consistent with expected patterns of mostly local TB transmission. Conclusions/Significance Standard MIRU-VNTR typing combined with spoligotyping can reveal epidemiologically meaningful clonal diversity behind a dominant M. tuberculosis strain lineage in a high TB-burden country and is useful to explore international phylogenetical ramifications. PMID:21464915

Investigation of genetic diversity and epidemiological characteristics of Pasteurella multocida isolates from poultry in southwest China by population structure, multi-locus sequence typing and virulence-associated gene profile analysis.

PubMed

Li, Zhangcheng; Cheng, Fangjun; Lan, Shimei; Guo, Jianhua; Liu, Wei; Li, Xiaoyan; Luo, Zeli; Zhang, Manli; Wu, Juan; Shi, Yang

2018-04-25

Fowl cholera caused by Pasteurella multocida has always been a disease of global importance for poultry production. The aim of this study was to obtain more information about the epidemiology of avian P. multocida infection in southwest China and the genetic characteristics of clinical isolates. P. multocida isolates were characterized by biochemical and molecular-biological methods. The distributions of the capsular serogroups, the phenotypic antimicrobial resistance profiles, lipopolysaccharide (LPS) genotyping and the presence of 19 virulence genes were investigated in 45 isolates of P. multocida that were associated with clinical disease in poultry. The genetic diversity of P. multocida strains was performed by 16S rRNA and rpoB gene sequence analysis as well as multilocus sequence typing (MLST). The results showed that most (80.0%) of the P. multocida isolates in this study represented special P. multocida subspecies, and 71.1% of the isolates showed multiple-drug resistance. 45 isolates belonged to capsular types: A (100%) and two LPS genotypes: L1 (95.6%) and L3 (4.4%). MLST revealed two new alleles (pmi77 and gdh57) and one new sequence type (ST342). ST129 types dominated in 45 P. multocida isolates. Isolates belonging to ST129 were with the genes ompH+plpB+ptfA+tonB, whereas ST342 included isolates with fur+hgbA+tonB genes. Population genetic analysis and the MLST results revealed that at least one new ST genotype was present in the avian P. multocida in China. These findings provide novel insights into the epidemiological characteristics of avian P. multocida isolates in southwest China.

[Precision medicine: new opportunities and challenges for molecular epidemiology].

PubMed

Song, Jing; Hu, Yonghua

2016-04-01

Since the completion of the Human Genome Project in 2003 and the announcement of the Precision Medicine Initiative by U.S. President Barack Obama in January 2015, human beings have initially completed the " three steps" of " genomics to biology, genomics to health as well as genomics to society". As a new inter-discipline, the emergence and development of precision medicine have relied on the support and promotion from biological science, basic medicine, clinical medicine, epidemiology, statistics, sociology and information science, etc. Meanwhile, molecular epidemiology is considered to be the core power to promote precision medical as a cross discipline of epidemiology and molecular biology. This article is based on the characteristics and research progress of medicine and molecular epidemiology respectively, focusing on the contribution and significance of molecular epidemiology to precision medicine, and exploring the possible opportunities and challenges in the future.

Mechanical failure modes of chronically implanted planar silicon-based neural probes for laminar recording

PubMed Central

Kozai, Takashi D. Y.; Catt, Kasey; Li, Xia; Gugel, Zhannetta V.; Olafsson, Valur T.; Vazquez, Alberto L.; Cui, X. Tracy

2014-01-01

Penetrating intracortical electrode arrays that record brain activity longitudinally are powerful tools for basic neuroscience research and emerging clinical applications. However, regardless of the technology used, signals recorded by these electrodes degrade over time. The failure mechanisms of these electrodes are understood to be a complex combination of the biological reactive tissue response and material failure of the device over time. While mechanical mismatch between the brain tissue and implanted neural electrodes have been studied as a source of chronic inflammation and performance degradation, the electrode failure caused by mechanical mismatch between different material properties and different structural components within a device have remained poorly characterized. Using Finite Element Model (FEM) we simulate the mechanical strain on a planar silicon electrode. The results presented here demonstrate that mechanical mismatch between iridium and silicon leads to concentrated strain along the border of the two materials. This strain is further focused on small protrusions such as the electrical traces in planar silicon electrodes. These findings are confirmed with chronic in vivo data (133–189 days) in mice by correlating a combination of single-unit electrophysiology, evoked multi-unit recordings, electrochemical impedance spectroscopy, and scanning electron microscopy from traces and electrode sites with our modeling data. Several modes of mechanical failure of chronically implanted planar silicon electrodes are found that result in degradation and/or loss of recording. These findings highlight the importance of strains and material properties of various subcomponents within an electrode array. PMID:25453935

Modified social ecological model: a tool to guide the assessment of the risks and risk contexts of HIV epidemics.

PubMed

Baral, Stefan; Logie, Carmen H; Grosso, Ashley; Wirtz, Andrea L; Beyrer, Chris

2013-05-17

Social and structural factors are now well accepted as determinants of HIV vulnerabilities. These factors are representative of social, economic, organizational and political inequities. Associated with an improved understanding of multiple levels of HIV risk has been the recognition of the need to implement multi-level HIV prevention strategies. Prevention sciences research and programming aiming to decrease HIV incidence requires epidemiologic studies to collect data on multiple levels of risk to inform combination HIV prevention packages. Proximal individual-level risks, such as sharing injection devices and unprotected penile-vaginal or penile-anal sex, are necessary in mediating HIV acquisition and transmission. However, higher order social and structural-level risks can facilitate or reduce HIV transmission on population levels. Data characterizing these risks is often far more actionable than characterizing individual-level risks. We propose a modified social ecological model (MSEM) to help visualize multi-level domains of HIV infection risks and guide the development of epidemiologic HIV studies. Such a model may inform research in epidemiology and prevention sciences, particularly for key populations including men who have sex with men (MSM), people who inject drugs (PID), and sex workers. The MSEM builds on existing frameworks by examining multi-level risk contexts for HIV infection and situating individual HIV infection risks within wider network, community, and public policy contexts as well as epidemic stage. The utility of the MSEM is demonstrated with case studies of HIV risk among PID and MSM. The MSEM is a flexible model for guiding epidemiologic studies among key populations at risk for HIV in diverse sociocultural contexts. Successful HIV prevention strategies for key populations require effective integration of evidence-based biomedical, behavioral, and structural interventions. While the focus of epidemiologic studies has traditionally been on describing individual-level risk factors, the future necessitates comprehensive epidemiologic data characterizing multiple levels of HIV risk.

Imperfect Vaccine Aggravates the Long-Standing Dilemma of Voluntary Vaccination

PubMed Central

Wu, Bin; Fu, Feng; Wang, Long

2011-01-01

Achieving widespread population immunity by voluntary vaccination poses a major challenge for public health administration and practice. The situation is complicated even more by imperfect vaccines. How the vaccine efficacy affects individuals' vaccination behavior has yet to be fully answered. To address this issue, we combine a simple yet effective game theoretic model of vaccination behavior with an epidemiological process. Our analysis shows that, in a population of self-interested individuals, there exists an overshooting of vaccine uptake levels as the effectiveness of vaccination increases. Moreover, when the basic reproductive number, , exceeds a certain threshold, all individuals opt for vaccination for an intermediate region of vaccine efficacy. We further show that increasing effectiveness of vaccination always increases the number of effectively vaccinated individuals and therefore attenuates the epidemic strain. The results suggest that ‘number is traded for efficiency’: although increases in vaccination effectiveness lead to uptake drops due to free-riding effects, the impact of the epidemic can be better mitigated. PMID:21687680

Influenza Research in the Eastern Mediterranean Region: A Review

PubMed Central

Khan, Wasiq; El Rifay, Amira S.; Malik, Mamun; Kayali, Ghazi

2017-01-01

Given the importance of influenza infections in the Eastern Mediterranean Region (EMR), we conducted a comprehensive literature review to analyze the status of influenza research in the region from 2012. Influenza research has gained more momentum recently with the emergence of H5N1 and new virus strains. Research covering epidemiological, veterinary, and basic science aspects is growing. More sequences were being generated per year, not only for diagnostic purposes but also for research. We included gray literature publications in our search and found several graduate student dissertations from Egypt, which were published on an online portal. However, the search revealed some weaknesses, mostly in the areas of study design and the lack of surveillance studies. Another weakness was the fact that the publications originated from very few countries, mainly Egypt and Iran. Although improving, influenza research in the EMR remains weak. We recommend encouraging countries in the EMR to conduct more influenza research using stronger methodologies. PMID:29026466

Echinococcus as a model system: biology and epidemiology.

PubMed

Thompson, R C A; Jenkins, D J

2014-10-15

The introduction of Echinococcus to Australia over 200 years ago and its establishment in sheep rearing areas of the country inflicted a serious medical and economic burden on the country. This resulted in an investment in both basic and applied research aimed at learning more about the biology and life cycle of Echinococcus. This research served to illustrate the uniqueness of the parasite in terms of developmental biology and ecology, and the value of Echinococcus as a model system in a broad range of research, from fundamental biology to theoretical control systems. These studies formed the foundation for an international, diverse and ongoing research effort on the hydatid organisms encompassing stem cell biology, gene regulation, strain variation, wildlife diseases and models of transmission dynamics. We describe the development, nature and diversity of this research, and how it was initiated in Australia but subsequently has stimulated much international and collaborative research on Echinococcus. Copyright © 2014 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Biochemical, genetic, and epidemiologic characterization of Haemophilus influenzae biogroup aegyptius (Haemophilus aegyptius) strains associated with Brazilian purpuric fever.

PubMed Central

Brenner, D J; Mayer, L W; Carlone, G M; Harrison, L H; Bibb, W F; Brandileone, M C; Sottnek, F O; Irino, K; Reeves, M W; Swenson, J M

1988-01-01

Brazilian purpuric fever (BPF) is a recently recognized fulminant pediatric disease characterized by fever, with rapid progression to purpura, hypotensive shock, and death. BPF is usually preceded by purulent conjunctivitis that has resolved before the onset of fever. Both the conjunctivitis and BPF are caused by Haemophilus influenzae biogroup aegyptius (formerly called H. aegyptius). Isolates from 15 BPF cases, mainly from blood or hemorrhagic cerebrospinal fluid, case-associated isolates from 42 persons in towns where BPF cases occurred, and control strains from 32 persons in towns without BPF cases were characterized biochemically, genetically, and epidemiologically. Results indicated that a single clone was responsible for all BPF cases identified in six Brazilian towns from 1984 through 1986. All of 15 (100%) case strains were the same clone as was 1 of 32 (3%) control strains (P = less than 10(-8). Isolates of the clone were preferentially intrarelated by DNA hybridization (99% relatedness, hydroxyapatite method at 60 and 75 degrees C) and were separable from other H. influenzae biogroup aegyptius strains (approximately 90% relatedness at 60 degrees C and 82% relatedness at 75 degrees C). All isolates of the BPF clone and no other strains contained a 24-megadalton plasmid of restriction endonuclease type 3031, were of a single multilocus enzyme mobility type, were of a single sodium dodecyl sulfate-polyacrylamide gel electrophoresis type, and were in one of two ribosomal DNA restriction patterns. All BPF clone isolates reacted with monoclonal antibodies produced from a case strain; only 3 of 62 (5%) other strains reacted with this monoclonal antibody. Ninety percent of BPF clone strains and 27% of other strains were relatively resistant to sulfamethoxazole-trimethoprim. Images PMID:3262623

Marked Genomic Diversity of Norovirus Genogroup I Strains in a Waterborne Outbreak

PubMed Central

Hannoun, Charles; Larsson, Charlotte U.; Bergström, Tomas

2012-01-01

Marked norovirus (NoV) diversity was detected in patient samples from a large community outbreak of gastroenteritis with waterborne epidemiology affecting approximately 2,400 people. NoV was detected in 33 of 50 patient samples examined by group-specific real-time reverse transcription-PCR. NoV genotype I (GI) strains predominated in 31 patients, with mixed GI infections occurring in 5 of these patients. Sequence analysis of RNA-dependent polymerase-N/S capsid-coding regions (∼900 nucleotides in length) confirmed the dominance of the GI strains (n = 36). Strains of NoV GI.4 (n = 21) and GI.7 (n = 9) were identified, but six strains required full capsid amino acid analyses (530 to 550 amino acids) based on control sequencing of cloned amplicons before the virus genotype could be determined. Three strains were assigned to a new NoV GI genotype, proposed as GI.9, based on capsid amino acid analyses showing 26% dissimilarity from the established genotypes GI.1 to GI.8. Three other strains grouped in a sub-branch of GI.3 with 13 to 15% amino acid dissimilarity to GI.3 GenBank reference strains. Phylogenetic analysis (2.1 kb) of 10 representative strains confirmed these genotype clusters. Strains of NoV GII.4 (n = 1), NoV GII.6 (n = 2), sapovirus GII.2 (n = 1), rotavirus (n = 3), adenovirus (n = 1), and Campylobacter spp. (n = 2) were detected as single infections or as mixtures with NoV GI. Marked NoV GI diversity detected in patients was consistent with epidemiologic evidence of waterborne NoV infections, suggesting human fecal contamination of the water supply. Recognition of NoV diversity in a cluster of patients provided a useful warning marker of waterborne contamination in the Lilla Edet outbreak. PMID:22247153

Application of whole genome sequence data in analyzing the molecular epidemiology of Shiga toxin-producing Escherichia coli O157:H7/H.

PubMed

Yokoyama, Eiji; Hirai, Shinichiro; Ishige, Taichiro; Murakami, Satoshi

2018-01-02

Seventeen clusters of Shiga toxin-producing Escherichia coli O157:H7/- (O157) strains, determined by cluster analysis of pulsed-field gel electrophoresis patterns, were analyzed using whole genome sequence (WGS) data to investigate this pathogen's molecular epidemiology. The 17 clusters included 136 strains containing strains from nine outbreaks, with each outbreak caused by a single source contaminated with the organism, as shown by epidemiological contact surveys. WGS data of these strains were used to identify single nucleotide polymorphisms (SNPs) by two methods: short read data were directly mapped to a reference genome (mapping derived SNPs) and common SNPs between the mapping derived SNPs and SNPs in assembled data of short read data (common SNPs). Among both SNPs, those that were detected in genes with a gap were excluded to remove ambiguous SNPs from further analysis. The effectiveness of both SNPs was investigated among all the concatenated SNPs that were detected (whole SNP set); SNPs were divided into three categories based on the genes in which they were located (i.e., backbone SNP set, O-island SNP set, and mobile element SNP set); and SNPs in non-coding regions (intergenic region SNP set). When SNPs from strains isolated from the nine single source derived outbreaks were analyzed using an unweighted pair group method with arithmetic mean tree (UPGMA) and a minimum spanning tree (MST), the maximum pair-wise distances of the backbone SNP set of the mapping derived SNPs were significantly smaller than those of the whole and intergenic region SNP set on both UPGMAs and MSTs. This significant difference was also observed when the backbone SNP set of the common SNPs were examined (Steel-Dwass test, P≤0.01). When the maximum pair-wise distances were compared between the mapping derived and common SNPs, significant differences were observed in those of the whole, mobile element, and intergenic region SNP set (Wilcoxon signed rank test, P≤0.01). When all the strains included in one complex on an MST or one cluster on a UPGMA were designated as the same genotype, the values of the Hunter-Gaston Discriminatory Power Index for the backbone SNP set of the mapping derived and common SNPs were higher than those of other SNP sets. In contrast, the mobile element SNP set could not robustly subdivide lineage I strains of tested O157 strains using both the mapping derived and common SNPs. These results suggested that the backbone SNP set were the most effective for analysis of WGS data for O157 in enabling an appropriation of its molecular epidemiology. Copyright © 2017 Elsevier B.V. All rights reserved.

Pulsotype Diversity of Clostridium botulinum Strains Containing Serotypes A and/or B Genes

PubMed Central

Halpin, Jessica L.; Joseph, Lavin; Dykes, Janet K.; McCroskey, Loretta; Smith, Elise; Toney, Denise; Stroika, Steven; Hise, Kelley; Maslanka, Susan; Lúquez, Carolina

2017-01-01

Clostridium botulinum strains are prevalent in the environment and produce a potent neurotoxin that causes botulism, a rare but serious paralytic disease. In 2010, a national PulseNet database was established to curate C. botulinum pulsotypes and facilitate epidemiological investigations, particularly for serotypes A and B strains frequently associated with botulism cases in the United States. Between 2010 and 2014 we performed pulsed-field gel electrophoresis (PFGE) using a PulseNet protocol, uploaded the resulting PFGE patterns into a national database, and analyzed data according to PulseNet criteria (UPGMA clustering, Dice coefficient, 1.5% position tolerance, and 1.5% optimization). A retrospective data analysis was undertaken on 349 entries comprised of type A and B strains isolated from foodborne and infant cases to determine epidemiological relevance, resolution of the method, and the diversity of the database. Most studies to date on the pulsotype diversity of C. botulinum have encompassed very small sets of isolates; this study, with over 300 isolates, is more comprehensive than any published to date. Epidemiologically linked isolates had indistinguishable patterns, except in four instances and there were no obvious geographic trends noted. Simpson’s Index of Diversity (D) has historically been used to demonstrate species diversity and abundance within a group, and is considered a standard descriptor for PFGE databases. Simpson’s Index was calculated for each restriction endonuclease (SmaI, XhoI), the pattern combination SmaI-XhoI, as well as for each toxin serotype. The D values indicate that both enzymes provided better resolution for serotype B isolates than serotype A. XhoI as the secondary enzyme provided little additional discrimination for C. botulinum. SmaI patterns can be used to exclude unrelated isolates during a foodborne outbreak, but pulsotypes should always be considered concurrently with available epidemiological data. PMID:28692343

Long-term dynamics of Mycoplasma conjunctivae at the wildlife-livestock interface in the Pyrenees

PubMed Central

Cabezón, Oscar; Frey, Joachim; Velarde, Roser; Serrano, Emmanuel; Colom-Cadena, Andreu; Gelormini, Giuseppina; Marco, Ignasi; Mentaberre, Gregorio; Lavín, Santiago; López-Olvera, Jorge Ramón

2017-01-01

Functional roles of domestic and wild host populations in infectious keratoconjunctivitis (IKC) epidemiology have been extensively discussed claiming a domestic reservoir for the more susceptible wild hosts, however, based on limited data. With the aim to better assess IKC epidemiology in complex host-pathogen alpine systems, the long-term infectious dynamics and molecular epidemiology of Mycoplasma conjunctivae was investigated in all host populations from six study areas in the Pyrenees and one in the Cantabrian Mountains (Northern Spain). Detection of M. conjunctivae was performed by qPCR on 3600 eye swabs collected during seven years from hunted wild ungulates and sympatric domestic sheep (n = 1800 animals), and cluster analyses of the strains were performed including previous reported local strains. Mycoplasma conjunctivae was consistently detected in three Pyrenean chamois (Rupicapra p. pyrenaica) populations, as well as in sheep flocks (17.0% of sheep) and occasionally in mouflon (Ovis aries musimon) from the Pyrenees (22.2% in one year/area); statistically associated with ocular clinical signs only in chamois. Chamois populations showed different infection dynamics with low but steady prevalence (4.9%) and significant yearly fluctuations (0.0%– 40.0%). Persistence of specific M. conjunctivae strain clusters in wild host populations is demonstrated for six and nine years. Cross-species transmission between chamois and sheep and chamois and mouflon were also sporadically evidenced. Overall, independent M. conjunctivae sylvatic and domestic cycles occurred at the wildlife-livestock interface in the alpine ecosystems from the Pyrenees with sheep and chamois as the key host species for each cycle, and mouflon as a spill-over host. Host population characteristics and M. conjunctivae strains resulted in different epidemiological scenarios in chamois, ranging from the fading out of the mycoplasma to the epidemic and endemic long-term persistence. These findings highlight the capacity of M. conjunctivae to establish diverse interactions and persist in host populations, also with different transmission conditions. PMID:29016676

Re-evaluation of a 2014 multi-country European outbreak of Salmonella Enteritidis phage type 14b using recent epidemiological and molecular data

PubMed Central

Hörmansdorfer, Stefan; Messelhäußer, Ute; Rampp, Albert; Schönberger, Katharina; Dallman, Tim; Allerberger, Franz; Kornschober, Christian; Sing, Andreas; Wallner, Peter; Zapf, Andreas

2017-01-01

A European multi-country outbreak of Salmonella Enteritidis phage type (PT) 14b occurred from March to November 2014 associated with the consumption of eggs. The outbreak involved more than 400 human cases from France, Luxembourg, Austria and the United Kingdom. In 2016–2017, it has been re-evaluated combining recent epidemiological results with latest molecular data. The outbreak was traced back to one large Bavarian egg producer with four distinct premises, three located in Bavaria, one in the Czech Republic. The outbreak isolates of S. Enteritidis PT 14b were grouped into three closely related clades by whole genome sequencing. Two of these clades could be referred to two Bavarian premises of the egg producer on the basis of epidemiological and molecular data, while epidemiological data presumably linked the third clade to another premises of the egg producer. Interestingly and in contrast to the situation in other European countries where several outbreaks were documented, all notified 91 laboratory-confirmed cases of S. Enteritidis PT 14b from Bavaria were sporadic, singular cases not belonging to any epidemiological outbreaks. In conclusion, as demonstrated here, the resolution of food-related outbreaks with such a high discriminatory power is rare in outbreak investigation. PMID:29258650

Re-evaluation of a 2014 multi-country European outbreak of Salmonella Enteritidis phage type 14b using recent epidemiological and molecular data.

PubMed

Hörmansdorfer, Stefan; Messelhäußer, Ute; Rampp, Albert; Schönberger, Katharina; Dallman, Tim; Allerberger, Franz; Kornschober, Christian; Sing, Andreas; Wallner, Peter; Zapf, Andreas

2017-12-01

A European multi-country outbreak of Salmonella Enteritidis phage type (PT) 14b occurred from March to November 2014 associated with the consumption of eggs. The outbreak involved more than 400 human cases from France, Luxembourg, Austria and the United Kingdom. In 2016-2017, it has been re-evaluated combining recent epidemiological results with latest molecular data. The outbreak was traced back to one large Bavarian egg producer with four distinct premises, three located in Bavaria, one in the Czech Republic. The outbreak isolates of S. Enteritidis PT 14b were grouped into three closely related clades by whole genome sequencing. Two of these clades could be referred to two Bavarian premises of the egg producer on the basis of epidemiological and molecular data, while epidemiological data presumably linked the third clade to another premises of the egg producer. Interestingly and in contrast to the situation in other European countries where several outbreaks were documented, all notified 91 laboratory-confirmed cases of S. Enteritidis PT 14b from Bavaria were sporadic, singular cases not belonging to any epidemiological outbreaks. In conclusion, as demonstrated here, the resolution of food-related outbreaks with such a high discriminatory power is rare in outbreak investigation.

Epidemiology and Clinical Research Design, Part 2: Principles.

PubMed

Manja, Veena; Lakshminrusimha, Satyan

This is the third article covering core knowledge in scholarly activities for neonatal physicians. In this article, we discuss various principles of epidemiology and clinical research design. A basic knowledge of these principles is necessary for conducting clinical research and for proper interpretation of studies. This article reviews bias and confounding, causation, incidence and prevalence, decision analysis, cost-effectiveness, sensitivity analysis, and measurement.

Taxonomic evaluation of putative Streptomyces scabiei strains held in the ARS (NRRL) Culture Collection using multi-locus sequence analysis

USDA-ARS?s Scientific Manuscript database

Multi-locus sequence analysis has been demonstrated to be a useful tool for identification of Streptomyces species and was previously applied to phylogenetically differentiate the type strains of species pathogenic on potatoes (Solanum tuberosum L.). The ARS Culture Collection (NRRL) contains 43 str...

Key Role of Sequencing to Trace Hepatitis A Viruses Circulating in Italy During a Large Multi-Country European Foodborne Outbreak in 2013

PubMed Central

Bruni, Roberto; Taffon, Stefania; Equestre, Michele; Chionne, Paola; Madonna, Elisabetta; Rizzo, Caterina; Tosti, Maria Elena; Alfonsi, Valeria; Ricotta, Lara; De Medici, Dario; Di Pasquale, Simona; Scavia, Gaia; Pavoni, Enrico; Losio, Marina Nadia; Romanò, Luisa; Zanetti, Alessandro Remo; Morea, Anna; Pacenti, Monia; Palù, Giorgio; Capobianchi, Maria Rosaria; Chironna, Maria; Pompa, Maria Grazia; Ciccaglione, Anna Rita

2016-01-01

Background Foodborne Hepatitis A Virus (HAV) outbreaks are being recognized as an emerging public health problem in industrialized countries. In 2013 three foodborne HAV outbreaks occurred in Europe and one in USA. During the largest of the three European outbreaks, most cases occurred in Italy (>1,200 cases as of March 31, 2014). A national Task Force was established at the beginning of the outbreak by the Ministry of Health. Mixed frozen berries were early demonstrated to be the source of infection by the identity of viral sequences in patients and in food. In the present study the molecular characterization of HAV isolates from 355 Italian cases is reported. Methods Molecular characterization was carried out by PCR/sequencing (VP1/2A region), comparison with reference strains and phylogenetic analysis. Results A unique strain was responsible for most characterized cases (235/355, 66.1%). Molecular data had a key role in tracing this outbreak, allowing 110 out of the 235 outbreak cases (46.8%) to be recognized in absence of any other link. The data also showed background circulation of further unrelated strains, both autochthonous and travel related, whose sequence comparison highlighted minor outbreaks and small clusters, most of them unrecognized on the basis of epidemiological data. Phylogenetic analysis showed most isolates from travel related cases clustering with reference strains originating from the same geographical area of travel. Conclusions In conclusion, the study documents, in a real outbreak context, the crucial role of molecular analysis in investigating an old but re-emerging pathogen. Improving the molecular knowledge of HAV strains, both autochthonous and circulating in countries from which potentially contaminated foods are imported, will become increasingly important to control outbreaks by supporting trace back activities, aiming to identify the geographical source(s) of contaminated food, as well as public health interventions. PMID:26901877

Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151.

PubMed

Arrieta-Ortiz, Mario L; Rodríguez-R, Luis M; Pérez-Quintero, Álvaro L; Poulin, Lucie; Díaz, Ana C; Arias Rojas, Nathalia; Trujillo, Cesar; Restrepo Benavides, Mariana; Bart, Rebecca; Boch, Jens; Boureau, Tristan; Darrasse, Armelle; David, Perrine; Dugé de Bernonville, Thomas; Fontanilla, Paula; Gagnevin, Lionel; Guérin, Fabien; Jacques, Marie-Agnès; Lauber, Emmanuelle; Lefeuvre, Pierre; Medina, Cesar; Medina, Edgar; Montenegro, Nathaly; Muñoz Bodnar, Alejandra; Noël, Laurent D; Ortiz Quiñones, Juan F; Osorio, Daniela; Pardo, Carolina; Patil, Prabhu B; Poussier, Stéphane; Pruvost, Olivier; Robène-Soustrade, Isabelle; Ryan, Robert P; Tabima, Javier; Urrego Morales, Oscar G; Vernière, Christian; Carrere, Sébastien; Verdier, Valérie; Szurek, Boris; Restrepo, Silvia; López, Camilo; Koebnik, Ralf; Bernal, Adriana

2013-01-01

Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus suggest that advanced draft genome sequences are valuable resources for molecular studies on their interaction with plants and could provide valuable tools for diagnostics and detection. Here we have generated the first manually annotated high-quality draft genome sequence of Xam strain CIO151. Its genomic structure is similar to that of other xanthomonads, especially Xanthomonas euvesicatoria and Xanthomonas citri pv. citri species. Several putative pathogenicity factors were identified, including type III effectors, cell wall-degrading enzymes and clusters encoding protein secretion systems. Specific characteristics in this genome include changes in the xanthomonadin cluster that could explain the lack of typical yellow color in all strains of this pathovar and the presence of 50 regions in the genome with atypical nucleotide composition. The genome sequence was used to predict and evaluate 22 variable number of tandem repeat (VNTR) loci that were subsequently demonstrated as polymorphic in representative Xam strains. Our results demonstrate that Xanthomonas axonopodis pv. manihotis strain CIO151 possesses ten clusters of pathogenicity factors conserved within the genus Xanthomonas. We report 126 genes that are potentially unique to Xam, as well as potential horizontal transfer events in the history of the genome. The relation of these regions with virulence and pathogenicity could explain several aspects of the biology of this pathogen, including its ability to colonize both vascular and non-vascular tissues of cassava plants. A set of 16 robust, polymorphic VNTR loci will be useful to develop a multi-locus VNTR analysis scheme for epidemiological surveillance of this disease.

Genomic Survey of Pathogenicity Determinants and VNTR Markers in the Cassava Bacterial Pathogen Xanthomonas axonopodis pv. Manihotis Strain CIO151

PubMed Central

Arrieta-Ortiz, Mario L.; Rodríguez-R, Luis M.; Pérez-Quintero, Álvaro L.; Poulin, Lucie; Díaz, Ana C.; Arias Rojas, Nathalia; Trujillo, Cesar; Restrepo Benavides, Mariana; Bart, Rebecca; Boch, Jens; Boureau, Tristan; Darrasse, Armelle; David, Perrine; Dugé de Bernonville, Thomas; Fontanilla, Paula; Gagnevin, Lionel; Guérin, Fabien; Jacques, Marie-Agnès; Lauber, Emmanuelle; Lefeuvre, Pierre; Medina, Cesar; Medina, Edgar; Montenegro, Nathaly; Muñoz Bodnar, Alejandra; Noël, Laurent D.; Ortiz Quiñones, Juan F.; Osorio, Daniela; Pardo, Carolina; Patil, Prabhu B.; Poussier, Stéphane; Pruvost, Olivier; Robène-Soustrade, Isabelle; Ryan, Robert P.; Tabima, Javier; Urrego Morales, Oscar G.; Vernière, Christian; Carrere, Sébastien; Verdier, Valérie; Szurek, Boris; Restrepo, Silvia; López, Camilo

2013-01-01

Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus suggest that advanced draft genome sequences are valuable resources for molecular studies on their interaction with plants and could provide valuable tools for diagnostics and detection. Here we have generated the first manually annotated high-quality draft genome sequence of Xam strain CIO151. Its genomic structure is similar to that of other xanthomonads, especially Xanthomonas euvesicatoria and Xanthomonas citri pv. citri species. Several putative pathogenicity factors were identified, including type III effectors, cell wall-degrading enzymes and clusters encoding protein secretion systems. Specific characteristics in this genome include changes in the xanthomonadin cluster that could explain the lack of typical yellow color in all strains of this pathovar and the presence of 50 regions in the genome with atypical nucleotide composition. The genome sequence was used to predict and evaluate 22 variable number of tandem repeat (VNTR) loci that were subsequently demonstrated as polymorphic in representative Xam strains. Our results demonstrate that Xanthomonas axonopodis pv. manihotis strain CIO151 possesses ten clusters of pathogenicity factors conserved within the genus Xanthomonas. We report 126 genes that are potentially unique to Xam, as well as potential horizontal transfer events in the history of the genome. The relation of these regions with virulence and pathogenicity could explain several aspects of the biology of this pathogen, including its ability to colonize both vascular and non-vascular tissues of cassava plants. A set of 16 robust, polymorphic VNTR loci will be useful to develop a multi-locus VNTR analysis scheme for epidemiological surveillance of this disease. PMID:24278159

Key Role of Sequencing to Trace Hepatitis A Viruses Circulating in Italy During a Large Multi-Country European Foodborne Outbreak in 2013.

PubMed

Bruni, Roberto; Taffon, Stefania; Equestre, Michele; Chionne, Paola; Madonna, Elisabetta; Rizzo, Caterina; Tosti, Maria Elena; Alfonsi, Valeria; Ricotta, Lara; De Medici, Dario; Di Pasquale, Simona; Scavia, Gaia; Pavoni, Enrico; Losio, Marina Nadia; Romanò, Luisa; Zanetti, Alessandro Remo; Morea, Anna; Pacenti, Monia; Palù, Giorgio; Capobianchi, Maria Rosaria; Chironna, Maria; Pompa, Maria Grazia; Ciccaglione, Anna Rita

2016-01-01

Foodborne Hepatitis A Virus (HAV) outbreaks are being recognized as an emerging public health problem in industrialized countries. In 2013 three foodborne HAV outbreaks occurred in Europe and one in USA. During the largest of the three European outbreaks, most cases occurred in Italy (>1,200 cases as of March 31, 2014). A national Task Force was established at the beginning of the outbreak by the Ministry of Health. Mixed frozen berries were early demonstrated to be the source of infection by the identity of viral sequences in patients and in food. In the present study the molecular characterization of HAV isolates from 355 Italian cases is reported. Molecular characterization was carried out by PCR/sequencing (VP1/2A region), comparison with reference strains and phylogenetic analysis. A unique strain was responsible for most characterized cases (235/355, 66.1%). Molecular data had a key role in tracing this outbreak, allowing 110 out of the 235 outbreak cases (46.8%) to be recognized in absence of any other link. The data also showed background circulation of further unrelated strains, both autochthonous and travel related, whose sequence comparison highlighted minor outbreaks and small clusters, most of them unrecognized on the basis of epidemiological data. Phylogenetic analysis showed most isolates from travel related cases clustering with reference strains originating from the same geographical area of travel. In conclusion, the study documents, in a real outbreak context, the crucial role of molecular analysis in investigating an old but re-emerging pathogen. Improving the molecular knowledge of HAV strains, both autochthonous and circulating in countries from which potentially contaminated foods are imported, will become increasingly important to control outbreaks by supporting trace back activities, aiming to identify the geographical source(s) of contaminated food, as well as public health interventions.

THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites

PubMed Central

Chang, Hsiao-Han; Worby, Colin J.; Yeka, Adoke; Nankabirwa, Joaniter; Kamya, Moses R.; Staedke, Sarah G.; Hubbart, Christina; Amato, Roberto; Kwiatkowski, Dominic P.

2017-01-01

As many malaria-endemic countries move towards elimination of Plasmodium falciparum, the most virulent human malaria parasite, effective tools for monitoring malaria epidemiology are urgent priorities. P. falciparum population genetic approaches offer promising tools for understanding transmission and spread of the disease, but a high prevalence of multi-clone or polygenomic infections can render estimation of even the most basic parameters, such as allele frequencies, challenging. A previous method, COIL, was developed to estimate complexity of infection (COI) from single nucleotide polymorphism (SNP) data, but relies on monogenomic infections to estimate allele frequencies or requires external allele frequency data which may not available. Estimates limited to monogenomic infections may not be representative, however, and when the average COI is high, they can be difficult or impossible to obtain. Therefore, we developed THE REAL McCOIL, Turning HEterozygous SNP data into Robust Estimates of ALelle frequency, via Markov chain Monte Carlo, and Complexity Of Infection using Likelihood, to incorporate polygenomic samples and simultaneously estimate allele frequency and COI. This approach was tested via simulations then applied to SNP data from cross-sectional surveys performed in three Ugandan sites with varying malaria transmission. We show that THE REAL McCOIL consistently outperforms COIL on simulated data, particularly when most infections are polygenomic. Using field data we show that, unlike with COIL, we can distinguish epidemiologically relevant differences in COI between and within these sites. Surprisingly, for example, we estimated high average COI in a peri-urban subregion with lower transmission intensity, suggesting that many of these cases were imported from surrounding regions with higher transmission intensity. THE REAL McCOIL therefore provides a robust tool for understanding the molecular epidemiology of malaria across transmission settings. PMID:28125584

Genome Sequence of Canine Parvovirus Strain SC02/2011, Isolated from a Puppy with Severe Diarrhea in South China

PubMed Central

Cheng, Yi; Ji, Yikuan; Wang, Yu; Sun, Leilei; Huang, Jiaxin

2012-01-01

A widespread hemorrhagic gastroenteritis in young dogs occurred in South China. A virulent field canine parvovirus (CPV) strain, SC02/2011, was isolated from a puppy showing enteric signs in Guangdong, China. The genome of CPV strain SC02/2011 was sequenced and analyzed, which will promote a better understanding of the molecular epidemiology and genetic diversity of CPV field isolates in South China. PMID:23166228

Toxoplasmic retinochoroiditis caused by Toxoplasma gondii strain ToxoDB#65.

PubMed

Brandão de Mattos, Cinara Cássia; Siqueira, Rubens Camargo; Frederico, Fábio Batista; Ferreira, Isabelle Martins Ribeiro; Ferreira, Ana Iara Costa; Previato, Mariana; Pereira-Chioccola, Vera Lucia; de Mattos, Luiz Carlos

2018-05-31

Ocular toxoplasmosis, caused by Toxoplasma gondii, is the most common cause of inflammation in the back of the eye. Analysis of the infecting strain may provide information regarding disease behavior and recurrence. Here, we describe clinical and epidemiological data for toxoplasmic retinochoroiditis in two Brazilian women infected by T. gondii strain ToxoDB#65, living in an urban region of São Paulo State, Brazil. Copyright © 2018 Elsevier B.V. All rights reserved.

Application of protein typing in molecular epidemiological investigation of nosocomial infection outbreak of aminoglycoside-resistant Pseudomonas aeruginosa.

PubMed

Song, Min; Tang, Min; Ding, Yinghuan; Wu, Zecai; Xiang, Chengyu; Yang, Kui; Zhang, Zhang; Li, Baolin; Deng, Zhenghua; Liu, Jinbo

2017-12-16

Pseudomonas aeruginosan has emerged as an important pathogen elated to serious infections and nosocomial outbreaks worldwide. This study was conducted to understand the prevalence of aminoglycoside (AMG)-resistant P. aeruginosa in our hospital and to provide a scientific basis for control measures against nosocomial infections. Eighty-two strains of P. aeruginosa were isolated from clinical departments and divided into AMG-resistant strains and AMG-sensitive strains based on susceptibility test results. AMG-resistant strains were typed by drug resistance gene typing (DRGT) and protein typing. Five kinds of aminoglycoside-modifying enzyme (AME) genes were detected in the AMG-resistant group. AMG-resistant P. aeruginosa strains were classified into three types and six subtypes by DRGT. Four protein peaks, namely, 9900.02, 7600.04, 9101.25 and 10,372.87 Da, were significantly and differentially expressed between the two groups. AMG-resistant P. aeruginosa strains were also categorised into three types and six subtypes at the distance level of 10 by protein typing. AMG-resistant P. aeruginosa was cloned spread in our hospital; the timely implementation of nosocomial infection prevention and control strategies were needed in preventing outbreaks and epidemic of AMG-resistant P. aeruginosa. SELDI-TOF MS technology can be used for bacterial typing, which provides a new method of clinical epidemiological survey and nosocomial infection control.

Molecular epidemiology of Staphylococcus aureus isolates at different sites in the milk producing dairy farms

PubMed Central

Souza, Viviane; Nader Filho, Antonio; de Castro Melo, Poliana; Ferraudo, Guilherme Moraes; Antônio Sérgio, Ferraudo; de Oliveira Conde, Sandra; Fogaça Junior, Flavio Augusto

2012-01-01

The epidemiological relationships between isolated Staphylococcus aureus strains in milk samples of dairy cows, reagent to California Mastitis Test, individual and group milk was demonstrated in different sites of the production fluxogram, in 12 milk-producing farms in the Gameleira region, municipality of Sacramento MG Brazil, so that localization and transmission modes may be identified. Two hundred and forty-four strains out of 446 samples collected at several sites were isolated and bio-chemically characterized as coagulase-positive staphylococcus. Specific chromosome DNA fragment of the species Staphylococcus aureus was amplified to 106 strains and 103 underwent (PFGE). Samples’ collection sites with the highest isolation frequency of Staphylococcus aureus strains comprised papillary ostia (31.1%), CMT-reagent cow milk (21.7%), mechanical milking machines’ insufflators (21,7%), milk in milk pails (6.6%) and the milk in community bulk tanks (5.6%). Genetic heterogeneity existed among the isolated 103 Staphylococcus aureus strains, since 32 different pulse-types were identified. Pulse-type 1 had the highest similarity among the isolated strains within the different sites of the milk-production fluxogram. Highest occurrence of pulsetype 1 isolates of Staphylococcus aureus strains was reported in samples collected from the papillary ostia (10.6%), followed by milk samples from CMT-reagent dairy cows (5.8%) and mechanical milking machine insufflators (3.8%). The above shows the relevance of these sites in the agents’ transmission mechanism within the context of the farms investigated. PMID:24031997

Using MOMP typing as an epidemiological tool to investigate outbreaks caused by milkborne Campylobacter jejuni isolates in California

USDA-ARS?s Scientific Manuscript database

We describe using major outer membrane protein (MOMP) typing as a screen to compare the C. jejuni porA gene sequences of clinical outbreak strains from human stool with the porA sequences of dairy farm strains isolated during two milkborne campylobacteriosis outbreak investigations in California. Th...

An Untypeable Shigella flexneri Strain Associated with an Outbreak in California

PubMed Central

Trevejo, Rosalie T.; Abbott, Sharon L.; Wolfe, Mitchell I.; Meshulam, Jerry; Yong, David; Flores, George R.

1999-01-01

Eleven Shigella flexneri (group B) isolates were recovered from epidemiologically linked patrons and food handlers from a restaurant-associated outbreak of shigellosis. Six isolates available for pulsed-field gel electrophoresis were identical. All strains agglutinated in group B and subgroup factor 6 sera but not in group 1 through group 6 sera. PMID:10364614

Bloodstream infection caused by nontoxigenic Corynebacterium diphtheriae in an immunocompromised host in the United States.

PubMed

Wojewoda, Christina M; Koval, Christine E; Wilson, Deborah A; Chakos, Mary H; Harrington, Susan M

2012-06-01

Corynebacterium species are well-known causes of catheter-related bloodstream infections. Toxigenic strains of Corynebacterium diphtheriae cause respiratory diphtheria. We report a bloodstream infection caused by a nontoxigenic strain of C. diphtheriae and discuss the epidemiology, possible sources of the infection, and the implications of rapid species identification of corynebacteria.

Bloodstream Infection Caused by Nontoxigenic Corynebacterium diphtheriae in an Immunocompromised Host in the United States

PubMed Central

Wojewoda, Christina M.; Koval, Christine E.; Wilson, Deborah A.; Chakos, Mary H.

2012-01-01

Corynebacterium species are well-known causes of catheter-related bloodstream infections. Toxigenic strains of Corynebacterium diphtheriae cause respiratory diphtheria. We report a bloodstream infection caused by a nontoxigenic strain of C. diphtheriae and discuss the epidemiology, possible sources of the infection, and the implications of rapid species identification of corynebacteria. PMID:22493337

Mumps Epidemiology and Mumps Virus Genotypes Circulating in Mainland China during 2013-2015.

PubMed

Cui, Aili; Zhu, Zhen; Hu, Ying; Deng, Xiuying; Sun, Zhaodan; Zhang, Yan; Mao, Naiying; Xu, Songtao; Fang, Xueqiang; Gao, Hui; Si, Yuan; Lei, Yake; Zheng, Huanying; He, Jilan; Wu, Hongwei; Xu, Wenbo

2017-01-01

With the implementation of mumps virus (MuV) vaccination in the expanded program on immunization (EPI) in mainland China since 2008, the incidence of mumps has decreased, and the natural epidemic pattern of mumps has slightly changed during 2013-2015. The two epidemic peaks (April-July and November-December) became less obvious than those observed from 2004 to 2012. Children and adolescents younger than 15, particularly in the five-to-nine-year-old age group, remain the target group and should be the focus of high-quality immunization activities in mainland China. However, it was also found that the incidence and reported cases of mumps decreased in each age group during 2013-2015, particularly in the five-to-nine-year-old and ten-to-fourteen-year-old age groups. The proportion of mumps cases among adults in some provinces also increased. Unlike the changes in the epidemiological characteristics of mumps affected by vaccination, the data of MuV virology surveillance indicated that most of the MuV transmission chains have not yet been effectively interrupted, and MuV remains a natural epidemic pattern in mainland China. In the MuV virology surveillance, 194 MuV strains during 2013-2015 were isolated from 10 of 31 provinces in mainland China. Based on the phylogenetic analysis of the small hydrophobic (SH) gene, both genotype F (99.0%) and G (1.0%) were identified, and genotype F was still the predominant genotype continuously circulating in mainland China. Representative genotype F and G strains isolated in China from 1995 to 2012 were selected for further analysis. The results indicated that there were multiple transmission chains within genotype F, with no obvious geographical or time differences. The high genetic diversity of genotype F strains could be a result of the continuous transmission and evolution of the MuV in mainland China. Genotype G was also detected in four provinces in mainland China. Because of the limited epidemiological data, it was uncertain whether the genotype G MuV strains found in 2011 and 2013 were imported from other countries. Therefore, combined high-quality epidemiological and virological surveillance is necessary for mumps control; it can also be used to observe the changes in epidemiological characteristics and viral transmission of mumps over time after mumps-containing vaccine (MuCV) implementation and to provide a comprehensive epidemiological and genetic baseline for mumps elimination in mainland China.

Mumps Epidemiology and Mumps Virus Genotypes Circulating in Mainland China during 2013-2015

PubMed Central

Cui, Aili; Zhu, Zhen; Hu, Ying; Deng, Xiuying; Sun, Zhaodan; Zhang, Yan; Mao, Naiying; Xu, Songtao; Fang, Xueqiang; Gao, Hui; Si, Yuan; Lei, Yake; Zheng, Huanying; He, Jilan; Wu, Hongwei; Xu, Wenbo

2017-01-01

With the implementation of mumps virus (MuV) vaccination in the expanded program on immunization (EPI) in mainland China since 2008, the incidence of mumps has decreased, and the natural epidemic pattern of mumps has slightly changed during 2013–2015. The two epidemic peaks (April-July and November-December) became less obvious than those observed from 2004 to 2012. Children and adolescents younger than 15, particularly in the five-to-nine-year-old age group, remain the target group and should be the focus of high-quality immunization activities in mainland China. However, it was also found that the incidence and reported cases of mumps decreased in each age group during 2013–2015, particularly in the five-to-nine-year-old and ten-to-fourteen-year-old age groups. The proportion of mumps cases among adults in some provinces also increased. Unlike the changes in the epidemiological characteristics of mumps affected by vaccination, the data of MuV virology surveillance indicated that most of the MuV transmission chains have not yet been effectively interrupted, and MuV remains a natural epidemic pattern in mainland China. In the MuV virology surveillance, 194 MuV strains during 2013–2015 were isolated from 10 of 31 provinces in mainland China. Based on the phylogenetic analysis of the small hydrophobic (SH) gene, both genotype F (99.0%) and G (1.0%) were identified, and genotype F was still the predominant genotype continuously circulating in mainland China. Representative genotype F and G strains isolated in China from 1995 to 2012 were selected for further analysis. The results indicated that there were multiple transmission chains within genotype F, with no obvious geographical or time differences. The high genetic diversity of genotype F strains could be a result of the continuous transmission and evolution of the MuV in mainland China. Genotype G was also detected in four provinces in mainland China. Because of the limited epidemiological data, it was uncertain whether the genotype G MuV strains found in 2011 and 2013 were imported from other countries. Therefore, combined high-quality epidemiological and virological surveillance is necessary for mumps control; it can also be used to observe the changes in epidemiological characteristics and viral transmission of mumps over time after mumps-containing vaccine (MuCV) implementation and to provide a comprehensive epidemiological and genetic baseline for mumps elimination in mainland China. PMID:28085897

Dynamics of two-strain influenza model with cross-immunity and no quarantine class.

PubMed

Chung, K W; Lui, Roger

2016-12-01

The question about whether a periodic solution can exists for a given epidemiological model is a complicated one and has a long history (Hethcote and Levin, Applied math. ecology, biomathematics, vol 18. Springer, Berlin, pp 193-211, 1989). For influenza models, it is well known that a periodic solution can exists for a single-strain model with periodic contact rate (Aron and Schwartz, J Math Biol 110:665-679, 1984; Kuznetsov and Piccardi, J Math Biol 32:109-121, 1994), or a multiple-strain model with cross-immunity and quarantine class or age-structure (Nuño et al., Mathematical epidemiology. Lecture notes in mathematics, vol 1945. Springer, Berlin, 2008, chapter 13). In this paper, we prove the local asymptotic stability of the interior steady-state of a two-strain influenza model with sufficiently close cross-immunity and no quarantine class or age-structure. We also show that if the cross-immunity between two strains are far apart; then it is possible for the interior steady-state to lose its stability and bifurcation of periodic solutions can occur. Our results extend those obtained by Nuño et.al. (SIAM J Appl Math 65:964-982, 2005). This problem is important because understanding the reasons behind periodic outbreaks of seasonal flu is an important issue in public health.

Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli.

PubMed

Christner, Martin; Trusch, Maria; Rohde, Holger; Kwiatkowski, Marcel; Schlüter, Hartmut; Wolters, Manuel; Aepfelbacher, Martin; Hentschke, Moritz

2014-01-01

In 2011 northern Germany experienced a large outbreak of Shiga-Toxigenic Escherichia coli O104:H4. The large amount of samples sent to microbiology laboratories for epidemiological assessment highlighted the importance of fast and inexpensive typing procedures. We have therefore evaluated the applicability of a MALDI-TOF mass spectrometry based strategy for outbreak strain identification. Specific peaks in the outbreak strain's spectrum were identified by comparative analysis of archived pre-outbreak spectra that had been acquired for routine species-level identification. Proteins underlying these discriminatory peaks were identified by liquid chromatography tandem mass spectrometry and validated against publicly available databases. The resulting typing scheme was evaluated against PCR genotyping with 294 E. coli isolates from clinical samples collected during the outbreak. Comparative spectrum analysis revealed two characteristic peaks at m/z 6711 and m/z 10883. The underlying proteins were found to be of low prevalence among genome sequenced E. coli strains. Marker peak detection correctly classified 292 of 293 study isolates, including all 104 outbreak isolates. MALDI-TOF mass spectrometry allowed for reliable outbreak strain identification during a large outbreak of Shiga-Toxigenic E. coli. The applied typing strategy could probably be adapted to other typing tasks and might facilitate epidemiological surveys as part of the routine pathogen identification workflow.

Molecular epidemiology of mumps virus in Japan and proposal of two new genotypes.

PubMed

Inou, Yoko; Nakayama, Tetsuo; Yoshida, Naoko; Uejima, Hajime; Yuri, Kenji; Kamada, Makoto; Kumagai, Takuji; Sakiyama, Hiroshi; Miyata, Akiko; Ochiai, Hitoshi; Ihara, Toshiaki; Okafuji, Teruo; Okafuji, Takao; Nagai, Takao; Suzuki, Eitaro; Shimomura, Kunihisa; Ito, Yuhei; Miyazaki, Chiaki

2004-05-01

We isolated 872 strains of mumps virus from naso-pharyngeal secretions in seven different districts of Japan from January 2000 to July 2001. Among them, 57 strains were geno-typed by nucleotide sequencing in part of the hemagglutinin-neuraminidase (HN) and small hydrophobic (SH) protein regions. Four different genotypes (B, G, K, and L) of mumps virus were co-circulating in Japan and the distribution of genotypes varied in geographically different districts. Two new clusters designated as genotypes K and L had more than 7% nucleotide variation in the SH gene. Among the 57 strains, 11 were classified as B, 35 as G, three as K, and eight as L, which was mainly isolated in Tokyo. We also examined 104 stains isolated in a clinic in Mie prefecture from 1993 to 2003. Genotype B was the indigenous strain and genotype K was introduced in 1994. Genotypes B and K co-circulated in the 1990s and were replaced by genotype G in 2000. There was no significant change in neutralizing test antibody titers against genotypes B, G, K, and L using seven post-vaccination sera with Hoshino strain (genotype B) and these four genotypes had a different antigenicity from genotype A. We should continue to watch on mumps virus molecular epidemiology. Copyright 2004 Wiley-Liss, Inc.

[Improvement of sanitary and epidemiological safety of rail transport--a requirement of the new legislation of the Russian Federation].

PubMed

2012-01-01

Brief analysis of the legal framework in recent years, both in the sphere of technical regulation, and in the field of sanitary and epidemiological welfare of the population is presented in this article. The necessity of inclusion in the technical regulations for the safety of railway rolling stock and elements of railway infrastructure the requirements for sanitary-epidemiological safety and hygiene regulations has been proved. Fragments of technical regulations for railway equipment and infrastructure elements, including the basic requirements for the sanitary-epidemiological security are presented. The position of authors in the processing of the regulatory framework in the field of sanitary-epidemiological welfare of population in standardization documents in accordance with the requirements of federal law "On technical regulation" has been reflected.

The changing epidemiology of invasive Haemophilus influenzae disease: Emergence and global presence of serotype a strains that may require a new vaccine for control.

PubMed

Tsang, Raymond S W; Ulanova, Marina

2017-07-24

More than two decades after the implementation of the Hib conjugate vaccine in North America, Haemophilus influenzae serotype a (Hia) has emerged as a significant cause of invasive disease in Indigenous communities. However, little is known about the global presence of this pathogen. We interrogated the H. influenzae Multi-Locus Sequence Typing (MLST) website (https://pubmlst.org/hinfluenzae/) by selecting for serotype a records. We also updated our previous literature review on this subject matter. Hia has been reported from at least 35 countries on six major continents. However, most Hia diseases were associated with Indigenous communities. Clonal analysis identified two clonal populations with one typified as ST-23 responsible for most invasive disease in North America and being the predominant clone described on the H. influenzae MLST website. Incidence of invasive Hia disease in Indigenous communities in North America are similar to the rates of Hib disease reported prior to the Hib conjugate vaccine era. Hia causes severe clinical diseases, such as meningitis, septicaemia, pneumonia, and septic arthritis with case-fatality rates between 5.6% and 33% depending on the age of the patient and the genetic makeup of the Hia strain. Although invasive Hia disease can be found globally, the current epidemiological data suggest that this infection predominantly affects Indigenous communities in North America. The clinical disease of Hia and the clonal nature of the bacteria resemble that of Hib. The high incidence of invasive Hia disease in Indigenous communities, along with potential fatality and severe sequelae causing long-term disability in survivors, may support the development of a new Hia conjugate vaccine for protection against this infection similar in design to the one introduced in the 1990s to control invasive Hib disease. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

An outbreak of serogroup C (ST-11) meningococcal disease in Tijuana, Mexico.

PubMed

Chacon-Cruz, Enrique; Espinosa-De Los Monteros, Luz Elena; Navarro-Alvarez, Samuel; Aranda-Lozano, Jose Luis; Volker-Soberanes, Maria Luisa; Rivas-Landeros, Rosa Maria; Alvelais-Arzamendi, Ariadna Annete; Vazquez, Julio Alberto

2014-05-01

Invasive meningococcal disease (IMD) has been reported to be endemic in children from Tijuana, Mexico and the risk of an outbreak was always a threat. To describe all clinical, epidemiological and microbiological features of a meningococcal outbreak that occurred in Tijuana, Mexico. All cases with IMD were admitted at different emergency departments within the city and diagnosed by culture and agglutination tests. Further restriction fragment length polymorphism pulse field gel electrophoresis (RFLP-PFGE) and multi locus sequence typing (MLST) were performed. All clinical and epidemiological characteristics and interventions were evaluated, as well as risk factors associated with mortality. From 30 January 2013 to 30 March 2013 there were 19 cases of IMD all caused by Neisseria meningitidis serogroup C. The median age was 16 years (2-47), with higher frequency among individuals at least 13 years old (73.7%). At admission, meningitis was the main clinical presentation (94.7%), followed by purpura (78.9%), septic shock (42.1%) and disseminated intravascular coagulation (DIC, 36.8%). Overall mortality was seven (36.8%). Variables associated with higher mortality were, at admission, presence of septic shock, DIC and thrombocytopenia less than 70,000. All 19 cases had no identifiable site or cluster as the source of the outbreak. RFLP-PFGE showed a discriminatory power for only one profile on all N. meningitidis strains analyzed and a clone ST-11 was identified in all strains. Public health interventions were continuous case reporting of all suspected cases of IMD, an increase in active surveillance in all hospitals, training of medical and laboratory personnel, massive and rapid chemoprophylaxis to all close contacts as indicated, and promotion of good health habits. An outbreak with high mortality of IMD occurred in Tijuana, Mexico. This event and evidence of endemicity should encourage health authorities to evaluate meningococcal vaccination in the region.

Evolving Epidemiology of Staphylococcus aureus Bacteremia.

PubMed

Rhee, Yoona; Aroutcheva, Alla; Hota, Bala; Weinstein, Robert A; Popovich, Kyle J

2015-12-01

Methicillin-resistant Staphylococcus aureus (MRSA) infections due to USA300 have become widespread in community and healthcare settings. It is unclear whether risk factors for bloodstream infections (BSIs) differ by strain type. To examine the epidemiology of S. aureus BSIs, including USA300 and non-USA300 MRSA strains. Retrospective observational study with molecular analysis. Large urban public hospital. Individuals with S. aureus BSIs from January 1, 2007 through December 31, 2013. We used electronic surveillance data to identify cases of S. aureus BSI. Available MRSA isolates were analyzed by pulsed-field gel electrophoresis. Poisson regression was used to evaluate changes in BSI incidence over time. Risk factor data were collected by medical chart review and logistic regression was used for multivariate analysis of risk factors. A total of 1,015 cases of S. aureus BSIs were identified during the study period; 36% were due to MRSA. The incidence of hospital-onset (HO) MRSA BSIs decreased while that of community-onset (CO) MRSA BSIs remained stable. The rate of CO- and HO- methicillin-susceptible S. aureus infections both decreased over time. More than half of HO-MRSA BSIs were due to the USA300 strain type and for 4 years, the proportion of HO-MRSA BSIs due to USA300 exceeded 60%. On multivariate analysis, current or former drug use was the only epidemiologic risk factor for CO- or HO-MRSA BSIs due to USA300 strains. USA300 MRSA is endemic in communities and hospitals and certain populations (eg, those who use illicit drugs) may benefit from enhanced prevention efforts in the community.

Molecular and Epidemiological Review of Toxigenic Diphtheria Infections in England between 2007 and 2013

PubMed Central

Both, Leonard; Collins, Sarah; de Zoysa, Aruni; White, Joanne; Mandal, Sema

2014-01-01

Human infections caused by toxigenic corynebacteria occur sporadically across Europe. In this report, we undertook the epidemiological and molecular characterization of all toxigenic corynebacterium strains isolated in England between January 2007 and December 2013. Epidemiological aspects include case demographics, risk factors, clinical presentation, treatment, and outcome. Molecular characterization was performed using multilocus sequence typing (MLST) alongside traditional phenotypic methods. In total, there were 20 cases of toxigenic corynebacteria; 12 (60.0%) were caused by Corynebacterium ulcerans, where animal contact was the predominant risk factor. The remaining eight (40.0%) were caused by Corynebacterium diphtheriae strains; six were biovar mitis, which were associated with recent travel abroad. Adults 45 years and older were particularly affected (55.0%; 11/20), and typical symptoms included sore throat and fever. Respiratory diphtheria with the absence of a pharyngeal membrane was the most common presentation (50.0%; 10/20). None of the eight C. diphtheriae cases were fully immunized. Diphtheria antitoxin was issued in two (9.5%) cases; both survived. Two (9.5%) cases died, one due to a C. diphtheriae infection and one due to C. ulcerans. MLST demonstrated that the majority (87.5%; 7/8) of C. diphtheriae strains represented new sequence types (STs). By adapting several primer sequences, the MLST genes in C. ulcerans were also amplified, thereby providing the basis for extension of the MLST scheme, which is currently restricted to C. diphtheriae. Despite high population immunity, occasional toxigenic corynebacterium strains are identified in England and continued surveillance is required. PMID:25502525

Epidemiology and phylogenetic analysis of hepatitis D virus infection in Australia.

PubMed

Jackson, Kathy; MacLachlan, Jennifer; Cowie, Benjamin; Locarnini, Stephen; Bowden, D Scott; Higgins, Nasra; Karapanagiotidis, Theo; Nicholson, Suellen; Littlejohn, Margaret

2018-05-14

The incidence and trends in hepatitis D virus (HDV) in Australia have not been recently assessed and the circulating genotypes have never been determined. This study aimed to characterise the current virology and epidemiology of HDV. Notifiable disease surveillance and laboratory testing data were analysed to assess demographics, risk factors, and trends. HDV serology and RNA testing were performed on requested samples from 2010-2016. Sequencing of a 500 nucleotides amplicon of the delta antigen and phylogenetic analysis of the strains from 2009-2016 was also conducted. Ninety HDV notifications were reported to the Victorian Department of Health and Human Services between 2010-2016. The majority (64.4%) of those diagnosed were born overseas, most commonly in Sudan, Pakistan and Vietnam. Over the same period 190 patients tested positive for anti-HDV serology and 166 for HDV RNA. Sequencing of isolates from 169 individuals between 2009 and 2016 revealed 80.5% strains were genotype 1, 16% genotype 5 and 3.5% genotype 2. Phylogenetic analysis confirmed relatedness of strains from birth country; revealed the presence of the "Pacific Island" genotype 1 strain in Queensland; and supported possible transmission in correctional facilities and within families. This study demonstrates the ongoing need for routine HDV screening and engagement in clinical care for people living with HBV in Australia. epidemiologic findings highlight the diversity in those affected and provides insights into the local and global geographic distribution and transmission patterns. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

[Enterohemorrhagic Escherichia coli as the cause of diarrhea in the Czech Republic, 1965-2013].

PubMed

Marejková, M; Petráš, P

2014-09-01

Enterohemorrhagic Escherichia coli (EHEC) is the cause of diarrhea, bloody diarrhea, and haemolytic uremic syndrome (HUS) worldwide. The role of EHEC in the etiology of HUS in the Czech Republic has recently been described, but the prevalence, characteristics, and epidemiology of EHEC causing diarrhea have not been fully known. Therefore, this study analyzed the serotypes, stx genotypes, and virulence factors in EHEC strains isolated in 1965-2013 from patients with diarrhea or bloody diarrhea and their family contacts. In addition, we characterized diagnostically relevant phenotypes of EHEC strains, their antimicrobial susceptibility, seasonal trends, and distribution by administrative region. Serogrouped E. coli isolates from patients were referred to the National Reference Laboratory (NRL) for E. coli and Shigella for the detection of Stx. Specimens of both human and non-human origin were referred to the NRL for epidemiological investigation. Serotyping was performed by conventional and molecular methods, PCR was applied to stx genotyping and identification of non-stx virulence factors, and standard methods were used for phenotypic analysis and antimicrobial susceptibility testing. The epidemiological link between the human and animal isolates was confirmed using pulsed-field gel electrophoresis (PFGE). Of 50 EHEC strains, 24 were recovered from patients with diarrhea without blood, 19 from patients with bloody diarrhea, six from family contacts, and one from an epidemiologically linked animal. EHEC cases were reported during the whole year, with peaks in May through October, most often in the Central Bohemian and Hradec Králové Regions. EHEC outbreaks occurred in three families: in one of them sheep-to-human transmission of EHEC was detected. The EHEC strains were assigned to five serotypes, with more than half of them being non-sorbitol fermenting (NSF) O157:H7/NM[fliCH7] and a third being strains O26:H11/NM[fliCH11]; serotypes O111:NM[fliCH8], O118:NM[fliCH25], and O104:H4, similarly to sorbitol-fermenting (SF) strains O157:NM[fliCH7], were rare. Of seven stx genotypes identified, all were present in NSF EHEC O157, two in each of EHEC O26 and O111, and one in each of EHEC O118, O104, and SF O157. All but one strain were Stx producers. Genes encoding other virulence factors including toxins (EHEC-hlyA, cdt-V, and espP) and adhesins (eae, efa1, iha, lpf, and sfpA) were detected in all strains and their occurrence was serotype specific. The most common of these genes were eae encoding adhesin intimin and EHEC-hlyA encoding EHEC hemolysin. All EHEC strains but SF O157 harboured terE encoding tellurite resistance. All strains except NSF EHEC O157 and EHEC O118 fermented sorbitol and produced ß-D-glucuronidase. Most (89.8%) EHEC strains were susceptible to all 12 antimicrobials tested. EHEC strains cause diarrhea and bloody diarrhea in the Czech Republic. Nevertheless, only a systematic screening of the stool from patients with diarrhea can make it possible to elucidate their actual role in the etiology of diarrheal diseases (as well as HUS) in the Czech Republic and to consider the data in the European context. EHEC cases are reported to the European Centre for Disease Prevention and Control (ECDC) within the Food and Waterborne Diseases Surveillance Network.

The Transition of Acute Postoperative Pain to Chronic Pain: An Integrative Overview of Research on Mechanisms.

PubMed

Chapman, C Richard; Vierck, Charles J

2017-04-01

The nature of the transition from acute to chronic pain still eludes explanation, but chronic pain resulting from surgery provides a natural experiment that invites clinical epidemiological investigation and basic scientific inquiry into the mechanisms of this transition. The primary purpose of this article is to review current knowledge and hypotheses on the transition from acute to persistent postsurgical pain, summarizing literature on clinical epidemiological studies of persistent postsurgical pain development, as well as basic neurophysiological studies targeting mechanisms in the periphery, spinal cord, and brain. The second purpose of this article is to integrate theory, information, and causal reasoning in these areas. Conceptual mapping reveals 5 classes of hypotheses pertaining to pain. These propose that chronic pain results from: 1) persistent noxious signaling in the periphery; 2) enduring maladaptive neuroplastic changes at the spinal dorsal horn and/or higher central nervous system structures reflecting a multiplicity of factors, including peripherally released neurotrophic factors and interactions between neurons and microglia; 3) compromised inhibitory modulation of noxious signaling in medullary-spinal pathways; 4) descending facilitatory modulation; and 5) maladaptive brain remodeling in function, structure, and connectivity. The third purpose of this article is to identify barriers to progress and review opportunities for advancing the field. This review reveals a need for a concerted, strategic effort toward integrating clinical epidemiology, basic science research, and current theory about pain mechanisms to hasten progress toward understanding, managing, and preventing persistent postsurgical pain. The development of chronic pain after surgery is a major clinical problem that provides an opportunity to study the transition from acute to chronic pain at epidemiologic and basic science levels. Strategic, coordinated, multidisciplinary research efforts targeting mechanisms of pain chronification can to help minimize or eliminate persistent postsurgical pain. Copyright © 2016 American Pain Society. Published by Elsevier Inc. All rights reserved.

[Molecular epidemiology in the epidemiological transition].

PubMed

Tapia-Conyer, R

1997-01-01

The epidemiological transition describes the changes in the health profile of populations where infectious diseases are substituted by chronic or non-communicable diseases. Even in industrialized countries, infectious diseases emerge as important public health problems and with a very important association with several type of neoplasm. Molecular epidemiology brings in new tools for the study of the epidemiological transition by discovering infectious agents as etiology of diseases, neither of both new. Much has been advanced in the understanding of the virulence and resistance mechanism of different strains, or improving the knowledge on transmission dynamics and dissemination pathways of infectious diseases. As to the non-communicable diseases, molecular epidemiology has enhanced the identification of endogenous risk factors link to alterations, molecular changes in genetic material, that will allow a more detail definition of risk and the identification of individual and groups at risk of several diseases. The potential impact of molecular epidemiology in other areas as environmental, lifestyles and nutritional areas are illustrated with several examples.

Genotype diversity in the honey bee parasite Nosema ceranae: multi-strain isolates, cryptic sex or both?

PubMed

Sagastume, Soledad; Martín-Hernández, Raquel; Higes, Mariano; Henriques-Gil, Nuno

2016-10-18

There is great controversy as to whether Microsporidia undergo a sexual cycle. In the paradigmatic case of Nosema ceranae, although there is no morphological evidence of sex, some meiosis-specific genes are present in its reduced genome and there is also high intraspecific variability, with incongruent phylogenies having been systematically obtained. The possibility of sexual recombination is important from an epidemiological standpoint, particularly as N. ceranae is considered to be a major factor in the current disquieting epidemic of widespread bee colony losses. This parasite apparently originated in oriental honey bees, spreading out of Asia and Australia to infect honey bees worldwide. This study had three main objectives: i) to obtain genetic markers that are not part of known multi-copy arrays for strain determination; ii) to shed light on the intraspecific variability and recombination of N. ceranae; and iii) to assess the variability in N. ceranae populations. The answers to these questions are critical to understand the capacity of adaptation of microsporidia. Biallelic polymorphisms were detected at a number of specific points in the five coding loci analyzed from European and Australian isolates of N. ceranae. Heterozygous genotypes were abundant and cloning experiments demonstrate that they reflect the existence of multiple alternative sequences in each isolate. The comparisons of different clones and genotypes clearly indicate that new haplotypes are generated by homologous recombination. The N. ceranae isolates from honey bees correspond to genotypically distinct populations, revealing that individual honey bees may not be infected by a particular clone but rather, a pool of different strains. Homologous recombination implies the existence of a cryptic sex cycle yet to be described in N. ceranae. There are no diagnostic alleles associated with Australian or European origins, nor are there differences between the two hosts, A. cerana and A. mellifera, supporting the absence of biological barriers for N. ceranae transmission. Diversity is high among microsporidia of both these origins, and the maintenance of a high heterozygosis in the recently invaded European populations, could hypothetically underlie the stronger virulence of N. ceranae observed in A. mellifera.

The novel 2016 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations: phenotypic, genetic and reference genome characterization.

PubMed

Unemo, Magnus; Golparian, Daniel; Sánchez-Busó, Leonor; Grad, Yonatan; Jacobsson, Susanne; Ohnishi, Makoto; Lahra, Monica M; Limnios, Athena; Sikora, Aleksandra E; Wi, Teodora; Harris, Simon R

2016-11-01

Gonorrhoea and MDR Neisseria gonorrhoeae remain public health concerns globally. Enhanced, quality-assured, gonococcal antimicrobial resistance (AMR) surveillance is essential worldwide. The WHO global Gonococcal Antimicrobial Surveillance Programme (GASP) was relaunched in 2009. We describe the phenotypic, genetic and reference genome characteristics of the 2016 WHO gonococcal reference strains intended for quality assurance in the WHO global GASP, other GASPs, diagnostics and research worldwide. The 2016 WHO reference strains (n = 14) constitute the eight 2008 WHO reference strains and six novel strains. The novel strains represent low-level to high-level cephalosporin resistance, high-level azithromycin resistance and a porA mutant. All strains were comprehensively characterized for antibiogram (n = 23), serovar, prolyliminopeptidase, plasmid types, molecular AMR determinants, N. gonorrhoeae multiantigen sequence typing STs and MLST STs. Complete reference genomes were produced using single-molecule PacBio sequencing. The reference strains represented all available phenotypes, susceptible and resistant, to antimicrobials previously and currently used or considered for future use in gonorrhoea treatment. All corresponding resistance genotypes and molecular epidemiological types were described. Fully characterized, annotated and finished references genomes (n = 14) were presented. The 2016 WHO gonococcal reference strains are intended for internal and external quality assurance and quality control in laboratory investigations, particularly in the WHO global GASP and other GASPs, but also in phenotypic (e.g. culture, species determination) and molecular diagnostics, molecular AMR detection, molecular epidemiology and as fully characterized, annotated and finished reference genomes in WGS analysis, transcriptomics, proteomics and other molecular technologies and data analysis. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Towards measles elimination: Phylogenetic analysis of measles viruses in Turkey (2012-2013) and identification of genotype D8.

PubMed

Kalaycioglu, Atila T; Yolbakan, Sultan; Guldemir, Dilek; Korukluoglu, Gulay; Coskun, Aslihan; Cosgun, Yasemin; Durmaz, Riza

2016-11-01

Molecular characterization of different measles virus (MV) strains is essential to combat the disease. Sixty measles MV strains were obtained from throat swabs or urine of patients in Turkey between 2012 and 2013 and characterized. MV RNA sequences (n = 60) were analysed for 456 nucleotides representing hypervariable domain of the nucleoprotein (N) gene. Of the 60 strains analysed 53 were the D8 genotype, 6 were B3, 1 was D4, and 1 was A. This report describes MV genotype D8 that was involved in a measles outbreak in Turkey. Sequences of most genotype D8 strains (n = 51) were identical to the sequence of variant D8-Frankfurt-Main, which has been associated with outbreaks throughout Europe. Despite the lack of epidemiologic information, a phylogenetic analysis suggested that the genotype D8 MV may have been brought to Turkey from elsewhere. Phylogenetic and epidemiological findings suggested that strains identified in tourists and associated with importation included one strain of genotype D8, one strain of genotype B3, and one strain of genotype D4. These findings from the 2012 to 2013 outbreak in Turkey confirm that pockets of unimmunised individuals are making the country susceptible to measles outbreaks. To prevent further outbreaks, deliberate and sustained effort must be made to reach, and immunise susceptible age groups. Towards measles elimination process, continued molecular surveillance of measles strains in Turkey will help identify transmission patterns of virus and evaluate vaccination efforts. J. Med. Virol. 88:1867-1873, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

High Prevalence of ESBL-Producing Klebsiella pneumoniae Causing Community-Onset Infections in China

PubMed Central

Zhang, Jing; Zhou, Kai; Zheng, Beiwen; Zhao, Lina; Shen, Ping; Ji, Jinru; Wei, Zeqing; Li, Lanjuan; Zhou, Jianying; Xiao, Yonghong

2016-01-01

The aim of this work was to investigate the epidemiological and genetic characteristics of ESBL-producing Klebsiella pneumoniae (ESBL-Kp) causing community-onset infections. K. pneumoniae isolates were collected from 31 Chinese secondary hospitals between August 2010 and 2011. Genes encoding ESBL and AmpC beta-lactamases were detected by PCR. The isolates were assigned to sequence types (STs) using multi-locus sequence typing (MLST). Eleven ESBL-Kp strains were selected for whole-genome sequencing (WGS) for investigating the genetic environment and plasmids encoding ESBL genes. A total of 578 K. pneumoniae isolates were collected, and 184 (31.8%) carried ESBL genes. The prevalence of ESBL-Kp varied from different geographical areas of China (10.2–50.3%). The three most prevalent ESBL genes were blaCTX-M-14 (n = 74), blaCTX-M-15 (n = 60), and blaCTX-M-3 (n = 40). MLST assigned 127 CTX-M-14 and CTX-M-15 producers to 54 STs, and CC17 was the most prevalent population (12.6%). STs (23, 37, and 86) that were known frequently associated with hypervirulent K. pneumoniae (hvKP) account for 14.1% (18/127). Phylogenetic analysis by concatenating the seven loci of MLST revealed the existence of ESBL-producing K. quasipneumoniae (two strains) and K. varricola (one strain), which was further confirmed by WGS. This study highlights the challenge of community-onset infections caused by ESBL-Kp in China. The prevalence of STs frequently associating with hvKP should be of concern. Surveillance of ESBL-KP causing community-onset infections now appears imperative. PMID:27895637

Cost–effectiveness analysis of quadrivalent influenza vaccine in Spain

PubMed Central

García, Amos; Ortiz de Lejarazu, Raúl; Reina, Jordi; Callejo, Daniel; Cuervo, Jesús; Morano Larragueta, Raúl

2016-01-01

ABSTRACT Influenza has a major impact on healthcare systems and society, but can be prevented using vaccination. The World Health Organization (WHO) currently recommends that influenza vaccines should include at least two virus A and one virus B lineage (trivalent vaccine; TIV). A new quadrivalent vaccine (QIV), which includes an additional B virus strain, received regulatory approval and is now recommended by several countries. The present study estimates the cost-effectiveness of replacing TIVs with QIV for risk groups and elderly population in Spain. A static, lifetime, multi-cohort Markov model with a one-year cycle time was adapted to assess the costs and health outcomes associated with a switch from TIV to QIV. The model followed a cohort vaccinated each year according to health authority recommendations, for the duration of their lives. National epidemiological data allowed the determination of whether the B strain included in TIVs matched the circulating one. Societal perspective was considered, costs and outcomes were discounted at 3% and one-way and probabilistic sensitivity analyses were performed. Compared to TIVs, QIV reduced more influenza cases and influenza-related complications and deaths during periods of B-mismatch strains in the TIV. The incremental cost-effectiveness ratio (ICER) was 8,748€/quality-adjusted life year (QALY). One-way sensitivity analysis showed mismatch with the B lineage included in the TIV was the main driver for ICER. Probabilistic sensitivity analysis shows ICER below 30,000€/QALY in 96% of simulations. Replacing TIVs with QIV in Spain could improve influenza prevention by avoiding B virus mismatch and provide a cost-effective healthcare intervention. PMID:27184622

Cost-effectiveness analysis of quadrivalent influenza vaccine in Spain.

PubMed

García, Amos; Ortiz de Lejarazu, Raúl; Reina, Jordi; Callejo, Daniel; Cuervo, Jesús; Morano Larragueta, Raúl

2016-09-01

Influenza has a major impact on healthcare systems and society, but can be prevented using vaccination. The World Health Organization (WHO) currently recommends that influenza vaccines should include at least two virus A and one virus B lineage (trivalent vaccine; TIV). A new quadrivalent vaccine (QIV), which includes an additional B virus strain, received regulatory approval and is now recommended by several countries. The present study estimates the cost-effectiveness of replacing TIVs with QIV for risk groups and elderly population in Spain. A static, lifetime, multi-cohort Markov model with a one-year cycle time was adapted to assess the costs and health outcomes associated with a switch from TIV to QIV. The model followed a cohort vaccinated each year according to health authority recommendations, for the duration of their lives. National epidemiological data allowed the determination of whether the B strain included in TIVs matched the circulating one. Societal perspective was considered, costs and outcomes were discounted at 3% and one-way and probabilistic sensitivity analyses were performed. Compared to TIVs, QIV reduced more influenza cases and influenza-related complications and deaths during periods of B-mismatch strains in the TIV. The incremental cost-effectiveness ratio (ICER) was 8,748€/quality-adjusted life year (QALY). One-way sensitivity analysis showed mismatch with the B lineage included in the TIV was the main driver for ICER. Probabilistic sensitivity analysis shows ICER below 30,000€/QALY in 96% of simulations. Replacing TIVs with QIV in Spain could improve influenza prevention by avoiding B virus mismatch and provide a cost-effective healthcare intervention.

Genome-Wide Immune Modulation of TLR3-Mediated Inflammation in Intestinal Epithelial Cells Differs between Single and Multi-Strain Probiotic Combination.

PubMed

MacPherson, Chad W; Shastri, Padmaja; Mathieu, Olivier; Tompkins, Thomas A; Burguière, Pierre

2017-01-01

Genome-wide transcriptional analysis in intestinal epithelial cells (IEC) can aid in elucidating the impact of single versus multi-strain probiotic combinations on immunological and cellular mechanisms of action. In this study we used human expression microarray chips in an in vitro intestinal epithelial cell model to investigate the impact of three probiotic bacteria, Lactobacillus helveticus R0052 (Lh-R0052), Bifidobacterium longum subsp. infantis R0033 (Bl-R0033) and Bifidobacterium bifidum R0071 (Bb-R0071) individually and in combination, and of a surface-layer protein (SLP) purified from Lh-R0052, on HT-29 cells' transcriptional profile to poly(I:C)-induced inflammation. Hierarchical heat map clustering, Set Distiller and String analyses revealed that the effects of Lh-R0052 and Bb-R0071 diverged from those of Bl-R0033 and Lh-R0052-SLP. It was evident from the global analyses with respect to the immune, cellular and homeostasis related pathways that the co-challenge with probiotic combination (PC) vastly differed in its effect from the single strains and Lh-R0052-SLP treatments. The multi-strain PC resulted in a greater reduction of modulated genes, found through functional connections between immune and cellular pathways. Cytokine and chemokine analyses based on specific outcomes from the TNF-α and NF-κB signaling pathways revealed single, multi-strain and Lh-R0052-SLP specific attenuation of the majority of proteins measured (TNF-α, IL-8, CXCL1, CXCL2 and CXCL10), indicating potentially different mechanisms. These findings indicate a synergistic effect of the bacterial combinations relative to the single strain and Lh-R0052-SLP treatments in resolving toll-like receptor 3 (TLR3)-induced inflammation in IEC and maintaining cellular homeostasis, reinforcing the rationale for using multi-strain formulations as a probiotic.

Genome-Wide Immune Modulation of TLR3-Mediated Inflammation in Intestinal Epithelial Cells Differs between Single and Multi-Strain Probiotic Combination

PubMed Central

MacPherson, Chad W.; Shastri, Padmaja; Mathieu, Olivier; Tompkins, Thomas A.; Burguière, Pierre

2017-01-01

Genome-wide transcriptional analysis in intestinal epithelial cells (IEC) can aid in elucidating the impact of single versus multi-strain probiotic combinations on immunological and cellular mechanisms of action. In this study we used human expression microarray chips in an in vitro intestinal epithelial cell model to investigate the impact of three probiotic bacteria, Lactobacillus helveticus R0052 (Lh-R0052), Bifidobacterium longum subsp. infantis R0033 (Bl-R0033) and Bifidobacterium bifidum R0071 (Bb-R0071) individually and in combination, and of a surface-layer protein (SLP) purified from Lh-R0052, on HT-29 cells’ transcriptional profile to poly(I:C)-induced inflammation. Hierarchical heat map clustering, Set Distiller and String analyses revealed that the effects of Lh-R0052 and Bb-R0071 diverged from those of Bl-R0033 and Lh-R0052-SLP. It was evident from the global analyses with respect to the immune, cellular and homeostasis related pathways that the co-challenge with probiotic combination (PC) vastly differed in its effect from the single strains and Lh-R0052-SLP treatments. The multi-strain PC resulted in a greater reduction of modulated genes, found through functional connections between immune and cellular pathways. Cytokine and chemokine analyses based on specific outcomes from the TNF-α and NF-κB signaling pathways revealed single, multi-strain and Lh-R0052-SLP specific attenuation of the majority of proteins measured (TNF-α, IL-8, CXCL1, CXCL2 and CXCL10), indicating potentially different mechanisms. These findings indicate a synergistic effect of the bacterial combinations relative to the single strain and Lh-R0052-SLP treatments in resolving toll-like receptor 3 (TLR3)-induced inflammation in IEC and maintaining cellular homeostasis, reinforcing the rationale for using multi-strain formulations as a probiotic. PMID:28099447

Multilocus Variable-Number-Tandem-Repeats Analysis (MLVA) distinguishes a clonal complex of Clavibacter michiganensis subsp. michiganensis strains isolated from recent outbreaks of bacterial wilt and canker in Belgium

PubMed Central

2013-01-01

Background Clavibacter michiganensis subsp. michiganensis (Cmm) causes bacterial wilt and canker in tomato. Cmm is present nearly in all European countries. During the last three years several local outbreaks were detected in Belgium. The lack of a convenient high-resolution strain-typing method has hampered the study of the routes of transmission of Cmm and epidemiology in tomato cultivation. In this study the genetic relatedness among a worldwide collection of Cmm strains and their relatives was approached by gyrB and dnaA gene sequencing. Further, we developed and applied a multilocus variable number of tandem repeats analysis (MLVA) scheme to discriminate among Cmm strains. Results A phylogenetic analysis of gyrB and dnaA gene sequences of 56 Cmm strains demonstrated that Belgian Cmm strains from recent outbreaks of 2010–2012 form a genetically uniform group within the Cmm clade, and Cmm is phylogenetically distinct from other Clavibacter subspecies and from non-pathogenic Clavibacter-like strains. MLVA conducted with eight minisatellite loci detected 25 haplotypes within Cmm. All strains from Belgian outbreaks, isolated between 2010 and 2012, together with two French strains from 2010 seem to form one monomorphic group. Regardless of the isolation year, location or tomato cultivar, Belgian strains from recent outbreaks belonged to the same haplotype. On the contrary, strains from diverse geographical locations or isolated over longer periods of time formed mostly singletons. Conclusions We hypothesise that the introduction might have originated from one lot of seeds or contaminated tomato seedlings that was the source of the outbreak in 2010 and that these Cmm strains persisted and induced infection in 2011 and 2012. Our results demonstrate that MLVA is a promising typing technique for a local surveillance and outbreaks investigation in epidemiological studies of Cmm. PMID:23738754

Multilocus variable-number-tandem-repeats analysis (MLVA) distinguishes a clonal complex of Clavibacter michiganensis subsp. michiganensis strains isolated from recent outbreaks of bacterial wilt and canker in Belgium.

PubMed

Zaluga, Joanna; Stragier, Pieter; Van Vaerenbergh, Johan; Maes, Martine; De Vos, Paul

2013-06-05

Clavibacter michiganensis subsp. michiganensis (Cmm) causes bacterial wilt and canker in tomato. Cmm is present nearly in all European countries. During the last three years several local outbreaks were detected in Belgium. The lack of a convenient high-resolution strain-typing method has hampered the study of the routes of transmission of Cmm and epidemiology in tomato cultivation. In this study the genetic relatedness among a worldwide collection of Cmm strains and their relatives was approached by gyrB and dnaA gene sequencing. Further, we developed and applied a multilocus variable number of tandem repeats analysis (MLVA) scheme to discriminate among Cmm strains. A phylogenetic analysis of gyrB and dnaA gene sequences of 56 Cmm strains demonstrated that Belgian Cmm strains from recent outbreaks of 2010-2012 form a genetically uniform group within the Cmm clade, and Cmm is phylogenetically distinct from other Clavibacter subspecies and from non-pathogenic Clavibacter-like strains. MLVA conducted with eight minisatellite loci detected 25 haplotypes within Cmm. All strains from Belgian outbreaks, isolated between 2010 and 2012, together with two French strains from 2010 seem to form one monomorphic group. Regardless of the isolation year, location or tomato cultivar, Belgian strains from recent outbreaks belonged to the same haplotype. On the contrary, strains from diverse geographical locations or isolated over longer periods of time formed mostly singletons. We hypothesise that the introduction might have originated from one lot of seeds or contaminated tomato seedlings that was the source of the outbreak in 2010 and that these Cmm strains persisted and induced infection in 2011 and 2012. Our results demonstrate that MLVA is a promising typing technique for a local surveillance and outbreaks investigation in epidemiological studies of Cmm.

Detection and phylogenetic analyses of spike genes in porcine epidemic diarrhea virus strains circulating in China in 2016-2017.

PubMed

Zhang, Qiaoling; Liu, Xinsheng; Fang, Yuzhen; Zhou, Peng; Wang, Yonglu; Zhang, Yongguang

2017-10-10

Large-scale outbreaks of porcine epidemic diarrhea (PED) have re-emerged in China in recent years. However, little is known about the genetic diversity and molecular epidemiology of field strains of PED virus (PEDV) in China in 2016-2017. To address this issue, in this study, 116 diarrhea samples were collected from pig farms in 6 Chinese provinces in 2016-2017 and were detected using PCR for main porcine enteric pathogens, including PEDV, porcine deltacoronavirus (PDCoV), porcine transmissible gastroenteritis virus (TGEV) and porcine kobuvirus (PKV). In addition, the complete S genes from 11 representative PEDV strains were sequenced and analyzed. PCR detection showed that 52.6% (61/116) of these samples were positive for PEDV. Furthermore, sequencing results for the spike (S) genes from 11 of the epidemic PEDV strains showed 93-94% nucleotide identity and 92-93% amino acid identity with the classical CV777 strain. Compared with the CV777 vaccine strain, these strains had an insertion (A 133 ), a deletion (G 155 ), and a continuous 4-amino-acid insertion ( 56 NNTN 59 ) in the S1 region. Phylogenetic analysis based on the S gene indicated that the 11 assessed PEDV strains were genetically diverse and clustered into the G2 group. These results demonstrate that the epidemic strains of PEDV in China in 2016-2017 are mainly virulent strains that belong to the G2 group and genetically differ from the vaccine strain. Importantly, this is the first report that the samples collected in Hainan Province were positive for PEDV (59.2%, 25/42). To our knowledge, this article presents the first report of a virulent PEDV strain isolated from Hainan Island, China. The results of this study will contribute to the understanding of the epidemiology and genetic characteristics of PEDV in China.

Molecular Epidemiology of Norovirus Outbreaks in Norway during 2000 to 2005 and Comparison of Four Norovirus Real-Time Reverse Transcriptase PCR Assays

PubMed Central

Vainio, Kirsti; Myrmel, Mette

2006-01-01

During the period from January 2000 to August 2005 a total of 204 outbreaks of norovirus gastroenteritis were diagnosed at the Norwegian Institute of Public Health. A clear increase in the norovirus activity was seen in healthcare institutions during the winter seasons. Polymerase sequence analysis of norovirus strains from 122 outbreaks showed that 112 were caused by GII strains (91.8%). Two norovirus variants seen during the study period—GIIb and GII.4—were predominant between January 2000 and September 2002, whereas GII.4 was predominant from September 2002 onward. The highest norovirus activity was seen during the 2002-2003 and 2004-2005 seasons with the emergence of new GII.4 variants. This study describes the molecular epidemiology of norovirus strains circulating in Norway during the five previous seasons and compares four norovirus real-time reverse transcriptase PCR assays. A suitable assay for routine diagnostics is suggested. PMID:17021099

Characterization of Austrian koi herpesvirus samples based on the ORF40 region.

PubMed

Marek, A; Schachner, O; Bilic, I; Hess, M

2010-02-17

Using a PCR that amplifies a region of the thymidine kinase (TK) gene, an epidemic spread of koi herpesvirus (KHV) was determined in koi carps in Austria in 2007. A total of 15 virus samples from different locations in Austria were analyzed to determine their genetic relatedness following PCR and nucleic acid sequencing of the open reading frame 40 (ORF40) region of the KHV genome. ORF40-specific PCR amplification products that were obtained from tissue samples shared 100% nucleotide sequence identity with the published sequence of the Japanese strain of KHV. The ORF40 sequence of one isolate from the UK that was included in the present study was 100% identical with the published sequence of an Israeli strain of KHV. This is the first study that used a larger number of samples and a PCR method, which allowed distinguishing all 3 strains of KHV. The present investigation provides information on the epidemiology of KHV infections in Europe and describes a useful molecular tool for epidemiological studies.

Epidemiology and Clinical Research Design, Part 2: Principles

PubMed Central

Manja, Veena; Lakshminrusimha, Satyan

2015-01-01

This is the third article covering core knowledge in scholarly activities for neonatal physicians. In this article, we discuss various principles of epidemiology and clinical research design. A basic knowledge of these principles is necessary for conducting clinical research and for proper interpretation of studies. This article reviews bias and confounding, causation, incidence and prevalence, decision analysis, cost-effectiveness, sensitivity analysis, and measurement. PMID:26236171

Molecular and epidemiological characterization of HIV-1 subtypes among Libyan patients.

PubMed

Daw, Mohamed A; El-Bouzedi, Abdallah; Ahmed, Mohamed O; Dau, Aghnyia A

2017-04-28

The epidemiological and clinical aspects of human immunodeficiency virus subtypes are of great interest worldwide. These subtypes are rarely studied in North African countries. Libya is a large country with the longest coast on the Mediterranean Sea, facing the Southern European countries. Studies on the characterization of HIV-1 subtypes are limited in Libya. This study aimed to determine the magnitude of the HIV problem among the Libyan population and to better understand the genetic diversity and the epidemiologic dynamics of HIV 1, as well as to correlate that with the risk factors involved. A total of 159 HIV-1 strains were collected from 814 HIV positive patients from the four Libyan regions during a 16-year period (1995-2010). To determine the HIV-1 subtypes, genetic analysis and molecular sequencing were carried out using provirus polygene. Epidemiologic and demographic information was obtained from each participant and correlated with HIV-1 subtypes using logistic regression. The overall prevalence of HIV among Libyans ranged from 5 to 10 per 100,000 during the study period. It was higher among intravenous drug users (IVDUs) (53.9%), blood recipients (25.9%) and heterosexuals (17.6%) than by vertical transmission (2.6%). Prevalence was higher among males aged 20-40 years (M:F 1:6, P > 0.001). Among the 159 strains of HIV-1 available for typing, 117 strains (73.6%) were subtype B, 29 (18.2%) were CRF02_AG, and 13 (8.2%) were subtype A. HIV-1 subtype B was the most prevalent all over the country, and it was more prevalent in the Northern region, particularly among IVDUs (P < 0.001). GRF02_AG was common in the Eastern region, particularly among blood recipients while subtype A emerged in the Western region, particularly among IVDUs. HIV-1 infection is emerging in Libya with a shifting prevalence of subtypes associated with the changing epidemiology of HIV-1 among risk groups. A genetic analysis of HIV-1 strains demonstrated low subtype heterogeneity with the evolution of subtype B, and CRF_20 AG, as well as HIV-1 subtype A. Our study highlights the importance of expanded surveillance programs to control HIV infection and the necessity of introducing public health strategies to target the risk groups, particularly IVDUs.

Multi-virulence-locus sequence typing of Staphylococcus lugdunensis generates results consistent with a clonal population structure and is reliable for epidemiological typing.

PubMed

Didi, Jennifer; Lemée, Ludovic; Gibert, Laure; Pons, Jean-Louis; Pestel-Caron, Martine

2014-10-01

Staphylococcus lugdunensis is an emergent virulent coagulase-negative staphylococcus responsible for severe infections similar to those caused by Staphylococcus aureus. To understand its potentially pathogenic capacity and have further detailed knowledge of the molecular traits of this organism, 93 isolates from various geographic origins were analyzed by multi-virulence-locus sequence typing (MVLST), targeting seven known or putative virulence-associated loci (atlLR2, atlLR3, hlb, isdJ, SLUG_09050, SLUG_16930, and vwbl). The polymorphisms of the putative virulence-associated loci were moderate and comparable to those of the housekeeping genes analyzed by multilocus sequence typing (MLST). However, the MVLST scheme generated 43 virulence types (VTs) compared to 20 sequence types (STs) based on MLST, indicating that MVLST was significantly more discriminating (Simpson's index [D], 0.943). No hypervirulent lineage or cluster specific to carriage strains was defined. The results of multilocus sequence analysis of known and putative virulence-associated loci are consistent with a clonal population structure for S. lugdunensis, suggesting a coevolution of these genes with housekeeping genes. Indeed, the nonsynonymous to synonymous evolutionary substitutions (dN/dS) ratio, the Tajima's D test, and Single-likelihood ancestor counting (SLAC) analysis suggest that all virulence-associated loci were under negative selection, even atlLR2 (AtlL protein) and SLUG_16930 (FbpA homologue), for which the dN/dS ratios were higher. In addition, this analysis of virulence-associated loci allowed us to propose a trilocus sequence typing scheme based on the intragenic regions of atlLR3, isdJ, and SLUG_16930, which is more discriminant than MLST for studying short-term epidemiology and further characterizing the lineages of the rare but highly pathogenic S. lugdunensis. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Polarized electron sources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prepost, R.

1994-12-01

The fundamentals of polarized electron sources are described with particular application to the Stanford Linear Accelerator Center. The SLAC polarized electron source is based on the principle of polarized photoemission from Gallium Arsenide. Recent developments using epitaxially grown, strained Gallium Arsenide cathodes have made it possible to obtain electron polarization significantly in excess of the conventional 50% polarization limit. The basic principles for Gallium and Arsenide polarized photoemitters are reviewed, and the extension of the basic technique to strained cathode structures is described. Results from laboratory measurements of strained photocathodes as well as operational results from the SLAC polarized sourcemore » are presented.« less

Deciphering the Possible Role of Strain Path on the Evolution of Microstructure, Texture, and Magnetic Properties in a Fe-Cr-Ni Alloy

NASA Astrophysics Data System (ADS)

Kumar, Amit; Khatirkar, Rajesh Kisni; Gupta, Aman; Shekhawat, Satish K.; Suwas, Satyam

2018-06-01

In the present work, the influence of strain path on the evolution of microstructure, crystallographic texture, and magnetic properties of a two-phase Fe-Cr-Ni alloy was investigated. The Fe-Cr-Ni alloy had nearly equal proportion of austenite and ferrite and was cold rolled up to a true strain of 1.6 (thickness reduction) using two different strain paths—unidirectional rolling and multi-step cross rolling. The microstructures were characterized by scanning electron microscopy (SEM) and electron backscattered diffraction (EBSD), while crystallographic textures were determined using X-ray diffraction. For magnetic characterization, B-H loops and M-H curves were measured and magnetic force microscopy was performed. After unidirectional rolling, ferrite showed the presence of strong α-fiber (rolling direction, RD//<110>) and austenite showed strong brass type texture (consisting of Brass (Bs) ({110}<112>), Goss ({110}<001>), and S ({123}<634>)). After multi-step cross rolling, strong rotated cube ({100}<110>) was developed in ferrite, while austenite showed ND (normal direction) rotated brass ( 10 deg) texture. The strain-induced martensite (SIM) was found to be higher in unidirectionally rolled samples than multi-step cross-rolled samples. The coherently diffracting domain size, micro-strain, coercivity, and core loss also showed a strong correlation with strain and strain path. More strain was partitioned into austenite than ferrite during deformation (unidirectional as well as cross rolling). Further, the strain partitioning (in both austenite and ferrite) was found to be higher in unidirectionally rolled samples.

Bridging Anticoagulation

MedlinePlus

... Customer Service and Ordering Information Subscribe to AHA Journals All Issues Subjects All Subjects Arrhythmia and Electrophysiology Basic, Translational, and Clinical Research Critical Care and Resuscitation Epidemiology, Lifestyle, and Prevention ...

Animal Movement and Establishment of Vaccinia Virus Cantagalo Strain in Amazon Biome, Brazil

PubMed Central

Quixabeira-Santos, Jociane Cristina; Medaglia, Maria Luiza G.; Pescador, Caroline A.

2011-01-01

To understand the emergence of vaccinia virus Cantagalo strain in the Amazon biome of Brazil, during 2008–2010 we conducted a molecular and epidemiologic survey of poxvirus outbreaks. Data indicate that animal movement was the major cause of virus dissemination within Rondônia State, leading to the establishment and spread of this pathogen. PMID:21470472

Molecular epidemiology of porcine reproductive and respiratory syndrome viruses isolated from 1991 to 2013 in Taiwan.

PubMed

Deng, Ming-Chung; Chang, Chia-Yi; Huang, Tien-Shine; Tsai, Hsiang-Jung; Chang, Chieh; Wang, Fun-In; Huang, Yu-Liang

2015-11-01

Porcine reproductive and respiratory syndrome virus (PRRSV) was first identified in Taiwan in 1991, but the genetic diversity and evolution of PRRSV has not been thoroughly investigated over the past 20 years. The aim of this study was to bridge the gap in understanding of its molecular epidemiology. A total of 31 PRRSV strains were collected and sequenced. The sequences were aligned using the MUSCLE program, and phylogenetic analysis were performed by the maximum-likelihood method and the neighbor-joining method using MEGA 5.2 software. In the early 1990s, two prototype strains, WSV and MD001 of the North American genotype, were first identified. Over the years, both viruses evolved separately. The population dynamics of PRRSV revealed that the strains of the MD001 group were predominant in Taiwan. Evolution was manifested in changes in the nsp2 and ORF5 genes. In addition, a suspected newly invading exotic strain was recovered in 2013, suggesting that international spread is still taking place and that it is affecting the population dynamics. Overall, the results provide an important basis for vaccine development for the control and prevention of PRRS.

Multiple-locus variable number of tandem repeat analysis as a tool for molecular epidemiology of botulism: The Italian experience.

PubMed

Anniballi, Fabrizio; Fillo, Silvia; Giordani, Francesco; Auricchio, Bruna; Tehran, Domenico Azarnia; di Stefano, Enrica; Mandarino, Giuseppina; De Medici, Dario; Lista, Florigio

2016-12-01

Clostridium botulinum is the bacterial agent of botulism, a rare but severe neuro-paralytic disease. Because of its high impact, in Italy botulism is monitored by an ad hoc surveillance system. The National Reference Centre for Botulism, as part of this system, collects and analyzes all demographic, epidemiologic, microbiological, and molecular data recovered during cases and/or outbreaks occurred in Italy. A panel of 312 C. botulinum strains belonging to group I were submitted to MLVA sub-typing. Strains, isolated from clinical specimens, food and environmental samples collected during the surveillance activities, were representative of all forms of botulism from all Italian regions. Through clustering analysis isolates were grouped into 12 main clusters. No regional or temporal clustering was detected, demonstrating the high heterogeneity of strains circulating in Italy. This study confirmed that MLVA is capable of sub-typing C. botulinum strains. Moreover, MLVA is effective at tracing and tracking the source of contamination and is helpful for the surveillance system in terms of planning and upgrading of procedures, activities and data collection forms. Copyright © 2016 Elsevier B.V. All rights reserved.

Crohns disease in Slovakia: prevalence, socioeconomic and psychological analysis.

PubMed

Príkazka, M; Letkovicová, M; Matejíckova, V

1998-01-01

The need for a basic epidemiological study, according to international standards, of the prevalence of IBD in Slovakia was increased by the dissolution of Czechoslovakia. This paper presents the results of CD prevalence to 30 April 1994 in Slovakia. To evaluate the statistical data of the prevalence of the disease according to age, sex, regions and districts, the authors employed the multi-dimensional Kruskal-Wallis test and cluster analysis and determined that the prevalence of CD in Slovakia is 6.75/100.000 inhabitants. The distribution differences indicate the need for further investigations of environmental differences. The socio-economic and psychological evaluation of the patients examined revealed some interesting associations. The psychological reaction to the disease is neurotic and depressive and a higher occurrence of affective symptomatology was observed in patients with permanent partnership and with children. On the other hand, the educational level and knowledge concerning the disease on the part of the patient had a positive influence on the reaction to the disease.

Rapid diagnostic testing for community-acquired pneumonia: can innovative technology for clinical microbiology be exploited?

PubMed

Yu, Victor L; Stout, Janet E

2009-12-01

Two nonsynchronous events have affected the management of community-acquired pneumonia (CAP): spiraling empiricism for CAP and the "golden era" of clinical microbiology. The development of broad-spectrum antibiotics has led to widespread empiric use without ascertaining the etiology of the infecting microbe. Unfortunately, this approach clashes with the second event, which is the advent of molecular-based microbiology that can identify the causative pathogen rapidly at the point of care. The urinary antigen is a most effective rapid test that has allowed targeted therapy for Legionnaire disease at the point of care. The high specificity (> 90%) allows the clinician to administer appropriate anti-Legionella therapy based on a single rapid test; however, its low sensitivity (76%) means that a notable number of cases of Legionnaire disease will go undiagnosed if other tests, especially culture, are not performed. Further, culture for Legionella is not readily available. If a culture is not performed, epidemiologic identification of the source of the bacterium cannot be ascertained by molecular fingerprinting of the patient and the putative source strain. We recommend resurrection of the basic principles of infectious disease, which are to identify the microbial etiology of the infection and to use narrow, targeted antimicrobial therapy. To reduce antimicrobial overuse with subsequent antimicrobial resistance, these basic principles must be applied in concert with traditional and newer tests in the clinical microbiology laboratory.

[Epidemiologic diagnostic of nosocomial suppurative-septic infections of Pseudomonas etiology based on intraspecies typing of causative agent].

PubMed

Fel'dblium, I V; Zakharova, Iu A; Nikolaeva, A M; Fedotova, O S

2013-01-01

Scientific justification of optimization of epidemiologic diagnostic of suppurative-septic infection (SSI) caused by Pseudomonas aeruginosa based on comparability of antibiotic sensitivity and beta-lactamase production. Intraspecies typing of 37 P. aeruginosa strains isolated during microbiological monitoring of 106 patients and 131 objects of clinical environment of surgical and obstetrician hospitals by using a complex ofphenotypic and molecular-biological methods including determination of sensitivity to antibiotics by serial dilutions method and PCR-diagnostics with determination of TEM, SHV, CTX, OXA, MBL, VIM genes was performed. P. aeruginosa strains combined into groups by isolation location during studies turned out to be heterogeneous by sensitivity to antibiotics and beta-lactamase production that allowed to form subgroups of strains by focality attribute. Isolates recovered from different SSI foci had significant differences in minimal inhibitory concentration (MIC) reaching 1024 times. MIC parameter within subgroups did not exceed 8 - 16 consequent dilutions. Use of a complex of phenotypic and molecular-biologic methods of causative agent typing including determination of sensitivity to antibiotics by serial dilutions method and evaluation of beta-lactamase production allowed to establish a mechanism of development of SSI epidemic process caused by P. aeruginosa, detect origins and reservoirs of infection in hospital, modes and factors of transmission and reach maximum justification of epidemiologic control and prophylaxis measures of localization of foci of nosocomial infections of pseudomonas etiology.

Molecular epidemiology of Mycobacterium avium subspecies paratuberculosis in ruminants in different parts of India.

PubMed

Sonawane, Ganesh G; Narnaware, Shirish D; Tripathi, Bhupendra N

2016-03-01

Paratuberculosis is an economically important, chronic, and incurable disease in ruminants, caused by Mycobacterium avium subspecies paratuberculosis (MAP). Understanding the genetic variability of MAP strains is important in diagnosis, epidemiological investigation, and the formation of strategies for prevention and control of the disease. In the present study, a total of 61 MAP isolates obtained from different parts and species of India were typed using IS1311 polymerase chain reaction-restriction endonuclease analysis (PCR-REA) to analyze the genetic difference(s), if any, between them and the host adaptation. Based on PCR-REA results, bison B type was detected in 54 (87%) MAP isolates obtained from cattle, sheep, and goats. Of these, 19 were from sheep of the Rajasthan (n=17) and Bareilly (n=2), North India regions, 28 were from cattle of Chennai, South India (n=3), Bareilly, North India (n=3), and Nagpur, West India (n=22), and seven goat isolates from Bareilly, North India region. The 'C' type strain was detected in only seven cattle isolates obtained from the Bareilly region. The study revealed that in India, bison B-type MAP strains were prevalent in most of the ruminant species. These results have important epidemiological implications with regard to control and prevention of paratuberculosis in India. Copyright © 2015 Asian African Society for Mycobacteriology. Published by Elsevier Ltd. All rights reserved.

Eco-epidemiology of Novel Bartonella Genotypes from Parasitic Flies of Insectivorous Bats.

PubMed

Sándor, Attila D; Földvári, Mihály; Krawczyk, Aleksandra I; Sprong, Hein; Corduneanu, Alexandra; Barti, Levente; Görföl, Tamás; Estók, Péter; Kováts, Dávid; Szekeres, Sándor; László, Zoltán; Hornok, Sándor; Földvári, Gábor

2018-04-29

Bats are important zoonotic reservoirs for many pathogens worldwide. Although their highly specialized ectoparasites, bat flies (Diptera: Hippoboscoidea), can transmit Bartonella bacteria including human pathogens, their eco-epidemiology is unexplored. Here, we analyzed the prevalence and diversity of Bartonella strains sampled from 10 bat fly species from 14 European bat species. We found high prevalence of Bartonella spp. in most bat fly species with wide geographical distribution. Bat species explained most of the variance in Bartonella distribution with the highest prevalence of infected flies recorded in species living in dense groups exclusively in caves. Bat gender but not bat fly gender was also an important factor with the more mobile male bats giving more opportunity for the ectoparasites to access several host individuals. We detected high diversity of Bartonella strains (18 sequences, 7 genotypes, in 9 bat fly species) comparable with tropical assemblages of bat-bat fly association. Most genotypes are novel (15 out of 18 recorded strains have a similarity of 92-99%, with three sequences having 100% similarity to Bartonella spp. sequences deposited in GenBank) with currently unknown pathogenicity; however, 4 of these sequences are similar (up to 92% sequence similarity) to Bartonella spp. with known zoonotic potential. The high prevalence and diversity of Bartonella spp. suggests a long shared evolution of these bacteria with bat flies and bats providing excellent study targets for the eco-epidemiology of host-vector-pathogen cycles.

Inferring epidemiological dynamics of infectious diseases using Tajima's D statistic on nucleotide sequences of pathogens.

PubMed

Kim, Kiyeon; Omori, Ryosuke; Ito, Kimihito

2017-12-01

The estimation of the basic reproduction number is essential to understand epidemic dynamics, and time series data of infected individuals are usually used for the estimation. However, such data are not always available. Methods to estimate the basic reproduction number using genealogy constructed from nucleotide sequences of pathogens have been proposed so far. Here, we propose a new method to estimate epidemiological parameters of outbreaks using the time series change of Tajima's D statistic on the nucleotide sequences of pathogens. To relate the time evolution of Tajima's D to the number of infected individuals, we constructed a parsimonious mathematical model describing both the transmission process of pathogens among hosts and the evolutionary process of the pathogens. As a case study we applied this method to the field data of nucleotide sequences of pandemic influenza A (H1N1) 2009 viruses collected in Argentina. The Tajima's D-based method estimated basic reproduction number to be 1.55 with 95% highest posterior density (HPD) between 1.31 and 2.05, and the date of epidemic peak to be 10th July with 95% HPD between 22nd June and 9th August. The estimated basic reproduction number was consistent with estimation by birth-death skyline plot and estimation using the time series of the number of infected individuals. These results suggested that Tajima's D statistic on nucleotide sequences of pathogens could be useful to estimate epidemiological parameters of outbreaks. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Molecular epidemiology of Vibrio cholerae associated with flood in Brahamputra River valley, Assam, India.

PubMed

Bhuyan, Soubhagya K; Vairale, Mohan G; Arya, Neha; Yadav, Priti; Veer, Vijay; Singh, Lokendra; Yadava, Pramod K; Kumar, Pramod

2016-06-01

Cholera is often caused when drinking water is contaminated through environmental sources. In recent years, the drastic cholera epidemics in Odisha (2007) and Haiti (2010) were associated with natural disasters (flood and Earthquake). Almost every year the state of Assam India witnesses flood in Brahamputra River valley during reversal of wind system (monsoon). This is often followed by outbreak of diarrheal diseases including cholera. Beside the incidence of cholera outbreaks, there is lack of experimental evidence for prevalence of the bacterium in aquatic environment and its association with cholera during/after flood in the state. A molecular surveillance during 2012-14 was carried out to study prevalence, strain differentiation, and clonality of Vibrio cholerae in inland aquatic reservoirs flooded by Brahamputra River in Assam. Water samples were collected, filtered, enriched in alkaline peptone water followed by selective culturing on thiosulfate bile salt sucrose agar. Environmental isolates were identified as V. cholerae, based on biochemical assays followed by sero-grouping and detailed molecular characterization. The incidence of the presence of the bacterium in potable water sources was higher after flood. Except one O1 isolate, all of the strains were broadly grouped under non-O1/non-O139 whereas some of them did have cholera toxin (CT). Surprisingly, we have noticed Haitian ctxB in two non-O1/non-O139 strains. MLST analyses based on pyrH, recA and rpoA genes revealed clonality in the environmental strains. The isolates showed varying degree of antimicrobial resistance including tetracycline and ciprofloxacin. The strains harbored the genetic elements SXT constins and integrons responsible for multidrug resistance. Genetic characterization is useful as phenotypic characters alone have proven to be unsatisfactory for strain discrimination. An assurance to safe drinking water, sanitation and monitoring of the aquatic reservoirs is of utmost importance for combating the impending epidemic threat in the flood affected areas. Further, the management of flood through multi-prong approaches and sustainable utilization of environmental resources would be effective in disease management. Copyright © 2015 Elsevier B.V. All rights reserved.

Dissemination of blaNDM-5 gene via an IncX3-type plasmid among non-clonal Escherichia coli in China.

PubMed

Li, Xi; Fu, Ying; Shen, Mengyuan; Huang, Danyan; Du, Xiaoxing; Hu, Qingfeng; Zhou, Yonglie; Wang, Dairong; Yu, Yunsong

2018-01-01

The emergence and spread of New Delhi metallo-β-lactamase-producing Enterobacteriaceae has been a serious challenge to manage in the clinic due to its rapid dissemination of multi-drug resistance worldwide. As one main type of carbapenemases, New Delhi metallo-β-lactamase (NDM)is able to confer resistance to almost all β-lactams, including carbapenems, in Enterobacteriaceae . Recently, New Delhi metallo-β-lactamase-5 attracted extensive attention because of increased resistance to carbapenems and widespread dissemination. However, the dissemination mechanism of bla NDM-5 gene remains unclear. A total of 224 carbapenem-resistant Enterobacteriaceae isolates (CRE) were collected from different hospitals in Zhejiang province. NDM-5-positive isolates were identified and subjected to genotyping, susceptibility testing, and clinical data analysis. We established the genetic location of bla NDM-5 with southern blot hybridisation, and analysed plasmids containing bla NDM-5 with filter mating and DNA sequencing. Eleven New Delhi metallo-β-lactamase-5 (NDM-5)-producing strains were identified, including 9 Escherichia coli strains, 1 Klebsiella pneumoniae strain, and 1 Citrobacter freundii strain. No epidemiological links for E. coli isolates were identified by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). S1-PFGE and southern blot suggested that the bla NDM-5 gene was located on a 46-kb IncX3-type plasmid in all isolates. Nine of the 11 isolates (81.8%) tested could successfully transfer their carbapenem-resistant phenotype to E. coli strain C600. Moreover, sequence analysis further showed that this plasmid possessed high sequence similarity to most of previously reported bla NDM-5 -habouring plasmids in China. The present data in this study showed the IncX3 type plasmid played an important role in the dissemination of bla NDM-5 in Enterobacteriaceae . In addition, to the best of our knowledge, this report is the first to isolate both E. coli and C. freundii strains carrying bla NDM-5 from one single patient, which further indicated the possibility of bla NDM-5 transmission among diverse species. Close surveillance is urgently needed to monitor the further dissemination of NDM-5-producing isolates.

Static and dynamic strain energy release rates in toughened thermosetting composite laminates

NASA Technical Reports Server (NTRS)

Cairns, Douglas S.

1992-01-01

In this work, the static and dynamic fracture properties of several thermosetting resin based composite laminates are presented. Two classes of materials are explored. These are homogeneous, thermosetting resins and toughened, multi-phase, thermosetting resin systems. Multi-phase resin materials have shown enhancement over homogenous materials with respect to damage resistance. The development of new dynamic tests are presented for composite laminates based on Width Tapered Double Cantilevered Beam (WTDCB) for Mode 1 fracture and the End Notched Flexure (ENF) specimen. The WTDCB sample was loaded via a low inertia, pneumatic cylinder to produce rapid cross-head displacements. A high rate, piezo-electric load cell and an accelerometer were mounted on the specimen. A digital oscilloscope was used for data acquisition. Typical static and dynamic load versus displacement plots are presented. The ENF specimen was impacted in three point bending with an instrumented impact tower. Fracture initiation and propagation energies under static and dynamic conditions were determined analytically and experimentally. The test results for Mode 1 fracture are relatively insensitive to strain rate effects for the laminates tested in this study. The test results from Mode 2 fracture indicate that the toughened systems provide superior fracture initiation and higher resistance to propagation under dynamic conditions. While the static fracture properties of the homogeneous systems may be relatively high, the apparent Mode 2 dynamic critical strain energy release rate drops significantly. The results indicate that static Mode 2 fracture testing is inadequate for determining the fracture performance of composite structures subjected to conditions such as low velocity impact. A good correlation between the basic Mode 2 dynamic fracture properties and the performance is a combined material/structural Compression After Impact (CAI) test is found. These results underscore the importance of examining rate-dependent behavior for determining the longevity of structures manufactured from composite materials.

Multi-target Parallel Processing Approach for Gene-to-structure Determination of the Influenza Polymerase PB2 Subunit

PubMed Central

Moen, Spencer O.; Smith, Eric; Raymond, Amy C.; Fairman, James W.; Stewart, Lance J.; Staker, Bart L.; Begley, Darren W.; Edwards, Thomas E.; Lorimer, Donald D.

2013-01-01

Pandemic outbreaks of highly virulent influenza strains can cause widespread morbidity and mortality in human populations worldwide. In the United States alone, an average of 41,400 deaths and 1.86 million hospitalizations are caused by influenza virus infection each year 1. Point mutations in the polymerase basic protein 2 subunit (PB2) have been linked to the adaptation of the viral infection in humans 2. Findings from such studies have revealed the biological significance of PB2 as a virulence factor, thus highlighting its potential as an antiviral drug target. The structural genomics program put forth by the National Institute of Allergy and Infectious Disease (NIAID) provides funding to Emerald Bio and three other Pacific Northwest institutions that together make up the Seattle Structural Genomics Center for Infectious Disease (SSGCID). The SSGCID is dedicated to providing the scientific community with three-dimensional protein structures of NIAID category A-C pathogens. Making such structural information available to the scientific community serves to accelerate structure-based drug design. Structure-based drug design plays an important role in drug development. Pursuing multiple targets in parallel greatly increases the chance of success for new lead discovery by targeting a pathway or an entire protein family. Emerald Bio has developed a high-throughput, multi-target parallel processing pipeline (MTPP) for gene-to-structure determination to support the consortium. Here we describe the protocols used to determine the structure of the PB2 subunit from four different influenza A strains. PMID:23851357

Isolation and molecular characterization of Leptospira borgpetersenii serovar Hardjo strain Hardjobovis in the urine of naturally infected cattle in Brazil.

PubMed

Chideroli, R T; Pereira, U P; Gonçalves, D D; Nakamura, A Y; Alfieri, A A; Alfieri, A F; Freitas, J C

2016-02-19

Most epidemiologic studies on bovine leptospirosis are based on serological tests that use antibodies against several serotypes, including the serovar Hardjo, which is widespread and considered to be the most adapted to bovine hosts. However, using only serological studies is not sufficient to identify and distinguish species of leptospires. The aim of this study was report the first isolation in Brazil of two strains serovar Hardjo obtained in urine samples from naturally infected cows in a small Brazilian dairy herd and find the genetic species and consequently the type strain Hardjobovis by molecular characterization. Fifteen dairy cows with a history of reproductive failure, such as abortion and infertility, were selected. Urine samples obtained from each animal were immediately seeded in tubes containing Ellinghausen-McCullough-Johnson-Harris culture medium. The identification of the isolates was performed by Multilocus variable-number tandem-repeat analysis (MLVA) technique and phylogenetic analysis of partial sequence of gene sec Y. From the 15 urine samples evaluated, two Leptospira were found and identified as the Londrina 49 and Londrina 54 strains. The MLVA profiles and sequencing of gene sec Y characterized the isolates as L. borgpetersenii serovar Hardjo strain Hadjobovis because it has different genetic pattern of Leptospira interrogans serovar Hardjo strain Hardjoprajitno. Therefore, more studies are needed including isolation and molecular characterization from regional strains to obtain a better knowledge about epidemiology of serovar Hardjo in bovine which may assist in future strategies of prevention and control of bovine leptospirosis.

Epidemiology of third-generation cephalosporin-resistant community-acquired Enterobacteria isolated from elderly patients.

PubMed

Thibaut, S; Caillon, J; Marquet, A; Grandjean, G; Potel, G; Ballereau, F

2014-02-01

This survey was made to study the epidemiology of multiresistant bacteria (MRB) in the French community, among elderly patients 65 years of age or more, carrying third-generation cephalosporin-resistant (3GC-resistant) Enterobacteriaceae, and the co-resistance of prescribed antibiotics. The data was collected in 2009 in the West of France by MedQual, a network of 174 private laboratories. Two thousand one hundred and sixty strains of the 88,255 identified Enterobacteria strains were 3GC-resistant (2.4%) and 945 of these strains (41.8%) were isolated from elderly patients 65 years of age or more. Escherichia coli was the predominant 3GC-resistant strain (72.7%). 51.4% of the 945 patients in whom a 3GC-resistant strain was isolated produced an extended-spectrum β-lactamase (ESBL). The main risk factors for infection with the 3GC-resistant strain were hospitalization and antibiotic treatment in the previous year (58.2 and 86.9%, respectively). Hospitalization during the previous year was more frequent among elderly patients who lived at home compared with those who lived in nursing homes (P<0.05). The production of ESBL, among the 945 patients who carried the 3GC-resistant strains, was similar among patients who lived at home compared with those who lived in nursing homes (51.4% versus 49.7%). Microbiologists should warn family physicians about MRB isolates with a specific antimicrobial resistance pattern (3GC-resistant, fluoroquinolone-resistant, etc.) to prescribe more effective medications. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

How medicine has become a science?

PubMed

Zieliński, Andrzej

2014-01-01

The historical review of medical activities draws attention how late in its very long history therapies of proven effectiveness were introduced. Author attributes it to the late development of methods which would be capable to determine the causal relations which would scientifically justified identification the causes and risk factors of diseases as well as checking the effectiveness of preventive and therapeutic procedures. Among the fundamental tools for scientific knowledge of the causes and mechanisms of diseases, the author indicates: achievements of basic science and the development of epidemiological methods used to study causal relationships. In the author's opinion the results of basic research are an essential source of variables among which, with an increased likelihood could be found the causes and risk factors of studied conditions, including diseases. The author also stresses the role of medical technology, which is the primary source of potential medicines, other therapeutic procedures and diagnostic methods whose effectiveness is tested in experimental epidemiological studies. Medical technologies create also tools for the development of basic sciences.

Track and field injuries.

PubMed

Zemper, Eric D

2005-01-01

A review of the existing literature on injuries to youth (< or =18 years old) in track and field or athletics. Searches of the Medline and SPORT Discus databases for English language articles through the end of 2003, using the search terms (adolescent or youth) and (track or field or running) and injuries. Only nine prospective or retrospective studies were found dealing with track and field injuries in children and that stated injury rates or provided enough information to allow the estimation of injury rates. Differences in study design and inconsistencies in the definition of a reportable injury provided major hindrances to making comparisons or combining data across studies. Among the few conclusions that can be drawn are that the lower extremities account for the majority of injuries, and muscle strains and ligament sprains are the predominant types of injury. While a majority of injuries may occur during training, since there is much more exposure during training than during competitions, the risk of injury is about four times higher during competitions. Informed decisions with regard to preventing injuries in youth track and field are dependent upon the quality of the basic epidemiological data available, and at this time such data are, for the most part, nonexistent. Because of the large numbers of participants and the large number and variety of activities involved in track and field, adequately designed epidemiological research is difficult, but opportunities for research in this sport are available for anyone willing to take on the challenge.

Whole genome sequencing identifies circulating Beijing-lineage Mycobacterium tuberculosis strains in Guatemala and an associated urban outbreak

PubMed Central

Saelens, Joseph W.; Lau-Bonilla, Dalia; Moller, Anneliese; Medina, Narda; Guzmán, Brenda; Calderón, Maylena; Herrera, Raúl; Sisk, Dana M.; Xet-Mull, Ana M.; Stout, Jason E.; Arathoon, Eduardo; Samayoa, Blanca; Tobin, David M.

2015-01-01

Summary Limited data are available regarding the molecular epidemiology of Mycobacterium tuberculosis (Mtb) strains circulating in Guatemala. Beijing-lineage Mtb strains have gained prevalence worldwide and are associated with increased virulence and drug resistance, but there have been only a few cases reported in Central America. Here we report the first whole genome sequencing of Central American Beijing-lineage strains of Mtb. We find that multiple Beijing-lineage strains, derived from independent founding events, are currently circulating in Guatemala, but overall still represent a relatively small proportion of disease burden. Finally, we identify a specific Beijing-lineage outbreak centered on a poor neighborhood in Guatemala City. PMID:26542222

Do factors related to combustion-based sources explain heterogeneity in PM-mortality associations across the United States?

EPA Science Inventory

Introduction: Spatial heterogeneity of effect estimates in associations between PM2.5 and total non-accidental mortality (TNA) in the United States (US), is an issue in epidemiology. This study uses rate ratios generated from the Multi-City/Multi-Pollutant study (1999-2005) for 3...

Phenotypic and Genomic Analysis of Hypervirulent Human-associated Bordetella bronchiseptica

PubMed Central

2012-01-01

Background B. bronchiseptica infections are usually associated with wild or domesticated animals, but infrequently with humans. A recent phylogenetic analysis distinguished two distinct B. bronchiseptica subpopulations, designated complexes I and IV. Complex IV isolates appear to have a bias for infecting humans; however, little is known regarding their epidemiology, virulence properties, or comparative genomics. Results Here we report a characterization of the virulence of human-associated complex IV B. bronchiseptica strains. In in vitro cytotoxicity assays, complex IV strains showed increased cytotoxicity in comparison to a panel of complex I strains. Some complex IV isolates were remarkably cytotoxic, resulting in LDH release levels in A549 cells that were 10- to 20-fold greater than complex I strains. In vivo, a subset of complex IV strains was found to be hypervirulent, with an increased ability to cause lethal pulmonary infections in mice. Hypercytotoxicity in vitro and hypervirulence in vivo were both dependent on the activity of the bsc T3SS and the BteA effector. To clarify differences between lineages, representative complex IV isolates were sequenced and their genomes were compared to complex I isolates. Although our analysis showed there were no genomic sequences that can be considered unique to complex IV strains, there were several loci that were predominantly found in complex IV isolates. Conclusion Our observations reveal a T3SS-dependent hypervirulence phenotype in human-associated complex IV isolates, highlighting the need for further studies on the epidemiology and evolutionary dynamics of this B. bronchiseptica lineage. PMID:22863321

A molecular epidemiology study based on VP2 gene sequences reveals that a new genotype of infectious bursal disease virus is dominantly prevalent in Italy.

PubMed

Lupini, Caterina; Giovanardi, Davide; Pesente, Patrizia; Bonci, Michela; Felice, Viviana; Rossi, Giulia; Morandini, Emilio; Cecchinato, Mattia; Catelli, Elena

2016-08-01

A distinctive infectious bursal disease (IBD) virus genotype (ITA) was detected in IBD-live vaccinated broilers in Italy without clinical signs of IBD. It was isolated in specific-pathogen-free eggs and molecularly characterized in the hypervariable region of the virus protein (VP) 2. Phylogenetic analysis showed that ITA strains clustered separately from other homologous reference sequences of IBDVs, either classical or very virulent, retrieved from GenBank or previously reported in Italy, and from vaccine strains. The new genotype shows peculiar molecular characteristics in key positions of the VP2 hypervariable region, which affect charged or potentially glycosylated amino acids virtually associated with important changes in virus properties. Characterization of 41 IBDV strains detected in Italy between 2013 and 2014 showed that ITA is emergent in densely populated poultry areas of Italy, being 68% of the IBDV detections made during routine diagnostic activity over a two-year period, in spite of the immunity induced by large-scale vaccination. Four very virulent strains (DV86) and one classical strain (HPR2), together with eight vaccine strains, were also detected. The currently available epidemiological and clinical data do not allow the degree of pathogenicity of the ITA genotype to be defined. Only in vivo experimental pathogenicity studies conducted in secure isolation conditions, through the evaluation of clinical signs and macro/microscopic lesions, will clarify conclusively the virulence of the new Italian genotype.

[Epidemiology of Staphylococcus aureus nosocomial infections in a high-risk neonatal unit].

PubMed

Velazco, Elsa; Nieves, Beatriz; Araque, María; Calderas, Zoila

2002-01-01

Nosocomial infections are a significant cause of morbidity and mortality throughout the world. In developing countries it is difficult to carry out effective surveillance and control programs for this type of infection because of the cost in both human and material resources. These considerations prompted us to perform a prospective study to determine the epidemiologic and microbiologic characteristics of nosocomial infections due to Staphylococcus aureus in the High-risk Neonatal Unit (HRNU) of the Instituto Autónomo Hospital Universitario de Los Andes (IAHULA), during the period of November 1997 to October 1998. Among a total of 120 microorganisms, 24 (20%) strains of Staphylococcus aureus were isolated; 47% were recovered from blood and 33% from conjunctive samples. Among the cases of conjunctivitis, S. aureus was the only pathogen isolated in 42%. Twenty of the 24 Staphylococcus aureus strains (83%) were methicillin-resistant (MRSA). According to their resistance profiles, we established 12 groups of strains from neonates with nosocomial infections and 1 group of strains from the two carriers among the healthcare personnel detected by microbiological screening. The MeRGmR pattern was the most frequent. Plasmid analysis disclosed two profiles, each having a plasmid molecular weight over 23.130 bp. The MRSA strains isolated from the neonates and those isolated from the carriers showed the same plasmid profile. This suggests that the healthcare personnel may have acted as reservoirs of the MRSA strains found in neonates with nosocomial infection.

Coordinating Centers in Cancer-Epidemiology Research: The Asia Cohort Consortium Coordinating Center

PubMed Central

Rolland, Betsy; Smith, Briana R; Potter, John D

2011-01-01

Although it is tacitly recognized that a good Coordinating Center (CC) is essential to the success of any multi-site collaborative project, very little study has been done on what makes a CC successful, why some CCs fail, or how to build a CC that meets the needs of a given project. Moreover, very little published guidance is available, as few CCs outside the clinical-trial realm write about their work. The Asia Cohort Consortium (ACC) is a collaborative cancer-epidemiology research project that has made strong scientific and organizational progress over the past three years by focusing its CC on the following activities: collaboration development; operations management; statistical and data management; and communications infrastructure and tool development. Our hope is that, by sharing our experience building the ACC CC, we can begin a conversation about what it means to run a coordinating center for multi-institutional collaboration in cancer epidemiology, help other collaborative projects solve some of the issues associated with collaborative research, and learn from others. PMID:21803842

[Epidemiological study on Streptococcus pyogenes strains isolated from the patients with streptococcal toxic shock syndrome (STSS) in Japan in 1992-2001].

PubMed

Okuno, Rumi; Endoh, Miyoko; Shimojima, Yukako; Yanagawa, Yoshitoki; Morozumi, Satoshi; Igarashi, Hideo; Ooe, Kenji

2004-01-01

To investigate clinical and microbiological features of streptococcal toxic shock syndrome (STSS), clinical, epidemiological, and bacteriological data obtained from 250 patients between 1992 and 2001 were analyzed. Among these 250 cases, 16 cases were excluded from the study because the causative microorganism were not Streptococcus pyogenes. 234 strains of S. pyogenes obtained from the aforementioned 234 cases were tested for T-type by a serological method, and for streptococcal pyrogenic exotoxin (SPE) by in vitro productivity of the toxin as well as molecular genetic methods. The number of patients was 141 (56.4%) for males, and 107 (42.8%) for females. The highest frequency of STSS was observed in those patients in their sixties in both sexes. The overall mortality rate was 43.2%. The mortality rate for male was 36.9%, and 52.3% for female. Bacteriological studies revealed that most common T types were T1 and T3. These strains consisted 54.3% of the strains collected. Among strains of T1 type, 98.8% possessed genes of spe A, and 46.1% were shown to produce SPE A in vitro. Among strains of T3 type, 82.9% possessed spe A gene, and all of these strains were shown to produce the toxin in vitro. It is concluded that certain strains of S. pyogenes, such as those with T1, or T3 type, and those with spe A gene or in vitro production of SPE A, are the most frequent cause of STSS. Although infections caused by such bacteria are quite common, STSS rarely occurs in most such patients. Additional factors, such as host factors, may play a crucial role in the pathogenesis of STSS.

Comparing in vitro and in vivo virulence phenotypes of Burkholderia pseudomallei type G strains.

PubMed

Lewis, Eric R G; Kilgore, Paul B; Mott, Tiffany M; Pradenas, Gonzalo A; Torres, Alfredo G

2017-01-01

Burkholderia pseudomallei (Bpm) is a saprophytic rod-shaped gram-negative bacterium and the causative agent of melioidosis. This disease has previously been described as endemic in areas such as northern Australia and Southeast Asia, but, more recently, a better understanding of the epidemiology of melioidosis indicated that the disease is distributed worldwide, including regions of the Americas and Africa. A 16S-23S rDNA internal transcribed spacer (ITS) typing system has been developed for Bpm and has revealed that ITS types C, E, and hybrid CE are mainly associated with Australia and Southeast Asia while type G strains are more associated with cases of melioidosis in the Western Hemisphere. The purpose of the current study was to determine the in vitro and in vivo virulence profiles of the understudied Bpm type G strains Ca2009, Ca2013a, Mx2013, and 724644 and compared such phenotypes to the commonly studied Bpm type C strain K96243. We evaluated virulence by measuring invasion/uptake and survival of these Bpm strains in murine respiratory epithelial LA-4 cells and alveolar macrophage MH-S cells using different multiplicity of infections (MOIs of 1 and 10). We also calculated the lethal dose 50 values (LD50) in BALB/c mice that were inoculated intranasally with either Ca2009, Ca2013a, or Mx2013. Overall, the virulence and lethality phenotypes of Bpm type G strains were similar to the Bpm type C strain K96243. Additional comparative analyses between the Bpm ITS types may lead to a better understanding of the contribution of the ITS type to the epidemiology and ecology of Bpm strains.

Comparing in vitro and in vivo virulence phenotypes of Burkholderia pseudomallei type G strains

PubMed Central

Mott, Tiffany M.; Pradenas, Gonzalo A.

2017-01-01

Burkholderia pseudomallei (Bpm) is a saprophytic rod-shaped gram-negative bacterium and the causative agent of melioidosis. This disease has previously been described as endemic in areas such as northern Australia and Southeast Asia, but, more recently, a better understanding of the epidemiology of melioidosis indicated that the disease is distributed worldwide, including regions of the Americas and Africa. A 16S-23S rDNA internal transcribed spacer (ITS) typing system has been developed for Bpm and has revealed that ITS types C, E, and hybrid CE are mainly associated with Australia and Southeast Asia while type G strains are more associated with cases of melioidosis in the Western Hemisphere. The purpose of the current study was to determine the in vitro and in vivo virulence profiles of the understudied Bpm type G strains Ca2009, Ca2013a, Mx2013, and 724644 and compared such phenotypes to the commonly studied Bpm type C strain K96243. We evaluated virulence by measuring invasion/uptake and survival of these Bpm strains in murine respiratory epithelial LA-4 cells and alveolar macrophage MH-S cells using different multiplicity of infections (MOIs of 1 and 10). We also calculated the lethal dose 50 values (LD50) in BALB/c mice that were inoculated intranasally with either Ca2009, Ca2013a, or Mx2013. Overall, the virulence and lethality phenotypes of Bpm type G strains were similar to the Bpm type C strain K96243. Additional comparative analyses between the Bpm ITS types may lead to a better understanding of the contribution of the ITS type to the epidemiology and ecology of Bpm strains. PMID:28414823

Genetic relatedness and recombination analysis of Allorhizobium vitis strains associated with grapevine crown gall outbreaks in Europe.

PubMed

Kuzmanović, N; Biondi, E; Bertaccini, A; Obradović, A

2015-09-01

To analyse genetic diversity and epidemiological relationships among 54 strains of Allorhizobium vitis isolated in Europe during an 8-year period and to assess the relative contribution of mutation and recombination in shaping their diversity. By using random amplified polymorphic DNA (RAPD) PCR, strains studied were distributed into 12 genetic groups. Sequence analysis of dnaK, gyrB and recA housekeeping genes was employed to characterize a representative subcollection of 28 strains. A total of 15 different haplotypes were found. Nucleotide sequence analysis suggested the presence of recombination events in A. vitis, particularly affecting dnaK locus. Although prevalence of mutation over recombination was found, impact of recombination was about two times greater than mutation in the evolution of the housekeeping genes analysed. The RAPD analysis indicated high degree of genetic diversity among the strains. However, the most abundant RAPD group was composed of 35 strains, which could lead to the conclusion that they share a common origin and were distributed by the movement of infected grapevine planting material as a most common way of crossing long distances. Furthermore, it seems that recombination is acting as an important driving force in the evolution of A. vitis. As no substantial evidence of recombination was detected within recA gene fragment, this phylogenetic marker could be reliable to characterize phylogenetic relationships among A. vitis strains. We demonstrated clear epidemiological relationship between majority of strains studied, suggesting a need for more stringent phytosanitary measures in international trade. Moreover, this is the first study to report recombination in A. vitis. © 2015 The Society for Applied Microbiology.

Co-Infection Dynamics of a Major Food-Borne Zoonotic Pathogen in Chicken

PubMed Central

Skånseng, Beate; Trosvik, Pål; Zimonja, Monika; Johnsen, Gro; Bjerrum, Lotte; Pedersen, Karl; Wallin, Nina; Rudi, Knut

2007-01-01

A major bottleneck in understanding zoonotic pathogens has been the analysis of pathogen co-infection dynamics. We have addressed this challenge using a novel direct sequencing approach for pathogen quantification in mixed infections. The major zoonotic food-borne pathogen Campylobacter jejuni, with an important reservoir in the gastrointestinal (GI) tract of chickens, was used as a model. We investigated the co-colonisation dynamics of seven C. jejuni strains in a chicken GI infection trial. The seven strains were isolated from an epidemiological study showing multiple strain infections at the farm level. We analysed time-series data, following the Campylobacter colonisation, as well as the dominant background flora of chickens. Data were collected from the infection at day 16 until the last sampling point at day 36. Chickens with two different background floras were studied, mature (treated with Broilact, which is a product consisting of bacteria from the intestinal flora of healthy hens) and spontaneous. The two treatments resulted in completely different background floras, yet similar Campylobacter colonisation patterns were detected in both groups. This suggests that it is the chicken host and not the background flora that is important in determining the Campylobacter colonisation pattern. Our results showed that mainly two of the seven C. jejuni strains dominated the Campylobacter flora in the chickens, with a shift of the dominating strain during the infection period. We propose a model in which multiple C. jejuni strains can colonise a single host, with the dominant strains being replaced as a consequence of strain-specific immune responses. This model represents a new understanding of C. jejuni epidemiology, with future implications for the development of novel intervention strategies. PMID:18020703

The evaluation and application of multilocus variable number tandem repeat analysis (MLVA) for the molecular epidemiological study of Salmonella enterica subsp. enterica serovar Enteritidis infection.

PubMed

Liu, Yao; Shi, Xiaolu; Li, Yinghui; Chen, Qiongcheng; Jiang, Min; Li, Wanli; Qiu, Yaqun; Lin, Yiman; Jiang, Yixiang; Kan, Biao; Sun, Qun; Hu, Qinghua

2016-01-29

Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) is one of the most prevalent Salmonella serotypes that cause gastroenteritis worldwide and the most prevalent serotype causing Salmonella infections in China. A rapid molecular typing method with high throughput and good epidemiological discrimination is urgently needed for detecting the outbreaks and finding the source for effective control of S. Enteritidis infections. In this study, 194 strains which included 47 from six outbreaks that were well-characterized epidemiologically were analyzed with pulse field gel electrophoresis (PFGE) and multilocus variable number tandem repeat analysis (MLVA). Seven VNTR loci published by the US Center for Disease Control and Prevention (CDC) were used to evaluate and develop MLVA scheme for S. Enteritidis molecular subtyping by comparing with PFGE, and then MLVA was applied to the suspected outbreaks detection. All S. Enteritidis isolates were analyzed with MLVA to establish a MLVA database in Shenzhen, Guangdong province, China to facilitate the detection of S. Enteritidis infection clusters. There were 33 MLVA types and 29 PFGE patterns among 147 sporadic isolates. These two measures had Simpson indices of 0.7701 and 0.8043, respectively, which did not differ significantly. Epidemiological concordance was evaluated by typing 47 isolates from six epidemiologically well-characterized outbreaks and it did not differ for PFGE and MLVA. We applied the well established MLVA method to detect two S. Enteritidis foodborne outbreaks and find their sources successfully in 2014. A MLVA database of 491 S. Enteritidis strains isolated from 2004 to 2014 was established for the surveillance of clusters in the future. MLVA typing of S. Enteritidis would be an effective tool for early warning and epidemiological surveillance of S. Enteritidis infections.

Extended Spectrum Beta-lactamases: Definition, Classification and Epidemiology.

PubMed

Ghafourian, Sobhan; Sadeghifard, Nourkhoda; Soheili, Sara; Sekawi, Zamberi

2015-01-01

Extended spectrum beta-lactamases (ESBLs) are defined as enzymes produced by certain bacteria that are able to hydrolyze extended spectrum cephalosporin. They are therefore effective against beta-lactam antibiotics such as ceftazidime, ceftriaxone, cefotaxime and oxyimino-monobactam. The objective of the current review is to provide a better understanding of ESBL and the epidemiology of ESBL producing organisms which are among those responsible for antibiotic resistant strains. Globally, ESBLs are considered to be problematic, particularly in hospitalized patients. There is an increasing frequency of ESBL in different parts of the world. The high risk patients are those contaminated with ESBL producer strains as it renders treatment to be ineffective in these patients. Thus, there an immediate needs to identify EBSL and formulate strategic policy initiatives to reduce their prevalence.

Unravelling the Molecular Epidemiology and Genetic Diversity among Burkholderia pseudomallei Isolates from South India Using Multi-Locus Sequence Typing.

PubMed

Tellapragada, Chaitanya; Kamthan, Aayushi; Shaw, Tushar; Ke, Vandana; Kumar, Subodh; Bhat, Vinod; Mukhopadhyay, Chiranjay

2016-01-01

There is a slow but steady rise in the case detection rates of melioidosis from various parts of the Indian sub-continent in the past two decades. However, the epidemiology of the disease in India and the surrounding South Asian countries remains far from well elucidated. Multi-locus sequence typing (MLST) is a useful epidemiological tool to study the genetic relatedness of bacterial isolates both with-in and across the countries. With this background, we studied the molecular epidemiology of 32 Burkholderia pseudomallei isolates (31 clinical and 1 soil isolate) obtained during 2006-2015 from various parts of south India using multi-locus sequencing typing and analysis. Of the 32 isolates included in the analysis, 30 (93.7%) had novel allelic profiles that were not reported previously. Sequence type (ST) 1368 (n = 15, 46.8%) with allelic profile (1, 4, 6, 4, 1, 1, 3) was the most common genotype observed. We did not observe a genotypic association of STs with geographical location, type of infection and year of isolation in the present study. Measure of genetic differentiation (FST) between Indian and the rest of world isolates was 0.14413. Occurrence of the same ST across three adjacent states of south India suggest the dispersion of B.pseudomallei across the south western coastal part of India with limited geographical clustering. However, majority of the STs reported from the present study remained as "outliers" on the eBURST "Population snapshot", suggesting the genetic diversity of Indian isolates from the Australasian and Southeast Asian isolates.

Epidemiology of Cystic Fibrosis.

PubMed

Spoonhower, Kimberly A; Davis, Pamela B

2016-03-01

Improved quality of care and rapidly emerging therapeutic strategies to restore chloride transport profoundly impact the epidemiology and pathobiology of cystic fibrosis (CF) in the twenty-first century. CF now serves as a model for chronic illness management, continuous quality improvement via registry data, and a seamless link between basic science research, translational studies, clinical trials, and outcomes research to enable rapid expansion of treatment options. Copyright © 2016 Elsevier Inc. All rights reserved.

Rabies Epidemiology and Control in Ecuador.

PubMed

Ortiz-Prado, Esteban; Ponce-Zea, Jorge; Ramirez, Dario; Stewart-Ibarra, Anna M; Armijos, Luciana; Yockteng, Jaime; Cardenas, Washington Bolivar

2015-07-12

Describe the epidemiology and the control effort for rabies in Ecuador. This observational study included data from the Ecuadorian National Institute of Census and Statistics (INEC), and mortality and morbidity data reported by the Ministry of Public Health and the National Institute for Social Security. We conducted a phylogeny analyses to compare the N gene from the Challenge Virus Standard (CVS) vaccine strain used in Ecuador with published Cosmopolitan, Asian and Sylvatic strains. Descriptive and inferential statistics were used to determine the significance of the data. In 1996 Ecuador suffered the highest rate of rabies per capita in the Americas, with an incidence rate of 0.56 cases per 100 000 people per year. Human and canine rabies showed a sharp decline until 2012. Between 1994 and 2014, we found a correlation of 0.925 (p<0.01) between annual cases of dog and human rabies. In 2011, there was an epidemic of sylvatic rabies transmitted to people by vampire bats (Desmodus rotundus) in the Amazon region, specifically in Morona Santiago, leading to 11 fatalities. Phylogenetic analyses of the CVS vaccine N gene showed an association with urban canine rabies strains (the Cosmopolitan lineage and Asian strains), whereas sylvatic rabies, like those reported in the Amazon region, were found to be grouped in a different clade represented mainly by bat-derived strains. This study presents the first compilation of epidemiological data on rabies in Ecuador. The incidence of human and canine rabies, also known as urban rabies, has clearly decreased due to massive canine vaccination campaigns. Phylogenetic analysis of the prevailing vaccine used in the country showed a clear separation from bat-derived rabies, the source of recent rabies outbreaks. Efforts are ongoing to develop rabies vaccines that are highly specific to the rabies virus genotype circulating in the region, including sylvatic rabies. These efforts include the implementation of reverse genetics to generate recombinant virus coding for the prevailing glycoprotein gene.

Rabies Epidemiology and Control in Ecuador

PubMed Central

Ortiz-Prado, Esteban; Ponce-Zea, Jorge; Ramirez, Dario; Stewart-Ibarra, Anna M.; Armijos, Luciana; Yockteng, Jaime; Cárdenas, Washington B.

2016-01-01

Objective: Describe the epidemiology and the control effort for rabies in Ecuador. Methods: This observational study included data from the Ecuadorian National Institute of Census and Statistics (INEC), and mortality and morbidity data reported by the Ministry of Public Health and the National Institute for Social Security. We conducted a phylogeny analyses to compare the N gene from the Challenge Virus Standard (CVS) vaccine strain used in Ecuador with published Cosmopolitan, Asian and Sylvatic strains. Descriptive and inferential statistics were used to determine the significance of the data. Results: In 1996 Ecuador suffered the highest rate of rabies per capita in the Americas, with an incidence rate of 0.56 cases per 100 000 people per year. Human and canine rabies showed a sharp decline until 2012. Between 1994 and 2014, we found a correlation of 0.925 (p<0.01) between annual cases of dog and human rabies. In 2011, there was an epidemic of sylvatic rabies transmitted to people by vampire bats (Desmodus rotundus) in the Amazon region, specifically in Morona Santiago, leading to 11 fatalities. Phylogenetic analyses of the CVS vaccine N gene showed an association with urban canine rabies strains (the Cosmopolitan lineage and Asian strains), whereas sylvatic rabies, like those reported in the Amazon region, were found to be grouped in a different clade represented mainly by bat-derived strains. Conclusions: This study presents the first compilation of epidemiological data on rabies in Ecuador. The incidence of human and canine rabies, also known as urban rabies, has clearly decreased due to massive canine vaccination campaigns. Phylogenetic analysis of the prevailing vaccine used in the country showed a clear separation from bat-derived rabies, the source of recent rabies outbreaks. Efforts are ongoing to develop rabies vaccines that are highly specific to the rabies virus genotype circulating in the region, including sylvatic rabies. These efforts include the implementation of reverse genetics to generate recombinant virus coding for the prevailing glycoprotein gene. PMID:26493436

Questionnaires for assessment of female sexual dysfunction: a review and proposal for a standardized screener.

PubMed

Giraldi, Annamaria; Rellini, Alessandra; Pfaus, James G; Bitzer, Johannes; Laan, Ellen; Jannini, Emmanuele A; Fugl-Meyer, Axel R

2011-10-01

There are many methods to evaluate female sexual function and dysfunction (FSD) in clinical and research settings, including questionnaires, structured interviews, and detailed case histories. Of these, questionnaires have become an easy first choice to screen individuals into different categories of FSD. The aim of this study was to review the strengths and weaknesses of different questionnaires currently available to assess different dimensions of women's sexual function and dysfunction, and to suggest a simple screener for FSD. A literature search of relevant databases, books, and articles in journals was used to identify questionnaires that have been used in basic or epidemiological research, clinical trials, or in clinical settings. Measures were grouped in four levels based on their purposes and degree of development, and were reviewed for their psychometric properties and utility in clinical or research settings. A Sexual Complaints Screener for Women (SCS-W) was then proposed based on epidemiological methods. Although many questionnaires are adequate for their own purposes, our review revealed a serious lack of standardized, internationally (culturally) acceptable questionnaires that are truly epidemiologically validated in general populations and that can be used to assess FSD in women with or without a partner and independent of the partner's gender. The SCS-W is proposed as a 10-item screener to aid clinicians in making a preliminary assessment of FSD. The definition of FSD continues to change and basic screening tools are essential to help advance clinical diagnosis and treatment, or to slate patients adequately into the right diagnostic categories for basic and epidemiological research or clinical trials. © 2011 International Society for Sexual Medicine.

Calibration of strain-gage installations in aircraft structures for the measurement of flight loads

NASA Technical Reports Server (NTRS)

Skopinski, T H; Aiken, William S , Jr; Huston, Wilber B

1954-01-01

A general method has been developed for calibrating strain-gage installations in aircraft structures, which permits the measurement in flight of the shear or lift, the bending moment, and the torque or pitching moment on the principal lifting or control surfaces. Although the stress in structural members may not be a simple function of the three loads of interest, a straightforward procedure is given for numerically combining the outputs of several bridges in such a way that the loads may be obtained. Extensions of the basic procedure by means of electrical combination of the strain-gage bridges are described which permit compromises between strain-gage installation time, availability of recording instruments, and data reduction time. The basic principles of strain-gage calibration procedures are illustrated by reference to the data for two aircraft structures of typical construction, one a straight and the other a swept horizontal stabilizer.

Molecular Typing of Vibrio parahaemolyticus Strains Isolated from Mollusks in the North Adriatic Sea.

PubMed

Rahman, Mohammad Shamsur; Carraro, Roberta; Cardazzo, Barbara; Carraro, Lisa; Meneguolo, Davide Boscolo; Martino, Maria Elena; Andreani, Nadia Andrea; Bordin, Paola; Mioni, Renzo; Barco, Lisa; Novelli, Enrico; Balzan, Stefania; Fasolato, Luca

2017-08-01

Vibrio parahaemolyticus is an emerging foodborne pathogen in the Mediterranean, usually associated with shellfish consumption. The increase in the number of outbreaks in Europe is primarily associated with the global warming of the ocean that has a great impact on the spread and genetic selection of waterborne pathogens. The primary role of Italy in Europe's mollusk production, together with the fact that cases of infections with V. parahaemolyticus are not always notified to the European community, highlighted the necessity of acquiring new information about the epidemiological involvement of shellfish products. The aim of the study was to provide useful insights into the first steps of the Risk Assessment associated with V. parahaemolyticus through the molecular characterization of isolates from commercialized mollusks. A total of 102 strains identified as V. parahaemolyticus were investigated as part of a larger sampling (1-year survey) from several shellfish species collected from the Venice lagoon and the North Adriatic sea. All strains were characterized by multilocus sequence typing and tested for the presence of virulence genes (trh and tdh). The study of sampling/environmental factors and epidemiological analyses was performed to describe the behaviors of the different genetic populations. The population structure analysis highlighted three genetic clusters that could be subject to temperature selection during cold (≤15°C) and warm (>16°C) seasons. Moreover, other factors, such as molluscan species (clams/mussels), probably played a role in the distribution of genetic clusters. Although few strains carried the virulence factors (n = 6 trh + ), epidemiological links with clinical isolates and a local dissemination of some sequence types were underlined. This work provides a useful background on the genotype spread as a first step in the Hazard Identification in light of future climate changes.

Epidemiology of Rickettsia sp. strain Atlantic rainforest in a spotted fever-endemic area of southern Brazil.

PubMed

Barbieri, Amalia R M; Filho, Jonas M; Nieri-Bastos, Fernanda A; Souza, Julio C; Szabó, Matias P J; Labruna, Marcelo B

2014-10-01

The present study was performed in Vila Itoupava, an area of the state of Santa Catarina, southern Brazil, in which a tick-borne spotted fever illness has been endemic since 2003. Notably, both the etiological agent and the vector of these spotted fever cases remain unknown. During January 2011, humans, domestic dogs, and their ticks were sampled in households that are typically surrounded by highly preserved Atlantic rainforest fragments. Ticks collected from dogs were Amblyomma ovale (34% prevalence), Amblyomma aureolatum (18.9%), and Rhipicephalus sanguineus (3.8%). A total of 7.8% (6/77) A. ovale and 9.3% (4/43) A. aureolatum were infected by Rickettsia sp. strain Atlantic rainforest, a Rickettsia parkeri-like agent recently shown to cause spotted fever illness in southeastern Brazil. Overall, 67.3% (35/52) of the dogs were seroreactive to spotted fever group rickettsiae, mostly with highest endpoint titers to R. parkeri. Among humans, 46.7% (7/15) reacted serologically to rickettsiae at low to moderate endpoint titers. Because canine seroreactivity to R. parkeri was strongly associated with frequent contact with forests (the preferred habitat for A. ovale and A. aureolatum), it is concluded that sampled dogs have been infected by strain Atlantic rainforest through the parasitism of these tick species. The present study provides epidemiological evidence that the spotted fever in the study area has been caused by Rickettsia sp. strain Atlantic rainforest, transmitted to humans by either A. ovale or A. aureolatum. Further studies encompassing direct diagnostic methods on clinical specimens from patients are needed to confirm the above epidemiological evidence. Copyright © 2014 Elsevier GmbH. All rights reserved.

Epidemiology of Clostridium difficile-associated disease at University Hospital Basel including molecular characterisation of the isolates 2006-2007.

PubMed

Fenner, L; Frei, R; Gregory, M; Dangel, M; Stranden, A; Widmer, A F

2008-12-01

A prospective study was conducted during a one-year period between 2006 and 2007 to describe the epidemiology of Clostridium difficile-associated disease (CDAD) at University Hospital Basel, Switzerland (UHBS) and to determine phenotypic and genotypic features of C. difficile strains isolated at the Microbiology Laboratory UHBS including strains from regional non-university hospitals. We prospectively identified 78 CDAD cases at UHBS with an incidence of 2.65/1,000 hospitalised patients or 2.3/10,000 patient-days. Sixteen patients (20.5%) were infected with clindamycin-resistant strains of PCR-ribotype 027 during an outbreak at the geriatric hospital. Among 124 single-patient isolates, 28 (22.6%) were resistant to moxifloxacin and 34 (27.4%) were resistant to clindamycin, but all remained susceptible to metronidazole and vancomycin. Of 102 toxigenic isolates, 19 (18.7%) had an 18-bp deletion in the tcdC gene, eight (7.8%) a 39-bp deletion, and one (1.0%) a 54-bp deletion. Genes for binary toxin were present in 27 (21.8%). PCR-ribotype 027 was associated with older age (median age 83.5 vs. 65.5 years, p < 0.0001) and longer duration of hospitalisation before onset of disease (median 15.5 vs. 9 days, p = 0.014) with a trend towards higher crude mortality, more severe disease, and previous use of macrolides compared to ribotype non-027. Overall, severe disease correlated with use of a nasogastric tube and surprisingly shorter duration of hospitalisation before onset of disease. Today, laboratory-based and epidemiological surveillance systems are required to monitor CDAD cases and emergence of new epidemic strains.

Epidemiological and molecular investigation of a measles outbreak in Punjab, Pakistan, 2013-2015.

PubMed

Zaidi, Syed Sohail Zahoor; Hameed, Abdul; Ali, Naeem; Rana, Muhammad Suleman; Umair, Massab; Alam, Muhammad Masroor; Aamir, Uzma Bashir; Khurshid, Adnan; Sharif, Salmaan; Shaukat, Shahzad; Angez, Mehar; Mujtaba, Ghulam; Arshad, Yasir; Akthar, Ribqa; Sufian, Mian Muhammad; Mehmood, Nayab

2018-04-28

Despite the availability of an effective vaccine, the measles virus continues to cause significant morbidity and mortality in children worldwide. Molecular characterization of wild-type measles strains is an invaluable component of epidemiological studies or surveillance systems that provides important information pertinent to outbreak linkages and transmission pathways. Serum samples and throat swabs were collected from suspected measles cases from the Punjab province of Pakistan (2013-2015) and further tested for measles immunoglobulin M (IgM) through enzyme-linked immunosorbent assay and reverse-transcriptase polymerase chain reaction for molecular characterization. Among the total of 5415 blood samples, 59% tested positive for measles IgM. Males had a higher infection rate (55%) than females (45%), and the highest frequency of positive cases (63%) was found in the age group of 0 to 5 years. Partial sequencing of the nucleoprotein gene showed that 27 strains belonged to the B3 genotype, whereas 2 viruses were identified as D4. On phylogenetic analysis, Pakistani B3 strains were found to be closely related to previously reported indigenous strains and those from neighboring countries of Iran and Qatar. This is the first report on the detection of the measles B3 genotype from Punjab, Pakistan. The current study shows a high burden of measles infections in Punjab province owing to poor routine immunization coverage in major cities. It is imperative that national health authorities adopt strategic steps on an urgent basis for improvement of routine immunization coverage. Molecular epidemiology of the measles viruses circulating in different parts of the country can provide useful data to manage future outbreaks. © 2018 Wiley Periodicals, Inc.

Screening of species-specific lactic acid bacteria for veal calves multi-strain probiotic adjuncts.

PubMed

Ripamonti, Barbara; Agazzi, Alessandro; Bersani, Carla; De Dea, Paola; Pecorini, Chiara; Pirani, Silvia; Rebucci, Raffaella; Savoini, Giovanni; Stella, Simone; Stenico, Alberta; Tirloni, Erica; Domeneghini, Cinzia

2011-06-01

The selection of promising specific species of lactic acid bacteria with potential probiotic characteristics is of particular interest in producing multi species-specific probiotic adjuncts in veal calves rearing. The aim of the present work was to select and evaluate in vitro the functional activity of lactic acid bacteria, Bifidobacterium longum and Bacillus coagulans strains isolated from veal calves in order to assess their potential use as multi species-specific probiotics for veal calves. For this purpose, bacterial strains isolated from faeces collected from 40 healthy 50-day-calves, were identified by RiboPrinter and 16s rRNA gene sequence. The most frequent strains belonged to the species B. longum, Streptococcus bovis, Lactobacillus animalis and Streptococcus macedonicus. Among these, 7 strains were chosen for testing their probiotic characteristics in vitro. Three strains, namely L. animalis SB310, Lactobacillus paracasei subsp. paracasei SB137 and B. coagulans SB117 showed varying individual but promising capabilities to survive in the gastrointestinal tract, to adhere, to produce antimicrobial compounds. These three selected species-specific bacteria demonstrated in vitro, both singularly and mixed, the functional properties needed for their use as potential probiotics in veal calves. Copyright © 2011 Elsevier Ltd. All rights reserved.

Chemical and morphological characterization of III-V strained layered heterostructures

NASA Astrophysics Data System (ADS)

Gray, Allen Lindsay

This dissertation describes investigations into the chemical and morphological characterization of III-V strained layered heterostructures by high-resolution x-ray diffraction. The purpose of this work is two-fold. The first was to use high-resolution x-ray diffraction coupled with transmission electron microscopy to characterize structurally a quaternary AlGaAsSb/InGaAsSb multiple quantum well heterostructure laser device. A method for uniquely determining the chemical composition of the strain quaternary quantum well, information previously thought to be unattainable using high resolution x-ray diffraction is thoroughly described. The misconception that high-resolution x-ray diffraction can separately find the well and barrier thickness of a multi-quantum well from the pendellosung fringe spacing is corrected, and thus the need for transmission electron microscopy is motivated. Computer simulations show that the key in finding the well composition is the intensity of the -3rd order satellite peaks in the diffraction pattern. The second part of this work addresses the evolution of strain relief in metastable multi-period InGaAs/GaAs multi-layered structures by high-resolution x-ray reciprocal space maps. Results are accompanied by transmission electron and differential contrast microscopy. The evolution of strain relief is tracked from a coherent "pseudomorphic" growth to a dislocated state as a function of period number by examining the x-ray diffuse scatter emanating from the average composition (zeroth-order) of the multi-layer. Relaxation is determined from the relative positions of the substrate with respect to the zeroth-order peak. For the low period number, the diffuse scatter from the multi-layer structure region arises from periodic, coherent crystallites. For the intermediate period number, the displacement fields around the multi-layer structure region transition to random coherent crystallites. At the higher period number, displacement fields of overlapping dislocations from relaxation of the random crystallites cause the initial stages of relaxation of the multi-layer structure. At the highest period number studied, relaxation of the multi-layer structure becomes bi-modal characterized by overlapping dislocations caused by mosaic block relaxation and periodically spaced misfit dislocations formed by 60°-type dislocations. The relaxation of the multi-layer structure has an exponential dependence on the diffuse scatter length-scale, which is shown to be a sensitive measure of the onset of relaxation.

Shape Sensing Using a Multi-Core Optical Fiber Having an Arbitrary Initial Shape in the Presence of Extrinsic Forces

NASA Technical Reports Server (NTRS)

Rogge, Matthew D. (Inventor); Moore, Jason P. (Inventor)

2014-01-01

Shape of a multi-core optical fiber is determined by positioning the fiber in an arbitrary initial shape and measuring strain over the fiber's length using strain sensors. A three-coordinate p-vector is defined for each core as a function of the distance of the corresponding cores from a center point of the fiber and a bending angle of the cores. The method includes calculating, via a controller, an applied strain value of the fiber using the p-vector and the measured strain for each core, and calculating strain due to bending as a function of the measured and the applied strain values. Additionally, an apparent local curvature vector is defined for each core as a function of the calculated strain due to bending. Curvature and bend direction are calculated using the apparent local curvature vector, and fiber shape is determined via the controller using the calculated curvature and bend direction.

[Epidemiological aspects relating to the determination of fosfomycin sensitivity: results of a study on 300 strains isolated in a hospital milieu in Turin].

PubMed

Vanini, G C; Moiraghi Ruggenini, A; Grassi, R; Maury, F; Giardini, F

1979-01-01

The AA. evaluated the sensitivity to Fosfomycin and to other commonly used antibiotics of 105 bacterial strains isolated from hospital environment and 195 from pathological materials. They also studied the problem of bacterial resistence to Fosfomycin considering the frequency of "inner colonies" and of bacterial cross-resistance to other antibiotics.

Resistance pattern of multi-drug resistant strains of Mycobacterium tuberculosis and characteristics of patients with multi-drug resistant tuberculosis.

PubMed

Moisoiu, Adriana; Mitran, Cristina Iulia; Mitran, Mãdãlina Irina; Huhu, Mihaela Roxana; Ioghen, Octavian Costin; Gheorghe, Adelina-Silvana; Tampa, Mircea; Georgescu, Simona Roxana; Popa, Mircea Ioan

2016-01-01

Multi-drug resistant tuberculosis (MDR-TB) is a major concern in the medical community. Knowledge about the drug resistance pattern of Mycobacterium tuberculosis strains plays an essential role in the management of the disease. We conducted a retrospective, 3-year study (2009-2011), in an urban area. We collected data on the drug resistance for 497 M. tuberculosis strains, isolated from patients with pulmonary TB. Among the 497 strains, we identified 158 MDR strains. Eighty medical recorders of patients infected with MDR strains were available and we included those patients in the study group. Of the 497 analysed strains, 8% were resistant to a single anti-TB drug. We identified 5.2% polyresistant drug strains, the most frequent combination being INH+EMB (1.4%). Of the 158 MDR strains identified (31.8%), over 60% were resistant to all first line anti-TB drugs tested. Most of them presented resistance to STM (86.1%) and EMB (67.7%). With respect to second line anti-TB drugs resistance to KM (23.4%) was the most common, followed by OFX (8.2%). With respect to the patients with MDR-TB, a percentage of 61.2% of them had a history of anti-TB treatment. Regarding lifestyle habits, 61.2% of the patients were smokers and 18.8% were abusing alcohol. Out of 51 patients, for whom information was available regarding their occupation, only 33.3 % were employees. MDR strains of Mycobacterium tuberculosis display an increased resistance to first line anti-TB drugs. Extension of resistance to second line anti-TB drugs narrows the therapeutic options. Knowledge of MDR-TB risk factors is imperative for the correct and rapid initiation of the treatment.

Multi-locus sequence typing of Salmonella enterica serovar Typhimurium isolates from wild birds in northern England suggests host-adapted strain.

PubMed

Hughes, L A; Wigley, P; Bennett, M; Chantrey, J; Williams, N

2010-10-01

Recent studies have suggested that Salmonella Typhimurium strains associated with mortality in UK garden birds are significantly different from strains that cause disease in humans and livestock and that wild bird strains may be host adapted. However, without further genomic characterization of these strains, it is not possible to determine whether they are host adapted. The aim of this study was to characterize a representative sample of Salm. Typhimurium strains detected in wild garden birds using multi-locus sequence typing (MLST)to investigate evolutionary relationships between them. Multi-locus sequence typing was performed on nine Salm. Typhimurium strains isolated from wild garden birds. Two sequence types were identified, the most common of which was ST568. Examination of the public Salmonella enterica MLST database revealed that only three other ST568 isolates had been cultured from a human in Scotland. Two further isolates of Salm. Typhimurium were determined to be ST19. Results of MLST analysis suggest that there is a predominant strain of Salm. Typhimurium circulating among garden bird populations in the United Kingdom, which is rarely detected in other species, supporting the hypothesis that this strain is host adapted. Host-pathogen evolution is often assumed to lead to pathogens becoming less virulent to avoid the death of their host; however, infection with ST568 led to high mortality rates among the wild birds examined, which were all found dead at wild bird-feeding stations. We hypothesize that by attracting unnaturally high densities of birds, wild bird-feeding stations may facilitate the transmission of ST568 between wild birds, therefore reducing the evolutionary cost of this pathogen killing its host, resulting in a host-adapted strain with increased virulence.

Genotype distribution of norovirus around the emergence of Sydney_2012 and the antigenic drift of contemporary GII.4 epidemic strains.

PubMed

Zhang, Jun; Shen, Zhen; Zhu, Zhaoqin; Zhang, Wanju; Chen, Huifen; Qian, Fangxing; Chen, Haili; Wang, Gang; Wang, Moying; Hu, Yunwen; Yuan, Zhenghong

2015-11-01

The pattern of epochal evolution of NoV is ongoing, while novel GII.4 variants emerge and cause new pandemics. Since, the emergence in March 2012, Sydney_2012 had replaced GII.4-2009 as the primary NoV strain in most countries in the northern hemisphere by November 2012. To determine the genotype distribution around the emergence of Sydney_2012 and to investigate the underlying evolution mechanisms of the contemporary GII.4 strains. From January 2012 to December 2013, molecular epidemiology of norovirus in 846 adults (≥16 years) in Shanghai were conducted. The VP1 proteins of the contemporary GII.4 strains (Den_Haag_2006b, New_Orleans_2009 and Sydney_2012) were expressed in vitro and purified. Receptor binding patterns of these three epidemic strains were determined through histo-blood group antigen (HBGA) binding assays. Convalescent serum from patients infected with GII.4 epidemic strains were employed to investigate the role of antigenic drift in the persistence of GII.4 epidemic strains through receptor-binding blockade assays. Epidemiological studies revealed that Sydeny_2012 has completely replaced Den_Haag_2006b and New_Orleans_2009 and has been the dominant circulating strain in Shanghai since its emergence in October 2012. Interestingly, Den_Haag_2006b and New_Orleans_2009 have been co-circulating in Shanghai before the emergence of Sydeny_2012. The contemporary GII.4 epidemic norovirus strains displayed commonly high tropism to the histo-blood group antigen receptors, whereas Sydeny_2012 was antigenically different from Den_Haag_2006b and New_Orleans_2009. Antigenic drift, rather than receptor switch, played a key role in the emergence and spreading of Sydney_2012. The contemporary GII.4 strains were evolving via epochal evolution without altered ligand binding profiles. Copyright © 2015 Elsevier B.V. All rights reserved.

Pyocine typing as an epidemiological marker in Pseudomonas aeruginosa mastitis in cattle

PubMed Central

Ziv, G.; Mushin, Rose; Tagg, J. R.

1971-01-01

Pyocine typing was used for the characterization of 134 Pseudomonas aeruginosa strains isolated from bovine mastitis. The scheme of Gillies & Govan (1966) was adopted with some modifications, and the procedure gave 89·6% typability. Pyocine type 1 strains were most commonly encountered and were followed in frequency by types 10 and 3. The introduction of two additional indicator strains allowed for division of these types into subtypes. In spite of some limitations, discussed in the paper, the pyocine typing scheme proved to be useful in `marking' P. aeruginosa strains and in following their association with bovine mastitis in various herds. PMID:4996924

Coexistence and specialization of pathogen strains on contact networks.

PubMed

Eames, Ken T D; Keeling, Matt J

2006-08-01

The coexistence of different pathogen strains has implications for pathogen variability and disease control and has been explained in a number of different ways. We use contact networks, which represent interactions between individuals through which infection could be transmitted, to investigate strain coexistence. For sexually transmitted diseases the structure of contact networks has received detailed study and has been shown to be a vital determinant of the epidemiological dynamics. By using analytical pairwise models and stochastic simulations, we demonstrate that network structure also has a profound influence on the interaction between pathogen strains. In particular, when the population is serially monogamous, fully cross-reactive strains can coexist, with different strains dominating in network regions with different characteristics. Furthermore, we observe specialization of different strains in different risk groups within the network, suggesting the existence of diverging evolutionary pressures.

Epidemiology and virulence of VIM-4 metallo-beta-lactamase-producing Pseudomonas aeruginosa isolated from burn patients in eastern Algeria.

PubMed

Meradji, Samah; Barguigua, Abouddihaj; Bentakouk, Mohamed Cherif; Nayme, Kaotar; Zerouali, Khalid; Mazouz, Dekhil; Chettibi, Houria; Timinouni, Mohammed

2016-06-01

In this study, we investigated the prevalence of carbapenem-resistant Pseudomonas aeruginosa (CRPA) in burn patients from eastern Algeria, CRPA virulence factors and the molecular epidemiology of CRPA. The overall prevalence of CRPA was 48.38%. Seven (46.66%) isolates were metallo-β-lactamases (MBL) producers and contained the MBL genes blaVIM-4 (n=6) and blaVIM-2 (n=1). Risk factors for CRPA infection were urinary catheter use and intubation (p=0.008). A high percentage of virulence factors (86.6% of these isolates were able to produce protease; 73.3% of isolates has DNase; and 66.6% were haemolysin positive) was observed in CRPA isolates. Among the seven MBL-producing isolates, four had the same clonal profile. The class 1 integrons, which contained the aadA7 gene cassette, were detected in six isolates. The 16SrRNA methylase gene, rmtB, was detected in one strain. All CRPA isolates were biofilm formers. A study on the kinetics of biofilm production revealed that biofilm production increased when the concentration of imipenem or ciprofloxacin and the incubation time increased. This is the first study to report the presence of VIM-4-producing P. aeruginosa from North Africa and also of the high prevalence of CRPA isolates. Based on our study of burn unit patients, the high percentage of P. aeruginosa with virulence factors and multi-drug resistance is alarming. Copyright © 2016 Elsevier Ltd and ISBI. All rights reserved.

Multiscale deformation behavior for multilayered steel by in-situ FE-SEM

NASA Astrophysics Data System (ADS)

Tanaka, Y.; Kishimoto, S.; Yin, F.; Kobayashi, M.; Tomimatsu, T.; Kagawa, K.

2010-03-01

The multi-scale deformation behavior of multi-layered steel during tensile loading was investigated by in-situ FE-SEM observation coupled with multi-scale pattern. The material used was multi-layered steel sheet consisting of martensitic and austenitic stainless steel layers. Prior to in-situ tensile testing, the multi-scale pattern combined with a grid and random dots were fabricated by electron beam lithography on the polished surface in the area of 1 mm2 to facilitate direct observation of multi-scale deformation. Both of the grids with pitches of 10 μm and a random speckle pattern ranging from 200 nm to a few μm sizes were drawn onto the specimen surface at same location. The electron moiré method was applied to measure the strain distribution in the deformed specimens at a millimeter scale and digital images correlation method was applied to measure the in-plane deformation and strain distribution at a micron meter scale acquired before and after at various increments of straining. The results showed that the plastic deformation in the austenitic stainless steel layer was larger than the martensitic steel layer at millimeter scale. However, heterogeneous intrinsic grain-scale plastic deformation was clearly observed and it increased with increasing the plastic deformation.

[The use of multilocus sequence typing (MLST) and randomly amplified polymorphic DNA (RAPD) for the differentiation between strains of Burkholderia mallei].

PubMed

Antonov, V A; Altukhova, V V; Savchenko, S S; Zamaraev, V S; Iliukhin, V I; Alekseev, V V

2007-01-01

Burkholderia mallei is highly pathogenic microorganism for both humans and animals. In this work, the possibility of the use of the genotyping method for differentiation between strains of B. mallei was studied. A collection of 14 isolates of B. mallei was characterized using randomly amplified polymorphic DNA (RAPD) and multilocus sequence typing (MLST). RAPD was the best method used for detecting strain differences of B. mallei. It was suggested that this method would be an increasingly useful molecular epidemiological tool.

Complete Genome Sequence and Comparative Genomics of a Streptococcus pyogenes emm3 Strain M3-b isolated from a Japanese Patient with Streptococcal Toxic Shock Syndrome.

PubMed

Ogura, Kohei; Watanabe, Shinya; Kirikae, Teruo; Miyoshi-Akiyama, Tohru

2017-01-01

Epidemiologic typing of Streptococcus pyogenes (GAS) is frequently based on the genotype of the emm gene, which encodes M/Emm protein. In this study, the complete genome sequence of GAS emm3 strain M3-b, isolated from a patient with streptococcal toxic shock syndrome (STSS), was determined. This strain exhibited 99% identity with other complete genome sequences of emm3 strains MGAS315, SSI-1, and STAB902. The complete genomes of five additional strains isolated from Japanese patients with and without STSS were also sequences. Maximum-likelihood phylogenetic analysis showed that strains M3-b, M3-e, and SSI-1, all which were isolated from STSS patients, were relatively close.

Global epidemiology of CTX-M β-lactamases: temporal and geographical shifts in genotype.

PubMed

Bevan, Edward R; Jones, Annie M; Hawkey, Peter M

2017-08-01

Globally, rates of ESBL-producing Enterobacteriaceae are rising. We undertook a literature review, and present the temporal trends in blaCTX-M epidemiology, showing that blaCTX-M-15 and blaCTX-M-14 have displaced other genotypes in many parts of the world. Explanations for these changes can be attributed to: (i) horizontal gene transfer (HGT) of plasmids; (ii) successful Escherichia coli clones; (iii) ESBLs in food animals; (iv) the natural environment; and (v) human migration and access to basic sanitation. We also provide explanations for the changing epidemiology of blaCTX-M-2 and blaCTX-M-27. Modifiable anthropogenic factors, such as poor access to basic sanitary facilities, encourage the spread of blaCTX-M and other antimicrobial resistance (AMR) genes, such as blaNDM, blaKPC and mcr-1. We provide further justification for novel preventative and interventional strategies to reduce transmission of these AMR genes. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Utilization and value of personal digital assistants on an epidemiology final examination.

PubMed

Lawler, Frank H; Cacy, Jim

2005-01-01

The utility of personal digital assistants (PDAs) in basic science medical education is uncertain. Student outcomes on an epidemiology course final examination for academic years 2003 and 2004 were examined. Students were given permission to use PDAs on the final examination, and self-selected whether these instruments were used. Performance on the examination based on use of a PDA and whether students thought it was useful for the examination was compared. A total of 389 students took the final examination, with an 88% response rate to the survey questions. No statistically significant differences were found on final examination scores. No trends toward significance were found on analyses of the total examination, specific topical domains, or on specific questions where a PDA might be expected to be especially useful. From this study, it can be concluded that use of PDAs and whether students thought they might be helpful had no measurable effect on performance on an epidemiology final examination. Further delineation of the possible use of PDAs in a basic science course and on the final examination is indicated.

Maximum stress estimation model for multi-span waler beams with deflections at the supports using average strains.

PubMed

Park, Sung Woo; Oh, Byung Kwan; Park, Hyo Seon

2015-03-30

The safety of a multi-span waler beam subjected simultaneously to a distributed load and deflections at its supports can be secured by limiting the maximum stress of the beam to a specific value to prevent the beam from reaching a limit state for failure or collapse. Despite the fact that the vast majority of accidents on construction sites occur at waler beams in retaining wall systems, no safety monitoring model that can consider deflections at the supports of the beam is available. In this paper, a maximum stress estimation model for a waler beam based on average strains measured from vibrating wire strain gauges (VWSGs), the most frequently used sensors in construction field, is presented. The model is derived by defining the relationship between the maximum stress and the average strains measured from VWSGs. In addition to the maximum stress, support reactions, deflections at supports, and the magnitudes of distributed loads for the beam structure can be identified by the estimation model using the average strains. Using simulation tests on two multi-span beams, the performance of the model is evaluated by estimating maximum stress, deflections at supports, support reactions, and the magnitudes of distributed loads.

Design of the Army Study to Assess Risk and Resilience in Servicemembers (Army STARRS)

PubMed Central

Kessler, Ronald C.; Colpe, Lisa J.; Fullerton, Carol S.; Gebler, Nancy; Naifeh, James A.; Nock, Matthew K.; Sampson, Nancy A.; Schoenbaum, Michael; Zaslavsky, Alan M.; Stein, Murray B.; Ursano, Robert J.; Heeringa, Steven G.

2014-01-01

The Army Study to Assess Risk and Resilience in Servicemembers (Army STARRS) is a multi-component epidemiological and neurobiological study designed to generate actionable evidence-based recommendations to reduce U.S. Army suicides and increase basic knowledge about the determinants of suicidality. This report presents an overview of the designs of the six component Army STARRS studies. These include: an integrated study of historical administrative data systems (HADS) designed to provide data on significant administrative predictors of suicides among the more than 1.6 million soldiers on active duty in 2004–2009; retrospective case-control studies of suicide attempts and fatalities; separate large-scale cross-sectional studies of new soldiers (i.e., those just beginning Basic Combat Training [BCT], who completed self-administered questionnaires [SAQ] and neurocognitive tests and provided blood samples) and soldiers exclusive of those in BCT (who completed SAQs); a pre-post deployment study of soldiers in three Brigade Combat Teams about to deploy to Afghanistan (who completed SAQs and provided blood samples) followed multiple times after returning from deployment; and a platform for following up Army STARRS participants who have returned to civilian life. DoD/Army administrative data records are linked with SAQ data to examine prospective associations between self-reports and subsequent suicidality. The presentation closes with a discussion of the methodological advantages of cross-component coordination. PMID:24318217

Design of the Army Study to Assess Risk and Resilience in Servicemembers (Army STARRS).

PubMed

Kessler, Ronald C; Colpe, Lisa J; Fullerton, Carol S; Gebler, Nancy; Naifeh, James A; Nock, Matthew K; Sampson, Nancy A; Schoenbaum, Michael; Zaslavsky, Alan M; Stein, Murray B; Ursano, Robert J; Heeringa, Steven G

2013-12-01

The Army Study to Assess Risk and Resilience in Servicemembers (Army STARRS) is a multi-component epidemiological and neurobiological study designed to generate actionable evidence-based recommendations to reduce US Army suicides and increase basic knowledge about the determinants of suicidality. This report presents an overview of the designs of the six components of the Army STARRS. These include: an integrated analysis of the Historical Administrative Data Study (HADS) designed to provide data on significant administrative predictors of suicides among the more than 1.6 million soldiers on active duty in 2004-2009; retrospective case-control studies of suicide attempts and fatalities; separate large-scale cross-sectional studies of new soldiers (i.e. those just beginning Basic Combat Training [BCT], who completed self-administered questionnaires [SAQs] and neurocognitive tests and provided blood samples) and soldiers exclusive of those in BCT (who completed SAQs); a pre-post deployment study of soldiers in three Brigade Combat Teams about to deploy to Afghanistan (who completed SAQs and provided blood samples) followed multiple times after returning from deployment; and a platform for following up Army STARRS participants who have returned to civilian life. Department of Defense/Army administrative data records are linked with SAQ data to examine prospective associations between self-reports and subsequent suicidality. The presentation closes with a discussion of the methodological advantages of cross-component coordination. Copyright © 2013 John Wiley & Sons, Ltd.

Prevalence and Psychosocial Correlates of Symptoms Suggestive of Painful Bladder Syndrome: Results from the Boston Area Community Health (BACH) Survey

PubMed Central

Link, Carol L.; Pulliam, Samantha J.; Hanno, Philip M.; Hall, Susan A.; Eggers, Paul W.; Kusek, John W.; McKinlay, John B.

2009-01-01

Purpose The objective is to estimate the prevalence of symptoms suggestive of Painful Bladder Syndrome (PBS) defined as pain increasing as the bladder fills and/or pain relieved by urination for at least three months and its association with socio-demographics (gender, age, race/ethnicity, and socioeconomic status), lifestyle (smoking, alcohol consumption, physical activity) and psychosocial variables (sexual, physical, emotional abuse experienced as a child or as an adult, worry, trouble paying for basics, depression). Materials and Methods The data used come from the Boston Area Community Health (BACH) survey, an epidemiologic study of 5506 randomly selected adults aged 30-79 of three race/ethnic groups (Black, Hispanic, White). Results The overall prevalence of symptoms suggestive of PBS is two percent (1.3% in men and 2.6% in women) with increased prevalence in middle aged adults and those of lower socioeconomic status. Symptoms suggestive of PBS are more common in those who have experienced abuse, in those who are worried about someone close to them, and in those who are having trouble paying for basics. This pattern holds even after adjusting for depression. Conclusions PBS is associated with a number of lifestyle and psychosocial correlates. This suggests that the management of patients with PBS (physical symptoms) may benefit from a multi-faceted approach of combining medical and psychological, and cognitive treatment. PMID:18554658

An epidemiological examination of the subluxation construct using Hill's criteria of causation.

PubMed

Mirtz, Timothy A; Morgan, Lon; Wyatt, Lawrence H; Greene, Leon

2009-12-02

Chiropractors claim to locate, analyze and diagnose a putative spinal lesion known as subluxation and apply the mode of spinal manipulation (adjustment) for the correction of this lesion. The purpose of this examination is to review the current evidence on the epidemiology of the subluxation construct and to evaluate the subluxation by applying epidemiologic criteria for it's significance as a causal factor. The databases of PubMed, Cinahl, and Mantis were searched for studies using the keywords subluxation, epidemiology, manipulation, dose-response, temporality, odds ratio, relative risk, biological plausibility, coherence, and analogy. The criteria for causation in epidemiology are strength (strength of association), consistency, specificity, temporality (temporal sequence), dose response, experimental evidence, biological plausibility, coherence, and analogy. Applied to the subluxation all of these criteria remain for the most part unfulfilled. There is a significant lack of evidence to fulfill the basic criteria of causation. This lack of crucial supportive epidemiologic evidence prohibits the accurate promulgation of the chiropractic subluxation.

An epidemiological examination of the subluxation construct using Hill's criteria of causation

PubMed Central

2009-01-01

Background Chiropractors claim to locate, analyze and diagnose a putative spinal lesion known as subluxation and apply the mode of spinal manipulation (adjustment) for the correction of this lesion. Aim The purpose of this examination is to review the current evidence on the epidemiology of the subluxation construct and to evaluate the subluxation by applying epidemiologic criteria for it's significance as a causal factor. Methods The databases of PubMed, Cinahl, and Mantis were searched for studies using the keywords subluxation, epidemiology, manipulation, dose-response, temporality, odds ratio, relative risk, biological plausibility, coherence, and analogy. Results The criteria for causation in epidemiology are strength (strength of association), consistency, specificity, temporality (temporal sequence), dose response, experimental evidence, biological plausibility, coherence, and analogy. Applied to the subluxation all of these criteria remain for the most part unfulfilled. Conclusion There is a significant lack of evidence to fulfill the basic criteria of causation. This lack of crucial supportive epidemiologic evidence prohibits the accurate promulgation of the chiropractic subluxation. PMID:19954544

Defining a Core Genome Multilocus Sequence Typing Scheme for the Global Epidemiology of Vibrio parahaemolyticus

PubMed Central

Jolley, Keith A.; Reed, Elizabeth; Martinez-Urtaza, Jaime

2017-01-01

ABSTRACT Vibrio parahaemolyticus is an important human foodborne pathogen whose transmission is associated with the consumption of contaminated seafood, with a growing number of infections reported over recent years worldwide. A multilocus sequence typing (MLST) database for V. parahaemolyticus was created in 2008, and a large number of clones have been identified, causing severe outbreaks worldwide (sequence type 3 [ST3]), recurrent outbreaks in certain regions (e.g., ST36), or spreading to other regions where they are nonendemic (e.g., ST88 or ST189). The current MLST scheme uses sequences of 7 genes to generate an ST, which results in a powerful tool for inferring the population structure of this pathogen, although with limited resolution, especially compared to pulsed-field gel electrophoresis (PFGE). The application of whole-genome sequencing (WGS) has become routine for trace back investigations, with core genome MLST (cgMLST) analysis as one of the most straightforward ways to explore complex genomic data in an epidemiological context. Therefore, there is a need to generate a new, portable, standardized, and more advanced system that provides higher resolution and discriminatory power among V. parahaemolyticus strains using WGS data. We sequenced 92 V. parahaemolyticus genomes and used the genome of strain RIMD 2210633 as a reference (with a total of 4,832 genes) to determine which genes were suitable for establishing a V. parahaemolyticus cgMLST scheme. This analysis resulted in the identification of 2,254 suitable core genes for use in the cgMLST scheme. To evaluate the performance of this scheme, we performed a cgMLST analysis of 92 newly sequenced genomes, plus an additional 142 strains with genomes available at NCBI. cgMLST analysis was able to distinguish related and unrelated strains, including those with the same ST, clearly showing its enhanced resolution over conventional MLST analysis. It also distinguished outbreak-related from non-outbreak-related strains within the same ST. The sequences obtained from this work were deposited and are available in the public database (http://pubmlst.org/vparahaemolyticus). The application of this cgMLST scheme to the characterization of V. parahaemolyticus strains provided by different laboratories from around the world will reveal the global picture of the epidemiology, spread, and evolution of this pathogen and will become a powerful tool for outbreak investigations, allowing for the unambiguous comparison of strains with global coverage. PMID:28330888

Optics and optronics in university courses for officers of the Federal Armed Forces - special curricula and hands-on lessons vs. academic requirements

NASA Astrophysics Data System (ADS)

Hahlweg, Cornelius; Rothe, Hendrik

2016-09-01

For more than two decades lessons in optics, digital image processing and optronics are compulsory optional subjects and as such integral parts of the courses in mechanical engineering at the University of the Federal Armed Forces in Hamburg. They are provided by the Chair for Measurement and Information Technology. Historically, the curricula started as typical basic lessons in optics and digital image processing and related sensors. Practical sessions originally concentrated on image processing procedures in Pascal, C and later Matlab. They evolved into a broad portfolio of practical hands-on lessons in lab and field, including high-tech and especially military equipment, but also homemaker style primitive experiments, of which the paper will give a methodical overview. A special topic - as always with optics in education - is the introduction to the various levels of abstraction in conjunction with the highly complex and wide-ranging matter squeezed into only two trimesters - instead of semesters at civil universities - for an audience being subject to strains from both study and duty. The talk will be accompanied by striking multi-media material, which will be also part of the multi-media attachment of the paper.

Experimental Investigations on Subsequent Yield Surface of Pure Copper by Single-Sample and Multi-Sample Methods under Various Pre-Deformation.

PubMed

Liu, Gui-Long; Huang, Shi-Hong; Shi, Che-Si; Zeng, Bin; Zhang, Ke-Shi; Zhong, Xian-Ci

2018-02-10

Using copper thin-walled tubular specimens, the subsequent yield surfaces under pre-tension, pre-torsion and pre-combined tension-torsion are measured, where the single-sample and multi-sample methods are applied respectively to determine the yield stresses at specified offset strain. The rule and characteristics of the evolution of the subsequent yield surface are investigated. Under the conditions of different pre-strains, the influence of test point number, test sequence and specified offset strain on the measurement of subsequent yield surface and the concave phenomenon for measured yield surface are studied. Moreover, the feasibility and validity of the two methods are compared. The main conclusions are drawn as follows: (1) For the single or multi-sample method, the measured subsequent yield surfaces are remarkably different from cylindrical yield surfaces proposed by the classical plasticity theory; (2) there are apparent differences between the test results from the two kinds of methods: the multi-sample method is not influenced by the number of test points, test order and the cumulative effect of residual plastic strain resulting from the other test point, while those are very influential in the single-sample method; and (3) the measured subsequent yield surface may appear concave, which can be transformed to convex for single-sample method by changing the test sequence. However, for the multiple-sample method, the concave phenomenon will disappear when a larger offset strain is specified.

Phylogenetic relationship of Ornithobacterium rhinotracheale strains.

PubMed

DE Oca-Jimenez, Roberto Montes; Vega-Sanchez, Vicente; Morales-Erasto, Vladimir; Salgado-Miranda, Celene; Blackall, Patrick J; Soriano-Vargas, Edgardo

2018-04-10

The bacterium Ornithobacterium rhinotracheale is associated with respiratory disease in wild birds and poultry. In this study, the phylogenetic analysis of nine reference strains of O. rhinotracheale belonging to serovars A to I, and eight Mexican isolates belonging to serovar A, was performed. The analysis was extended to include available sequences from another 23 strains available in the public domain. The analysis showed that the 40 sequences formed six clusters, I to VI. All eight Mexican field isolates were placed in cluster I. One of the reference strains appears to present genetic diversity not previously recognized and was placed in a new genetic cluster. In conclusion, the phylogenetic analysis of O. rhinotracheale strains, based on the 16S rRNA gene, is a suitable tool for epidemiologic studies.

Whole genome sequencing identifies circulating Beijing-lineage Mycobacterium tuberculosis strains in Guatemala and an associated urban outbreak.

PubMed

Saelens, Joseph W; Lau-Bonilla, Dalia; Moller, Anneliese; Medina, Narda; Guzmán, Brenda; Calderón, Maylena; Herrera, Raúl; Sisk, Dana M; Xet-Mull, Ana M; Stout, Jason E; Arathoon, Eduardo; Samayoa, Blanca; Tobin, David M

2015-12-01

Limited data are available regarding the molecular epidemiology of Mycobacterium tuberculosis (Mtb) strains circulating in Guatemala. Beijing-lineage Mtb strains have gained prevalence worldwide and are associated with increased virulence and drug resistance, but there have been only a few cases reported in Central America. Here we report the first whole genome sequencing of Central American Beijing-lineage strains of Mtb. We find that multiple Beijing-lineage strains, derived from independent founding events, are currently circulating in Guatemala, but overall still represent a relatively small proportion of disease burden. Finally, we identify a specific Beijing-lineage outbreak centered on a poor neighborhood in Guatemala City. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Genetic Characterization of Bacillus anthracis 17 JB strain.

PubMed

Seyed-Mohamadi, Sakineh; Moradi Bidhendi, Soheila; Tadayon, Keyvan; Ghaderi, Rainak

2015-06-01

Bacillus anthracis is one of the most homogenous bacteria ever described. Some level of diversity. Bacillus anthracis 17JB is a laboratory strain It is broadly used as a challenge strain in guinea pigs for potency test of anthrax vaccine. This work describes genetic characterization of B. anthracis 17 JB strain using the SNPs and MLVA genotyping. In SNPs typing, the originally French 17JB strain represented the A.Br. 008/009 subgroup. In Levy's genotyping method, 843, 451 and 864 bp long fragments were identified at AA03, AJ03 and AA07 loci, respectively. In the vaccine manufacturer perspective these findings are much valuable on their own account, but similar research is required to extend molecular knowledge of B. anthracis epidemiology in Persia.

Analyzing Fourier Transforms for NASA DFRC's Fiber Optic Strain Sensing System

NASA Technical Reports Server (NTRS)

Fiechtner, Kaitlyn Leann

2010-01-01

This document provides a basic overview of the fiber optic technology used for sensing stress, strain, and temperature. Also, the document summarizes the research concerning speed and accuracy of the possible mathematical algorithms that can be used for NASA DFRC's Fiber Optic Strain Sensing (FOSS) system.

Molecular epidemiology is becoming complex under the dynamic HIV prevalence: The perspective from Harbin, China.

PubMed

Shao, Bing; Song, Bo; Cao, Lijun; Du, Juan; Sun, Dongying; Lin, Yuanlong; Wang, Binyou; Wang, Fuxiang; Wang, Sunran

2016-05-01

Unlike most areas of China, HIV transmission via men who have sex with men (MSM) is increasing rapidly, and has become the main route of HIV transmission in Harbin city. The purpose of the current study was to elaborate the molecular epidemiologic characteristics of the new HIV epidemic. Eighty-one HIV-1 gag gene sequences (HXB2:806-1861) from local HIV infections were isolated; CRF01_AE predominated among HIV infections (71.6%), followed by subtype B (16.5%), CRF07_BC (6.2%), and unique recombinant strains (URFs; 6.2%). URFs were most often identified in the MSM population, which consisted of a recombination of CRF01_AE with subtype B or CRF07_BC. Six clusters were formed in this analysis; clusters I and II mainly circulated in southwest China. Clusters III and IV mainly circulated in southwest, southeast, and central China. Clusters V and VI mainly circulated in north and northeast China. Clusters III and IV may facilitate the transmission of the CRF01_AE strain from the southwest to the north and northeast regions of China. HIV subtypes are becoming diverse with the persistent epidemic in this geographic region. In brief, our results indicate that the molecular epidemiology of HIV is trending to be more complex. Thus, timely molecular epidemiologic supervision of HIV is necessary, especially for the MSM population. © 2015 Wiley Periodicals, Inc.

Molecular epidemiology of HIV: tracking AIDS pandemic.

PubMed

TakebE, Yutaka; Kusagawa, Shigeru; Motomura, Kazushi

2004-04-01

Human immunodeficiency virus (HIV) and acquired immunodeficiency syndrome (AIDS) epidemic is a global threat to maternal and child health, especially in developing countries. It is estimated that 800 000 children are infected and 580 000 children die of AIDS-related illnesses every year. Molecular epidemiology has been a useful tool in analyzing the origin of HIV and tracking the course of global HIV spread. This article provides an overview of recent advances in the field of molecular epidemiology of HIV across the world, and discuss the biological implications. Based on the near full-length or partial nucleotide sequence information, the phylogeny and recombinant structure of HIV strains are analyzed. Using genotype classification of HIV as a molecular marker, the origin and the genesis of HIV epidemic are investigated. The HIV-1 group M, a major HIV group responsible for current AIDS pandemic, began its expansion in human population approximately 70 years ago and diversified rapidly over time, now comprising a number of different subtypes and circulating recombinant forms (CRF). Of note, recent studies revealed that new recombinant strains are arising continually, becoming a powerful force in the spread of HIV-1 across the globe. Global dissemination of HIV is a dramatic and deadly example of recent genome emergence and expansion. Molecular epidemiological investigation is expected to provide information critical for prevention and future vaccine strategies.

Molecular Epidemiology and Prevalence of Echovirus 30 in Zhejiang Province, China, from 2002 to 2015.

PubMed

Chen, Yin; Sun, Yi; Yan, Juying; Miao, Ziping; Xu, Changping; Zhang, Yanjun; Mao, Haiyan; Gong, Liming

2017-12-28

Echovirus serotype 30 (ECHO30) has been responsible for several recent worldwide outbreaks of viral meningitis. In Zhejiang Province, China, ECHO30 has been one of the main causes of viral meningitis for years. This study, using phylogenetic analysis of the VP1 gene, was performed to investigate the general molecular epidemiology and genetic patterns of ECHO30 circulating in Zhejiang Province between the years 2002 and 2015. The nucleotide sequences of ECHO30 VP1 showed that they were 64.8% identical with the prototype strain, Bastianni, while the amino acids were 84.9% identical. Phylogenetic analyses showed that ECHO30 in the Zhejiang area has diverged into two genotypes. Genotype I consists of strains isolated since 2002, whereas genotype II includes strains that were mainly isolated during the 2002 to 2004 outbreak. ECHO30 has been endemically circulating in both humans and the environment for a long period of time. Additionally, we evaluated the significance of recombination presented during the years 2005 to 2007 to demonstrate that recombination plays an important role in the prevalence of ECHO30 in the Zhejiang area.

Genome characterization of Turkey Rotavirus G strains from the United States identifies potential recombination events with human Rotavirus B strains.

PubMed

Chen, Fangzhou; Knutson, Todd P; Porter, Robert E; Ciarlet, Max; Mor, Sunil Kumar; Marthaler, Douglas G

2017-12-01

Rotavirus G (RVG) strains have been detected in a variety of avian species, but RVG genomes have been published from only a single pigeon and two chicken strains. Two turkey RVG strains were identified and characterized, one in a hatchery with no reported health issues and the other in a hatchery with high embryo/poult mortality. The two turkey RVG strains shared only an 85.3 % nucleotide sequence identity in the VP7 gene while the other genes possessed high nucleotide identity among them (96.3-99.9 %). Low nucleotide percentage identities (31.6-87.3 %) occurred among the pigeon and chicken RVG strains. Interestingly, potential recombination events were detected between our RVG strains and a human RVB strain, in the VP6 and NSP3 segments. The epidemiology of RVG in avian flocks and the pathogenicity of the two different RVG strains should be further investigated to understand the ecology and impact of RVG in commercial poultry flocks.

Genomic Epidemiology of Salmonella enterica Serotype Enteritidis based on Population Structure of Prevalent Lineages

PubMed Central

Desai, Prerak T.; den Bakker, Henk C.; Mikoleit, Matthew; Tolar, Beth; Trees, Eija; Hendriksen, Rene S.; Frye, Jonathan G.; Porwollik, Steffen; Weimer, Bart C.; Wiedmann, Martin; Weinstock, George M.; Fields, Patricia I.; McClelland, Michael

2014-01-01

Salmonella enterica serotype Enteritidis is one of the most commonly reported causes of human salmonellosis. Its low genetic diversity, measured by fingerprinting methods, has made subtyping a challenge. We used whole-genome sequencing to characterize 125 S. enterica Enteritidis and 3 S. enterica serotype Nitra strains. Single-nucleotide polymorphisms were filtered to identify 4,887 reliable loci that distinguished all isolates from each other. Our whole-genome single-nucleotide polymorphism typing approach was robust for S. enterica Enteritidis subtyping with combined data for different strains from 2 different sequencing platforms. Five major genetic lineages were recognized, which revealed possible patterns of geographic and epidemiologic distribution. Analyses on the population dynamics and evolutionary history estimated that major lineages emerged during the 17th–18th centuries and diversified during the 1920s and 1950s. PMID:25147968

Molecular epidemiology of Oropouche virus, Brazil.

PubMed

Vasconcelos, Helena Baldez; Nunes, Márcio R T; Casseb, Lívia M N; Carvalho, Valéria L; Pinto da Silva, Eliana V; Silva, Mayra; Casseb, Samir M M; Vasconcelos, Pedro F C

2011-05-01

Oropouche virus (OROV) is the causative agent of Oropouche fever, an urban febrile arboviral disease widespread in South America, with >30 epidemics reported in Brazil and other Latin American countries during 1960-2009. To describe the molecular epidemiology of OROV, we analyzed the entire N gene sequences (small RNA) of 66 strains and 35 partial Gn (medium RNA) and large RNA gene sequences. Distinct patterns of OROV strain clustered according to N, Gn, and large gene sequences, which suggests that each RNA segment had a different evolutionary history and that the classification in genotypes must consider the genetic information for all genetic segments. Finally, time-scale analysis based on the N gene showed that OROV emerged in Brazil ≈223 years ago and that genotype I (based on N gene data) was responsible for the emergence of all other genotypes and for virus dispersal.

Tawny owl (Strix aluco) as a potential transmitter of Enterobacteriaceae epidemiologically relevant for forest service workers, nature protection service and ornithologists.

PubMed

Grzywaczewski, Grzegorz; Kowalczyk-Pecka, Danuta; Cios, Szymon; Bojar, Wiktor; Jankuszew, Andrzej; Bojar, Hubert; Kolejko, Marcin

2017-03-31

Established taxa within the Enterobacteriaceae wereisolated from cloacal swabs of Strix aluco chicks in nest boxes located at five research sites. ChromID ESBL medium (bioMerieux) was used to select a pool of Enterobacteriaceae strains producing extended-spectrum beta-lactamases. Drug sensitivity of the chosen strains was determined from the full pool of Enterobacteriaceae to 6 chemotherapeutics of different mechanisms of action. The study evaluated the sensitivity of ESBL-synthesizing isolates to substances belonging to penicillins, cephalosporins, cephamycins, clavams, carbapenems and monobactams. Analysis of the results indicated a potential role of Strix aluco in the dissemination of epidemiologically-relevant Enterobacteriaceae, and, importantly, pose health risks to forest service workers, nature protection service and ornithologists. The results can also serve as the basis for further environmental studies.

Application of Pulsed-Field Gel Electrophoresis and Binary Typing as Tools in Veterinary Clinical Microbiology and Molecular Epidemiologic Analysis of Bovine and Human Staphylococcus aureus Isolates

PubMed Central

Zadoks, Ruth; van Leeuwen, Willem; Barkema, Herman; Sampimon, Otlis; Verbrugh, Henri; Schukken, Ynte Hein; van Belkum, Alex

2000-01-01

Thirty-eight bovine mammary Staphylococcus aureus isolates from diverse clinical, temporal, and geographical origins were genotyped by pulsed-field gel electrophoresis (PFGE) after SmaI digestion of prokaryotic DNA and by means of binary typing using 15 strain-specific DNA probes. Seven pulsed-field types and four subtypes were identified, as were 16 binary types. Concordant delineation of genetic relatedness was documented by both techniques, yet based on practical and epidemiological considerations, binary typing was the preferable method. Genotypes of bovine isolates were compared to 55 previously characterized human S. aureus isolates through cluster analysis of binary types. Genetic clusters containing strains of both human and bovine origin were found, but bacterial genotypes were predominantly associated with a single host species. Binary typing proved an excellent tool for comparison of S. aureus strains, including methicillin-resistant S. aureus, derived from different host species and from different databases. For 28 bovine S. aureus isolates, detailed clinical observations in vivo were compared to strain typing results in vitro. Associations were found between distinct genotypes and severity of disease, suggesting strain-specific bacterial virulence. Circumstantial evidence furthermore supports strain-specific routes of bacterial dissemination. We conclude that PFGE and binary typing can be successfully applied for genetic analysis of S. aureus isolates from bovine mammary secretions. Binary typing in particular is a robust and simple method and promises to become a powerful tool for strain characterization, for resolution of clonal relationships of bacteria within and between host species, and for identification of sources and transmission routes of bovine S. aureus. PMID:10790124

High-resolution typing of Chlamydia trachomatis: epidemiological and clinical uses.

PubMed

de Vries, Henry J C; Schim van der Loeff, Maarten F; Bruisten, Sylvia M

2015-02-01

A state-of-the-art overview of molecular Chlamydia trachomatis typing methods that are used for routine diagnostics and scientific studies. Molecular epidemiology uses high-resolution typing techniques such as multilocus sequence typing, multilocus variable number of tandem repeats analysis, and whole-genome sequencing to identify strains based on their DNA sequence. These data can be used for cluster, network and phylogenetic analyses, and are used to unveil transmission networks, risk groups, and evolutionary pathways. High-resolution typing of C. trachomatis strains is applied to monitor treatment efficacy and re-infections, and to study the recent emergence of lymphogranuloma venereum (LGV) amongst men who have sex with men in high-income countries. Chlamydia strain typing has clinical relevance in disease management, as LGV needs longer treatment than non-LGV C. trachomatis. It has also led to the discovery of a new variant Chlamydia strain in Sweden, which was not detected by some commercial C. trachomatis diagnostic platforms. After a brief history and comparison of the various Chlamydia typing methods, the applications of the current techniques are described and future endeavors to extend scientific understanding are formulated. High-resolution typing will likely help to further unravel the pathophysiological mechanisms behind the wide clinical spectrum of chlamydial disease.

Identification and pathogenicity of Vibrio ponticus affecting cultured Japanese sea bass, Lateolabrax japonicus (Cuvier in Cuvier and Valenciennes).

PubMed

Xie, Z Y; Hu, C Q; Zhang, L P; Chen, C; Ren, C H; Shen, Q

2007-07-01

To rapidly determine the causative agent of mass death in Lateolabrax japonicus in Zhelin Bay of Guangdong Province in China in April 2004. Thirty-six strains, numbered sequentially from RP01 to RP36, were isolated from six diseased fish. All of the strains were identified as being of the same vibrio species according to the results of universal primer PCR combined with DGGE (UPPCR-DGGE). RP30 was one of these strains that was randomly selected and analysed by using a morphological, physiological and biochemical plate, Biolog GN2 Microplate System and API 20E system. Furthermore, RP30' 16S rDNA was sequenced and aligned in Genbank. Its virulence to Lateolabrax japonicus (Cuvier in Cuvier and Valenciennes) was also tested. RP30 is most closely related to four Vibrio ponticus strains (99.3% similarity). LD50s were 2.5 (x103 CFU per fish for intraperitoneal inoculation (IP) and 3.2 (x103 CFU per fish for intramuscular inoculation (IM), respectively. The investigated pathogenic agent of Lateolabrax japonicus (Cuvier in Cuvier and Valenciennes) was V. ponticus. UPPCR-DGGE is very helpful in epidemiologic investigation. Interestingly, this is the first report that V. ponticus infects cultured marine fish. DGGE was likewise first introduced to epidemiologic investigation of fish disease.

Spoligotyping of Mycobacterium tuberculosis isolates at a tertiary care hospital in India.

PubMed

Suzana, Shirly; Shanmugam, Sivakumar; Uma Devi, K R; Swarna Latha, P N; Michael, Joy S

2017-06-01

Spoligotyping is a valuable genotyping tool to study the genetic diversity and molecular epidemiology of Mycobacterium tuberculosis (M. tb). The aim of this study was to analyse different spoligotype patterns of M. tb strains isolated from patients with tuberculosis from different parts of India. A total of 163 M. tb isolates were spoligotyped between January 2014 and January 2015. About 47% (n = 77) were from patients with extrapulmonary tuberculosis; of these, 10 were MDR, and seven were Pre-XDR. Of the 86 M. tb isolates from patients with pulmonary tuberculosis, 25 were MDR, and 25 were Pre-XDR. We found 61 spoligo patterns, 128 clusters in the spoligotype data base (spoldb4 data base) with spoligo international type (SIT) number and 35 true unique isolates. The most pre-dominant spoligotype was EAI lineage (56), followed by Beijing (28), CAS (20), T(9), U(7), X(3), H(3), BOVIS_1 BCG(1) and LAM(1). Although our study identified EAI, CAS and Beijing strain lineages as pre-dominant, we also found a large number of orphan strains (20%) in our study. Beijing strains were more significantly associated with MDR TB than CAS and EAI lineages. Further studies on large sample sizes would help to clearly describe the epidemiology of M. tb in India. © 2017 John Wiley & Sons Ltd.

[Epidemiological profile and antibiotic resistance of Pseudomonas aeruginosa isolates in burn and traumatology center in Tunisia over a three-year period].

PubMed

Zoghlami, Ayoub; Kanzari, Lamia; Boukadida, Jalel; Messadi, Amen Allah; Ghanem, Abdelraouef

2012-11-01

Pseudomonas aeruginosa is a known opportunistic pathogen frequently causing serious infections in burned patients. To analyze the epidemiological profile of Pseudomonas aeruginosa isolated in a Tunisian burn unit. During a 3-year period (from 01 July 2008 to 30 June 2011), 544 non repetitive strains of P. aeruginosa were isolated from burn patients. Susceptibility to antibiotics was assessed according to CA-SFM guidelines. Serotypes were identified by slide agglutination test using P.aeruginosa O antisera (Biorad). Producing carbapenemase was analyzed for 202 imipenem resistant isolates by EDTA test. Susceptibility testing data were stored in a laboratory data base using whonet 5.3 software. The most frequent sites of isolation were cutaneous infections and blood cultures (83.4%). The percentages of resistant isolates were as follows: ceftazidime: 34%; imipenem: 37.1%, ciprofloxacin: 27.1% and amikacin: 29.6%. The most prevalent serotypes were: 011(51%), 06(17%), 03 (8%), 04(12%), 012(5%). Among the 202 imipenem resistant strains, 58% expressed a metallocarbapenemase. All theses strains were resistant to all tested antibiotics except colistin and belonged to the serotype O11. The dissemination of carbapenemases strains must be contained by implementation of timely identification, strict isolation methods and better hygienic procedures.

Bacterial genomics reveal the complex epidemiology of an emerging pathogen in arctic and boreal ungulates

USGS Publications Warehouse

Forde, Taya L.; Orsel, Karin; Zadoks, Ruth N.; Biek, Roman; Adams, Layne G.; Checkley, Sylvia L.; Davison, Tracy; De Buck, Jeroen; Dumond, Mathieu; Elkin, Brett T.; Finnegan, Laura; Macbeth, Bryan J.; Nelson, Cait; Niptanatiak, Amanda; Sather, Shane; Schwantje, Helen M.; van der Meer, Frank; Kutz, Susan J.

2016-01-01

Northern ecosystems are currently experiencing unprecedented ecological change, largely driven by a rapidly changing climate. Pathogen range expansion, and emergence and altered patterns of infectious disease, are increasingly reported in wildlife at high latitudes. Understanding the causes and consequences of shifting pathogen diversity and host-pathogen interactions in these ecosystems is important for wildlife conservation, and for indigenous populations that depend on wildlife. Among the key questions are whether disease events are associated with endemic or recently introduced pathogens, and whether emerging strains are spreading throughout the region. In this study, we used a phylogenomic approach to address these questions of pathogen endemicity and spread for Erysipelothrix rhusiopathiae, an opportunistic multi-host bacterial pathogen associated with recent mortalities in arctic and boreal ungulate populations in North America. We isolated E. rhusiopathiae from carcasses associated with large-scale die-offs of muskoxen in the Canadian Arctic Archipelago, and from contemporaneous mortality events and/or population declines among muskoxen in northwestern Alaska and caribou and moose in western Canada. Bacterial genomic diversity differed markedly among these locations; minimal divergence was present among isolates from muskoxen in the Canadian Arctic, while in caribou and moose populations, strains from highly divergent clades were isolated from the same location, or even from within a single carcass. These results indicate that mortalities among northern ungulates are not associated with a single emerging strain of E. rhusiopathiae, and that alternate hypotheses need to be explored. Our study illustrates the value and limitations of bacterial genomic data for discriminating between ecological hypotheses of disease emergence, and highlights the importance of studying emerging pathogens within the broader context of environmental and host factors.

Genotypic and Phenotypic Properties of Cattle-Associated Campylobacter and Their Implications to Public Health in the USA

PubMed Central

Sanad, Yasser M.; Kassem, Issmat I.; Abley, Melanie; Gebreyes, Wondwossen; LeJeune, Jeffrey T.; Rajashekara, Gireesh

2011-01-01

Since cattle are a major source of food and the cattle industry engages people from farms to processing plants and meat markets, it is conceivable that beef-products contaminated with Campylobacter spp. would pose a significant public health concern. To better understand the epidemiology of cattle-associated Campylobacter spp. in the USA, we characterized the prevalence, genotypic and phenotypic properties of these pathogens. Campylobacter were detected in 181 (19.2%) out of 944 fecal samples. Specifically, 71 C. jejuni, 132 C. coli, and 10 other Campylobacter spp. were identified. The prevalence of Campylobacter varied regionally and was significantly (P<0.05) higher in fecal samples collected from the South (32.8%) as compared to those from the North (14.8%), Midwest (15.83%), and East (12%). Pulsed Field Gel Electrophoresis (PFGE) analysis showed that C. jejuni and C. coli isolates were genotypically diverse and certain genotypes were shared across two or more of the geographic locations. In addition, 13 new C. jejuni and two C. coli sequence types (STs) were detected by Multi Locus Sequence Typing (MLST). C. jejuni associated with clinically human health important sequence type, ST-61 which was not previously reported in the USA, was identified in the present study. Most frequently observed clonal complexes (CC) were CC ST-21, CC ST-42, and CC ST-61, which are also common in humans. Further, the cattle associated C. jejuni strains showed varying invasion and intracellular survival capacity; however, C. coli strains showed a lower invasion and intracellular survival potential compared to C. jejuni strains. Furthermore, many cattle associated Campylobacter isolates showed resistance to several antimicrobials including ciprofloxacin, erythromycin, and gentamicin. Taken together, our results highlight the importance of cattle as a potential reservoir for clinically important Campylobacter. PMID:22046247

The clinical and molecular epidemiology of Staphylococcus aureus infections in Fiji.

PubMed

Jenney, Adam; Holt, Deborah; Ritika, Roselyn; Southwell, Paul; Pravin, Shalini; Buadromo, Eka; Carapetis, Jonathan; Tong, Steven; Steer, Andrew

2014-03-24

There are few data describing the microbiology and genetic typing of Staphylococcus aureus that cause infections in developing countries. In this study we observed S. aureus infections in Pacific Island nation of Fiji in both the community and hospital setting with an emphasis on clonal complex (CC) genotyping and antimicrobial susceptibility. S. aureus was commonly found in impetigo lesions of school children and was recovered from 57% of impetigo lesions frequently in conjunction with group A streptococcal infection. Methicillin-resistant S. aureus (MRSA) comprised 7% (20/299) of isolates and were all non-multi-resistant and all genotyped as CC1. In contrast, there was a diverse selection of 17 CCs among the 105 genotyped methicillin-susceptible S.aureus (MSSA) strains. Isolates of the rare, phylogenetically divergent and non-pigmented CC75 lineage (also called S. argenteus) were found in Fiji.From hospitalized patients the available 36 MRSA isolates from a 9-month period were represented by five CCs. The most common CCs were CC1 and CC239. CC1 is likely to be a community-acquired strain, reflecting what was found in the school children, whereas the CC239 is the very successful multi-drug resistant MRSA nosocomial lineage. Of 17 MSSA isolates, 59% carried genes for Panton-Valentine leukocidin. The S. aureus bacteraemia incidence rate of 50 per 100,000 population is among the highest reported in the literature and likely reflects the high overall burden of staphylococcal infections in this population. S. aureus is an important cause of disease in Fiji and there is considerable genotypic diversity in community skin infections in Fijian schoolchildren. Community acquired- (CA)- MRSA is present at a relatively low prevalence (6.7%) and was solely to CC1 (CA-MRSA). The globally successful CC239 is also a significant pathogen in Fiji.

Emergence of carbapenem non-susceptible multidrug resistant Acinetobacter baumannii strains of clonal complexes 103(B) and 92(B) harboring OXA-type carbapenemases and metallo-β-lactamases in Southern India.

PubMed

Saranathan, Rajagopalan; Vasanth, Vaidyanathan; Vasanth, Thamodharan; Shabareesh, Pidathala Raghavendra Venkata; Shashikala, P; Devi, Chandrakesan Sheela; Kalaivani, Ramakrishnan; Asir, Johny; Sudhakar, Pagal; Prashanth, K

2015-05-01

The molecular epidemiology and carbapenem resistance mechanisms of clinical isolates of Acinetobacter baumannii obtained from a south Indian tertiary care hospital were investigated by repetitive extragenic palindromic sequence PCR (REP-PCR) and multi-locus sequence typing (MLST). Analysis of resistant determinants was achieved by PCR screening for the presence of genes encoding OXA-carbapenemases, metallo-β-lactamases (MBLs) and efflux pumps. REP-PCR generated around eight clusters of high heterogeneity; of these, two major clusters (I and V) appeared to be clonal in origin. Analysis of representative isolates from different clusters by MLST revealed that most of the isolates belonged to sequence type 103 of CC103(B) . Second most prevalent ST belonged to clonal complex (CC) 92(B) which is also referred to as international clone II. Most of the isolates were multi-drug resistant, being susceptible only to polymyxin-B and newer quinolones. Class D β-lactamases such as blaOXA-51-like (100%), blaOXA-23-like (56.8%) and blaOXA-24-like (14.8%) were found to be predominant, followed by a class B β-lactamase, namely blaIMP-1 (40.7%); none of the isolates had blaOXA-58 like, blaNDM-1 or blaSIM-1 . Genes of efflux-pump adeABC were predominant, most of isolates being biofilm producers that were PCR-positive for autoinducer synthase gene (>94%). Carbapenem non-susceptible isolates were highly diverse and present throughout the hospital irrespective of type of ward or intensive care unit. Although previous reports have documented diverse resistant mechanisms in A. baumannii, production of MBL and OXA-type of carbapenamases were found to be the predominant mechanism(s) of carbapenem resistance identified in strains isolated from Southern India. © 2015 The Societies and Wiley Publishing Asia Pty Ltd.

Constructing rigorous and broad biosurveillance networks for detecting emerging zoonotic outbreaks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, Mac; Moore, Leslie; McMahon, Benjamin

Determining optimal surveillance networks for an emerging pathogen is difficult since it is not known beforehand what the characteristics of a pathogen will be or where it will emerge. The resources for surveillance of infectious diseases in animals and wildlife are often limited and mathematical modeling can play a supporting role in examining a wide range of scenarios of pathogen spread. We demonstrate how a hierarchy of mathematical and statistical tools can be used in surveillance planning help guide successful surveillance and mitigation policies for a wide range of zoonotic pathogens. The model forecasts can help clarify the complexities ofmore » potential scenarios, and optimize biosurveillance programs for rapidly detecting infectious diseases. Using the highly pathogenic zoonotic H5N1 avian influenza 2006-2007 epidemic in Nigeria as an example, we determined the risk for infection for localized areas in an outbreak and designed biosurveillance stations that are effective for different pathogen strains and a range of possible outbreak locations. We created a general multi-scale, multi-host stochastic SEIR epidemiological network model, with both short and long-range movement, to simulate the spread of an infectious disease through Nigerian human, poultry, backyard duck, and wild bird populations. We chose parameter ranges specific to avian influenza (but not to a particular strain) and used a Latin hypercube sample experimental design to investigate epidemic predictions in a thousand simulations. We ranked the risk of local regions by the number of times they became infected in the ensemble of simulations. These spatial statistics were then complied into a potential risk map of infection. Finally, we validated the results with a known outbreak, using spatial analysis of all the simulation runs to show the progression matched closely with the observed location of the farms infected in the 2006-2007 epidemic.« less

The clinical and molecular epidemiology of Staphylococcus aureus infections in Fiji

PubMed Central

2014-01-01

Background There are few data describing the microbiology and genetic typing of Staphylococcus aureus that cause infections in developing countries. Methods In this study we observed S. aureus infections in Pacific Island nation of Fiji in both the community and hospital setting with an emphasis on clonal complex (CC) genotyping and antimicrobial susceptibility. Results S. aureus was commonly found in impetigo lesions of school children and was recovered from 57% of impetigo lesions frequently in conjunction with group A streptococcal infection. Methicillin-resistant S. aureus (MRSA) comprised 7% (20/299) of isolates and were all non-multi-resistant and all genotyped as CC1. In contrast, there was a diverse selection of 17 CCs among the 105 genotyped methicillin-susceptible S.aureus (MSSA) strains. Isolates of the rare, phylogenetically divergent and non-pigmented CC75 lineage (also called S.argenteus) were found in Fiji. From hospitalized patients the available 36 MRSA isolates from a 9-month period were represented by five CCs. The most common CCs were CC1 and CC239. CC1 is likely to be a community-acquired strain, reflecting what was found in the school children, whereas the CC239 is the very successful multi-drug resistant MRSA nosocomial lineage. Of 17 MSSA isolates, 59% carried genes for Panton-Valentine leukocidin. The S. aureus bacteraemia incidence rate of 50 per 100,000 population is among the highest reported in the literature and likely reflects the high overall burden of staphylococcal infections in this population. Conclusions S. aureus is an important cause of disease in Fiji and there is considerable genotypic diversity in community skin infections in Fijian schoolchildren. Community acquired- (CA)- MRSA is present at a relatively low prevalence (6.7%) and was solely to CC1 (CA-MRSA). The globally successful CC239 is also a significant pathogen in Fiji. PMID:24655406

Constructing rigorous and broad biosurveillance networks for detecting emerging zoonotic outbreaks

DOE PAGES

Brown, Mac; Moore, Leslie; McMahon, Benjamin; ...

2015-05-06

Determining optimal surveillance networks for an emerging pathogen is difficult since it is not known beforehand what the characteristics of a pathogen will be or where it will emerge. The resources for surveillance of infectious diseases in animals and wildlife are often limited and mathematical modeling can play a supporting role in examining a wide range of scenarios of pathogen spread. We demonstrate how a hierarchy of mathematical and statistical tools can be used in surveillance planning help guide successful surveillance and mitigation policies for a wide range of zoonotic pathogens. The model forecasts can help clarify the complexities ofmore » potential scenarios, and optimize biosurveillance programs for rapidly detecting infectious diseases. Using the highly pathogenic zoonotic H5N1 avian influenza 2006-2007 epidemic in Nigeria as an example, we determined the risk for infection for localized areas in an outbreak and designed biosurveillance stations that are effective for different pathogen strains and a range of possible outbreak locations. We created a general multi-scale, multi-host stochastic SEIR epidemiological network model, with both short and long-range movement, to simulate the spread of an infectious disease through Nigerian human, poultry, backyard duck, and wild bird populations. We chose parameter ranges specific to avian influenza (but not to a particular strain) and used a Latin hypercube sample experimental design to investigate epidemic predictions in a thousand simulations. We ranked the risk of local regions by the number of times they became infected in the ensemble of simulations. These spatial statistics were then complied into a potential risk map of infection. Finally, we validated the results with a known outbreak, using spatial analysis of all the simulation runs to show the progression matched closely with the observed location of the farms infected in the 2006-2007 epidemic.« less

Staphylococcus aureus strains associated with food poisoning outbreaks in France: comparison of different molecular typing methods, including MLVA

PubMed Central

Roussel, Sophie; Felix, Benjamin; Vingadassalon, Noémie; Grout, Joël; Hennekinne, Jacques-Antoine; Guillier, Laurent; Brisabois, Anne; Auvray, Fréderic

2015-01-01

Staphylococcal food poisoning outbreaks (SFPOs) are frequently reported in France. However, most of them remain unconfirmed, highlighting a need for a better characterization of isolated strains. Here we analyzed the genetic diversity of 112 Staphylococcus aureus strains isolated from 76 distinct SFPOs that occurred in France over the last 30 years. We used a recently developed multiple-locus variable-number tandem-repeat analysis (MLVA) protocol and compared this method with pulsed field gel electrophoresis (PFGE), spa-typing and carriage of genes (se genes) coding for 11 staphylococcal enterotoxins (i.e., SEA, SEB, SEC, SED, SEE, SEG, SEH, SEI, SEJ, SEP, SER). The strains known to have an epidemiological association with one another had identical MLVA types, PFGE profiles, spa-types or se gene carriage. MLVA, PFGE and spa-typing divided 103 epidemiologically unrelated strains into 84, 80, and 50 types respectively demonstrating the high genetic diversity of S. aureus strains involved in SFPOs. Each MLVA type shared by more than one strain corresponded to a single spa-type except for one MLVA type represented by four strains that showed two different-but closely related-spa-types. The 87 enterotoxigenic strains were distributed across 68 distinct MLVA types that correlated all with se gene carriage except for four MLVA types. The most frequent se gene detected was sea, followed by seg and sei and the most frequently associated se genes were sea-seh and sea-sed-sej-ser. The discriminatory ability of MLVA was similar to that of PFGE and higher than that of spa-typing. This MLVA protocol was found to be compatible with high throughput analysis, and was also faster and less labor-intensive than PFGE. MLVA holds promise as a suitable method for investigating SFPOs and tracking the source of contamination in food processing facilities in real time. PMID:26441849

Mycobacterium tuberculosis population structure and molecular epidemiological analysis in Sucre municipality, Miranda state, Venezuela.

PubMed

Patiño, Margareth A; Abadía, Edgar; Solalba Gómez; Maes, Mailis; Muñoz, Mariana; Gómez, Daniela; Guzmán, Patricia; Méndez, María Victoria; Ramirez, Carmen; Mercedes, España; de Waard, Jacobus; Takiff, Howard

2014-12-01

Sucre municipality is a large, densely populated marginal area in the eastern part of Caracas, Venezuela that consistently has more cases of tuberculosis than other municipalities in the country. To identify the neighborhoods in the municipality with the highest prevalence of tuberculosis, and determine whether the Mycobacterium tuberculosis strain distribution in this municipality is different from that previously found in the western part of Caracas and the rest of Venezuela, we collected data on all tuberculosis cases in the municipality diagnosed in 2005-6. We performed two separate molecular epidemiological studies, spoligotyping 44 strains in a first study, and spoligotyping 131 strains, followed by MIRU-VNTR 15 on 21 clustered isolates in the second. With spoligotyping, the most common patterns were Shared International Type SIT17 (21%); SIT42 (15%); SIT93 (11%); SIT20 (7%); SIT53 (6%), a distribution similar to other parts of Venezuela, except that SIT42 and SIT20 were more common. MIRU-VNTR 15 showed that six of seven SIT17 strains examined belonged to a large cluster previously found circulating in Venezuela, but all of the SIT42 strains were related to a cluster centered in the neighborhoods of Unión and Maca, with a MIRU-VNTR pattern not previously seen in Venezuela. It appears that a large percentage of the tuberculosis in the Sucre municipality is caused by the active transmission of two strain families centered within distinct neighborhoods, one reflecting communication with the rest of the country, and the other suggesting the insular, isolated nature of some sectors.

The incidence of antibiotic resistance and other characteristics amongst Escherichia coli strains causing fatal infection in chickens: the utilization of these characteristics to study the epidemiology of the infection

PubMed Central

Heller, E. D.; Smith, H. Williams

1973-01-01

Of 173 epidemiologically unrelated strains of Escherichia coli isolated from the pericardial sac of chickens that had died from infection with these organisms in England in 1972, approximately 1 year after the introduction of legislation forbidding the routine use of feeds containing `therapeutic' antibiotics, 83·8% were resistant to sulphonamides, 31·2% to tetracyclines, 20·8% to furazolidone, 18·5% to streptomycin, 2·9% to spectinomycin and 1·2% to ampicillin; none of the strains were resistant to chloramphenicol, neomycin, polymixin, trimethoprim or nalidixic acid. The sulphonamide resistance and possibly some of the resistance to other agents might have been the consequence of sulphonamides being exempted from the legislation. Much of the resistance, with the exception of that to furazolidone, was of the transferable type. Many strains possessed transfer factors in the absence of any known transferable characteristic. Colicine production was twice as common in the pathogenic strains as in a collection of strains isolated from the faeces of healthy chickens; about half of it was transferable. By means of serology, antibiotic resistance and other markers, it was found that several different kinds of E. coli were usually incriminated in any one outbreak of E. coli infection in broiler chickens. Sometimes the same kinds of E. coli were found in outbreaks in consecutive crops of chickens on the same farm. New kinds, too, appeared to be brought in by replacement chickens. PMID:4272208

[Molecular strain typing contribution to epidemiology of tuberculosis in Limousin (1998 to 2006)].

PubMed

Bezanahary, H; Baclet, M-C; Sola, C; Gazaille, V; Turlure, P; Weinbreck, P; Denis, F; Martin, C

2008-06-01

We conducted a molecular epidemiology of Mycobacterium tuberculosis in Limousin, a French area with a low incidence of tuberculosis (4.8/100,000 inhabitants in 2005) to define the molecular diversity and the pattern of transmission. Two hundred and fifty-nine strains were isolated (each strain corresponds to one patient) from 1998 to 2006. Both spoligotyping and MIRU15 were chosen for our study because of their discriminatory power. Only 165 medical records were available: 99M/66F, mean age 56.4 years (14-94), 32.7% foreign-born patients, 16.9% homeless or living in shelters, 21.8% of immunocompromised patients (three HIV positive), 14.5% of alcohol addicts. Pulmonary manifestations were predominant (81.8%) with 45.1% of positive smears. Two strains among the 259 presented a multidrug resistance. Spoligotyping identified 136/259 spoligotypes (110 unique, 26 clusters composed of two to 36 isolates); within these 26 clusters, ST53 (n=36) and ST50 (n=19) were the most frequent. Three major families were observed as follow: T1 (30%), Haarlem (30%) and LAM (20%). MIRU15 identified 28/36 isolates in the ST53 group and 14/19 in the ST50 group. Eleven clusters (32 strains) with identical ST-MIRU15 were obtained with a proved case of recent transmission. Alcohol dependence, immunosuppression and pulmonary infections seem to be involved in transmission factors. M. tuberculosis strains isolated in Limousin are characterized by their high genetic diversity. The rate of recent transmission (8.1%) is low and therefore a reactivation process is predominant in this area.

The emergence of translational epidemiology: from scientific discovery to population health impact.

PubMed

Khoury, Muin J; Gwinn, Marta; Ioannidis, John P A

2010-09-01

Recent emphasis on translational research (TR) is highlighting the role of epidemiology in translating scientific discoveries into population health impact. The authors present applications of epidemiology in TR through 4 phases designated T1-T4, illustrated by examples from human genomics. In T1, epidemiology explores the role of a basic scientific discovery (e.g., a disease risk factor or biomarker) in developing a "candidate application" for use in practice (e.g., a test used to guide interventions). In T2, epidemiology can help to evaluate the efficacy of a candidate application by using observational studies and randomized controlled trials. In T3, epidemiology can help to assess facilitators and barriers for uptake and implementation of candidate applications in practice. In T4, epidemiology can help to assess the impact of using candidate applications on population health outcomes. Epidemiology also has a leading role in knowledge synthesis, especially using quantitative methods (e.g., meta-analysis). To explore the emergence of TR in epidemiology, the authors compared articles published in selected issues of the Journal in 1999 and 2009. The proportion of articles identified as translational doubled from 16% (11/69) in 1999 to 33% (22/66) in 2009 (P = 0.02). Epidemiology is increasingly recognized as an important component of TR. By quantifying and integrating knowledge across disciplines, epidemiology provides crucial methods and tools for TR.

The Emergence of Translational Epidemiology: From Scientific Discovery to Population Health Impact

PubMed Central

Khoury, Muin J.; Gwinn, Marta; Ioannidis, John P. A.

2010-01-01

Recent emphasis on translational research (TR) is highlighting the role of epidemiology in translating scientific discoveries into population health impact. The authors present applications of epidemiology in TR through 4 phases designated T1–T4, illustrated by examples from human genomics. In T1, epidemiology explores the role of a basic scientific discovery (e.g., a disease risk factor or biomarker) in developing a “candidate application” for use in practice (e.g., a test used to guide interventions). In T2, epidemiology can help to evaluate the efficacy of a candidate application by using observational studies and randomized controlled trials. In T3, epidemiology can help to assess facilitators and barriers for uptake and implementation of candidate applications in practice. In T4, epidemiology can help to assess the impact of using candidate applications on population health outcomes. Epidemiology also has a leading role in knowledge synthesis, especially using quantitative methods (e.g., meta-analysis). To explore the emergence of TR in epidemiology, the authors compared articles published in selected issues of the Journal in 1999 and 2009. The proportion of articles identified as translational doubled from 16% (11/69) in 1999 to 33% (22/66) in 2009 (P = 0.02). Epidemiology is increasingly recognized as an important component of TR. By quantifying and integrating knowledge across disciplines, epidemiology provides crucial methods and tools for TR. PMID:20688899

Carbon nanotubes (CNTs) based strain sensors for a wearable monitoring and biofeedback system for pressure ulcer prevention and rehabilitation.

PubMed

Boissy, Patrick; Genest, Jonathan; Patenaude, Johanne; Poirier, Marie-Sol; Chenel, Vanessa; Béland, Jean-Pierre; Legault, Georges-Auguste; Bernier, Louise; Tapin, Danielle; Beauvais, Jacques

2011-01-01

This paper presents an overview of the functioning principles of CNTs and their electrical and mechanical properties when used as strain sensors and describes a system embodiment for a wearable monitoring and biofeedback platform for use in pressure ulcer prevention and rehabilitation. Two type of CNTs films (multi-layered CNTs film vs purified film) were characterized electrically and mechanically for potential use as source material. The loosely woven CNTs film (multi-layered) showed substantial less sensitivity than the purified CNTs film but had an almost linear response to stress and better mechanical properties. CNTs have the potential to achieve a much higher sensitivity to strain than other piezoresistors based on regular of conductive particles such as commercially available resistive inks and could become an innovative source material for wearable strain sensors. We are currently continuing the characterization of CNTs based strain sensors and exploring their use in a design for 3-axis strain sensors.

Advances in studies of disease-navigating webs: Sarcoptes scabiei as a case study

PubMed Central

2014-01-01

The discipline of epidemiology is the study of the patterns, causes and effects of health and disease conditions in defined anima populations. It is the key to evidence-based medicine, which is one of the cornerstones of public health. One of the important facets of epidemiology is disease-navigating webs (disease-NW) through which zoonotic and multi-host parasites in general move from one host to another. Epidemiology in this context includes (i) classical epidemiological approaches based on the statistical analysis of disease prevalence and distribution and, more recently, (ii) genetic approaches with approximations of disease-agent population genetics. Both approaches, classical epidemiology and population genetics, are useful for studying disease-NW. However, both have strengths and weaknesses when applied separately, which, unfortunately, is too often current practice. In this paper, we use Sarcoptes scabiei mite epidemiology as a case study to show how important an integrated approach can be in understanding disease-NW and subsequent disease control. PMID:24406101

An ontologically founded architecture for information systems in clinical and epidemiological research.

PubMed

Uciteli, Alexandr; Groß, Silvia; Kireyev, Sergej; Herre, Heinrich

2011-08-09

This paper presents an ontologically founded basic architecture for information systems, which are intended to capture, represent, and maintain metadata for various domains of clinical and epidemiological research. Clinical trials exhibit an important basis for clinical research, and the accurate specification of metadata and their documentation and application in clinical and epidemiological study projects represents a significant expense in the project preparation and has a relevant impact on the value and quality of these studies.An ontological foundation of an information system provides a semantic framework for the precise specification of those entities which are presented in this system. This semantic framework should be grounded, according to our approach, on a suitable top-level ontology. Such an ontological foundation leads to a deeper understanding of the entities of the domain under consideration, and provides a common unifying semantic basis, which supports the integration of data and the interoperability between different information systems.The intended information systems will be applied to the field of clinical and epidemiological research and will provide, depending on the application context, a variety of functionalities. In the present paper, we focus on a basic architecture which might be common to all such information systems. The research, set forth in this paper, is included in a broader framework of clinical research and continues the work of the IMISE on these topics.

Epidemiology of Resistant Microbial Strains Among Different Groups of People (Healthy, Infected and Exposed to Animals)

ClinicalTrials.gov

2017-11-10

ESBL Producing E.Coli; ESBL Producing K.Pneumoniae; Multidrug Resistant P.Aeruginosa; Carbapenem Resistant P.Aeruginosa; Methicillin Resistant Staphylococcus Aureus (MRSA); Vancomycin (Glycopeptide) Resistant Enterococcus (VRE)

Poliovirus strain characterization: a WHO Memorandum*

PubMed Central

1980-01-01

Reliable laboratory techniques for the intratypic characterization of poliovirus types 1, 2, and 3 isolates have an important role in the epidemiological surveillance of poliomyelitis and in studies of the safety and efficacy of poliovirus vaccines. Of the techniques available for poliovirus strain characterization, those potentially most useful are intratypic serodifferentiation and the biochemical techniques. The value of strain-specific (absorbed) antisera for antigenic characterization of strains has been clearly established for the identification of both vaccine-like viruses and different epidemic wild strains. Single-radial-diffusion techniques appear to be promising and should be further explored. Biochemical techniques involving studies of both virus polypeptides and nucleic acids are also capable of providing valuable information for strain characterization. Biological and physico-chemical tests are generally of limited value but their application may be useful in certain circumstances. PMID:6170471

Dynamics of a stochastic multi-strain SIS epidemic model driven by Lévy noise

NASA Astrophysics Data System (ADS)

Chen, Can; Kang, Yanmei

2017-01-01

A stochastic multi-strain SIS epidemic model is formulated by introducing Lévy noise into the disease transmission rate of each strain. First, we prove that the stochastic model admits a unique global positive solution, and, by the comparison theorem, we show that the solution remains within a positively invariant set almost surely. Next we investigate stochastic stability of the disease-free equilibrium, including stability in probability and pth moment asymptotic stability. Then sufficient conditions for persistence in the mean of the disease are established. Finally, based on an Euler scheme for Lévy-driven stochastic differential equations, numerical simulations for a stochastic two-strain model are carried out to verify the theoretical results. Moreover, numerical comparison results of the stochastic two-strain model and the deterministic version are also given. Lévy noise can cause the two strains to become extinct almost surely, even though there is a dominant strain that persists in the deterministic model. It can be concluded that the introduction of Lévy noise reduces the disease extinction threshold, which indicates that Lévy noise may suppress the disease outbreak.

Oligonucleotide (GTG)5 as a marker for Mycobacterium tuberculosis strain identification.

PubMed Central

Wiid, I J; Werely, C; Beyers, N; Donald, P; van Helden, P D

1994-01-01

Culture of Mycobacterium tuberculosis provides no information on the identity of a strain or the distribution of such a strain in the community. Strain identification of M. tuberculosis can help to address important epidemiological questions, e.g., the origin of an infection in a patient's household or community, whether reactivation of infection is endogenous or exogenous in origin, and the spread and early detection of organisms with acquired antibiotic resistance. To research this problem, strain identification must be reliable and accurate. Although genetic identification techniques already exist, it is valuable to have genetic identification techniques based on a number of genetic markers to improve the accurate identification of M. tuberculosis strains. We show that oligonucleotide (GTG)5 can be successfully applied to the identification of M. tuberculosis strains. This technique may be particularly useful in cases in which M. tuberculosis strains have few or no insertion elements (e.g., IS6110) or in identifying other strains of mycobacteria when informative probes are lacking. Images PMID:7914207

In Search of Multi-Peaked Reflective Spectrum with Optic Fiber Bragg Grating Sensor for Dynamic Strain Measurement

NASA Technical Reports Server (NTRS)

Tai, Hsiang

2006-01-01

In a typical optic fiber Bragg grating (FBG) strain measurement, unless in an ideal static laboratory environment, the presence of vibration or often disturbance always exists, which often creates spurious multiple peaks in the reflected spectrum, resulting in a non-unique determination of strain value. In this report we attempt to investigate the origin of this phenomenon by physical arguments and simple numerical simulation. We postulate that the fiber gratings execute small amplitude transverse vibrations changing the optical path in which the reflected light traverses slightly and non-uniformly. Ultimately, this causes the multi-peak reflected spectrum.

Inter- and intracontinental migrations and local differentiation have shaped the contemporary epidemiological landscape of canine parvovirus in South America

PubMed Central

Grecco, Sofía; Iraola, Gregorio; Decaro, Nicola; Alfieri, Alice; Alfieri, Amauri; Gallo Calderón, Marina; da Silva, Ana Paula; Name, Daniela; Aldaz, Jaime; Calleros, Lucía; Marandino, Ana; Tomás, Gonzalo; Maya, Leticia; Francia, Lourdes; Panzera, Yanina; Pérez, Ruben

2018-01-01

Abstract Canine parvovirus (CPV) is a fast-evolving single-stranded DNA virus that causes one of the most significant infectious diseases of dogs. Although the virus dispersed over long distances in the past, current populations are considered to be spatially confined and with only a few instances of migration between specific localities. It is unclear whether these dynamics occur in South America where global studies have not been performed. The aim of this study is to analyze the patterns of genetic variability in South American CPV populations and explore their evolutionary relationships with global strains. Genomic sequences of sixty-three strains from South America and Europe were generated and analyzed using a phylodynamic approach. All the obtained strains belong to the CPV-2a lineage and associate with global strains in four monophyletic groups or clades. European and South American strains from all the countries here analyzed are representative of a widely distributed clade (Eur-I) that emerged in Southern Europe during 1990–98 to later spread to South America in the early 2000s. The emergence and spread of the Eur-I clade were correlated with a significant rise in the CPV effective population size in Europe and South America. The Asia-I clade includes strains from Asia and Uruguay. This clade originated in Asia during the late 1980s and evolved locally before spreading to South America during 2009–10. The third clade (Eur-II) comprises strains from Italy, Brazil, and Ecuador. This clade appears in South America as a consequence of an early introduction from Italy to Ecuador in the middle 1980s and has experienced extensive local genetic differentiation. Some strains from Argentina, Uruguay, and Brazil constitute an exclusive South American clade (SA-I) that emerged in Argentina in the 1990s. These results indicate that the current epidemiological scenario is a consequence of inter- and intracontinental migrations of strains with different geographic and temporal origins that set the conditions for competition and local differentiation of CPV populations. The coexistence and interaction of highly divergent strains are the main responsible for the drastic epidemiological changes observed in South America in the last two decades. This highlights the threat of invasion from external sources and the importance of whole-genome resolution to robustly infer the origin and spread of new CPV variants. From a taxonomic standpoint, the findings herein show that the classification system that uses a single amino acid to identify variants (2a, 2b, and 2c) within the CPV-2a lineage does not reflect phylogenetic relationships and is not suitable to analyze CPV evolution. In this regard, the identification of clades or sublineages within circulating CPV strains is the first step towards a genetic and evolutionary classification of the virus. PMID:29657837

Inter- and intracontinental migrations and local differentiation have shaped the contemporary epidemiological landscape of canine parvovirus in South America.

PubMed

Grecco, Sofía; Iraola, Gregorio; Decaro, Nicola; Alfieri, Alice; Alfieri, Amauri; Gallo Calderón, Marina; da Silva, Ana Paula; Name, Daniela; Aldaz, Jaime; Calleros, Lucía; Marandino, Ana; Tomás, Gonzalo; Maya, Leticia; Francia, Lourdes; Panzera, Yanina; Pérez, Ruben

2018-01-01

Canine parvovirus (CPV) is a fast-evolving single-stranded DNA virus that causes one of the most significant infectious diseases of dogs. Although the virus dispersed over long distances in the past, current populations are considered to be spatially confined and with only a few instances of migration between specific localities. It is unclear whether these dynamics occur in South America where global studies have not been performed. The aim of this study is to analyze the patterns of genetic variability in South American CPV populations and explore their evolutionary relationships with global strains. Genomic sequences of sixty-three strains from South America and Europe were generated and analyzed using a phylodynamic approach. All the obtained strains belong to the CPV-2a lineage and associate with global strains in four monophyletic groups or clades. European and South American strains from all the countries here analyzed are representative of a widely distributed clade (Eur-I) that emerged in Southern Europe during 1990-98 to later spread to South America in the early 2000s. The emergence and spread of the Eur-I clade were correlated with a significant rise in the CPV effective population size in Europe and South America. The Asia-I clade includes strains from Asia and Uruguay. This clade originated in Asia during the late 1980s and evolved locally before spreading to South America during 2009-10. The third clade (Eur-II) comprises strains from Italy, Brazil, and Ecuador. This clade appears in South America as a consequence of an early introduction from Italy to Ecuador in the middle 1980s and has experienced extensive local genetic differentiation. Some strains from Argentina, Uruguay, and Brazil constitute an exclusive South American clade (SA-I) that emerged in Argentina in the 1990s. These results indicate that the current epidemiological scenario is a consequence of inter- and intracontinental migrations of strains with different geographic and temporal origins that set the conditions for competition and local differentiation of CPV populations. The coexistence and interaction of highly divergent strains are the main responsible for the drastic epidemiological changes observed in South America in the last two decades. This highlights the threat of invasion from external sources and the importance of whole-genome resolution to robustly infer the origin and spread of new CPV variants. From a taxonomic standpoint, the findings herein show that the classification system that uses a single amino acid to identify variants (2a, 2b, and 2c) within the CPV-2a lineage does not reflect phylogenetic relationships and is not suitable to analyze CPV evolution. In this regard, the identification of clades or sublineages within circulating CPV strains is the first step towards a genetic and evolutionary classification of the virus.

Centers of Excellence on Environmental Health Disparities Research

EPA Pesticide Factsheets

collaborative effort that encourages basic, biological, clinical, epidemiological, behavioral, and/or social scientific investigations of disease conditions that are known to be a significant burden in low socioeconomic and health disparate populations

12th International Conference on Malignancies in AIDS and Other Acquired Immunodeficiencies

Cancer.gov

Summary of speakers and events from the 2010 ICMAOI conference, focused on presenting basic, epidemiologic, and clinical aspects of research on malignancies in HIV-infected and other immunosuppressed individuals.

Rivaroxaban to Prevent Pulmonary Embolism after Hip or Knee Replacement

MedlinePlus

... Customer Service and Ordering Information Subscribe to AHA Journals All Issues Subjects All Subjects Arrhythmia and Electrophysiology Basic, Translational, and Clinical Research Critical Care and Resuscitation Epidemiology, Lifestyle, and Prevention ...

8th International Conference on Malignancies in AIDS and Other Immunodeficiencies

Cancer.gov

Program guide of speakers and events from the 2004 ICMAOI conference, focused on presenting basic, epidemiologic, and clinical aspects of research on malignancies in HIV-infected and other immunosuppressed individuals.

13th International Conference on Malignancies in AIDS and Other Acquired Immunodeficiencies

Cancer.gov

Summary of speakers and events from the 2011 ICMAOI conference, focused on presenting basic, epidemiologic, and clinical aspects of research on malignancies in HIV-infected and other immunosuppressed individuals.

Final Technical Report for Award # ER64999

DOE Office of Scientific and Technical Information (OSTI.GOV)

Metcalf, William W.

2014-10-08

This report provides a summary of activities for Award # ER64999, a Genomes to Life Project funded by the Office of Science, Basic Energy Research. The project was entitled "Methanogenic archaea and the global carbon cycle: a systems biology approach to the study of Methanosarcina species". The long-term goal of this multi-investigator project was the creation of integrated, multiscale models that accurately and quantitatively predict the role of Methanosarcina species in the global carbon cycle under dynamic environmental conditions. To achieve these goals we pursed four specific aims: (1) genome sequencing of numerous members of the Order Methanosarcinales, (2) identificationmore » of genomic sources of phenotypic variation through in silico comparative genomics, (3) elucidation of the transcriptional networks of two Methanosarcina species, and (4) development of comprehensive metabolic network models for characterized strains to address the question of how metabolic models scale with genetic distance.« less

Bioreactor concepts for cell culture-based viral vaccine production.

PubMed

Gallo-Ramírez, Lilí Esmeralda; Nikolay, Alexander; Genzel, Yvonne; Reichl, Udo

2015-01-01

Vaccine manufacturing processes are designed to meet present and upcoming challenges associated with a growing vaccine market and to include multi-use facilities offering a broad portfolio and faster reaction times in case of pandemics and emerging diseases. The final products, from whole viruses to recombinant viral proteins, are very diverse, making standard process strategies hardly universally applicable. Numerous factors such as cell substrate, virus strain or expression system, medium, cultivation system, cultivation method, and scale need consideration. Reviewing options for efficient and economical production of human vaccines, this paper discusses basic factors relevant for viral antigen production in mammalian cells, avian cells and insect cells. In addition, bioreactor concepts, including static systems, single-use systems, stirred tanks and packed-beds are addressed. On this basis, methods towards process intensification, in particular operational strategies, the use of perfusion systems for high product yields, and steps to establish continuous processes are introduced.

Epidemics with pathogen mutation on small-world networks

NASA Astrophysics Data System (ADS)

Shao, Zhi-Gang; Tan, Zhi-Jie; Zou, Xian-Wu; Jin, Zhun-Zhi

2006-05-01

We study the dynamical behavior of the epidemiological model with pathogen mutation on small-world networks, and discuss the influence of the immunity duration τR, the cross-immunity threshold hthr, and system size N on epidemic dynamics. A decaying oscillation occurs because of the interplay between the immune response and the pathogen mutation. These results have implications for the interpretation of longitudinal epidemiological data on strain abundance, and they will be helpful to assess the threat of highly pathogenic and mutative viruses, such as avian influenza.

Strengths and limitations of molecular subtyping in a community outbreak of Legionnaires' disease.

PubMed

Kool, J L; Buchholz, U; Peterson, C; Brown, E W; Benson, R F; Pruckler, J M; Fields, B S; Sturgeon, J; Lehnkering, E; Cordova, R; Mascola, L M; Butler, J C

2000-12-01

An epidemiological and microbiological investigation of a cluster of eight cases of Legionnaires' disease in Los Angeles County in November 1997 yielded conflicting results. The epidemiological part of the investigation implicated one of several mobile cooling towers used by a film studio in the centre of the outbreak area. However, water sampled from these cooling towers contained L. pneumophila serogroup 1 of another subtype than the strain that was recovered from case-patients in the outbreak. Samples from two cooling towers located downwind from all of the case-patients contained a Legionella strain that was indistinguishable from the outbreak strain by four subtyping techniques (AP-PCR, PFGE, MAb, and MLEE). It is unlikely that these cooling towers were the source of infection for all the case-patients, and they were not associated with risk of disease in the case-control study. The outbreak strain also was not distinguishable, by three subtyping techniques (AP-PCR, PFGE, and MAb), from a L. pneumophila strain that had caused an outbreak in Providence, RI, in 1993. Laboratory cross-contamination was unlikely because the initial subtyping was done in different laboratories. In this investigation, microbiology was helpful for distinguishing the outbreak cluster from unrelated cases of Legionnaires' disease occurring elsewhere. However, multiple subtyping techniques failed to distinguish environmental sources that were probably not associated with the outbreak. Persons investigating Legionnaires' disease outbreaks should be aware that microbiological subtyping does not always identify a source with absolute certainty.

An agent-based modeling framework linking inflammation and cancer using evolutionary principles: description of a generative hierarchy for the hallmarks of cancer and developing a bridge between mechanism and epidemiological data.

PubMed

An, Gary; Kulkarni, Swati

2015-02-01

Inflammation plays a critical role in the development and progression of cancer, evident in multiple patient populations manifesting increased, non-resolving inflammation, such as inflammatory bowel disease, viral hepatitis and obesity. Given the complexity of both the inflammatory response and the process of oncogenesis, we utilize principles from the field of Translational Systems Biology to bridge the gap between basic mechanistic knowledge and clinical/epidemiologic data by integrating inflammation and oncogenesis within an agent-based model, the Inflammation and Cancer Agent-based Model (ICABM). The ICABM utilizes two previously published and clinically/epidemiologically validated mechanistic models to demonstrate the role of an increased inflammatory milieu on oncogenesis. Development of the ICABM required the creation of a generative hierarchy of the basic hallmarks of cancer to provide a foundation to ground the plethora of molecular and pathway components currently being studied. The ordering schema emphasizes the essential role of a fitness/selection frame shift to sub-organismal evolution as a basic property of cancer, where the generation of genetic instability as a negative effect for multicellular eukaryotic organisms represents the restoration of genetic plasticity used as an adaptive strategy by colonies of prokaryotic unicellular organisms. Simulations with the ICABM demonstrate that inflammation provides a functional environmental context that drives the shift to sub-organismal evolution, where increasingly inflammatory environments led to increasingly damaged genomes in microtumors (tumors below clinical detection size) and cancers. The flexibility of this platform readily facilitates tailoring the ICABM to specific cancers, their associated mechanisms and available epidemiological data. One clinical example of an epidemiological finding that could be investigated with this platform is the increased incidence of triple negative breast cancers in the premenopausal African-American population, which has been identified as having up-regulated of markers of inflammation. The fundamental nature of the ICABM suggests its usefulness as a base platform upon which additional molecular detail could be added as needed. Copyright © 2014 Elsevier Inc. All rights reserved.

Central line-associated bloodstream infection in a trauma intensive care unit: impact of implementation of Society for Healthcare Epidemiology of America/Infectious Diseases Society of America practice guidelines.

PubMed

Mazi, Waleed; Begum, Zikra; Abdulla, Diaa; Hesham, Ahmed; Maghari, Sami; Assiri, Abdullah; Senok, Abiola

2014-08-01

This study aimed to assess the impact implementation of the basic Society for Healthcare Epidemiology of America/Infectious Diseases Society of America (SHEA/IDSA) practice recommendations in reducing central line-associated bloodstream infection (CLABSI) in intensive care units (ICUs). The prospective study was conducted from January 2011-December 2012 at the 23-bed trauma ICU in Saudi Arabia. The basic SHEA/IDSA practice recommendations were introduced and implemented during the year 2012. Laboratory-confirmed CLABSIs were identified, and the antimicrobial susceptibility of isolates was determined. Data were collected and analyzed for benchmarking with the National Healthcare Safety Network. There was a 58% decline in the CLABSI incidence rate from 3.87 to 1.5 per 1,000 central line days in 2011 and 2012, respectively (standardized infection ratio, 0.42; P = .043). Three institutional risk factors were identified and resolved: health care personnel education, removal of nonessential catheters, and use of a catheter cart. Three Klebsiella pneumoniae isolates susceptible only to imipenem, 1 pandrug resistant Acinetobacter baumannii, and 2 Enterococcus faecalis, with 1 isolate resistant to vancomycin, were identified in 2012. The basic SHEA/ISDA practice recommendation is an effective prevention model for the reduction of CLABSIs in the ICU. Additional measures are needed to control the spread of multidrug-resistant organisms. Copyright © 2014 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.

"Zero-Mass" Noninvasive Pressure Transducers

NASA Technical Reports Server (NTRS)

Hartley, Frank T.

2009-01-01

Extremely lightweight, compact, noninvasive, rugged, relatively inexpensive strain-gauge transducers have been developed for use in measuring pressures of fluids in tubes. These gauges were originally intended for measuring pressures of spacecraft-propulsion fluids, but they are also attractive for use in numerous terrestrial applications especially those involving fluids that are extremely chemically reactive, fluids that must be isolated for hygienic purposes, fluids that must be allowed to flow without obstruction, and fluid-containing tubes exposed to severe environments. A basic pressure transducer of this type comprises one or more pair(s) of thin-film strain gauges integral with a tube that contains the fluid of interest. Following established strain-gauge practice, the gauges in each pair are connected into opposite arms of a Wheatstone bridge (see figure). Typically, each pressure transducer includes one pair (the active pair) of strain gauges for measuring the hoop stress proportional to the pressure of the fluid in the tube and another pair (the dummy pair) of strain gauges that are nominally unstrained: The dummy gauges are mounted on a substrate that is made of the same material as that of the tube. The substrate is welded to the tube at only one spot so that stresses and strains are not coupled from the tube into the substrate. The dummy strain gauges measure neutral strains (basically, strains associated with thermal expansion), so that the neutral-strain contribution can be subtracted out of the final gauge reading.

Splitting of the neutral mechanical plane depends on the length of the multi-layer structure of flexible electronics.

PubMed

Li, Shuang; Su, Yewang; Li, Rui

2016-06-01

Multi-layer structures with soft (compliant) interlayers have been widely used in flexible electronics and photonics as an effective design for reducing interactions among the hard (stiff) layers and thus avoiding the premature failure of an entire device. The analytic model for bending of such a structure has not been well established due to its complex mechanical behaviour. Here, we present a rational analytic model, without any parameter fitting, to study the bending of a multi-layer structure on a cylinder, which is often regarded as an important approach to mechanical reliability testing of flexible electronics and photonics. For the first time, our model quantitatively reveals that, as the key for accurate strain control, the splitting of the neutral mechanical plane depends not only on the relative thickness of the middle layer, but also on the length-to-thickness ratio of the multi-layer structure. The model accurately captures the key quantities, including the axial strains in the top and bottom layers, the shear strain in the middle layer and the locations of the neutral mechanical planes of the top and bottom layers. The effects of the length of the multi-layer and the thickness of the middle layer are elaborated. This work is very useful for the design of multi-layer structure-based flexible electronics and photonics.

Splitting of the neutral mechanical plane depends on the length of the multi-layer structure of flexible electronics

PubMed Central

Li, Shuang; Li, Rui

2016-01-01

Multi-layer structures with soft (compliant) interlayers have been widely used in flexible electronics and photonics as an effective design for reducing interactions among the hard (stiff) layers and thus avoiding the premature failure of an entire device. The analytic model for bending of such a structure has not been well established due to its complex mechanical behaviour. Here, we present a rational analytic model, without any parameter fitting, to study the bending of a multi-layer structure on a cylinder, which is often regarded as an important approach to mechanical reliability testing of flexible electronics and photonics. For the first time, our model quantitatively reveals that, as the key for accurate strain control, the splitting of the neutral mechanical plane depends not only on the relative thickness of the middle layer, but also on the length-to-thickness ratio of the multi-layer structure. The model accurately captures the key quantities, including the axial strains in the top and bottom layers, the shear strain in the middle layer and the locations of the neutral mechanical planes of the top and bottom layers. The effects of the length of the multi-layer and the thickness of the middle layer are elaborated. This work is very useful for the design of multi-layer structure-based flexible electronics and photonics. PMID:27436977

Early detection and control of an Acinetobacter baumannii multi-resistant outbreak in a hospital in Quito, Ecuador.

PubMed

Cartelle Gestal, Monica; Zurita, Jeannete; Gualpa, Gabriela; Gonzalez, Cecibel; Paz Y Mino, Ariane

2016-12-30

Acinetobacter baumannii (ABA) is an important opportunistic pathogen associated with high mortality rates in intensive care units (ICUs). An outbreak in the ICU of a secondary-level hospital in Quito, Ecuador, occurred during April and May 2015 and was successfully controlled. Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) and repetitive element palindromic (REP)-PCR was conducted on all isolates recovered from patients, as well as environmental samples, to confirm the presence of an outbreak. A case-control study was conducted by comparing the clinical histories of the affected patients and of control patients present in the ICU during the outbreak period who did not present a positive culture for ABA. Five patients were infected and two were colonized with the same clonal strain of ABA, which was also identified on the stethoscope and a monitor associated with an isolation room. Statistical analysis of case histories did not identify any additional risk factors, but the outbreak was initiated by one patient in the isolation room of the ICU who was infected with the outbreak strain. All patients who ocupied that room after the index case tested positive for at least one culture of ABA. The outbreak strain was found on the stethoscope, and a subclone was found on the monitor of that room. Having access to basic equipment will enable well-trained professionals to rapidly detect and initiate the control process of an outbreak, saving lives and money spent on nosocomial infection treatments.

Prevalence of three campylobacter species, C. jejuni, C. coli, and C. lari, using multilocus sequence typing in wild birds of the Mid-Atlantic region, USA.

PubMed

Keller, Judith I; Shriver, W Gregory

2014-01-01

Campylobacter jejuni is responsible for the majority of bacterial foodborne gastroenteritis in the US, usually due to the consumption of undercooked poultry. Research on which avian species transmit the bacterium is limited, especially in the US. We sampled wild birds in three families-Anatidae, Scolopacidae, and Laridae-in eastern North America to determine the prevalence and specific strains of Campylobacter. The overall prevalence of Campylobacter spp. was 9.2% for all wild birds sampled (n = 781). Campylobacter jejuni was the most prevalent species (8.1%), while Campylobacter coli and Campylobacter lari prevalence estimates were low (1.4% and 0.3%, respectively). We used multilocus sequence typing PCR specific to C. jejuni to characterize clonal complexes and sequence types isolated from wild bird samples and detected 13 novel sequence types, along with a clonal complex previously only associated with human disease (ST-658). Wild birds share an increasing amount of habitat with humans as more landscapes become fragmented and developed for human needs. Wild birds are and will remain an important aspect of public health due to their ability to carry and disperse emerging zoonotic pathogens or their arthropod vectors. As basic information such as prevalence is limited or lacking from a majority of wild birds in the US, this study provides further insight into Campylobacter epidemiology, host preference, and strain characterization of C. jejuni.