Science.gov

Sample records for molecular epidemiological study

  1. Usefulness of ribotyping in a molecular epidemiology study of shigellosis.

    PubMed Central

    Mendoza, M. C.; Martín, M. C.; González-Hevia, M. A.

    1996-01-01

    Ribotyping performed with six restriction endonucleases was used to study the molecular epidemiology of shigellosis in Asturias, Spain. The series included Shigella sonnei from 34 sporadic cases, 3 outbreaks and 3 reference strains, and S. Flexneri from sporadic cases and 1 reference strain. The S. sonnei strains were grouped into 5 ribotypes with Sal I, 4 with Hind III and Pvu II, 3 with Bgl II and EcoR I and 2 with Hinc II (Discriminatory Index (DI) between 0.54 and 0.14); the S. flexneri into 5 ribotypes with Sal I, Hinc II and Hind III, and 4 with the other enzymes (DI = 0.71 - 0.63). The combination of results for 2 or more enzymes facilitated and additional discrimination, the highest values in S. sonnei were for the 6 enzymes (16 types, DI = 0.91) and in S. flexneri for some combinations of 3 or more enzymes (7 types, DI = 0.81). Ribotypes with the 6 enzymes defined 16 clonal lines in S. sonnei and 7 in S. flexneri, which showed a different degree of genetic heterogeneity, and all the lines of each species falling into a different cluster. No line appeared as clearly endemic in the bowels of Asturian people. Images Fig. 1 Fig. 2 PMID:8620903

  2. Molecular epidemiological study of dengue virus type 1 in Taiwan.

    PubMed

    Hwang, Kao-Pin; Chu, Pei-Yu; Tung, Yi-Ching; Wang, Heng-Lin; Yueh, Yi-Yun; Wu, Ying-Chang; Chin, Chuan; Lin, Kuei-Hsiang

    2003-07-01

    Taiwan has experienced several major outbreaks of dengue (DEN) virus since 1981. The predominant virus type involved has been dengue virus type one (DEN-1), which first appeared in 1987. To understand the molecular epidemiology of this virus, 15 strains of DEN-1 isolated during 1987-1991 and 1994-1995, including 11 epidemic strains, two sporadic strains, and two imported strains have been studied. Fragments of 490 nucleotides (nt) from the E/NS1 junction were amplified by reverse transcription-polymerase chain reaction and the nt sequences were determined. Of the 490 nt of the E/NS1 junction, 240 nt (nt 2282-2521) were aligned and compared. Nucleotide substitutions were found at 54 positions among 15 isolates. Most nt changes were synonymous substitutions, and only three amino acid changes were found. A total of 61 strains isolated worldwide were analyzed by the Neighbor-joining method, and separated phylogenetically into three distinct genotypes, I-III. Genotype I comprised isolates from Japan and Hawaii collected in the 1940s. Genotype II included most strains isolated from Asia in 1977-1995. Genotype III consisted of isolates from three continents in 1964-1995: Asia, the Americas, and Africa. Genotype III was divided further into two subgenotypes, IIIA and IIIB. Most recent isolates from Taiwan, except for the sporadic strain isolated in 1995, were similar genetically and have been classified as Genotype II. PMID:12767004

  3. Molecular markers for the study of streptococcal epidemiology.

    PubMed

    McMillan, David J; Sanderson-Smith, Martina L; Smeesters, Pierre Robert; Sriprakash, Kadaba S

    2013-01-01

    Diseases caused by Streptococcus pyogenes (Group A streptococcus, GAS) range from superficial infections such as pharyngitis and impetigo to potentially fatal rheumatic heart disease and invasive disease. Studies spanning emm-typing surveillance to population genomics are providing new insights into the epidemiology, pathogenesis, and biology of this organism. Such studies have demonstrated the differences that exist in the epidemiology of streptococcal disease between developing and developed nations. In developing nations, where streptococcal disease is endemic, the diversity of GAS emm-types circulating is much greater than that found in developed nations. An association between emm-type and disease, as observed in developed countries is also lacking. Intriguingly, comparative genetic studies suggest that emm-type is not always a good predictor of the evolutionary relatedness of geographically distant isolates. A view of GAS as a highly dynamic organism, in possession of a core set of virulence genes that contribute to host niche specialization and common pathogenic processes, augmented by accessory genes that change the relative virulence of specific lineages is emerging. Our inability to definitively identify genetic factors that contribute to specific disease outcome underscores the complex nature of streptococcal diseases. PMID:23179674

  4. Molecular Epidemiology of Amebiasis

    PubMed Central

    Ali, Ibne Karim M.; Clark, C. Graham; Petri, William A.

    2008-01-01

    Entamoeba histolytica, the causative agent of human amebiasis, remains a significant cause of morbidity and mortality in developing countries and is responsible for up to 100,000 deaths worldwide each year. Entamoeba dispar, morphologically indistinguishable from E. histolytica, is more common in humans in many parts of the world. Similarly Entamoeba moshkovskii, which was long considered to be a free-living ameba, is also morphologically identical to E. histolytica and E. dispar, and is highly prevalent in some E. histolytica endemic countries. However, the only species to cause disease in humans is E. histolytica. Most old epidemiological data on E. histolytica are unusable as the techniques employed do not differentiate between the above three Entamoeba species. Molecular tools are now available not only to diagnose these species accurately but also to study intra-species genetic diversity. Recent studies suggest that only a minority of all E. histolytica infections progress to development of clinical symptoms in the host and there exist population level differences between the E. histolytica strains isolated from the asymptomatic and symptomatic individuals. Nevertheless the underlying factors responsible for variable clinical outcome of infection by E. histolytica remain largely unknown. We anticipate that the recently completed E. histolytica genome sequence and new molecular techniques will rapidly advance our understanding of the epidemiology and pathogenicity of amebiasis. PMID:18571478

  5. Epidemiological and molecular characteristics of meticillin-resistant Staphylococcus aureus in Turkey: A multicentre study.

    PubMed

    Dündar, Devrim; Willke, Ayse; Sayan, Murat; Koc, Meliha Meric; Akan, Ozay Arıkan; Sumerkan, Bulent; Saltoglu, Nese; Yaman, Akgun; Ayaz, Celal; Koksal, Iftihar

    2016-09-01

    The aim of this study was to investigate the epidemiological and molecular features of clinical meticillin-resistant Staphylococcus aureus (MRSA) isolates in Turkey. MRSA isolates were collected from six regions of Turkey. The mecA and nuc genes were detected by PCR. Antimicrobial susceptibilities were determined by the disk diffusion method. Staphylococcal cassette chromosome mec (SCCmec) and staphylococcal protein A (spa) typing were performed by the sequencing method for 270 randomly selected MRSA isolates. The US Centers for Disease Control and Prevention (CDC) definition was used for epidemiological diagnosis of community-associated MRSA (CA-MRSA). Resistance rates of MRSA to ciprofloxacin, gentamicin, clindamycin, erythromycin, rifampicin, trimethoprim/sulfamethoxazole and tetracycline were 93.4%, 81.2%, 38.5%, 57.8%, 93.9%, 1.1% and 93.1%, respectively. The most frequent SCCmec type was SCCmec III (91.1%). SCCmec type IV was found in 5.2% of the isolates. The most frequent spa type was t030 (81.1%). Five isolates were CA-MRSA if only the epidemiological definition was used (5/725; 0.7%). Two isolates were defined as CA-MRSA both by epidemiological features and SCCmec typing (2/270; 0.7%). Of 14 SCCmec type IV isolates, 12 were not defined as CA-MRSA by epidemiological features. In conclusion, this is the most comprehensive multicentre study in Turkey investigating MRSA using both epidemiological and genotypic features. The CA-MRSA rate is low in Turkey. Combined use of epidemiological and genotypic methods is the most accurate approach for the diagnosis of CA-MRSA. PMID:27530838

  6. A molecular epidemiological study of rabies in Cuba.

    PubMed

    Nadin-Davis, S A; Torres, G; Ribas, M De Los Angeles; Guzman, M; De La Paz, R Cruz; Morales, M; Wandeler, A I

    2006-12-01

    To investigate the emergence and current situation of terrestrial rabies in Cuba, a collection of rabies virus specimens was employed for genetic characterization. These data supported the monophyletic nature of all terrestrial rabies viruses presently circulating in Cuba but additionally delineated several distinct variants exhibiting limited spatial distribution which may reflect the history of rabies spread on the island. The strain of rabies currently circulating in Cuba, which emerged on the island in the early 20th century, has very close evolutionary ties to the Mexican dog type and is a member of the cosmopolitan lineage widely distributed during the colonial period. The Cuban rabies viruses, which circulate predominantly within the mongoose population, are phylogenetically distant from viruses circulating in mongooses in other parts of the world. These studies illustrate, at a global level, the adaptation of multiple strains of rabies to mongoose species which should be regarded as important wildlife hosts for rabies re-emergence. Given the recent emergence of human cases due to bat contact in Cuba, this study also included a single insectivorous bat specimen which was found to most closely resemble the rabies viruses known to circulate in Mexican vampire bats. PMID:16740188

  7. Low-dose ionising radiation and cardiovascular diseases--Strategies for molecular epidemiological studies in Europe.

    PubMed

    Kreuzer, Michaela; Auvinen, Anssi; Cardis, Elisabeth; Hall, Janet; Jourdain, Jean-Rene; Laurier, Dominique; Little, Mark P; Peters, Annette; Raj, Ken; Russell, Nicola S; Tapio, Soile; Zhang, Wei; Gomolka, Maria

    2015-01-01

    It is well established that high-dose ionising radiation causes cardiovascular diseases. In contrast, the evidence for a causal relationship between long-term risk of cardiovascular diseases after moderate doses (0.5-5 Gy) is suggestive and weak after low doses (<0.5 Gy). However, evidence is emerging that doses under 0.5 Gy may also increase long-term risk of cardiovascular disease. This would have major implications for radiation protection with respect to medical use of radiation for diagnostic purposes and occupational or environmental radiation exposure. Therefore, it is of great importance to gain information about the presence and possible magnitude of radiation-related cardiovascular disease risk at doses of less than 0.5 Gy. The biological mechanisms implicated in any such effects are unclear and results from epidemiological studies are inconsistent. Molecular epidemiological studies can improve the understanding of the pathogenesis and the risk estimation of radiation-induced circulatory disease at low doses. Within the European DoReMi (Low Dose Research towards Multidisciplinary Integration) project, strategies to conduct molecular epidemiological studies in this field have been developed and evaluated. Key potentially useful European cohorts are the Mayak workers, other nuclear workers, uranium miners, Chernobyl liquidators, the Techa river residents and several diagnostic or low-dose radiotherapy patient cohorts. Criteria for informative studies are given and biomarkers to be investigated suggested. A close collaboration between epidemiology, biology and dosimetry is recommended, not only among experts in the radiation field, but also those in cardiovascular diseases. PMID:26041268

  8. Metabolism and Biomarkers of Heterocyclic Aromatic Amines in Molecular Epidemiology Studies: Lessons Learned from Aromatic Amines

    PubMed Central

    2011-01-01

    Aromatic amines and heterocyclic aromatic amines (HAAs) are structurally related classes of carcinogens that are formed during the combustion of tobacco or during the high-temperature cooking of meats. Both classes of procarcinogens undergo metabolic activation by N-hydroxylation of the exocyclic amine group, to produce a common proposed intermediate, the arylnitrenium ion, which is the critical metabolite implicated in toxicity and DNA damage. However, the biochemistry and chemical properties of these compounds are distinct and different biomarkers of aromatic amines and HAAs have been developed for human biomonitoring studies. Hemoglobin adducts have been extensively used as biomarkers to monitor occupational and environmental exposures to a number of aromatic amines; however, HAAs do not form hemoglobin adducts at appreciable levels and other biomarkers have been sought. A number of epidemiologic studies that have investigated dietary consumption of well-done meat in relation to various tumor sites reported a positive association between cancer risk and well-done meat consumption, although some studies have shown no associations between well-done meat and cancer risk. A major limiting factor in most epidemiological studies is the uncertainty in quantitative estimates of chronic exposure to HAAs and, thus, the association of HAAs formed in cooked meat and cancer risk has been difficult to establish. There is a critical need to establish long-term biomarkers of HAAs that can be implemented in molecular epidemioIogy studies. In this review article, we highlight and contrast the biochemistry of several prototypical carcinogenic aromatic amines and HAAs to which humans are chronically exposed. The biochemical properties and the impact of polymorphisms of the major xenobiotic-metabolizing enzymes on the biological effects of these chemicals are examined. Lastly, the analytical approaches that have been successfully employed to biomonitor aromatic amines and HAAs, and

  9. Molecular epidemiology studies on occupational and environmental exposure to mutagens and carcinogens, 1997-1999.

    PubMed Central

    Srám, R J; Binková, B

    2000-01-01

    Molecular epidemiology is a new and evolving area of research, combining laboratory measurement of internal dose, biologically effective dose, biologic effects, and influence of individual susceptibility with epidemiologic methodologies. Biomarkers evaluated were selected according to basic scheme: biomarkers of exposure--metabolites in urine, DNA adducts, protein adducts, and Comet assay parameters; biomarkers of effect--chromosomal aberrations, sister chromatid exchanges, micronuclei, mutations in the hypoxanthine-guanine phosphoribosyltransferase gene, and the activation of oncogenes coding for p53 or p21 proteins as measured on protein levels; biomarkers of susceptibility--genetic polymorphisms of genes CYP1A1, GSTM1, GSTT1, NAT2. DNA adducts measured by 32P-postlabeling are the biomarker of choice for the evaluation of exposure to polycyclic aromatic hydrocarbons. Protein adducts are useful as a biomarker for exposure to tobacco smoke (4-aminobiphenyl) or to smaller molecules such as acrylonitrile or 1,3-butadiene. Of the biomarkers of effect, the most common are cytogenetic end points. Epidemiologic studies support the use of chromosomal breakage as a relevant biomarker of cancer risk. The use of the Comet assay and methods analyzing oxidative DNA damage needs reliable validation for human biomonitoring. Until now there have not been sufficient data to interpret the relationship between genotypes, biomarkers of exposure, and biomarkers of effect for assessing the risk of human exposure to mutagens and carcinogens. PMID:10698723

  10. [Opportunity and challenge on molecular epidemiology].

    PubMed

    Duan, G C; Chen, S Y

    2016-08-10

    Molecular epidemiology, a branch of epidemiology, combines the theories and methods, both in epidemiology and molecular biology. Molecular epidemiology mainly focuses on biological markers, describing the distribution, occurrence, development and prognosis of diseases at the molecular level. The completion of Human Genome Project and rapid development of Precision Medicine and Big Data not only offer the new development opportunities but also bring about a higher demand and new challenge for molecular epidemiology. PMID:27539332

  11. Molecular Epidemiology of Tuberculosis: Current Insights

    PubMed Central

    Mathema, Barun; Kurepina, Natalia E.; Bifani, Pablo J.; Kreiswirth, Barry N.

    2006-01-01

    Molecular epidemiologic studies of tuberculosis (TB) have focused largely on utilizing molecular techniques to address short- and long-term epidemiologic questions, such as in outbreak investigations and in assessing the global dissemination of strains, respectively. This is done primarily by examining the extent of genetic diversity of clinical strains of Mycobacterium tuberculosis. When molecular methods are used in conjunction with classical epidemiology, their utility for TB control has been realized. For instance, molecular epidemiologic studies have added much-needed accuracy and precision in describing transmission dynamics, and they have facilitated investigation of previously unresolved issues, such as estimates of recent-versus-reactive disease and the extent of exogenous reinfection. In addition, there is mounting evidence to suggest that specific strains of M. tuberculosis belonging to discrete phylogenetic clusters (lineages) may differ in virulence, pathogenesis, and epidemiologic characteristics, all of which may significantly impact TB control and vaccine development strategies. Here, we review the current methods, concepts, and applications of molecular approaches used to better understand the epidemiology of TB. PMID:17041139

  12. Epidemiological and molecular study of Ehrlichia canis in dogs in Bahia, Brazil.

    PubMed

    Carvalho, F S; Wenceslau, A A; Carlos, R S A; Albuquerque, G R

    2008-01-01

    The objective of the present article was an epidemiological and molecular study of Ehrlichia canis in dogs of Ilhéus and Itabuna in Bahia, as well as an evaluation of associated risk factors. Blood samples were collected from 153 dogs and DNA was extracted and analyzed by the nested-polymerase chain reaction, using one pair of primers to detect Ehrlichia bacteria and another pair to detect the presence of E. canis. Of the 153 animals, 12 (7.8%) were polymerase chain reaction-positive for E. canis, indicating the presence of the parasite in dogs of the Ilhéus-Itabuna microregion. The associated risk factors were exposure to tick-infested habitats and the fact that the dogs lived in the countryside. PMID:18752193

  13. Whole genome sequencing: the future for molecular epidemiological studies on aquatic pathogens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The advent of next generation sequencing (NGS) has transformed our ability to analyze the genomic content of isolated strains and communities of microorganisms. An important application of the new technology is for molecular epidemiology, as single sequencing reactions can generate nearly complete ...

  14. Molecular epidemiology in environmental carcinogenesis.

    PubMed Central

    Perera, F P; Mooney, L A; Dickey, C P; Santella, R M; Bell, D; Blaner, W; Tang, D; Whyatt, R M

    1996-01-01

    Molecular epidemiology has significant potential in preventing cancer and other diseases caused by environmental exposures (related to lifestyle, occupation, or ambient pollution). This approach attempts to prevent cancer by incorporating laboratory methods to document the molecular dose and preclinical effects of carcinogens, as well as factors that increases individual susceptibility to carcinogens. Recently we have carried out validation studies of biologic markers such as carcinogen--DNA and carcinogen--protein adducts, gene and chromosomal mutations, alterations in target oncogenes or tumor suppressor genes, polymorphisms in putative susceptibility genes (individual P450s, glutathione transferase M1), and serum levels of micronutrients. This research involves adults, infants, and children exposed to varying levels of carcinogens, as well as cancer cases and controls. On a group level, dose-response relationships have frequently been seen between various biomarkers and environmental exposures such as polycyclic aromatic hydrocarbons, cigarette smoke (active and passive), and ambient indoor and workplace air pollution. However, there is significant interindividual variation in biomarkers that appears to reflect a modulating effect on biomarkers (hence potential risk) by genetic and acquired susceptibility factors. Ongoing retrospective and nested case-control studies of lung and breast cancer are examining the association between biomarkers and cancer risk. Results of these studies are encouraging; they suggest that biomarkers, once validated, can be useful in identifying populations and individuals at risk in time to intervene effectively. PMID:8781360

  15. [Future prospects of molecular epidemiology in tuberculosis].

    PubMed

    Matsumoto, Tomoshige; Iwamoto, Tomotada

    2009-12-01

    Before the availability of high-resolution genotyping tools in 1990s, there was a prevailing dogma of little genomic sequence diversity in Mycobacterium tuberculosis. Due to the low levels of genetic variation, it was assumed that M. tuberculosis exhibit very little phenotypic variation in immunologic and virulence factors. The fingerprinting method based on restriction fragment length polymorphisms (RFLP) of IS6110 insertion sequences had unveiled the underestimation of the sequence variation in M. tuberculosis and the importance of strain-to-strain variation for understanding pathogenesis, immune mechanisms, bacterial evolution, and host adaptation. This method became a gold standard for strain differentiation in the molecular epidemiological study. It had lead to a profusion of studies in molecular epidemiology such as the detection of unsuspected transmission, the estimation of the extent of recent transmission, the identification of laboratory cross-contamination, the identification of outbreaks, and distinction between reinfection and relapse. This, in 1990s, is the opening of the molecular epidemiology of tuberculosis. After the completion of genome project of the M. tuberculosis laboratory strain H37Rv, some of the clinical isolates were completely sequenced. This prompted the in silico genome comparison and identified various genomic markers which can give a unifying framework for both epidemiology and evolutionary analysis of M. tuberculosis population. Of them, variable numbers of tandem repeats (VNTR) was found as the most promising PCR-based method which can provide adequate discrimination of M. tuberculosis strains in many cases, including the estimation of M. tuberculosis transmission and the identification of genetic lineages. PCR-based VNTR analysis is easy, rapid, and highly specific and can generate portable digit-based data, unlike the analog information obtained from IS6110 RFLP which is labor intensive. In this regards, investigators can

  16. Molecular Epidemiology of Amoebiasis: A Cross-Sectional Study among North East Indian Population

    PubMed Central

    Nath, Joyobrato; Ghosh, Sankar Kumar; Singha, Baby; Paul, Jaishree

    2015-01-01

    Background Epidemiological studies carried out using culture or microscopy in most of the amoebiasis endemic developing countries, yielded confusing results since none of these could differentiate the pathogenic Entamoeba histolytica from the non-pathogenic Entamoeba dispar and Entamoeba moshkovskii. The Northeastern part of India is a hot spot of infection since the climatic conditions are most conducive for the infection and so far no systemic study has been carried out in this region. Methodology/Principal Findings Following a cross-sectional study designed during the period 2011–2014, a total of 1260 fecal samples collected from the Northeast Indian population were subjected to microscopy, fecal culture and a sensitive and specific DNA dot blot screening assay developed in our laboratory targeting the Entamoeba spp. Further species discrimination using PCR assay performed in microscopy, culture and DNA dot blot screening positive samples showed E. histolytica an overall prevalence rate of 11.1%, 8.0% and 13.7% respectively. In addition, infection rates of nonpathogenic E. dispar and E. moshkovskii were 11.8% (95% CI = 10.2, 13.8) and 7.8% (95% CI = 6.4, 9.4) respectively. The spatial distributions of infection were 18.2% (107/588) of Assam, 11.7% (23/197) of Manipur, 10.2% (21/207) of Meghalaya, and 8.2% (22/268) of Tripura states. Association study of the disease with demographic features suggested poor living condition (OR = 3.21; 95% CI = 1.83, 5.63), previous history of infection in family member (OR = 3.18; 95% CI = 2.09, 4.82) and unhygienic toilet facility (OR = 1.79; 95% CI = 1.28, 2.49) as significant risk factors for amoebiasis. Children in age group <15 yr, participants having lower levels of education, and daily laborers exhibited a higher infection rate. Conclusions/Significance Despite the importance of molecular diagnosis of amoebiasis, molecular epidemiological data based on a large sample size from endemic countries are rarely reported in the

  17. Prevalence of mitochondrial diabetes in southwestern Finland: a molecular epidemiological study.

    PubMed

    Martikainen, Mika H; Rönnemaa, Tapani; Majamaa, Kari

    2013-10-01

    Mitochondrial diabetes and deafness (MIDD) is a subtype of diabetes mellitus (DM) that most commonly results from the m.3243A > G mutation in mitochondrial DNA (mtDNA). Sensorineural hearing loss is a typical accompanying feature. Previous studies have suggested a prevalence of ~1-1.5 % for MIDD. We studied the molecular epidemiology of MIDD among young (aged 18-45 years) adults in a defined population in southwestern Finland. Of the identified cohort of 1,532 patients with DM, we received blood samples of 299 patients and analyzed them for the m.3243A > G mutation and for mtDNA haplogroups. We found three DM patients (1.0 %) with the m.3243A > G mutation. All the three patients with DM and m.3243A > G also had severe hearing impairment that required use of hearing aid. MtDNA haplogroup U was more prevalent among patients with maternal family history of DM. We conclude that among young adults, ~1 % of all DM is associated with the m.3243A > G mutation. We suggest that all patients with both DM and hearing impairment, at least in this age group, should undergo investigation for this mutation. Furthermore, our results suggest that mtDNA haplogroup U is associated with maternal family history of DM. PMID:22492248

  18. Pathogenesis of Helicobacter pylori-Related Gastroduodenal Diseases from Molecular Epidemiological Studies

    PubMed Central

    Yamaoka, Yoshio

    2012-01-01

    Helicobacter pylori is a major human pathogen that infects the stomach and produces inflammation that is responsible for various gastroduodenal diseases. Despite the high prevalence of H. pylori infections in Africa and South Asia, the incidence of gastric cancer in these areas is much lower than in other countries. The incidence of gastric cancer also tends to decrease from north to south in East Asia. Data from molecular epidemiological studies show that this variation in different geographic areas could be explained in part by different types of H. pylori virulence factors, especially CagA, VacA, and OipA. H. pylori infection is thought to be involved in both gastric cancer and duodenal ulcer, which are at opposite ends of the disease spectrum. This discrepancy can also be explained in part by another H. pylori factor, DupA, as well as by CagA typing (East Asian type versus Western type). H. pylori has a genome of approximately 1,600 genes; therefore, there might be other novel virulence factors. Because genome wide analyses using whole-genome sequencing technology give a broad view of the genome of H. pylori, we hope that next-generation sequencers will enable us to efficiently investigate novel virulence factors. PMID:22829807

  19. Pathogenesis of Helicobacter pylori-Related Gastroduodenal Diseases from Molecular Epidemiological Studies.

    PubMed

    Yamaoka, Yoshio

    2012-01-01

    Helicobacter pylori is a major human pathogen that infects the stomach and produces inflammation that is responsible for various gastroduodenal diseases. Despite the high prevalence of H. pylori infections in Africa and South Asia, the incidence of gastric cancer in these areas is much lower than in other countries. The incidence of gastric cancer also tends to decrease from north to south in East Asia. Data from molecular epidemiological studies show that this variation in different geographic areas could be explained in part by different types of H. pylori virulence factors, especially CagA, VacA, and OipA. H. pylori infection is thought to be involved in both gastric cancer and duodenal ulcer, which are at opposite ends of the disease spectrum. This discrepancy can also be explained in part by another H. pylori factor, DupA, as well as by CagA typing (East Asian type versus Western type). H. pylori has a genome of approximately 1,600 genes; therefore, there might be other novel virulence factors. Because genome wide analyses using whole-genome sequencing technology give a broad view of the genome of H. pylori, we hope that next-generation sequencers will enable us to efficiently investigate novel virulence factors. PMID:22829807

  20. Molecular and epidemiological studies of Porcine rubulavirus infection – an overview

    PubMed Central

    Cuevas-Romero, Julieta Sandra; Blomström, Anne-Lie; Berg, Mikael

    2015-01-01

    Porcine rubulavirus-La Piedad-Michoacan-Mexico virus (PorPV-LPMV) was identified as the causative agent of a viral disease that emerged spontaneously in Mexican swine in the 1980s. Since the report of the initial outbreak of the disease, only one full-length genome from a strain isolated in 1984 (PorPV-LPMV/1984) has been sequenced; sequence data are scarce from other isolates. The genetic variation of this virus that has spread throughout the main endemic region of Mexico is almost a complete mystery. The development of molecular techniques for improved diagnostics and to investigate the persistence, molecular epidemiology, and the possible reservoirs of PorPV are needed. Together, this will provide greater knowledge regarding the molecular genetic changes and useful data to establish new strategies in the control of this virus in Mexico. PMID:26584829

  1. [Application of molecular methods in the diagnosis and epidemiological study of viral respiratory infections].

    PubMed

    Pozo, Francisco; Casas, Inmaculada; Ruiz, Guillermo; Falcón, Ana; Pérez-Breña, Pilar

    2008-07-01

    To date, more than two hundred viruses, belonging to six different taxonomic families, have been associated with human respiratory tract infection. The widespread incorporation of molecular methods into clinical microbiology laboratories has not only led to notable advances in the etiological diagnosis of viral respiratory infections but has also increased insight into the pathology and epidemiological profiles of the causative viruses. Because of their high sensitivity, molecular techniques markedly increase the efficiency of viral detection in respiratory specimens, particularly those that fail to propagate successfully in common cell cultures, thus allowing more rapid etiologic diagnosis. However, there are also some disadvantages in the use of these new technologies such as detection of viruses that merely colonize the respiratory tract of healthy people, or those found in the nasopharyngeal secretions of patients who have recovered from respiratory infections, due to longterm viral shedding, when the viruses are unlikely to act as pathogens. Additionally, sequencing of the amplification products allows further characterization of detected viruses, including molecular epidemiology, genotyping, or detection of antiviral resistance, to cite only a few examples. PMID:19195443

  2. Navigating the future of bacterial molecular epidemiology

    PubMed Central

    Baker, Stephen; Hanage, William P; Holt, Kathryn E

    2010-01-01

    Technological advances in high-throughput genome sequencing have led to an enhanced appreciation of the genetic diversity found within populations of pathogenic bacteria. Methods based on single nucleotide polymorphisms (SNPs) and insertions or deletions (indels) build upon the framework established by multi-locus sequence typing (MLST) and permit a detailed, targeted analysis of variation within related organisms. Robust phylogenetics, when combined with epidemiologically informative data, can be applied to study ongoing temporal and geographical fluctuations in bacterial pathogens. As genome sequencing, SNP detection and geospatial information become more accessible these methods will continue to transform the way molecular epidemiology is used to study populations of bacterial pathogens. PMID:20846899

  3. Longitudinal Molecular Epidemiological Study of Thermophilic Campylobacters on One Conventional Broiler Chicken Farm▿

    PubMed Central

    Ridley, Anne M.; Morris, Victoria K.; Cawthraw, Shaun A.; Ellis-Iversen, Johanne; Harris, Jillian A.; Kennedy, Emma M.; Newell, Diane G.; Allen, Vivien M.

    2011-01-01

    Improved understanding of the ecology and epidemiology of Campylobacter in the poultry farm environment is key to developing appropriate farm-based strategies for preventing flock colonization. The sources of Campylobacter causing broiler flock colonization were investigated on one poultry farm and its environment, from which samples were obtained on three occasions during each of 15 crop cycles. The farm was adjacent to a dairy farm, with which there was a shared concreted area and secondary entrance. There was considerable variation in the Campylobacter status of flocks at the various sampling times, at median ages of 20, 26, and 35 days, with 3 of the 15 flocks remaining negative at slaughter. Campylobacters were recoverable from various locations around the farm, even while the flock was Campylobacter negative, but the degree of environmental contamination increased substantially once the flock was positive. Molecular typing showed that strains from house surroundings and the dairy farm were similar to those subsequently detected in the flock and that several strains intermittently persisted through multiple crop cycles. The longitudinal nature of the study suggested that bovine fecal Campylobacter strains, initially recovered from the dairy yard, may subsequently colonize poultry. One such strain, despite being repeatedly recovered from the dairy areas, failed to colonize the concomitant flock during later crop cycles. The possibility of host adaptation of this strain was investigated with 16-day-old chickens experimentally exposed to this strain naturally present in, or spiked into, bovine feces. Although the birds became colonized by this infection model, the strain may preferentially infect cattle. The presence of Campylobacter genotypes in the external environment of the poultry farm, prior to their detection in broiler chickens, confirms the horizontal transmission of these bacteria into the flock and highlights the risk from multispecies farms. PMID

  4. A unified approach to molecular epidemiology investigations: tools and patterns in California as a case study for endemic shigellosis

    PubMed Central

    2009-01-01

    Background Shigellosis causes diarrheal disease in humans from both developed and developing countries, and multi-drug resistance is an emerging problem. The objective of this study is to present a unified approach that can be used to characterize endemic and outbreak patterns of shigellosis using use a suite of epidemiologic and molecular techniques. The approach is applied to a California case study example of endemic shigellosis at the population level. Methods Epidemiologic patterns were evaluated with respect to demographics, multi-drug resistance, antimicrobial resistance genes, plasmid profiles, and pulsed-field gel electrophoresis (PFGE) fingerprints for the 43 Shigella isolates obtained by the Monterey region health departments over the two year period from 2004-2005. Results The traditional epidemiologic as well as molecular epidemiologic findings were consistent with endemic as compared to outbreak shigellosis in this population. A steady low level of cases was observed throughout the study period and high diversity was observed among strains. In contrast to most studies in developed countries, the predominant species was Shigella flexneri (51%) followed closely by S. sonnei (49%). Over 95% of Shigella isolates were fully resistant to three or more antimicrobial drug subclasses, and 38% of isolates were resistant to five or more subclasses. More than half of Shigella strains tested carried the tetB, catA, or blaTEM genes for antimicrobial resistance to tetracycline, chloramphenicol, and ampicillin, respectively. Conclusion This study shows how epidemiologic patterns at the host and bacterial population levels can be used to investigate endemic as compared to outbreak patterns of shigellosis in a community. Information gathered as part of such investigations will be instrumental in identifying emerging antimicrobial resistance, for developing treatment guidelines appropriate for that community, and to provide baseline data with which to compare outbreak

  5. MOLECULAR EPIDEMIOLOGICAL STUDIES ON TWO CYCLOSPORIASIS OUTBREAKS IN VANCOUVER, BRITISH COLUMBIA

    EPA Science Inventory

    Two cyclosporiasis outbreaks in Vancouver, British Columbia (BC) were investigated using molegular epidemiology. The cause of the 1999 outbreak has not been identiifed whereas the 2001 oubreak has been linked epidemiologically to the consumption of Thai basil. The internal tran...

  6. Molecular epidemiology of Legionnaires' disease in Israel.

    PubMed

    Moran-Gilad, J; Mentasti, M; Lazarovitch, T; Huberman, Z; Stocki, T; Sadik, C; Shahar, T; Anis, E; Valinsky, L; Harrison, T G; Grotto, I

    2014-07-01

    National surveillance of Legionnaires' disease (LD) is important to inform control measures and facilitate international networking for timely reporting. This study is the first to describe the molecular epidemiology of LD in Israel. Case notifications for 2006-2011, collated through mandatory reporting, were identified and demographic, clinical and laboratory data were extracted. Unrelated clinical and environmental Legionella pneumophila strains were characterized using standard procedures, Dresden panel of monoclonal antibodies and the ESCMID Study Group for Legionella Infections (ESGLI) Sequence-Based Typing scheme. In all, 294 cases were reported (crude incidence 0.67 cases/100 000; age-standardized incidence 1/100 000). LD epidemiological trends and features largely resembled those of the EU, except for a larger proportion of nosocomial cases. Of 28 clinical and 23 environmental strains analysed, 71.4% and 21.7% were serogroup (sg) 1 and the most common immunological subgroup was OLDA/Oxford (64%). Of the clinical strains, OLDA/Oxford, ST1 was the most common (43%) followed by Allentown/France, ST40 (14%). The unusual sg 3 ST338 was found in 17.4% of environmental strains. Novel STs were detected amongst 23.5% of strains. These findings warrant further molecular investigation. Molecular epidemiology data generated from neighbouring countries newly adopting the ESGLI typing scheme for L. pneumophila contribute to understanding of regional strain diversity. PMID:24118162

  7. Molecular epidemiological studies in 1,3-butadiene exposed Czech workers: female-male comparisons.

    PubMed

    Albertini, Richard J; Sram, Radim J; Vacek, Pamela M; Lynch, Jeremiah; Rossner, Pavel; Nicklas, Janice A; McDonald, Jake D; Boysen, Gunnar; Georgieva, Nadia; Swenberg, James A

    2007-03-20

    Results of a recent molecular epidemiological study of 1,3-butadiene (BD) exposed Czech workers, conducted to compare female to male responses, have confirmed and extended the findings of a previously reported males only study (HEI Research Report 116, 2003). The initial study found that urine concentrations of the metabolites 1,2-dihydroxy-4-(acetyl) butane (M1) and 1-dihydroxy-2-(N-acetylcysteinyl)-3-butene (M2) and blood concentrations of the hemoglobin adducts N-[2-hydroxy-3-butenyl] valine (HB-Val) and N-[2,3,4-trihydroxy-butyl] valine (THB-Val) constitute excellent biomarkers of exposure, both being highly correlated with BD exposure levels, and that GST genotypes modulate at least one metabolic pathway, but that irreversible genotoxic effects such as chromosome aberrations and HPRT gene mutations are neither associated with BD exposure levels nor with worker genotypes (GST [glutathione-S-transferase]-M1, GSTT1, CYP2E1 (5' promoter), CYP2E1 (intron 6), EH [epoxide hydrolase] 113, EH139, ADH [alcohol dehydrogenase]2 and ADH3). The no observed adverse effect level (NOAEL) for chromosome aberrations and HPRT mutations was 1.794 mg/m(3) (0.812 ppm)--the mean exposure level for the highest exposed worker group in this initial study. The second Czech study, reported here, initiated in 2003, included 26 female control workers, 23 female BD exposed workers, 25 male control workers and 30 male BD exposed workers (some repeats from the first study). Multiple external exposure measurements (10 full 8-h shift measures by personal monitoring per worker) over a 4-month period before biological sample collections showed that BD workplace levels were lower than in the first study. Mean 8-h TWA exposure levels were 0.008 mg/m(3) (0.0035 ppm) and 0.397 mg/m(3) (0.180 ppm) for female controls and exposed, respectively, but with individual single 8-h TWA values up to 9.793 mg/m(3) (4.45 ppm) in the exposed group. Mean male 8-h TWA exposure levels were 0.007 mg/m(3) (0.0032 ppm

  8. A molecular epidemiological study of rabies epizootics in kudu (Tragelaphus strepsiceros) in Namibia

    PubMed Central

    Mansfield, Karen; McElhinney, Lorraine; Hübschle, Otto; Mettler, Felix; Sabeta, Claude; Nel, Louis H; Fooks, Anthony R

    2006-01-01

    Background A panel of 37 rabies virus isolates were collected and studied, originating mainly from the northern and central regions of Namibia, between 1980 and 2003. Results These virus isolates demonstrated a high degree of genetic similarity with respect to a 400 bp region of the nucleoprotein gene, with the virus isolates originating from kudu antelope (n = 10) sharing 97.2–100% similarity with jackal isolates, and 97–100% similarity with those isolated from domestic dogs. Phylogenetic analysis suggested that these viruses were all of the canid rabies biotype of southern Africa. The viruses from kudu were closely associated with jackal isolates (n = 6), bat-eared fox isolates (n = 2) and domestic dog isolates (n = 2) at the genetic level and identical at the amino acid level, irrespective of the year of isolation. Conclusion These data suggest that jackal and kudu may form part of the same epidemiological cycle of rabies in Namibian wildlife, and might demonstrate the close-relationship between rabies virus strains that circulate within Namibia and those that circulate between Namibia and its neighbouring countries such as Botswana and South Africa. PMID:16412222

  9. Molecular epidemiological and serological studies of bovine leukemia virus (BLV) infection in Thailand cattle.

    PubMed

    Lee, EunJung; Kim, Eun-Ju; Ratthanophart, Jadsada; Vitoonpong, Ratchaneekorn; Kim, Bo-Hye; Cho, In-Soo; Song, Jae-Young; Lee, Kyoung-Ki; Shin, Yeun-Kyung

    2016-07-01

    BLV is the etiological agent of enzootic bovine leucosis. BLV has negative effects on animal health and causes economic losses worldwide. However, epidemiological studies on BLV are relatively unknown in many parts of Asian countries. Thus, this study sought to explore BLV infections in cattle in Thailand to determine the extent of the geographic distribution of BLV and to measure its prevalence rates. For this study, 744 cattle from 11 farms in 9 provinces of Thailand were screened in 2013 and 2014 by ELISA and nested PCR. Of those cattle, 41 BLVs were genetically characterized using 188 BLV gp51 env gene sequences available in GenBank. The BLV prevalence in Thailand was high, ranging from 5.3% to 87.8%, as determined by PCR and 11.0% to 100% as determined by ELISA, according to geographical region. Phylogenetic analysis showed that Thailand BLVs belonged to genotypes 1 and 6 and a new genotype 10, which are sporadically observed across Thailand with a prevalence of 31.7%, 19.5%, and 48.8%, respectively. A significant number of amino acid substitutions were also found in the gp51 sequences, of which unique changes in genotype 10 have not been reported previously. Briefly, the majority of substitutions were confined to CD4+/CD8+ T-cell epitopes, neutralizing domains, and E-D-A epitopes. Those observations indicate that BLV infections in Thailand cattle are prevalent and that the geographic distribution of BLV is dynamic, with a high level of genetic diversity. This distribution implies a long-term BLV infection in cattle populations and the movement of infected cattle. In sum, this study suggests that intensive surveillance and effective prevention strategies are required to determine the prevalence of BLV in Thailand and control continuous infections with BLVs. PMID:27090024

  10. Molecular epidemiology: new rules for new tools?

    PubMed

    Merlo, Domenico Franco; Sormani, Maria Pia; Bruzzi, Paolo

    2006-08-30

    Molecular epidemiology combines biological markers and epidemiological observations in the study of the environmental and genetic determinants of cancer and other diseases. The potential advantages associated with biomarkers are manifold and include: (a) increased sensitivity and specificity to carcinogenic exposures; (b) more precise evaluation of the interplay between genetic and environmental determinants of cancer; (c) earlier detection of carcinogenic effects of exposure; (d) characterization of disease subtypes-etiologies patterns; (e) evaluation of primary prevention measures. These, in turn, may translate into better tools for etiologic research, individual risk assessment, and, ultimately, primary and secondary prevention. An area that has not received sufficient attention concerns the validation of these biomarkers as surrogate endpoints for cancer risk. Validation of a candidate biomarker's surrogacy is the demonstration that it possesses the properties required for its use as a substitute for a true endpoint. The principles underlying the validation process underwent remarkable developments and discussion in therapeutic research. However, the challenges posed by the application of these principles to epidemiological research, where the basic tool for this validation (i.e., the randomized study) is seldom possible, have not been thoroughly explored. The validation process of surrogacy must be applied rigorously to intermediate biomarkers of cancer risk before using them as risk predictors at the individual as well as at the population level. PMID:16843503

  11. Applying molecular epidemiology in pediatric leukemia.

    PubMed

    Schiffman, Joshua D

    2016-02-01

    Molecular epidemiology is the study of genetic and environmental risk for disease, with much effort centered on cancer. Childhood leukemia occurs in nearly a third of all patients newly diagnosed with pediatric cancer. only a small percentage of these new cases of childhood leukemia are associated with high penetrant hereditary cancer syndromes. Childhood leukemia, especially acute lymphoblastic leukemia, has been associated with a dysregulated immune system due to delayed infectious exposure at a young age. Identical twins with childhood leukemia suggest that acute lymphoblastic leukemia begins in utero and that the concordant presentation is due to a shared preleukemia subclone via placental transfer. Investigation of single nucleotide polymorphisms within candidate genes find that leukemia risk may be attributed to population-based polymorphisms affecting folate metabolism, xenobiotic metabolism, DNA repair, immunity, and B-cell development. More recently, genome-wide association studies for leukemia risk has led investigators to genes associated with B-cell development. When describing leukemia predisposition due to hereditary cancer syndromes, the following 6 categories become apparent on the basis of biology and clinical presentation: (1) genetic instability/DNA repair syndromes, (2) cell cycle/differentiation syndromes, (3) bone marrow failure syndromes, (4) telomere maintenance syndromes, (5) immunodeficiency syndromes, and (6) transcription factor syndromes and pure familial leukemia. understanding the molecular epidemiology of childhood leukemia can affect the treatment and tumor surveillance strategies for these high risk patients and their family members. PMID:25973690

  12. Molecular epidemiology of Giardia and Cryptosporidium infections.

    PubMed

    Thompson, R C A; Ash, A

    2016-06-01

    Giardia and Cryptosporidium are ubiquitous enteric protozoan pathogens of vertebrates. Although recognised as the aetiological agents of disease in humans and domestic animals for many years, fundamental questions concerning their ecology have been unresolved. Molecular tools have helped to better understand their genetic diversity and in so doing have helped to resolve questions about their transmission patterns and associated impacts on public health. However, the value of molecular tools is often complicated by questions concerning their applications, interpretation of results and terminology. Taxonomic issues have, until recently, made it difficult to determine the epidemiology of infections with both Giardia and Cryptosporidium. Similarly, improved understanding of their respective phylogenetic relationships has helped to resolve questions about zoonotic potential and distribution in wildlife. In the case of Cryptosporidium, imaging technologies have complemented phylogenetic studies in demonstrating the parasite's affinities with gregarine protozoa and have further supported its extracellular developmental capability and potential role as an environmental pathogen. PMID:26458528

  13. Incidence of Sarcoma Histotypes and Molecular Subtypes in a Prospective Epidemiological Study with Central Pathology Review and Molecular Testing

    PubMed Central

    Ducimetière, Françoise; Lurkin, Antoine; Ranchère-Vince, Dominique; Decouvelaere, Anne-Valérie; Péoc'h, Michel; Istier, Luc; Chalabreysse, Philippe; Muller, Christine; Alberti, Laurent; Bringuier, Pierre-Paul; Scoazec, Jean-Yves; Schott, Anne-Marie; Bergeron, Christophe; Cellier, Dominic; Blay, Jean-Yves; Ray-Coquard, Isabelle

    2011-01-01

    Background The exact overall incidence of sarcoma and sarcoma subtypes is not known. The objective of the present population-based study was to determine this incidence in a European region (Rhone-Alpes) of six million inhabitants, based on a central pathological review of the cases. Methodology/Principal Findings From March 2005 to February 2007, pathology reports and tumor blocks were prospectively collected from the 158 pathologists of the Rhone-Alpes region. All diagnosed or suspected cases of sarcoma were collected, reviewed centrally, examined for molecular alterations and classified according to the 2002 World Health Organization classification. Of the 1287 patients screened during the study period, 748 met the criteria for inclusion in the study. The overall crude and world age-standardized incidence rates were respectively 6.2 and 4.8 per 100,000/year. Incidence rates for soft tissue, visceral and bone sarcomas were respectively 3.6, 2.0 and 0.6 per 100,000. The most frequent histological subtypes were gastrointestinal stromal tumor (18%; 1.1/100,000), unclassified sarcoma (16%; 1/100,000), liposarcoma (15%; 0.9/100,000) and leiomyosarcoma (11%; 0.7/100,000). Conclusions/Significance The observed incidence of sarcomas was higher than expected. This study is the first detailed investigation of the crude incidence of histological and molecular subtypes of sarcomas. PMID:21826194

  14. Multicentre study highlighting clinical relevance of new high-throughput methodologies in molecular epidemiology of Pneumocystis jirovecii pneumonia.

    PubMed

    Esteves, F; de Sousa, B; Calderón, E J; Huang, L; Badura, R; Maltez, F; Bassat, Q; de Armas, Y; Antunes, F; Matos, O

    2016-06-01

    Pneumocystis jirovecii causes severe interstitial pneumonia (PcP) in immunosuppressed patients. This multicentre study assessed the distribution frequencies of epidemiologically relevant genetic markers of P. jirovecii in different geographic populations from Portugal, the USA, Spain, Cuba and Mozambique, and the relationship between the molecular data and the geographical and clinical information, based on a multifactorial approach. The high-throughput typing strategy for P. jirovecii characterization consisted of DNA pooling using quantitative real-time PCR followed by multiplex-PCR/single base extension. The frequencies of relevant P. jirovecii single nucleotide polymorphisms (mt85, SOD110, SOD215, DHFR312, DHPS165 and DHPS171) encoded at four loci were estimated in ten DNA pooled samples representing a total of 182 individual samples. Putative multilocus genotypes of P. jirovecii were shown to be clustered due to geographic differences but were also dependent on clinical characteristics of the populations studied. The haplotype DHFR312T/SOD110C/SOD215T was associated with severe AIDS-related PcP and high P. jirovecii burdens. The frequencies of this genetic variant of P. jirovecii were significantly higher in patients with AIDS-related PcP from Portugal and the USA than in the colonized patients from Portugal, and Spain, and children infected with P. jirovecii from Cuba or Mozambique, highlighting the importance of this haplotype, apparently associated with the severity of the disease and specific clinical groups. Patients from the USA and Mozambique showed higher rates of DHPS mutants, which may suggest the circulation of P. jirovecii organisms potentially related with trimethoprim-sulfamethoxazole resistance in those geographical regions. This report assessed the worldwide distribution of P. jirovecii haplotypes and their epidemiological impact in distinct geographic and clinical populations. PMID:27021425

  15. Molecular epidemiology of norovirus in South Korea.

    PubMed

    Lee, Sung-Geun; Cho, Han-Gil; Paik, Soon-Young

    2015-02-01

    Norovirus is a major cause of viral gastroenteritis and a common cause of foodborne and waterborne outbreaks. Norovirus outbreaks are responsible for economic losses, most notably to the public health and food industry field. Norovirus has characteristics such as low infectious dose, prolonged shedding period, strong stability, great diversity, and frequent genome mutations. Besides these characteristics, they are known for rapid and extensive spread in closed settings such as hospitals, hotels, and schools. Norovirus is well known as a major agent of food-poisoning in diverse settings in South Korea. For these reasons, nationwide surveillance for norovirus is active in both clinical and environmental settings in South Korea. Recent studies have reported the emergence of variants and novel recombinants of norovirus. In this review, we summarized studies on the molecular epidemiology and nationwide surveillance of norovirus in South Korea. This review will provide information for vaccine development and prediction of new emerging variants of norovirus in South Korea. PMID:25441425

  16. A reassessment of the epidemiology of Rice yellow mottle virus following recent advances in field and molecular studies.

    PubMed

    Traoré, O; Pinel-Galzi, A; Sorho, F; Sarra, S; Rakotomalala, M; Sangu, E; Kanyeka, Z; Séré, Y; Konaté, G; Fargette, D

    2009-05-01

    The available knowledge on the epidemiology of Rice yellow mottle virus (RYMV) is reassessed in the light of major advances in field and molecular studies of the disease it causes in rice. Previously un-described means of transmission by mammals and through leaf contact have been discovered recently. Several agricultural practices, including the use of seedbed nurseries, have also contributed to a massive build-up of RYMV inoculum. Phytosanitation is now known to be critical to reduce disease incidence in rice. A new model of the ecology of RYMV in which man plays a central role has emerged. Furthermore, estimates of the evolutionary rate of change of RYMV provided a time-frame for its epidemiology, the first attempt for a plant virus. Earlier interpretations of the patterns of virus diversity which assumed a long-term evolution, and assigned a major role to adaptive events had to be discarded. In contrast, a wave-like model of dispersal of RYMV, which postulates its initial diversification in East Africa, followed by westward spread across the continent, was developed, refined and dated. The most salient -- and largely unexpected -- finding is that RYMV emerged recently and subsequently spread rapidly throughout Africa in the last two centuries. Diversification and spread of RYMV has been concomitant with an extension of rice cultivation in Africa since the 19th century. This major agro-ecological change increased the encounters between primary hosts of RYMV and cultivated rice. It also modified the landscape ecology in ways that facilitated virus spread. PMID:19195488

  17. Neuronal ceroid lipofuscinosis in Border Collie dogs in Japan: clinical and molecular epidemiological study (2000-2011).

    PubMed

    Mizukami, Keijiro; Kawamichi, Takuji; Koie, Hiroshi; Tamura, Shinji; Matsunaga, Satoru; Imamoto, Shigeki; Saito, Miyoko; Hasegawa, Daisuke; Matsuki, Naoaki; Tamahara, Satoshi; Sato, Shigenobu; Yabuki, Akira; Chang, Hye-Sook; Yamato, Osamu

    2012-01-01

    Neuronal ceroid lipofuscinosis (NCL) is an inherited, neurodegenerative lysosomal disease that causes premature death. The present study describes the clinical and molecular epidemiologic findings of NCL in Border Collies in Japan for 12 years, between 2000 and 2011. The number of affected dogs was surveyed, and their clinical characteristics were analyzed. In 4 kennels with affected dogs, the dogs were genotyped. The genetic relationships of all affected dogs and carriers identified were analyzed. The survey revealed 27 affected dogs, but there was a decreasing trend at the end of the study period. The clinical characteristics of these affected dogs were updated in detail. The genotyping survey demonstrated a high mutant allele frequency in examined kennels (34.8%). The pedigree analysis demonstrated that all affected dogs and carriers in Japan are related to some presumptive carriers imported from Oceania and having a common ancestor. The current high prevalence in Japan might be due to an overuse of these carriers by breeders without any knowledge of the disease. For NCL control and prevention, it is necessary to examine all breeding dogs, especially in kennels with a high prevalence. Such endeavors will reduce NCL prevalence and may already be contributing to the recent decreasing trend in Japan. PMID:22919312

  18. Neuronal Ceroid Lipofuscinosis in Border Collie Dogs in Japan: Clinical and Molecular Epidemiological Study (2000–2011)

    PubMed Central

    Mizukami, Keijiro; Kawamichi, Takuji; Koie, Hiroshi; Tamura, Shinji; Matsunaga, Satoru; Imamoto, Shigeki; Saito, Miyoko; Hasegawa, Daisuke; Matsuki, Naoaki; Tamahara, Satoshi; Sato, Shigenobu; Yabuki, Akira; Chang, Hye-Sook; Yamato, Osamu

    2012-01-01

    Neuronal ceroid lipofuscinosis (NCL) is an inherited, neurodegenerative lysosomal disease that causes premature death. The present study describes the clinical and molecular epidemiologic findings of NCL in Border Collies in Japan for 12 years, between 2000 and 2011. The number of affected dogs was surveyed, and their clinical characteristics were analyzed. In 4 kennels with affected dogs, the dogs were genotyped. The genetic relationships of all affected dogs and carriers identified were analyzed. The survey revealed 27 affected dogs, but there was a decreasing trend at the end of the study period. The clinical characteristics of these affected dogs were updated in detail. The genotyping survey demonstrated a high mutant allele frequency in examined kennels (34.8%). The pedigree analysis demonstrated that all affected dogs and carriers in Japan are related to some presumptive carriers imported from Oceania and having a common ancestor. The current high prevalence in Japan might be due to an overuse of these carriers by breeders without any knowledge of the disease. For NCL control and prevention, it is necessary to examine all breeding dogs, especially in kennels with a high prevalence. Such endeavors will reduce NCL prevalence and may already be contributing to the recent decreasing trend in Japan. PMID:22919312

  19. Molecular epidemiology and evolution of fish Novirhabdoviruses

    USGS Publications Warehouse

    Kurath, Gael

    2014-01-01

    The genus Novirhabdoviridae contains several of the important rhabdoviruses that infect fish hosts. There are four established virus species: Infectious hematopoietic necrosis virus (IHNV), Viral hemorrhagic septicemia virus (VHSV), Hirame rhabdovirus(HIRRV), and Snakehead rhabdovirus (SHRV). Viruses of these species vary in host and geographic range, and they have all been studied at the molecular and genomic level. As globally significant pathogens of cultured fish, IHNV and VHSV have been particularly well studied in terms of molecular epidemiology and evolution. Phylogenic analyses of hundreds of field isolates have defined five major genogroups of IHNV and four major genotypes of VHSV worldwide. These phylogenies are informed by the known histories of IHNV and VHSV, each involving a series of viral emergence events that are sometimes associated with host switches, most often into cultured rainbow trout. In general, IHNV has relatively low genetic diversity and a narrow host range, and has been spread from its endemic source in North American to Europe and Asia due to aquaculture activities. In contrast, VHSV has broad host range and high genetic diversity, and the source of emergence events is virus in widespread marine fish reservoirs in the northern Atlantic and Pacific Oceans. Common mechanisms of emergence and host switch events include use of raw feed, proximity to wild fish reservoirs of virus, and geographic translocations of virus or naive fish hosts associated with aquaculture.

  20. [Seroepidemiology and molecular epidemiology of enterovirus type 71 in the world and the Russian Federation].

    PubMed

    Akhmadishina, L V; Koroleva, G A; Ivanova, O E; Trotsenko, O E; Mikhaĭlov, M I; Lukashev, A N

    2013-01-01

    A review of recent publications on epidemiology and seroepidemiology of enterovirus type 71 in various regions of the world and authors' own results of study of seroepidemiology and molecular epidemiology of EV71 in Russia are presented. PMID:24605685

  1. Molecular Epidemiology of Mycobacterium avium subsp. paratuberculosis in a Longitudinal Study of Three Dairy Herds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to evaluate whether cows that were low shedders of Mycobacterium avium subsp. paratuberculosis (MAP) were passive shedding animals or whether they were truly infected with MAP. We also evaluated whether these MAP-infected animals could have been infected as adults by ...

  2. Non-maternal transmission is the major mode of ovine lentivirus transmission in a ewe flock: A molecular epidemiology study

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transmission of ovine progressive pneumonia virus (OPPV), a lentivirus of sheep, occurs through both maternal and non-maternal means. Currently, the contribution of each route to the overall flock OPPV prevalence is poorly understood since previous serological epidemiologic studies lacked the abilit...

  3. Phylogenetic and molecular epidemiological studies reveal evidence of multiple past recombination events between infectious laryngotracheitis viruses.

    PubMed

    Lee, Sang-Won; Devlin, Joanne M; Markham, John F; Noormohammadi, Amir H; Browning, Glenn F; Ficorilli, Nino P; Hartley, Carol A; Markham, Philip F

    2013-01-01

    In contrast to the RNA viruses, the genome of large DNA viruses such as herpesviruses have been considered to be relatively stable. Intra-specific recombination has been proposed as an important, but underestimated, driving force in herpesvirus evolution. Recently, two distinct field strains of infectious laryngotracheitis virus (ILTV) have been shown to have arisen from independent recombination events between different commercial ILTV vaccines. In this study we sequenced the genomes of additional ILTV strains and also utilized other recently updated complete genome sequences of ILTV to confirm the existence of a number of ILTV recombinants in nature. Multiple recombination events were detected in the unique long and repeat regions of the genome, but not in the unique short region. Most recombinants contained a pair of crossover points between two distinct lineages of ILTV, corresponding to the European origin and the Australian origin vaccine strains of ILTV. These results suggest that there are two distinct genotypic lineages of ILTV and that these commonly recombine in the field. PMID:23383306

  4. Phylogenetic and Molecular Epidemiological Studies Reveal Evidence of Multiple Past Recombination Events between Infectious Laryngotracheitis Viruses

    PubMed Central

    Lee, Sang-Won; Devlin, Joanne M.; Markham, John F.; Noormohammadi, Amir H.; Browning, Glenn F.; Ficorilli, Nino P.; Hartley, Carol A.; Markham, Philip F.

    2013-01-01

    In contrast to the RNA viruses, the genome of large DNA viruses such as herpesviruses have been considered to be relatively stable. Intra-specific recombination has been proposed as an important, but underestimated, driving force in herpesvirus evolution. Recently, two distinct field strains of infectious laryngotracheitis virus (ILTV) have been shown to have arisen from independent recombination events between different commercial ILTV vaccines. In this study we sequenced the genomes of additional ILTV strains and also utilized other recently updated complete genome sequences of ILTV to confirm the existence of a number of ILTV recombinants in nature. Multiple recombination events were detected in the unique long and repeat regions of the genome, but not in the unique short region. Most recombinants contained a pair of crossover points between two distinct lineages of ILTV, corresponding to the European origin and the Australian origin vaccine strains of ILTV. These results suggest that there are two distinct genotypic lineages of ILTV and that these commonly recombine in the field. PMID:23383306

  5. Physical activity and lung cancer among non-smokers: A pilot molecular epidemiologic study within EPIC

    PubMed Central

    RUNDLE, ANDREW; RICHIE, JOHN; STEINDORF, KAREN; PELUSO, MARCO; OVERVAD, KIM; RAASCHOU-NIELSEN, OLE; CLAVEL-CHAPELON, FRANCOISE; LINSEISEN, JACOB P.; BOEING, HEINER; TRICHOPOULOU, ANTONIA; PALLI, DOMENICO; KROGH, VITTORIO; TUMINO, ROSARIO; PANICO, SALVATORE; BUENO-DE-MESQUITA, HENDRIK B.; PEETERS, PETRA H.; LUND, EILIV; GONZALEZ, CARLOS A.; MARTINEZ, CARMEN; DORRONSORO, MIREN; BARRICARTE, AURELIO; TORMO, M. JOSE; QUIROS, JOSÈ R.; AGUDO, ANTONIO; BERGLUND, GORAN; JARVHOLM, BENGT; BINGHAM, SHEILA; KEY, TIMOTHY J.; GORMALLY, EMMANUELLE; SARACCI, RODOLFO; KAAKS, RUDOLF; RIBOLI, ELIO; VINEIS, PAOLO

    2013-01-01

    The association between physical activity, potential intermediate biomarkers and lung cancer risk was investigated in a study of 230 cases and 648 controls nested within the European Prospective Investigation of Cancer and Nutrition. Data on white blood cell aromatic-DNA adducts by 32P-postlabeling and glutathione (GSH) in red blood cells were available from a subset of cases and controls. Compared to the first quartile, the fourth quartile of recreational physical activity was associated with lower lung cancer risk [odds ratio=0.56 (0.35–0.90)], higher GSH levels [+1.87 micro mole GSH/gram haemoglobin, p=0.04] but not with the presence of high levels of adducts [odds ratio=1.05 (0.38–2.86)]. Despite being associated with recreational physical activity, in these small scale pilot analyses GSH levels were not associated with lung cancer risk, [odds ratio=0.95 (0.84 – 1.07) per unit increase in glutathione levels]. Household and occupational activity was not associated with lung cancer risk or biomarker levels. PMID:20050820

  6. Full-Genome Sequencing as a Basis for Molecular Epidemiology Studies of Bluetongue Virus in India

    PubMed Central

    Maan, Sushila; Maan, Narender S.; Belaganahalli, Manjunatha N.; Rao, Pavuluri Panduranga; Singh, Karam Pal; Hemadri, Divakar; Putty, Kalyani; Kumar, Aman; Batra, Kanisht; Krishnajyothi, Yadlapati; Chandel, Bharat S.; Reddy, G. Hanmanth; Nomikou, Kyriaki; Reddy, Yella Narasimha; Attoui, Houssam; Hegde, Nagendra R.; Mertens, Peter P. C.

    2015-01-01

    Since 1998 there have been significant changes in the global distribution of bluetongue virus (BTV). Ten previously exotic BTV serotypes have been detected in Europe, causing severe disease outbreaks in naïve ruminant populations. Previously exotic BTV serotypes were also identified in the USA, Israel, Australia and India. BTV is transmitted by biting midges (Culicoides spp.) and changes in the distribution of vector species, climate change, increased international travel and trade are thought to have contributed to these events. Thirteen BTV serotypes have been isolated in India since first reports of the disease in the country during 1964. Efficient methods for preparation of viral dsRNA and cDNA synthesis, have facilitated full-genome sequencing of BTV strains from the region. These studies introduce a new approach for BTV characterization, based on full-genome sequencing and phylogenetic analyses, facilitating the identification of BTV serotype, topotype and reassortant strains. Phylogenetic analyses show that most of the equivalent genome-segments of Indian BTV strains are closely related, clustering within a major eastern BTV ‘topotype’. However, genome-segment 5 (Seg-5) encoding NS1, from multiple post 1982 Indian isolates, originated from a western BTV topotype. All ten genome-segments of BTV-2 isolates (IND2003/01, IND2003/02 and IND2003/03) are closely related (>99% identity) to a South African BTV-2 vaccine-strain (western topotype). Similarly BTV-10 isolates (IND2003/06; IND2005/04) show >99% identity in all genome segments, to the prototype BTV-10 (CA-8) strain from the USA. These data suggest repeated introductions of western BTV field and/or vaccine-strains into India, potentially linked to animal or vector-insect movements, or unauthorised use of ‘live’ South African or American BTV-vaccines in the country. The data presented will help improve nucleic acid based diagnostics for Indian serotypes/topotypes, as part of control strategies. PMID

  7. Molecular epidemiology and cancer prevention

    SciTech Connect

    Perera, F.P.; Jeffrey, A.M.; Brandt-Rauf, P.W.; Brenner, D.; Mayer, J.L.; Smith, S.J.; Latriano, L.; Hemminki, K.; Santella, R.M. )

    1990-01-01

    A review of recent studies of biologic markers in populations with model exposures to carcinogens (cigarette smoke and polycyclic aromatic hydrocarbons) illustrates their potential role in cancer prevention. Data on macromolecular adducts and oncogene activation from cross-sectional, serial sampling and case-control studies demonstrate the usefulness of biologic markers in signalling a potential carcinogenic risk and in estimating the magnitude of interindividual variation within exposed groups. Recommendations for future research include nested case-control studies to establish the relationship between markers of biologic dose and effect (e.g., adducts, gene mutation, oncogene activation) and cancer risk. 31 references.

  8. Molecular Epidemiology of Enterococcal Bacteremia in Australia

    PubMed Central

    Pearson, Julie C.; Daley, Denise A.; Le, Tam; Robinson, Owen J.; Gottlieb, Thomas; Howden, Benjamin P.; Johnson, Paul D. R.; Bennett, Catherine M.; Stinear, Timothy P.; Turnidge, John D.

    2014-01-01

    Enterococci are a major cause of health care-associated infections and account for approximately 10% of all bacteremias globally. The aim of this study was to determine the proportion of enterococcal bacteremia isolates in Australia that are antimicrobial resistant, with particular emphasis on susceptibility to ampicillin and the glycopeptides, and to characterize the molecular epidemiology of the Enterococcus faecalis and Enterococcus faecium isolates. From 1 January to 31 December 2011, 1,079 unique episodes of bacteremia were investigated, of which 95.8% were caused by either E. faecalis (61.0%) or E. faecium (34.8%). The majority of bacteremias were health care associated, and approximately one-third were polymicrobial. Ampicillin resistance was detected in 90.4% of E. faecium isolates but was not detected in E. faecalis isolates. Vancomycin nonsusceptibility was reported in 0.6% and 36.5% of E. faecalis and E. faecium isolates, respectively. Unlike Europe and the United States, where vancomycin resistance in E. faecium is predominately due to the acquisition of the vanA operon, 98.4% of E. faecium isolates harboring van genes carried the vanB operon, and 16.1% of the vanB E. faecium isolates had vancomycin MICs at or below the susceptible breakpoint of the CLSI. Although molecular typing identified 126 E. faecalis pulsed-field gel electrophoresis pulsotypes, >50% belonged to two pulsotypes that were isolated across Australia. E. faecium consisted of 73 pulsotypes from which 43 multilocus sequence types were identified. Almost 90% of the E. faecium isolates were identified as CC17 clones, of which approximately half were characterized as ST203, which was isolated Australia-wide. In conclusion, the Australian Enterococcal Sepsis Outcome Programme (AESOP) study has shown that although they are polyclonal, enterococcal bacteremias in Australia are frequently caused by ampicillin-resistant vanB E. faecium. PMID:24391201

  9. MOLECULAR EPIDEMIOLOGY OF BLUETONGUE VIRUS IN NORTHERN COLORADO

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The molecular epidemiology of bluetongue virus serotype 11 in an enzootic focus in northern Colorado was investigated. Viruses isolated up to 12 years apart, from both vertebrate and invertebrate hosts, were compared by genetic analysis. This study demonstrated that multiple genes need to be compa...

  10. MOLECULAR EPIDEMIOLOGY: POTENTIAL IMPACTS ON THE ASSESSMENT OF PUBLIC HEALTH

    EPA Science Inventory

    Introduction

    The term "molecular epidemiology" has been used to cover a broad range of scientific activities, often without specific reference to epidemiology. In fact, as noted by Foxman and Riley [1],molecular epidemiology has often been described almost exclusively in...

  11. Molecular epidemiology, phylogeny and evolution of Legionella.

    PubMed

    Khodr, A; Kay, E; Gomez-Valero, L; Ginevra, C; Doublet, P; Buchrieser, C; Jarraud, S

    2016-09-01

    Legionella are opportunistic pathogens that develop in aquatic environments where they multiply in protozoa. When infected aerosols reach the human respiratory tract they may accidentally infect the alveolar macrophages leading to a severe pneumonia called Legionnaires' disease (LD). The ability of Legionella to survive within host-cells is strictly dependent on the Dot/Icm Type 4 Secretion System that translocates a large repertoire of effectors into the host cell cytosol. Although Legionella is a large genus comprising nearly 60 species that are worldwide distributed, only about half of them have been involved in LD cases. Strikingly, the species Legionella pneumophila alone is responsible for 90% of all LD cases. The present review summarizes the molecular approaches that are used for L. pneumophila genotyping with a major focus on the contribution of whole genome sequencing (WGS) to the investigation of local L. pneumophila outbreaks and global epidemiology studies. We report the newest knowledge regarding the phylogeny and the evolution of Legionella and then focus on virulence evolution of those Legionella species that are known to have the capacity to infect humans. Finally, we discuss the evolutionary forces and adaptation mechanisms acting on the Dot/Icm system itself as well as the role of mobile genetic elements (MGE) encoding T4ASSs and of gene duplications in the evolution of Legionella and its adaptation to different hosts and lifestyles. PMID:27180896

  12. Epidemiologic and Molecular Prognostic Review of Glioblastoma

    PubMed Central

    Thakkar, Jigisha P.; Dolecek, Therese A.; Horbinski, Craig; Ostrom, Quinn T.; Lightner, Donita D.; Barnholtz-Sloan, Jill S.; Villano, John L.

    2014-01-01

    Glioblastoma (GBM) is the most common and aggressive primary CNS malignancy with a median survival of 15 months. The average incidence rate (IR) of GBM is 3.19/100,000 population and the median age of diagnosis is 64 years. Incidence is higher in men and individuals of white race and non-Hispanic ethnicity. Many genetic and environmental factors have been studied in GBM but the majority are sporadic and no risk factor accounting for a large proportion of GBMs has been identified. However, several favorable clinical prognostic factors are identified including, younger age at diagnosis, cerebellar location, high performance status and maximal tumor resection. GBMs comprise of primary and secondary subtypes which evolve through different genetic pathways, affect patients at different ages and have differences in outcomes. We report the current epidemiology of GBM with new data from the Central Brain Tumor Registry of the United States (CBTRUS) 2006–2010 as well as demonstrate and discuss trends in incidence and survival. We also provide a concise review on molecular markers in GBM that have helped distinguish biologically similar subtypes of GBM and have prognostic and predictive value. PMID:25053711

  13. A Multi-Site Study of Norovirus Molecular Epidemiology in Australia and New Zealand, 2013-2014

    PubMed Central

    Lim, Kun Lee; Hewitt, Joanne; Sitabkhan, Alefiya; Eden, John-Sebastian; Lun, Jennifer; Levy, Avram; Merif, Juan; Smith, David; Rawlinson, William D.; White, Peter A.

    2016-01-01

    Background Norovirus (NoV) is the major cause of acute gastroenteritis across all age groups. In particular, variants of genogroup II, genotype 4 (GII.4) have been associated with epidemics globally, occurring approximately every three years. The pandemic GII.4 variant, Sydney 2012, was first reported in early 2012 and soon became the predominant circulating NoV strain globally. Despite its broad impact, both clinically and economically, our understanding of the fundamental diversity and mechanisms by which new NoV strains emerge remains limited. In this study, we describe the molecular epidemiological trends of NoV-associated acute gastroenteritis in Australia and New Zealand between January 2013 and June 2014. Methodology Overall, 647 NoV-positive clinical faecal samples from 409 outbreaks and 238 unlinked cases of acute gastroenteritis were examined by RT-PCR and sequencing. Phylogenetic analysis was then performed to identify NoV capsid genotypes and to establish the temporal dominance of circulating pandemic GII.4 variants. Recombinant viruses were also identified based on analysis of the ORF1/2 overlapping region. Findings Peaks in NoV activity were observed, however the timing of these epidemics varied between different regions. Overall, GII.4 NoVs were the dominant cause of both outbreaks and cases of NoV-associated acute gastroenteritis (63.1%, n = 408/647), with Sydney 2012 being the most common GII.4 variant identified (98.8%, n = 403/408). Of the 409 reported NoV outbreaks, aged-care facilities were the most common setting in both Western Australia (87%, n = 20/23) and New Zealand (58.1%, n = 200/344) while most of the NoV outbreaks were reported from hospitals (38%, n = 16/42) in New South Wales, Australia. An analysis of a subset of non-GII.4 viruses from all locations (125/239) showed the majority (56.8%, n = 71/125) were inter-genotype recombinants. These recombinants were surprisingly diverse and could be classified into 18 distinct recombinant

  14. Review Article: The Role of Molecular Pathological Epidemiology in the Study of Neoplastic and Non-neoplastic Diseases in the Era of Precision Medicine.

    PubMed

    Ogino, Shuji; Nishihara, Reiko; VanderWeele, Tyler J; Wang, Molin; Nishi, Akihiro; Lochhead, Paul; Qian, Zhi Rong; Zhang, Xuehong; Wu, Kana; Nan, Hongmei; Yoshida, Kazuki; Milner, Danny A; Chan, Andrew T; Field, Alison E; Camargo, Carlos A; Williams, Michelle A; Giovannucci, Edward L

    2016-07-01

    Molecular pathology diagnostics to subclassify diseases based on pathogenesis are increasingly common in clinical translational medicine. Molecular pathological epidemiology (MPE) is an integrative transdisciplinary science based on the unique disease principle and the disease continuum theory. While it has been most commonly applied to research on breast, lung, and colorectal cancers, MPE can investigate etiologic heterogeneity in non-neoplastic diseases, such as cardiovascular diseases, obesity, diabetes mellitus, drug toxicity, and immunity-related and infectious diseases. This science can enhance causal inference by linking putative etiologic factors to specific molecular biomarkers as outcomes. Technological advances increasingly enable analyses of various -omics, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, microbiome, immunomics, interactomics, etc. Challenges in MPE include sample size limitations (depending on availability of biospecimens or biomedical/radiological imaging), need for rigorous validation of molecular assays and study findings, and paucities of interdisciplinary experts, education programs, international forums, and standardized guidelines. To address these challenges, there are ongoing efforts such as multidisciplinary consortium pooling projects, the International Molecular Pathological Epidemiology Meeting Series, and the Strengthening the Reporting of Observational Studies in Epidemiology-MPE guideline project. Efforts should be made to build biorepository and biobank networks, and worldwide population-based MPE databases. These activities match with the purposes of the Big Data to Knowledge (BD2K), Genetic Associations and Mechanisms in Oncology (GAME-ON), and Precision Medicine Initiatives of the United States National Institute of Health. Given advances in biotechnology, bioinformatics, and computational/systems biology, there are wide open opportunities in MPE to contribute to public

  15. Molecular Epidemiology of Hemoglobinopathies in Cambodia.

    PubMed

    Munkongdee, Thongperm; Tanakulmas, Jatuporn; Butthep, Punnee; Winichagoon, Pranee; Main, Barbara; Yiannakis, Miriam; George, Joby; Devenish, Robyn; Fucharoen, Suthat; Svasti, Saovaros

    2016-06-01

    Determining the magnitude of the thalassemia problem in a country is important for implementing a national prevention and control program. In order to acquire accurate thalassemia prevalence data, the gene frequency of α- and β-thalassemia (α- and β-thal) in different regions of a country should be determined. The molecular basis of thalassemia in Cambodia was performed by polymerase chain reaction (PCR)-based techniques in a community-based cross-sectional survey of 1631 unrelated individuals from three regions, Battambang, Preah Vihear and Phnom Penh. Thalassemia mutations were detected in 62.7% of the three studied population of Cambodia. Hb E (HBB: c.79G > A) was the most common β-globin gene mutation with a frequency ranging from 0.139 to 0.331, while the most frequent α-globin gene mutation was the -α(3.7) (rightward) deletion (0.098-0.255). The other frequencies were 0.001-0.003 for β-thal, 0.008-0.011 for α-thal-1 (- -(SEA)), 0.003-0.008 for α-thal-2 [-α(4.2) (leftward deletion)], 0.021-0.044 for Hb Constant Spring (Hb CS, HBA2: c.427T > C) and 0.009-0.036 for Hb Paksé (HBA2: c.429A > T). A regional specific thalassemia gene frequency was observed. Preah Vihear had the highest prevalence of Hb E (55.9%), α-thal-2 (24.0%) and nondeletional α-thal (15.1%), whereas Phnom Penh had the lowest frequency of thalassemia genes. Interestingly, in Preah Vihear, the frequency of Hb Paksé was extremely high (0.036), almost equivalent to that of Hb CS (0.044). Our results indicate the importance of micromapping and epidemiology studies of thalassemia, which will assist in establishing the national prevention and control program in Cambodia. PMID:27117566

  16. 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

  17. Molecular Epidemiology of Mycobacterium bovis in Humans and Cattle.

    PubMed

    El-Sayed, A; El-Shannat, S; Kamel, M; Castañeda-Vazquez, M A; Castañeda-Vazquez, H

    2016-06-01

    Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis), is a serious re-emerging disease in both animals and humans. The evolution of the Multi- and Extensively drug-resistant M. bovis strains (MDR-TB and XDR-TB) represents a global threat to public health. Worldwide, the disease is responsible for great economic losses in the veterinary field, serious threat to the ecosystem, and about 3.1% of human TB cases, up to 16% in Tanzania. Only thorough investigation to understand the pathogen's epidemiology can help in controlling the disease and minimizing its threat. For this purpose, various tools have been developed for use in advanced molecular epidemiological studies of bTB, either alone or in combination with standard conventional epidemiological approaches. These techniques enable the analysis of the intra- and inter-species transmission dynamics of bTB. The delivered data can reveal detailed insights into the source of infection, correlations among human and bovine isolates, strain diversity and evolution, spread, geographical localization, host preference, tracing of certain virulence factors such as antibiotic resistance genes, and finally the risk factors for the maintenance and spread of M. bovis. They also allow for the determination of epidemic and endemic strains. This, in turn, has a significant diagnostic impact and helps in vaccine development for bTB eradication programs. The present review discusses many topics including the aetiology, epidemiology and importance of M. bovis, the prevalence of bTB in humans and animals in various countries, the molecular epidemiology of M. bovis, and finally applied molecular epidemiological techniques. PMID:26684712

  18. Molecular Epidemiology of Human Intestinal Amoebas in Iran

    PubMed Central

    Hooshyar, H; Rostamkhani, P; Rezaian, M

    2012-01-01

    Many microscopic-based epidemiological surveys on the prevalence of human intestinal pathogenic and non-pathogenic protozoa including intestinal amoeba performed in Iran show a high prevalence of human intestinal amoeba in different parts of Iran. Such epidemiological studies on amoebiasis are confusing, mainly due to recently appreciated distinction between the Entamoeba histolytica, E. dispar and E. moshkovskii. Differential diagnosis can be done by some methods such as PCR-based methods, monoclonal antibodies and the analysis of isoenzyme typing, however the molecular study of these protozoa in Iran is low. Based on molecular studies, it seems that E. dispar is predominant species especially in the central and northern areas of Iran and amoebiasis due to E. histolytica is a rare infection in the country. It is suggested that infection with E. moshkovskii may be common among Iranians. Considering the importance of molecular epidemiology of amoeba in Iran and also the current data, the present study reviews the data currently available on the molecular distribution of intestinal human amoeba in Iran. PMID:23193500

  19. Zoonotic Potential and Molecular Epidemiology of Giardia Species and Giardiasis†

    PubMed Central

    Feng, Yaoyu; Xiao, Lihua

    2011-01-01

    Summary: Molecular diagnostic tools have been used recently in assessing the taxonomy, zoonotic potential, and transmission of Giardia species and giardiasis in humans and animals. The results of these studies have firmly established giardiasis as a zoonotic disease, although host adaptation at the genotype and subtype levels has reduced the likelihood of zoonotic transmission. These studies have also identified variations in the distribution of Giardia duodenalis genotypes among geographic areas and between domestic and wild ruminants and differences in clinical manifestations and outbreak potentials of assemblages A and B. Nevertheless, our efforts in characterizing the molecular epidemiology of giardiasis and the roles of various animals in the transmission of human giardiasis are compromised by the lack of case-control and longitudinal cohort studies and the sampling and testing of humans and animals living in the same community, the frequent occurrence of infections with mixed genotypes and subtypes, and the apparent heterozygosity at some genetic loci for some G. duodenalis genotypes. With the increased usage of multilocus genotyping tools, the development of next-generation subtyping tools, the integration of molecular analysis in epidemiological studies, and an improved understanding of the population genetics of G. duodenalis in humans and animals, we should soon have a better appreciation of the molecular epidemiology of giardiasis, the disease burden of zoonotic transmission, the taxonomy status and virulences of various G. duodenalis genotypes, and the ecology of environmental contamination. PMID:21233509

  20. Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management

    PubMed Central

    Grossmann, Sebastian; Nowak, Piotr; Neogi, Ujjwal

    2015-01-01

    Introduction HIV-1 near full-length genome (HIV-NFLG) sequencing from plasma is an attractive multidimensional tool to apply in large-scale population-based molecular epidemiological studies. It also enables genotypic resistance testing (GRT) for all drug target sites allowing effective intervention strategies for control and prevention in high-risk population groups. Thus, the main objective of this study was to develop a simplified subtype-independent, cost- and labour-efficient HIV-NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies. Methods Plasma samples (n=30) were obtained from HIV-1B (n=10), HIV-1C (n=10), CRF01_AE (n=5) and CRF01_AG (n=5) infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV-NFLG. GRT was validated against ViroSeq™ HIV-1 Genotyping System. Results After excluding four plasma samples with low-quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92%) samples with the lowest viral load being 3000 copies/ml. High (>99%) concordance was observed between HIV-NFLG and ViroSeq™ when determining the drug resistance mutations (DRMs). The N384I connection mutation was additionally detected by NFLG in two samples. Conclusions Our high efficiency subtype-independent HIV-NFLG is a simple and promising approach to be used in large-scale molecular epidemiological studies. It will facilitate the understanding of the HIV-1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay. PMID:26115688

  1. Malaria Molecular Epidemiology: Lessons from the International Centers of Excellence for Malaria Research Network

    PubMed Central

    Escalante, Ananias A.; Ferreira, Marcelo U.; Vinetz, Joseph M.; Volkman, Sarah K.; Cui, Liwang; Gamboa, Dionicia; Krogstad, Donald J.; Barry, Alyssa E.; Carlton, Jane M.; van Eijk, Anna Maria; Pradhan, Khageswar; Mueller, Ivo; Greenhouse, Bryan; Andreina Pacheco, M.; Vallejo, Andres F.; Herrera, Socrates; Felger, Ingrid

    2015-01-01

    Molecular epidemiology leverages genetic information to study the risk factors that affect the frequency and distribution of malaria cases. This article describes molecular epidemiologic investigations currently being carried out by the International Centers of Excellence for Malaria Research (ICEMR) network in a variety of malaria-endemic settings. First, we discuss various novel approaches to understand malaria incidence and gametocytemia, focusing on Plasmodium falciparum and Plasmodium vivax. Second, we describe and compare different parasite genotyping methods commonly used in malaria epidemiology and population genetics. Finally, we discuss potential applications of molecular epidemiological tools and methods toward malaria control and elimination efforts. PMID:26259945

  2. Molecular epidemiology of PRRSV: a phylogenetic perspective.

    PubMed

    Shi, Mang; Lam, Tommy Tsan-Yuk; Hon, Chung-Chau; Hui, Raymond Kin-Hei; Faaberg, Kay S; Wennblom, Trevor; Murtaugh, Michael P; Stadejek, Tomasz; Leung, Frederick Chi-Ching

    2010-12-01

    Since its first discovery two decades ago, porcine reproductive and respiratory syndrome virus (PRRSV) has been the subject of intensive research due to its huge impact on the worldwide swine industry. Thanks to the phylogenetic analyses, much has been learned concerning the genetic diversity and evolution history of the virus. In this review, we focused on the evolutionary and epidemiological aspects of PRRSV from a phylogenetic perspective. We first described the diversity and transmission dynamics of Type 1 and 2 PRRSV, respectively. Then, we focused on the more ancient evolutionary history of PRRSV: the time of onset of all existing PRRSV and an origin hypothesis were discussed. Finally, we summarized the results from previous recombination studies to assess the potential impact of recombination on the virus epidemiology. PMID:20837072

  3. The Role of Epidemiology in the Era of Molecular Epidemiology and Genomics: Summary of the 2013 AJE-sponsored Society of Epidemiologic Research Symposium

    PubMed Central

    Kuller, Lewis H.; Bracken, Michael B.; Ogino, Shuji; Prentice, Ross L.; Tracy, Russell P.

    2013-01-01

    On June 20, 2013, the American Journal of Epidemiology sponsored a symposium at the Society for Epidemiologic Research's 46th Annual Meeting in Boston, Massachusetts, entitled, “What Is the Role of Epidemiology in the Era of Molecular Biology and Genomics?” The future of epidemiology depends on innovation in generating interesting and important testable hypotheses that are relevant to population health. These new strategies will depend on new technology, both in measurement of agents and environment and in the fields of pathophysiology and outcomes, such as cellular epidemiology and molecular pathology. The populations to be studied, sample sizes, and study designs should be selected based on the hypotheses to be tested and include case-control, cohort, and clinical trials. Developing large mega cohorts without attention to specific hypotheses is inefficient, will fail to address many associations with high-quality data, and may well produce spurious results. PMID:24105654

  4. Idiopathic environmental intolerances (IEI): from molecular epidemiology to molecular medicine.

    PubMed

    De Luca, C; Scordo, G; Cesareo, E; Raskovic, D; Genovesi, G; Korkina, L

    2010-07-01

    Inherited or acquired impairment of xenobiotics metabolism is a postulated mechanism underlying environment-associated pathologies such as multiple chemical sensitivity, fibromyalgia, chronic fatigue syndrome, dental amalgam disease, and others, also collectively named idiopathic environmental intolerances (IEI). In view of the poor current knowledge of their etiology and pathogenesis, and the absence of recognised genetic and metabolic markers of the diseases. They are often considered "medically unexplained syndromes",. These disabling conditions share the features of polysymptomatic multi-organ syndromes, considered by part of the medical community to be aberrant responses triggered by exposure to low-dose organic and inorganic chemicals and metals, in concentrations far below average reference levels admitted for environmental toxicants. A genetic predisposition to altered biotransformation of environmental chemicals, drugs, and metals, and of endogenous low-molecular weight metabolites, caused by polymorphisms of genes coding for xenobiotic metabolizing enzymes, their receptors and transcription factors appears to be involved in the susceptibility to these environment-associated pathologies, along with epigenetic factors. Free radical/antioxidant homeostasis may also be heavily implicated, indirectly by affecting the regulation of xenobiotic metabolizing enzymes, and directly by causing increased levels of oxidative products, implicated in the chronic damage of cells and tissues, which is in part correlated with clinical symptoms. More systematic studies of molecular epidemiology, toxico- and pharmaco-genomics, elucidating the mechanisms of regulation, expression, induction, and activity of antioxidant/detoxifying enzymes, and the possible role of inflammatory mediators, promise a better understanding of this pathologically increased sensitivity to low-level chemical stimuli, and a solid basis for effective individualized antioxidant- and/or chelator

  5. Tumor-based case-control studies of infection and cancer: muddling the when and where of molecular epidemiology.

    PubMed

    Engels, Eric A; Wacholder, Sholom; Katki, Hormuzd A; Chaturvedi, Anil K

    2014-10-01

    We describe the "tumor-based case-control" study as a type of epidemiologic study used to evaluate associations between infectious agents and cancer. These studies assess exposure using diseased tissues from affected individuals (i.e., evaluating tumor tissue for cancer cases), but they must utilize nondiseased tissues to assess control subjects, who do not have the disease of interest. This approach can lead to exposure misclassification in two ways. First, concerning the "when" of exposure assessment, retrospective assessment of tissues may not accurately measure exposure at the key earlier time point (i.e., during the etiologic window). Second, concerning the "where" of exposure assessment, use of different tissues in cases and controls can have different accuracy for detecting the exposure (i.e., differential exposure misclassification). We present an example concerning the association of human papillomavirus with various cancers, where tumor-based case-control studies likely overestimate risk associated with infection. In another example, we illustrate how tumor-based case-control studies of Helicobacter pylori and gastric cancer underestimate risk. Tumor-based case-control studies can demonstrate infection within tumor cells, providing qualitative information about disease etiology. However, measures of association calculated in tumor-based case-control studies are prone to over- or underestimating the relationship between infections and subsequent cancer risk. PMID:25063520

  6. Molecular epidemiology of infectious laryngotracheitis: a review.

    PubMed

    Menendez, Kimberly R; García, Maricarmen; Spatz, Stephen; Tablante, Nathaniel L

    2014-01-01

    Infectious laryngotracheitis (ILT) is an economically important respiratory disease of poultry that affects the poultry industry worldwide. The disease is caused by gallid herpesvirus I (GaHV-1), a member of the genus Iltovirus, family Herpesviridae, subfamily Alphaherpesvirinae. The current incidence of the disease is heavily influenced by live attenuated vaccines, which have been used extensively since their introduction in the mid-twentieth century. The capability of current live attenuated vaccine viruses to revert to virulence and spread from bird to bird has shaped the molecular epidemiology of ILT. Because of the antigenic homogeneity among GaHV-1 strains, differentiation of strains has been achieved by targeting genomic differences between outbreak-related isolates and vaccine strains. Numerous genes and genomic regions have been utilized in the development of DNA-based diagnostic assays to differentiate outbreak-related isolates from vaccine strains in countries where ILT outbreaks have occurred. More recently, full genome sequences have allowed determination of the origin of some of the outbreak-related isolates circulating in some poultry production countries. Overall, molecular typing data collected worldwide have identified live attenuated vaccine-related isolates as the primary source for outbreaks of the disease. PMID:24460399

  7. Molecular Epidemiology of Invasive Listeriosis due to Listeria monocytogenes in a Spanish Hospital over a Nine-Year Study Period, 2006–2014

    PubMed Central

    Ariza-Miguel, Jaime; Fernández-Natal, María Isabel; Soriano, Francisco; Hernández, Marta; Stessl, Beatrix; Rodríguez-Lázaro, David

    2015-01-01

    We investigated the pathogenicity, invasiveness, and genetic relatedness of 17 clinical Listeria monocytogenes stains isolated over a period of nine years (2006–2014). All isolates were phenotypically characterised and growth patterns were determined. The antimicrobial susceptibility of L. monocytogenes isolates was determined in E-tests. Invasion assays were performed with epithelial HeLa cells. Finally, L. monocytogenes isolates were subtyped by PFGE and MLST. All isolates had similar phenotypic characteristics (β-haemolysis and lecithinase activity), and three types of growth curve were observed. Bacterial recovery rates after invasion assays ranged from 0.09% to 7.26% (1.62 ± 0.46). MLST identified 11 sequence types (STs), and 14 PFGE profiles were obtained, indicating a high degree of genetic diversity. Genetic studies unequivocally revealed the occurrence of one outbreak of listeriosis in humans that had not previously been reported. This outbreak occurred in October 2009 and affected three patients from neighbouring towns. In conclusion, the molecular epidemiological analysis clearly revealed a cluster (three human cases, all ST1) of not previously reported listeriosis cases in northwestern Spain. Our findings indicate that molecular subtyping, in combination with epidemiological case analysis, is essential and should be implemented in routine diagnosis, to improve the tracing of the sources of outbreaks. PMID:26539467

  8. [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. PMID:27087232

  9. Nationwide Study of the Prevalence, Characteristics, and Molecular Epidemiology of Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae in France▿

    PubMed Central

    Galas, Muriel; Decousser, Jean-Winoc; Breton, Nelly; Godard, Thierry; Allouch, Pierre Yves; Pina, Patrick

    2008-01-01

    Among 10,872 isolates of Enterobacteriaceae from a nationwide study of 88 French hospitals in 2005, 169 (1.7%) expressed an extended-spectrum β-lactamase. The most prevalent species were Escherichia coli (48.5%), Enterobacter aerogenes (23.7%), and Klebsiella pneumoniae (14.8%). Molecular analysis underlined the polyclonal spread of CTX-M-expressing E. coli, primarily isolates of the CTX-M-1 subgroup. PMID:18025119

  10. Application of PCR-SSCP for molecular epidemiological studies on the exposure of farm children to bacteria in environmental dust.

    PubMed

    Korthals, Melanie; Ege, Markus J; Tebbe, Christoph C; von Mutius, Erika; Bauer, Johann

    2008-04-01

    epidemiological studies characterizing the exposure of farmers using environmental dust. PMID:18321601

  11. How to assess epidemiological studies

    PubMed Central

    Zaccai, J

    2004-01-01

    Assessing the quality of an epidemiological study equates to assessing whether the inferences drawn from it are warranted when account is taken of the methods, the representativeness of the study sample, and the nature of the population from which it is drawn. Bias, confounding, and chance can threaten the quality of an epidemiological study at all its phases. Nevertheless, their presence does not necessarily imply that a study should be disregarded. The reader must first balance any of these threats or missing information with their potential impact on the conclusions of the report. PMID:15016934

  12. Molecular Epidemiology of Candida albicans and Its Closely Related Yeasts Candida dubliniensis and Candida africana▿

    PubMed Central

    Romeo, Orazio; Criseo, Giuseppe

    2009-01-01

    We performed a molecular study to determine the occurrence of Candida albicans, Candida africana, and Candida dubliniensis in different clinical samples. The study provides new insights into the epidemiology of candidiasis in hospitalized patients in three hospitals in southern Italy. It also reports the first detailed epidemiological data concerning the occurrence of C. africana in clinical samples. PMID:18987171

  13. Molecular epidemiology of Candida albicans and its closely related yeasts Candida dubliniensis and Candida africana.

    PubMed

    Romeo, Orazio; Criseo, Giuseppe

    2009-01-01

    We performed a molecular study to determine the occurrence of Candida albicans, Candida africana, and Candida dubliniensis in different clinical samples. The study provides new insights into the epidemiology of candidiasis in hospitalized patients in three hospitals in southern Italy. It also reports the first detailed epidemiological data concerning the occurrence of C. africana in clinical samples. PMID:18987171

  14. The epidemiology and molecular mechanisms linking obesity, diabetes, and cancer.

    PubMed

    Ferguson, Rosalyn D; Gallagher, Emily J; Scheinman, Eyal J; Damouni, Rawan; LeRoith, Derek

    2013-01-01

    The worldwide epidemic of obesity is associated with increasing rates of the metabolic syndrome and type 2 diabetes. Epidemiological studies have reported that these conditions are linked to increased rates of cancer incidence and mortality. Obesity, particularly abdominal obesity, is associated with insulin resistance and the development of dyslipidemia, hyperglycemia, and ultimately type 2 diabetes. Although many metabolic abnormalities occur with obesity and type 2 diabetes, insulin resistance and hyperinsulinemia appear to be central to these conditions and may contribute to dyslipidemia and altered levels of circulating estrogens and androgens. In this review, we will discuss the epidemiological and molecular links between obesity, type 2 diabetes, and cancer, and how hyperinsulinemia and dyslipidemia may contribute to cancer development. We will discuss how these metabolic abnormalities may interact with estrogen signaling in breast cancer growth. Finally, we will discuss the effects of type 2 diabetes medications on cancer risk. PMID:23810003

  15. Use of Case Studies to Introduce Undergraduate Students to Principles of Food Microbiology, Molecular Biology, and Epidemiology of Food-Borne Disease

    ERIC Educational Resources Information Center

    Ponder, Monica A.; Sumner, Susan

    2009-01-01

    Mock outbreaks of infectious disease offer the ability to introduce principles of food microbiology, ecology, and epidemiology to undergraduate students using an inquiry driven process. Students were presented with an epidemiological case study detailing patient history, clinical presentation, and foods recently consumed. The students then had to…

  16. SITVITWEB--a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology.

    PubMed

    Demay, Christophe; Liens, Benjamin; Burguière, Thomas; Hill, Véronique; Couvin, David; Millet, Julie; Mokrousov, Igor; Sola, Christophe; Zozio, Thierry; Rastogi, Nalin

    2012-06-01

    Among various genotyping methods to study Mycobacterium tuberculosis complex (MTC) genotypic polymorphism, spoligotyping and mycobacterial interspersed repetitive units-variable number of DNA tandem repeats (MIRU-VNTRs) have recently gained international approval as robust, fast, and reproducible typing methods generating data in a portable format. Spoligotyping constituted the backbone of a publicly available database SpolDB4 released in 2006; nonetheless this method possesses a low discriminatory power when used alone and should be ideally used in conjunction with a second typing method such as MIRU-VNTRs for high-resolution epidemiological studies. We hereby describe a publicly available international database named SITVITWEB which incorporates such multimarker data allowing to have a global vision of MTC genetic diversity worldwide based on 62,582 clinical isolates corresponding to 153 countries of patient origin (105 countries of isolation). We report a total of 7105 spoligotype patterns (corresponding to 58,180 clinical isolates) - grouped into 2740 shared-types or spoligotype international types (SIT) containing 53,816 clinical isolates and 4364 orphan patterns. Interestingly, only 7% of the MTC isolates worldwide were orphans whereas more than half of SITed isolates (n=27,059) were restricted to only 24 most prevalent SITs. The database also contains a total of 2379 MIRU patterns (from 8161 clinical isolates) from 87 countries of patient origin (35 countries of isolation); these were grouped in 847 shared-types or MIRU international types (MIT) containing 6626 isolates and 1533 orphan patterns. Lastly, data on 5-locus exact tandem repeats (ETRs) were available on 4626 isolates from 59 countries of patient origin (22 countries of isolation); a total of 458 different VNTR patterns were observed - split into 245 shared-types or VNTR International Types (VIT) containing 4413 isolates) and 213 orphan patterns. Datamining of SITVITWEB further allowed to update

  17. Twin Studies: A Unique Epidemiological Tool

    PubMed Central

    Sahu, Monalisha; Prasuna, Josyula G

    2016-01-01

    Twin studies are a special type of epidemiological studies designed to measure the contribution of genetics as opposed to the environment, to a given trait. Despite the facts that the classical twin studies are still being guided by assumptions made back in the 1920s and that the inherent limitation lies in the study design itself, the results suggested by earlier twin studies have often been confirmed by molecular genetic studies later. Use of twin registries and various innovative yet complex software packages such as the (SAS) and their extensions (e.g., SAS PROC GENMOD and SAS PROC PHREG) has increased the potential of this epidemiological tool toward contributing significantly to the field of genetics and other life sciences. PMID:27385869

  18. The contribution of molecular epidemiology to the understanding and control of viral diseases of salmonid aquaculture

    PubMed Central

    2011-01-01

    Molecular epidemiology is a science which utilizes molecular biology to define the distribution of disease in a population (descriptive epidemiology) and relies heavily on integration of traditional (or analytical) epidemiological approaches to identify the etiological determinants of this distribution. The study of viral pathogens of aquaculture has provided many exciting opportunities to apply such tools. This review considers the extent to which molecular epidemiological studies have contributed to better understanding and control of disease in aquaculture, drawing on examples of viral diseases of salmonid fish of commercial significance including viral haemorrhagic septicaemia virus (VHSV), salmonid alphavirus (SAV) and infectious salmon anaemia virus (ISAV). Significant outcomes of molecular epidemiological studies include: Improved taxonomic classification of viruses A better understanding of the natural distribution of viruses An improved understanding of the origins of viral pathogens in aquaculture An improved understanding of the risks of translocation of pathogens outwith their natural host range An increased ability to trace the source of new disease outbreaks Development of a basis for ensuring development of appropriate diagnostic tools An ability to classify isolates and thus target future research aimed at better understanding biological function While molecular epidemiological studies have no doubt already made a significant contribution in these areas, the advent of new technologies such as pyrosequencing heralds a quantum leap in the ability to generate descriptive molecular sequence data. The ability of molecular epidemiology to fulfil its potential to translate complex disease pathways into relevant fish health policy is thus unlikely to be limited by the generation of descriptive molecular markers. More likely, full realisation of the potential to better explain viral transmission pathways will be dependent on the ability to assimilate and

  19. Molecular epidemiology of canine parvovirus in Morocco.

    PubMed

    Amrani, Nadia; Desario, Costantina; Kadiri, Ahlam; Cavalli, Alessandra; Berrada, Jaouad; Zro, Khalil; Sebbar, Ghizlane; Colaianni, Maria Loredana; Parisi, Antonio; Elia, Gabriella; Buonavoglia, Canio; Malik, Jamal; Decaro, Nicola

    2016-07-01

    Since it first emergence in the mid-1970's, canine parvovirus 2 (CPV-2) has evolved giving rise to new antigenic variants termed CPV-2a, CPV-2b and CPV-2c, which have completely replaced the original strain and had been variously distributed worldwide. In Africa limited data are available on epidemiological prevalence of these new types. Hence, the aim of the present study was to determine circulating variants in Morocco. Through TaqMan-based real-time PCR assay, 91 samples, collected from symptomatic dogs originating from various cities between 2011 and 2015, were diagnosed. Positive specimens were characterised by means of minor groove binder (MGB) probe PCR. The results showed that all samples but one (98.9%) were CPV positive, of which 1 (1.1%) was characterised as CPV-2a, 43 (47.7%) as CPV-2b and 39 (43.3%) as CPV-2c. Interestingly, a co-infection with CPV-2b and CPV-2c was detected in 4 (4.4%) samples and 3 (3.3%) samples were not characterised. Sequencing of the full VP2 gene revealed these 3 uncharacterised strains as CPV-2c, displaying a change G4068A responsible for the replacement of aspartic acid with asparagine at residue 427, impacting the MGB probe binding. In this work we provide a better understanding of the current status of prevailing CPV strains in northern Africa. PMID:27083072

  20. Vitamin D and colorectal cancer: molecular, epidemiological and clinical evidence.

    PubMed

    Dou, Ruoxu; Ng, Kimmie; Giovannucci, Edward L; Manson, JoAnn E; Qian, Zhi Rong; Ogino, Shuji

    2016-05-01

    In many cells throughout the body, vitamin D is converted into its active form calcitriol and binds to the vitamin D receptor (VDR), which functions as a transcription factor to regulate various biological processes including cellular differentiation and immune response. Vitamin D-metabolising enzymes (including CYP24A1 and CYP27B1) and VDR play major roles in exerting and regulating the effects of vitamin D. Preclinical and epidemiological studies have provided evidence for anti-cancer effects of vitamin D (particularly against colorectal cancer), although clinical trials have yet to prove its benefit. In addition, molecular pathological epidemiology research can provide insights into the interaction of vitamin D with tumour molecular and immunity status. Other future research directions include genome-wide research on VDR transcriptional targets, gene-environment interaction analyses and clinical trials on vitamin D efficacy in colorectal cancer patients. In this study, we review the literature on vitamin D and colorectal cancer from both mechanistic and population studies and discuss the links and controversies within and between the two parts of evidence. PMID:27245104

  1. 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. PMID:27108539

  2. Colorectal Cancer in Iran: Molecular Epidemiology and Screening Strategies

    PubMed Central

    Dolatkhah, Roya; Somi, Mohammad Hossein; Bonyadi, Mortaza Jabbarpour; Asvadi Kermani, Iraj; Farassati, Faris; Dastgiri, Saeed

    2015-01-01

    Purpose. The increasing incidence of colorectal cancer (CRC) in the past three decades in Iran has made it a major public health burden. This study aimed to report its epidemiologic features, molecular genetic aspects, survival, heredity, and screening pattern in Iran. Methods. A comprehensive literature review was conducted to identify the relevant published articles. We used medical subject headings, including colorectal cancer, molecular genetics, KRAS and BRAF mutations, screening, survival, epidemiologic study, and Iran. Results. Age standardized incidence rate of Iranian CRCs was 11.6 and 10.5 for men and women, respectively. Overall five-year survival rate was 41%, and the proportion of CRC among the younger age group was higher than that of western countries. Depending on ethnicity, geographical region, dietary, and genetic predisposition, mutation genes were considerably diverse and distinct among CRCs across Iran. The high occurrence of CRC in records of relatives of CRC patients showed that family history of CRC was more common among young CRCs. Conclusion. Appropriate screening strategies for CRC which is amenable to early detection through screening, especially in relatives of CRCs, should be considered as the first step in CRC screening programs. PMID:25685149

  3. Analysis of phenanthrene diol epoxide mercapturic acid detoxification products in human urine: relevance to molecular epidemiology studies of glutathione S-transferase polymorphisms

    PubMed Central

    Hecht, Stephen S.; Villalta, Peter W.; Hochalter, J.Bradley

    2008-01-01

    Many studies have investigated the effects of glutathione S-transferase (GST) polymorphisms on cancer incidence in people exposed to carcinogenic polycyclic aromatic hydrocarbons (PAHs). The basis for this is that the carcinogenic bay region diol epoxide metabolites of several PAH are detoxified by GSTs in in vitro studies. However, there are no reports in the literature on the identification in urine of the mercapturic acid metabolites that would result from this process in humans. We addressed this by developing a method for quantitation in human urine of mercapturic acids which would be formed from angular ring diol epoxides of phenanthrene (Phe), the simplest PAH with a bay region, and a common environmental pollutant. We prepared standard mercapturic acids by reactions of syn- or anti-Phe-1,2-diol-3,4-epoxide and syn- or anti-Phe-3,4-diol-1,2-epoxide with N-acetylcysteine. Analysis of human urine conclusively demonstrated that the only detectable mercapturic acid of this type—N-acetyl-S-(r-4,t-2,3-trihydroxy-1,2,3,4-tetrahydro-c/t-1-phenanthryl)-L-cysteine (anti-PheDE-1-NAC)—was derived from the ‘reverse diol epoxide’, anti-Phe-3,4-diol-1,2-epoxide, and not from the bay region diol epoxides, syn- or anti-Phe-1,2-diol-3,4-epoxide. Levels of anti-PheDE-1-NAC in the urine of 36 smokers were (mean ± SD) 728 ± 859 fmol/ml urine. The results of this study provide the first evidence for a mercapturic acid of a PAH diol epoxide in human urine, but it was not derived from a bay region diol epoxide as molecular epidemiologic studies have presumed, but rather from a reverse diol epoxide, representative of metabolites with little if any carcinogenic activity. These results demonstrate the need for integration of genotyping and phenotyping information in molecular epidemiology studies. PMID:18477646

  4. Epidemiology and molecular pathology of gallbladder cancer.

    PubMed

    Lazcano-Ponce, E C; Miquel, J F; Muñoz, N; Herrero, R; Ferrecio, C; Wistuba, I I; Alonso de Ruiz, P; Aristi Urista, G; Nervi, F

    2001-01-01

    Gallbladder cancer is usually associated with gallstone disease, late diagnosis, unsatisfactory treatment, and poor prognosis. We report here the worldwide geographical distribution of gallbladder cancer, review the main etiologic hypotheses, and provide some comments on perspectives for prevention. The highest incidence rate of gallbladder cancer is found among populations of the Andean area, North American Indians, and Mexican Americans. Gallbladder cancer is up to three times higher among women than men in all populations. The highest incidence rates in Europe are found in Poland, the Czech Republic, and Slovakia. Incidence rates in other regions of the world are relatively low. The highest mortality rates are also reported from South America, 3.5-15.5 per 100,000 among Chilean Mapuche Indians, Bolivians, and Chilean Hispanics. Intermediate rates, 3.7 to 9.1 per 100,000, are reported from Peru, Ecuador, Colombia, and Brazil. Mortality rates are low in North America, with the exception of high rates among American Indians in New Mexico (11.3 per 100,000) and among Mexican Americans. The main associated risk factors identified so far include cholelithiasis (especially untreated chronic symptomatic gallstones), obesity, reproductive factors, chronic infections of the gallbladder, and environmental exposure to specific chemicals. These suspected factors likely represent promoters of carcinogenesis. The main limitations of epidemiologic studies on gallbladder cancer are the small sample sizes and specific problems in quantifying exposure to putative risk factors. The natural history of gallbladder disease should be characterized to support the allocation of more resources for early treatment of symptomatic gallbladder disease in high-risk populations. Secondary prevention of gallbladder cancer could be effective if supported by cost-effective studies of prophylactic cholecystectomy among asymptomatic gallstone patients in high-risk areas. PMID:11760569

  5. [Lichen striatus. Epidemiologic study].

    PubMed

    Sittart, J A; Pegas, J R; Sant'Ana, L A; Pires, M C

    1989-01-01

    The authors are showing a retrospective study of 53 cases of lichen striatus concerning sex, colour, age, place of lesions, associated diseases and period of the year of occurrence of the dermatosis. There was a larger number of cases in females of white race and age-between 2 and 5 years old. A greater occurrence was observed in the months of September and March which correspond to spring and summer. Adding the fact that there have been more cases in children, at times in brothers and the trend to spontaneous involution, the authors suggest the possibility of a virus as etiology to this entity. PMID:2666785

  6. Epidemiological studies in psychosomatic medicine.

    PubMed

    Eastwood, M R

    1975-01-01

    The epidemiological triad of host, agent and environment used conceptually in infectious disease may serve as a model for psychosomatic disorders, despite the involvement of many more variables. There are major problems with diagnosis and measurement, however, and the term "psychosomatic" has several meanings. The two main senses are "specific" psychosomatic disorders and an ecological view of illness. The association between psychiatric and physical disorder has been examined in a variety of settings and the findings have suggested that there is a positive relationship. Despite considerable methodological and sampling difficulties in epidemiological research into psychosomatic illness, recent efforts have been made to overcome these. The results of ecological studies appear to be more consistent that those dealing with "specific" psychosomatic disorders and suggest that man has a general psychophysical propensity to disease. Although physical and mental illness do seem to be intimately linked, the reasons for "vulnerability" to illness and "clustering" of illness are obscure. The clarification of these areas appears to be the main task ahead for epidemiology in the field of psychosomatic medicine. PMID:773850

  7. [Molecular epidemiology of cystic fibrosis in Tunisia].

    PubMed

    Messaoud, T; Bel Haj Fredj, S; Bibi, A; Elion, J; Férec, C; Fattoum, S

    2005-01-01

    Cystic fibrosis is the most frequent autosomal recessive genetic disease in North European population. This pathology seems to not be rare in Tunisia. On another hand, development of molecular biology techniques has largely contributed to implement the study of the different mutations in the CFTR gene where over 1,300 mutations were reported. Herein, we describe the strategy used to detect molecular defects responsible of cystic fibrosis on 390 children (383 families) in Tunisian population. Several techniques were performed for genotype diagnosis: DNA extraction was from peripheral blood. Polymerase chain reaction (PCR) and polyacylamide gel electrophoresis, and reverse dot blot procedures were used to detect known point mutations. Denaturant gradient gel electrophoresis (DGGE) were used in a next step searching for the unknown point mutations that are later identified by automated sequencing on ABIprism 310. This strategy allowed us to detect 17 different mutations located on the different exons of the CFTR gene. The most frequent was the F508del (50.74%) followed by three other mutations (G542X, W1282X and N1303K) known to be common in the Mediterranean area. For mutations (T665S, 2766 del8, F1166C, L1043R) were exclusively found, up to now, in the Tunisian population. Our results permitted to establish cystic fibrosis mutations and their distribution in Tunisia and to implement an appropriate prevention program of these diseases through the genetic council and prenatal diagnosis. PMID:16330381

  8. The Current Status of the Disease Caused by Enterovirus 71 Infections: Epidemiology, Pathogenesis, Molecular Epidemiology, and Vaccine Development.

    PubMed

    Chang, Ping-Chin; Chen, Shou-Chien; Chen, Kow-Tong

    2016-01-01

    Enterovirus 71 (EV71) infections have a major public health impact in the Asia-Pacific region. We reviewed the epidemiology, pathogenesis, and molecular epidemiology of EV71 infection as well as EV71 vaccine development. Previous studies were found using the search terms "enterovirus 71" and "epidemiology" or "pathogenesis" or "molecular epidemiology" or "vaccine" in Medline and PubMed. Articles that were not published in the English language, manuscripts without an abstract, and opinion articles were excluded from the review. The reported epidemiology of cases caused by EV71 infection varied from country to country; seasonal variations in incidence were observed. Most cases of EV71 infection that resulted in hospitalization for complications occurred in children less than five years old. The brainstem was the most likely major target of EV71 infection. The emergence of the EV71 epidemic in the Asia-Pacific region has been associated with the circulation of different genetic lineages (genotypes B3, B4, C1, C2, and C4) that appear to be undergoing rapid evolutionary changes. The relationship between the gene structure of the EV71 virus and the factors that ensure its survival, circulation, and evasion of immunity is still unknown. EV71 infection has emerged as an important global public health problem. Vaccine development, including the development of inactivated whole-virus live attenuated, subviral particles, and DNA vaccines, has been progressing. PMID:27618078

  9. Molecular epidemiology of coxsackievirus type B1.

    PubMed

    Abdelkhalek, Ichrak; Seghier, Mohamed; Yahia, Ahlem Ben; Touzi, Henda; Meddeb, Zina; Triki, Henda; Rezig, Dorra

    2015-11-01

    Coxsackievirus type B1 (CVB1) has emerged globally as the predominant enterovirus serotype and is associated with epidemics of meningitis and chronic diseases. In this report, the phylogeny of CVB1 was studied based on the VP1 sequences of 11 North African isolates and 81 published sequences. All CVB1 isolates segregated into four distinct genogroups and 10 genotypes. Most of the identified genotypes of circulating CVB1 strains appear to have a strict geographical specificity. The North African strains were of a single genotype and probably evolved distinctly. Using a relaxed molecular clock model and three different population models (constant population, exponential growth and Bayesian skyline demographic models) in coalescent analysis using the BEAST program, the substitution rate in CVB1 varied between 6.95 × 10(-3) and 7.37 × 10(-3) substitutions/site/year in the VP1 region. This study permits better identification of circulating CVB1, which has become one of the most predominant enterovirus serotypes in humans. PMID:26243282

  10. Molecular epidemiology of norovirus in Singapore, 2004-2011.

    PubMed

    Lim, Kun Lee; Eden, John-Sebastian; Oon, Lynette L E; White, Peter A

    2013-10-01

    Norovirus (NoV) is the most common cause of sporadic and epidemic gastroenteritis, globally. This study aimed to investigate the molecular epidemiology of NoV-associated acute gastroenteritis in Singapore by classifying circulating NoV genotypes and genogroup II, genotype 4 (GII.4) variants between September 2004 and February 2011. The temporal dominance and antigenic variation within the circulating epidemic NoV GII.4 variants was also examined, in order to compare the trends in Singapore to those observed globally during the same period. A total of 312 of 1,060 fecal specimens were positive for NoV RNA, using a quantitative RT-PCR. In a subset (125 of 312) of NoV positive samples, the 5' end of ORF2 (region C) of the GI or GII NoV genome was amplified and sequenced. Subsequent phylogenetic analysis identified GII.4 was the most commonly identified genotype representing 80.8% (101/125) of NoV sequenced in this study. The predominant GII.4 variants in circulation during the 2004-2011 epidemic periods were Hunter 2004 (2004-2005), Den Haag 2006b (2006-2009), and New Orleans 2009 (2009-2011). Amino acid variation within the P2 domain of the major capsid protein, VP1, was followed longitudinally within the GII.4 lineage. A constant turnover of variant-specific amino acid change was observed, particularly within the antigenic epitopes A, C and E. In conclusion, this study has characterized the NoV strains in circulation in Singapore between 2004 and 2011. The molecular epidemiology and persistence of GII.4 pandemic NoV lineages in Singapore was similar to trends seen globally, with a noted absence of the Asia 2003 variant. PMID:23868077

  11. Molecular Epidemiology of Brucella abortus in Northern Ireland—1991 to 2012

    PubMed Central

    Byrne, Andrew; Mallon, Thomas; Skuce, Robin; Groussaud, Pauline; Dainty, Amanda; Graham, Judith; Jones, Kerri; Pollock, Lorraine; Whatmore, Adrian

    2015-01-01

    Background Brucellosis is the most common bacterial zoonoses worldwide. Bovine brucellosis caused by Brucella abortus has far reaching animal health and economic impacts at both the local and national levels. Alongside traditional veterinary epidemiology, the use of molecular typing has recently been applied to inform on bacterial population structure and identify epidemiologically-linked cases of infection. Multi-locus variable number tandem repeat VNTR analysis (MLVA) was used to investigate the molecular epidemiology of a well-characterised Brucella abortus epidemic in Northern Ireland involving 387 herds between 1991 and 2012. Results MLVA identified 98 unique B. abortus genotypes from disclosing isolates in the 387 herds involved in the epidemic. Clustering algorithms revealed the relatedness of many of these genotypes. Combined with epidemiological information on chronology of infection and geographic location, these genotype data helped to identify 7 clonal complexes which underpinned the outbreak over the defined period. Hyper-variability of some VNTR loci both within herds and individual animals led to detection of multiple genotypes associated with single outbreaks. However with dense sampling, these genotypes could still be associated with specific clonal complexes thereby permitting inference of epidemiological links. MLVA- based epidemiological monitoring data were congruent with an independent classical veterinary epidemiology study carried out in the same territory. Conclusions MLVA is a useful tool in ongoing disease surveillance of B. abortus outbreaks, especially when combined with accurate epidemiological information on disease tracings, geographical clustering of cases and chronology of infection. PMID:26325586

  12. Impairment of Colour Vision in Diabetes with No Retinopathy: Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetics Study (SNDREAMS- II, Report 3)

    PubMed Central

    Gella, Laxmi; Raman, Rajiv; Kulothungan, Vaitheeswaran; Pal, Swakshyar Saumya; Ganesan, Suganeswari; Sharma, Tarun

    2015-01-01

    Purpose To assess impairment of colour vision in type 2 diabetics with no diabetic retinopathy and elucidate associated risk factors in a population-based cross-sectional study. Methods This is part of Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular-genetics Study (SN-DREAMS II) which was conducted between 2007–2010. FM 100 hue-test was performed in 253 subjects with no clinical evidence of diabetic retinopathy. All subjects underwent detailed ophthalmic evaluation including cataract grading using LOCS III and 45° 4-field stereoscopic fundus photography. Various ocular and systemic risk factors for impairment of colour vision (ICV) were assessed in subjects with diabetes but no retinopathy. P value of < 0.05 was considered statistically significant. Results The mean age of the study sample was 57.08 ± 9.21 (range: 44–86 years). Gender adjusted prevalence of ICV among subjects with diabetes with no retinopathy was 39.5% (CI: 33.5–45.5). The mean total error score in the study sample was 197.77 ± 100 (range: 19–583). The risk factors for ICV in the study were women OR: 1.79 (1.00–3.18), increased resting heart rate OR: 1.04 (1.01–1.07) and increased intraocular pressure OR: 1.12 (1.00–1.24). Significant protective factor was serum high-density lipoprotein OR: 0.96 (0.93–0.99). Conclusions Acquired ICV is an early indicator of neurodegenerative changes in the retina. ICV found in diabetic subjects without retinopathy may be of non-vascular etiology. PMID:26053017

  13. Initial Data on the Molecular Epidemiology of Cryptosporidiosis in Lebanon

    PubMed Central

    Osman, Marwan; El Safadi, Dima; Benamrouz, Sadia; Guyot, Karine; Dei-Cas, Eduardo; Aliouat, El Moukhtar; Creusy, Colette; Mallat, Hassan; Hamze, Monzer; Dabboussi, Fouad; Viscogliosi, Eric; Certad, Gabriela

    2015-01-01

    Cryptosporidium spp. represent a major public health problem worldwide and infect the gastrointestinal tract of both immunocompetent and immunocompromised persons. The prevalence of these parasites varies by geographic region, and no data are currently available in Lebanon. To promote an understanding of the epidemiology of cryptosporidiosisin this country, the main aim of this study was to determine the prevalence Cryptosporidium in symptomatic hospitalized patients, and to analyze the genetic diversity of the corresponding isolates. Fecal specimens were collected in four hospitals in North Lebanon from 163 patients (77 males and 86 females, ranging in age from 1 to 88 years, with a mean age of 22 years) presenting gastrointestinal disorders during the period July to December 2013. The overall prevalence of Cryptosporidium spp. infection obtained by modified Ziehl-Neelsen staining and/or nested PCR was 11%, and children <5 years old showed a higher rate of Cryptosporidium spp. The PCR products of the 15 positive samples were successfully sequenced. Among them, 10 isolates (66.7%) were identified as C. hominis, while the remaining 5 (33.3%) were identified as C. parvum. After analysis of the gp60 locus, C. hominis IdA19, a rare subtype, was found to be predominant. Two C. parvum subtypes were found: IIaA15G1R1 and IIaA15G2R1. The molecular characterization of Cryptosporidium isolates is an important step in improving our understanding of the epidemiology and transmission of the infection. PMID:25950832

  14. Choosing an appropriate bacterial typing technique for epidemiologic studies

    PubMed Central

    Foxman, Betsy; Zhang, Lixin; Koopman, James S; Manning, Shannon D; Marrs, Carl F

    2005-01-01

    A wide variety of bacterial typing systems are currently in use that vary greatly with respect to the effort required, cost, reliability and ability to discriminate between bacterial strains. No one technique is optimal for all forms of investigation. We discuss the desired level of discrimination and need for a biologic basis for grouping strains of apparently different types when using bacterial typing techniques for different epidemiologic applications: 1) confirming epidemiologic linkage in outbreak investigations, 2) generating hypotheses about epidemiologic relationships between bacterial strains in the absence of epidemiologic information, and 3) describing the distributions of bacterial types and identifying determinants of those distributions. Inferences made from molecular epidemiologic studies of bacteria depend upon both the typing technique selected and the study design used; thus, choice of typing technique is pivotal for increasing our understanding of the pathogenesis and transmission, and eventual disease prevention. PMID:16309556

  15. MOLECULAR EPIDEMIOLOGY OF BLUETONGUE VIRUS IN NORTHERN COLORADO

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The molecular epidemiology of Bluetongue virus serotype 11 (BTV11) in an enzootic focus in northern Colorado was investigated. Viruses isolated up to 12 years apart, from both vertebrate and invertebrate hosts, were compared by phylogenetic analysis of nucleotide sequence data from three genome seg...

  16. Invasive Streptococcus pneumoniae in France: Antimicrobial Resistance, Serotype, and Molecular Epidemiology Findings from a Monthly National Study in 2000 to 2002

    PubMed Central

    Decousser, Jean-Winoc; Pina, Patrick; Viguier, Florent; Picot, Franc; Courvalin, Patrice; Allouch, Pierre

    2004-01-01

    A study of 257 French invasive pneumococci isolated between 2000 and 2002 showed high rates of nonsusceptibility to penicillin and macrolides (50%), contrasting with a low frequency of resistance to amoxicillin or levofloxacin (<1%) and tolerance to vancomycin (0%). The genetic homogeneity of some serogroups, including serogroup 1, enhanced the risk of epidemiological changes. PMID:15328146

  17. A first molecular epidemiological study of SAT-2 type foot-and-mouth disease viruses in West Africa.

    PubMed Central

    Sangaré, O.; Bastos, A. D.; Venter, E. H.; Vosloo, W.

    2004-01-01

    Thirty-one viruses causing SAT-2 outbreaks in seven West African countries between 1974 and 1991, and four viruses representative of East and Central Africa were genetically characterized in this study. Four major viral lineages (I-IV) were identified by phylogenetic analysis of an homologous 480 nucleotide region corresponding to the C-terminus end of VP1. Lineage I comprised two West African genotypes with viruses clustering according to year of isolation rather than geographical origin. Lineage II was represented by viruses isolated between 1979 and 1983 in two neighbouring West African countries, Senegal and The Gambia. Viruses from Nigeria and Eritrea, representative of West and East Africa respectively, constituted lineage III, whilst lineage IV, comprising viruses from Central and East Africa, was regionally and genetically distinct. This study revealed that unrestricted animal movement in West Africa is a major factor in disease dissemination and has also provided the first indication of trans-regional virus transmission. PMID:15188721

  18. A molecular epidemiology project on diet and cancer: the EPIC-Italy Prospective Study. Design and baseline characteristics of participants.

    PubMed

    Palli, Domenico; Berrino, Franco; Vineis, Paolo; Tumino, Rosario; Panico, Salvatore; Masala, Giovanna; Saieva, Calogero; Salvini, Simonetta; Ceroti, Marco; Pala, Valeria; Sieri, Sabina; Frasca, Graziella; Giurdanella, Maria Concetta; Sacerdote, Carlotta; Fiorini, Laura; Celentano, Egidio; Galasso, Rocco; Decarli, Adriano; Krogh, Vittorio

    2003-01-01

    EPIC-Italy is the Italian section of a larger project known as EPIC (European Prospective Investigation into Cancer and Nutrition), a prospective study on diet and cancer carried out in 10 European countries. In the period 1993-1998, EPIC-Italy completed the recruitment of 47,749 volunteers (15,171 men, 32,578 women, aged 35-65 years) in 4 different areas covered by cancer registries: Varese (12,083 volunteers) and Turin (10,604) in the Northern part of the country; Florence (13,597) and Ragusa (6,403) in Central and Southern Italy, respectively. An associate center in Naples enrolled 5,062 women. Detailed information for each individual volunteer about diet and life-style habits, anthropometric measurements and a blood sample was collected, after signing an informed consent form. A food frequency questionnaire specifically developed for the Italian dietary pattern was tested in a pilot phase. A computerized data base with the dietary and life-style information of each participant was completed. Blood samples were processed in the same day of collection, aliquoted (RBC, WBC, serum and plasma) and stored in liquid nitrogen containers. Follow-up procedures were validated and implemented for the identification of newly diagnosed cancer cases. Cancer incidence was related to dietary habits and biochemical markers of food consumption and individual susceptibility in order to test the role of diet-related exposure in the etiology of cancer and its interaction with other environmental or genetic determinants. The comparability of information in a prospective study design is much higher than in other studies. The availability of such a large biological bank linked to individual data on dietary and life-style exposures also provides the unique opportunity of evaluating the role of selected genotypes involved in the metabolism of chemical compounds and DNA repair, potentially related to the risk of cancer, in residents of geographic areas of Italy characterized by specific

  19. Global Molecular Epidemiology of Cryptococcus neoformans and Cryptococcus gattii: An Atlas of the Molecular Types

    PubMed Central

    Cogliati, Massimo

    2013-01-01

    Cryptococcosis is a fungal disease affecting more than one million people per year worldwide. The main etiological agents of cryptococcosis are the two sibling species Cryptococcus neoformans and Cryptococcus gattii that present numerous differences in geographical distribution, ecological niches, epidemiology, pathobiology, clinical presentation and molecular characters. Genotyping of the two Cryptococcus species at subspecies level supplies relevant information to understand how this fungus has spread worldwide, the nature of its population structure, and how it evolved to be a deadly pathogen. At present, nine major molecular types have been recognized: VNI, VNII, VNB, VNIII, and VNIV among C. neoformans isolates, and VGI, VGII, VGIII, and VGIV among C. gattii isolates. In this paper all the information available in the literature concerning the isolation of the two Cryptococcus species has been collected and analyzed on the basis of their geographical origin, source of isolation, level of identification, species, and molecular type. A detailed analysis of the geographical distribution of the major molecular types in each continent has been described and represented on thematic maps. This study represents a useful tool to start new epidemiological surveys on the basis of the present knowledge. PMID:24278784

  20. [Epidemiological and molecular study of autosomal dominant polycystic kidney disease (ADPKD) in the province of Vicenza, Italy: possible founder effect?].

    PubMed

    Corradi, Valentina; Gastaldon, Fiorella; Virzi', Grazia Maria; Clementi, Maurizio; Nalesso, Federico; Cruz, Dinna N; de Cal, Massimo; Torregrossa, Rossella; Ronco, Claudio

    2010-01-01

    Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic renal disorder, with a prevalence of 1:400 to 1:1000. ADPKD is genetically and clinically heterogeneous. In addition, significant intrafamilial renal disease variability is evident. The prevalence of ADPKD patients on renal replacement therapy in Italy has been reported to be 8.2%. In the dialysis population of Vicenza province (northeast Italy), in one area especially, ADPKD cases account for 13.4%. We hypothesize that this high frequency is related to a founder effect in this geographically isolated population. Since April 2007 we have studied the characteristics of ADPKD patients and the presence of haplotypes shared by several families. The clinical profile of patients in the Vicenza province is similar to that described in the literature but there is a high prevalence of ADPKD in several isolated areas. These areas are characterized by the presence of three distinct haplotypes, suggesting a strong lineage-specific gene. PMID:21132648

  1. Molecular epidemiology of Shigella infections in Israel.

    PubMed Central

    Yavzori, M.; Cohen, D.; Bercovier, H.

    1992-01-01

    The DNAs of Shigella sonnei or Shigella dysenteriae type 1 strains isolated in outbreaks of shigellosis or in sporadic cases were analysed by restriction fragment length polymorphism (RFLP). Southern blots of the DNAs of 36 S. sonnei isolates digested by 8 restriction enzymes were hybridized with an Escherichia coli rRNA probe. The S. sonnei strains were unexpectedly diverse in their RFLP. Antibiotypes of the same isolates showed clusters of strains corresponding to the various outbreaks. On the other hand, RFLP analysis suggested concomitant multiple sources of infection rather than a common source and thereby introduced a new insight in the epidemiology of shigellosis. RFLP was also used to trace S. dysenteriae type 1 transmission in a recent cluster of clinical cases. Although antibiotic resistance patterns indicated the presence of more than one strain, RFLP analysis showed that the six isolates were identical clones and suggested the loss of an R episome after one person-to-person passage. Images Fig. 1 Fig. 2 Fig. 3 PMID:1356821

  2. Molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae in Greece.

    PubMed

    Karampatakis, Theodoros; Antachopoulos, Charalampos; Iosifidis, Elias; Tsakris, Athanassios; Roilides, Emmanuel

    2016-06-01

    Hospital infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) constitute a worldwide problem associated with high rates of treatment failure and mortality. In Greece, CRKP have emerged in 2002 due to VIM carbapenemase production and later due to KPC, NDM and OXA-48-like carbapenemases that have become endemic. The molecular epidemiology of CRKP strains is dynamic, as antibiotic consumption and worldwide traveling are strongly associated with global spread of CRKP isolates. Lately, porin defects, such as disruption of OmpK35 and production of OmpK36 variant, have also contributed to carbapenem resistance. In the coming years, the high prevalence of CRKP will require intense infection control measures, while novel molecular patterns may appear. To our knowledge, this is the first review analyzing the molecular epidemiology of CRKP strains in Greece. PMID:27206024

  3. Molecular epidemiology of pneumococcal isolates from children in China

    PubMed Central

    Kang, Li-Hua; Liu, Meng-Juan; Xu, Wen-Chun; Cui, Jing-Jing; Zhang, Xue-Mei; Wu, Kai-Feng; Zhang, Qun

    2016-01-01

    Objectives: To investigate the molecular epidemiology of pneumococcal isolates in Chongqing, China. Methods: In this cross-sectional study, 51 invasive Streptococcus pneumoniae (S. pneumoniae) strains were from children with invasive pneumococcal disease (IPD) and 32 carriage strains from healthy children from January 2010 to December 2013 at the Children’s Hospital of Chongqing Medical University, Chongqing, China. Multilocus sequence typing was used to identify the sequence types (STs). Capsular serotypes were determined by multiplex polymerase chain reaction. Drug susceptibility and resistance was determined by minimum inhibitory concentrations. Results: In this study, 11 serotypes were identified among the 83 S. pneumoniae clinical isolates tested. Prevalent serotypes were 19A (20.4%), 6A/B (20.4%), 19F (15.7%), 14 (14.5%), and 23F (10.8%). Serotype 19F was the most frequent carriage strain, and serotype 19A was the most frequent invasive strain. The ST983 was the most prevalent ST for carriage strains, and ST320 was the most prevalent ST for invasive strains. For gene analysis, psaA (99.5%) and piaA (98.6%) were present and much conserved in all pneumococci tested. The cps2A and pcsB genes were more frequent in invasive isolates than carriage strains. Antimicrobial resistance rates of invasive pneumococcal isolates to erythromycin, penicillin, meropenem, cefotaxime, and clindamycin were higher than the carriage isolates from children. Conclusion: Our epidemiological evidence shows that 19A, 6A/B, 19F, 14, and 23F remain the most prevalent serotypes, which can be targeted by PCV13. Genotypes and drug resistance varied between carriage and invasive strains. The PsaA and PiaA may be good protein vaccine candidates. PMID:27052283

  4. A prospective case–control and molecular epidemiological study of human cases of Shiga toxin-producing Escherichia coli in New Zealand

    PubMed Central

    2013-01-01

    Background Shiga toxin-producing Escherichia coli (STEC) O157:H7 and related non-O157 STEC strains are enteric pathogens of public health concern worldwide, causing life-threatening diseases. Cattle are considered the principal hosts and have been shown to be a source of infection for both foodborne and environmental outbreaks in humans. The aims of this study were to investigate risk factors associated with sporadic STEC infections in humans in New Zealand and to provide epidemiological information about the source and exposure pathways. Methods During a national prospective case–control study from July 2011 to July 2012, any confirmed case of STEC infection notified to regional public health units, together with a random selection of controls intended to be representative of the national demography, were interviewed for risk factor evaluation. Isolates from each case were genotyped using pulsed-field gel electrophoresis (PFGE) and Shiga toxin-encoding bacteriophage insertion (SBI) typing. Results Questionnaire data from 113 eligible cases and 506 controls were analysed using multivariate logistic regression. Statistically significant animal and environmental risk factors for human STEC infections were identified, notably 'Cattle livestock present in meshblock’ (the smallest geographical unit) (odds ratio 1.89, 95% CI 1.04–3.42), 'Contact with animal manure’ (OR 2.09, 95% CI 1.12–3.90), and 'Contact with recreational waters’ (OR 2.95, 95% CI 1.30–6.70). No food-associated risk factors were identified as sources of STEC infection. E. coli O157:H7 caused 100/113 (88.5%) of clinical STEC infections in this study, and 97/100 isolates were available for molecular analysis. PFGE profiles of isolates revealed three distinctive clusters of genotypes, and these were strongly correlated with SBI type. The variable 'Island of residence’ (North or South Island of New Zealand) was significantly associated with PFGE genotype (p = 0.012). Conclusions Our

  5. Molecular epidemiology and evolution of porcine parvoviruses.

    PubMed

    Streck, André Felipe; Canal, Cláudio Wageck; Truyen, Uwe

    2015-12-01

    Porcine parvovirus (PPV), recently named Ungulate protoparvovirus 1, is considered to be one of the most important causes of reproductive failure in swine. Fetal death, mummification, stillbirths and delayed return to estrus are predominant clinical signs commonly associated with PPV infection in a herd. It has recently been shown that certain parvoviruses exhibit a nucleotide substitution rate close to that commonly determined for RNA viruses. However, the PPV vaccines broadly used in the last 30 years have most likely reduced the genetic diversity of the virus and led to the predominance of strains with a capsid profile distinct from that of the original vaccine-based strains. Furthermore, a number of novel porcine parvovirus species with yet-unknown veterinary relevance and characteristics have been described during the last decade. In this review, an overview of PPV molecular evolution is presented, highlighting characteristics of the various genetic elements, their evolutionary rate and the discovery of new capsid profiles driven by the currently used vaccines. PMID:26453771

  6. The use of genetic markers in the molecular epidemiology of histoplasmosis: a systematic review.

    PubMed

    Damasceno, L S; Leitão, T M J S; Taylor, M L; Muniz, M M; Zancopé-Oliveira, R M

    2016-01-01

    Histoplasmosis is a systemic mycosis caused by Histoplasma capsulatum, a dimorphic fungal pathogen that can infect both humans and animals. This disease has worldwide distribution and affects mainly immunocompromised individuals. In the environment, H. capsulatum grows as mold but undergoes a morphologic transition to the yeast morphotype under special conditions. Molecular techniques are important tools to conduct epidemiologic investigations for fungal detection, identification of infection sources, and determination of different fungal genotypes associated to a particular disease symptom. In this study, we performed a systematic review in the PubMed database to improve the understanding about the molecular epidemiology of histoplasmosis. This search was restricted to English and Spanish articles. We included a combination of specific keywords: molecular typing [OR] genetic diversity [OR] polymorphism [AND] H. capsulatum; molecular epidemiology [AND] histoplasmosis; and molecular epidemiology [AND] Histoplasma. In addition, we used the specific terms: histoplasmosis [AND] outbreaks. Non-English or non-Spanish articles, dead links, and duplicate results were excluded from the review. The results reached show that the main methods used for molecular typing of H. capsulatum were: restriction fragment length polymorphism, random amplified polymorphic DNA, microsatellites polymorphism, sequencing of internal transcribed spacers region, and multilocus sequence typing. Different genetic profiles were identified among H. capsulatum isolates, which can be grouped according to their source, geographical origin, and clinical manifestations. PMID:26589702

  7. [Computerization of data collection in epidemiological studies].

    PubMed

    Galasso, R; Celentano, E

    1992-01-01

    Data collected in epidemiological studies on large cohorts need to be evaluated through the organization of a specific computer laboratory in order to make all procedures simple and fast. This paper describes the basic elements composing a computer laboratory and discusses its implementation in epidemiological investigations. PMID:1492737

  8. Molecular epidemiology of selected sexually transmitted infections.

    PubMed

    Jalal, Hamid; Delaney, Andrew; Bentley, Neil; Sonnex, Christopher; Carne, Christopher A

    2013-01-01

    Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT), Trichomonas vaginalis (TV) and Mycoplasma genitalium (MG) are established pathogens for human genital tract. However, the role of Ureaplasma urealyticum (UU) and Ureaplasma parvum (UP) in genital pathology is poorly unerstood. A prospective study to investigate the prevalence of above infections was performed on a cohort of 1,718 consecutive patients attending a Genitourinary Medicine (GUM) clinic. A previously published in-house real-time PCR assay, for the detection of CT DNA in genital swabs, was modified for this study. Two amplification reactions detected the DNAs of TV, NG, MG, CT, UU and UP in genital swabs from 4 (0.2%), 11 (0.6%), 17 (1%), 129 (8%), 282 (16%) and 636 (37%) patients, respectively. 594 (70%) of 848 women and 333 (38%) of 870 men were infected with at least one type of microorganism. Among 594 infected females, 485 (82%) had a single infection, 97 (16%) had a double infection, and 12 (2%) had a triple infection. Of the 333 infected men, 304 (91%) had a single infection, 27 (8%) had a double infection, and 2 (1%) had a triple infection. The prevalence of infection in both genders decreased with increasing age. The prevalence proportion of UP was significantly higher in women (54%) compared with men (18%). The high prevalence of UU and UP suggests that these bacteria are commensals of genital tract. PMID:24046809

  9. Molecular epidemiology of human coxsackievirus A16 strains

    PubMed Central

    YU, WENMIN; XU, HUANXIN; YIN, CHANGCHANG

    2016-01-01

    The hand, foot and mouth disease (HFMD) epidemics have mainly been caused by human enterovirus 71 and human coxsackievirus A16 (CA16), which circulated alternatively or together in the epidemic area. The aim of the present study was to provide guidance in the prevention and control of HFMD from CA16 infection. The molecular epidemiology of the human CA16 strains was investigated. Overall, 1,151 specimens (throat swabs) were collected from 1,151 patients with HFMD symptoms. The results of the homology comparison in the VP1 of CA16 strains showed that the CA16 strains belonged to the B1b subgenotype. The difference of the 6 CA16 strains analyzed showed that the most prominent strain was the A genotype, and the most close strains were the B1 gene subtype, particularly the B1b gene subtype. With regards to the amino acids, in addition to the A genotype, the differences of amino acids with other gene subtype was not significant. The present data suggest that more effective and highly targeted intervention mechanisms could be developed for the prevention and control of HFMD. PMID:27284420

  10. 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

  11. Molecular Epidemiology of Human Oral Chagas Disease Outbreaks in Colombia

    PubMed Central

    Ramírez, Juan David; Montilla, Marleny; Cucunubá, Zulma M.; Floréz, Astrid Carolina; Zambrano, Pilar; Guhl, Felipe

    2013-01-01

    Background Trypanosoma cruzi, the causative agent of Chagas disease, displays significant genetic variability revealed by six Discrete Typing Units (TcI-TcVI). In this pathology, oral transmission represents an emerging epidemiological scenario where different outbreaks associated to food/beverages consumption have been reported in Argentina, Bolivia, Brazil, Ecuador and Venezuela. In Colombia, six human oral outbreaks have been reported corroborating the importance of this transmission route. Molecular epidemiology of oral outbreaks is barely known observing the incrimination of TcI, TcII, TcIV and TcV genotypes. Methodology and Principal Findings High-throughput molecular characterization was conducted performing MLMT (Multilocus Microsatellite Typing) and mtMLST (mitochondrial Multilocus Sequence Typing) strategies on 50 clones from ten isolates. Results allowed observing the occurrence of TcI, TcIV and mixed infection of distinct TcI genotypes. Thus, a majority of specific mitochondrial haplotypes and allelic multilocus genotypes associated to the sylvatic cycle of transmission were detected in the dataset with the foreseen presence of mitochondrial haplotypes and allelic multilocus genotypes associated to the domestic cycle of transmission. Conclusions These findings suggest the incrimination of sylvatic genotypes in the oral outbreaks occurred in Colombia. We observed patterns of super-infection and/or co-infection with a tailored association with the severe forms of myocarditis in the acute phase of the disease. The transmission dynamics of this infection route based on molecular epidemiology evidence was unraveled and the clinical and biological implications are discussed. PMID:23437405

  12. Molecular Epidemiology of Cases of Mycoplasma californicum Infection in Japan

    PubMed Central

    Suzuki, Kan-ichiro; Hanyu, Hideki; Itoh, Megumi; Higuchi, Hidetoshi; Kobayashi, Hideki

    2014-01-01

    Bovine mastitis due to Mycoplasma californicum is often accompanied by huge economic losses, and the disease spreads very quickly. An appropriate molecular epidemiological analysis is needed to prevent and control infectious disease, but molecular epidemiological analysis methods for M. californicum have not yet been reported. Here we developed a combination of multiple-locus variable-number tandem repeat analysis (MLVA) and pulsed-field gel electrophoresis (PFGE) methods, which are common genotyping methods for various bacteria, for M. californicum. The MLVA is based on four interspersed repeat units that were found in the M. californicum genome data. The MLVA using these repeat units showed sufficient discriminatory power for a molecular epidemiological analysis; i.e., a Hunter-Gaston diversity index (HGDI) of 0.949, against M. californicum strains in Japan and M. californicum strain ATCC 33461. The PFGE for M. californicum also showed sufficient discriminatory power, with an HGDI of 0.985. Strain ATCC 33461 showed MLVA profiles and pulsotypes that differed greatly from those of strains from Japan. These results indicate that MLVA and PFGE are good tools for identifying M. californicum transmission events more accurately. Our combined MLVA and PFGE analysis suggests the persistence of M. californicum infection among herds in a specific area for a long period of time, as well as the movement of cows and heifers accompanying the expansion of M. californicum infection. Failure to identify asymptomatic infected cows is suspected as one of the central causes of the present M. californicum infection scenario in Japan. PMID:25281385

  13. Molecular mistletoe therapy: friend or foe in established anti-tumor protocols? A multicenter, controlled, retrospective pharmaco-epidemiological study in pancreas cancer.

    PubMed

    Matthes, H; Friedel, W E; Bock, P R; Zänker, K S

    2010-06-01

    Mistletoe is often used as complementary therapy in oncology. The anti-tumor effects of mistletoe (Iscador) are well documented in-vitro in respect to inhibition of cell proliferation, induction of apoptosis, segmental activation of immune competent cells and trapping of chemotherapeutic drugs within cancer cells by modulating the inhibitory potential of P-glycoprotein (P-gp)-mediated transport of cell toxifying substances (cytotoxic drugs). However, the clinical activity of mistletoe treatment remains still controversial. Implementation of mistletoe therapy as supportive care into anti-cancer programs should be based on the best evidence and must continually be evaluated to ensure safety, efficacy, collection of new data, and cost-effectiveness. Useful domains that can be evaluated include symptom control, adherence to conventional treatment protocols, quality of life, individual outcome and potential advantages of a whole-system health approach. Here we report the results of a multicenter, controlled, retrospective and observational pharmaco-epidemiological study in patients suffering from a pancreatic carcinoma. After surgery the patients were treated by adjuvant chemotherapy with gemcitabine supported by Iscador, or with gemcitabine alone, or any other best of care, but not including Iscador. Using a novel methodological pharmaco-epidemiological design and statistical approach it could be shown that Iscador offers benefits--symptom control, overall survival--as supportive care within gemcitabine protocols of patients with surgically resected pancreatic carcinoma. PMID:20455850

  14. Use of case studies to introduce undergraduate students to principles of food microbiology, molecular biology, and epidemiology of food-borne disease.

    PubMed

    Ponder, Monica A; Sumner, Susan

    2009-05-01

    Mock outbreaks of infectious disease offer the ability to introduce principles of food microbiology, ecology, and epidemiology to undergraduate students using an inquiry driven process. Students were presented with an epidemiological case study detailing patient history, clinical presentation, and foods recently consumed. The students then had to form hypotheses about the causative agents and attempt to identify the vehicle of transmission from foods their patient consumed. Students applied biochemical testing protocols to explore bacterial metabolism that are used to identify pathogens. After biochemically identifying their case's causative agent, the students were introduced to rapid methods that are used by health departments. Students extracted DNA, performed PCR reactions to amplify the 16s rDNA gene and identified it by comparing the PCR product sequence to a database using BLAST. Rapid methods, which do not employ time-consuming culturing methods, are increasingly being used; this exercise ensures that students have the technical skills necessary to compete in an increasingly technological global market. PMID:21567725

  15. Malignant Catarrhal Fever: Understanding Molecular Diagnostics in Context of Epidemiology

    PubMed Central

    Li, Hong; Cunha, Cristina W.; Taus, Naomi S.

    2011-01-01

    Malignant catarrhal fever (MCF) is a frequently fatal disease, primarily of ruminants, caused by a group of gammaherpesviruses. Due to complexities of pathogenesis and epidemiology in various species, which are either clinically-susceptible or reservoir hosts, veterinary clinicians face significant challenges in laboratory diagnostics. The recent development of specific assays for viral DNA and antibodies has expanded and improved the inventory of laboratory tests and opened new opportunities for use of MCF diagnostics. Issues related to understanding and implementing appropriate assays for specific diagnostic needs must be addressed in order to take advantage of molecular diagnostics in the laboratory. PMID:22072925

  16. [Molecular epidemiology of hepatitis B virus in Northern Cyprus].

    PubMed

    Arıkan, Ayşe; Şanlıdağ, Tamer; Süer, Kaya; Sayan, Murat; Akçalı, Sinem; Güler, Emrah

    2016-01-01

    Identification of hepatitis B virus (HBV) strains and understanding of molecular epidemiological characteristics are important for the effective surveillance of HBV infections. Genotype D is dominant in studies performed in Turkey but it is known that cases infected with genotypes A, E, G and H also exists. In contrast, there are no data regarding the molecular epidemiologic characteristics of the HBV in Northern Cyprus. The aim of this study was to determine the distribution of genotypes and subgenotypes of HBV among the people living, educating and working in Northern Cyprus. A total of 160 cases (1.2%) who were HBsAg seropositive out of 13.892 subjects admitted to Nicosia, Near East University Hospital microbiology laboratory for the routine control and to blood center for donor screening tests between November 2011 to September 2014, were included in the study. HBV-DNA levels in the HBsAg positive cases were detected by real-time polymerase chain reaction and genotypes/subgenotypes were determined by sequence analysis of the viral pol gene (reverse transcriptase [rt] region, between 80-250. aminoacids). Sixty samples (60/160, 37.5%) were excluded from sequencing analysis due to negative and/or very low (< 30 IU/ml) HBV-DNA levels, so 100 samples were included in sequence analysis. Ninety-six of those cases (13 female, 87 male; mean age: 35.51 ± 12.88 years) were anti-HBc IgG, 95 were anti-HBe and five were HBeAg positive, with a mean HBV-DNA level of 5.36 x 10(6) ± 3.58 x 10(7) IU/ml. As 32 (32%) samples yielded HBV-DNA level below the threshold of 1000 IU/ml, sequence analyses were unsuccesful, eventually 68 (68/160, 42.5%) samples could be phylogenetically analyzed. The distribution of HBV genotypes/subgenotypes were found as follows: 48 were (70.6%) D/D1; four were (5.9%) D/D2; one was (1.5%) D/D3, five were (7.4%) A/A1, two were (2.9%) A/A2 and eight were (11.8%) genotype E. Among the most frequent D1 strains, 60.4% (29/48) cases were from Turkish; single

  17. Molecular epidemiologic study of community-associated methicillin-resistant Staphylococcus aureus with Panton-Valentine leukocidin gene among family members in Japan.

    PubMed

    Uehara, Yuki; Ito, Teruyo; Ogawa, Yu; Hirotaki, Shintaro; Shoji, Takayo; Tame, Tomoyuki; Horikoshi, Yuho; Hiramatsu, Keiichi

    2015-09-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is one of the worldwide concerns of antimicrobial chemotherapy. An accumulation of ten patients in five families (A-E) suffering from skin and soft tissue infection (SSTI) of CA-MRSA was experienced in 2012, in Fuchu-shi, Tokyo, Japan. Molecular epidemiological investigation was performed for the 10 MRSA strains obtained from 8 children and 2 of their parents to assess endemic patterns of CA-MRSA in the community. Results of molecular typing, presence of toxin genes and antimicrobial susceptibilities were analyzed combined with the patients' clinical information. Each family had its own unique MRSA strain: A, ST30-SCCmec IVd; B, ST8-SCCmec IVd; C, ST8-SCCmec IVa; D, ST8-SCCmec IVl; E, ST8-SCCmec IVl and ST858-SCCmec IVl. Seven strains from the families A-C carried Panton-Valentine leukocidin gene. Three strains from the families D and E carried toxic shock syndrome toxin gene. Strains belonged to the same family demonstrated genetically related banding patterns of pulsed-filed gel electrophoresis. The family C experienced intrafamilial transmission of USA300-0114. Our data showed the MRSA clones disseminating in this community were highly diverse. They contained USA300-0114 clone, the rapidly distributing clone in the world, as well as MRSA clones identified in Japan. Our results suggested intrafamilial transmission of MRSA could be initial phenomenon of wide transmission in a community, therefore CA-MRSA SSTI in children and their family members should be monitored closely in order to notice the spread of highly pathogenic and transmittable strains. PMID:26091885

  18. A prospective epidemiological study of new incident GISTs during two consecutive years in Rhône Alpes region: incidence and molecular distribution of GIST in a European region

    PubMed Central

    Cassier, P A; Ducimetière, F; Lurkin, A; Ranchère-Vince, D; Scoazec, J-Y; Bringuier, P-P; Decouvelaere, A-V; Méeus, P; Cellier, D; Blay, J-Y; Ray-Coquard, I

    2010-01-01

    Background: Preliminary data indicate that the molecular epidemiology of localised gastrointestinal stromal tumour (GIST) may be different from that of advanced GIST. We sought to investigate the molecular epidemiology of sarcomas, including GIST, in the Rhone-Alpes region in France. Patients and methods: A prospective and exhaustive study in the Rhone-Alpes Region in France to assess the precise incidence of primary sarcomas with systematic centralised pathological review and molecular analysis was conducted for 2 consecutive years. Results: Among 760 patients with a confirmed diagnosis of sarcoma, 131 (17%) had a GIST. The majority of patients had gastric primaries (61%). Mutational analysis could be performed in 106 tumour samples (74%), and 71 (67%) had exon 11 mutations. PDGFRA mutations were found in 16% of cases, which is twice as high as previously reported for advanced GIST. Conclusion: Data indicate that PDGFRA mutations in localised GIST may be twice as high as what was previously reported in patients with advanced disease. This finding may have important consequences for patients offered adjuvant imatinib, although most of these tumours are in the low-risk group. PMID:20588273

  19. Protocol for a population-based molecular epidemiology study of tuberculosis transmission in a high HIV-burden setting: the Botswana Kopanyo study

    PubMed Central

    Zetola, N M; Modongo, C; Moonan, P K; Click, E; Oeltmann, J E; Shepherd, J; Finlay, A

    2016-01-01

    Introduction Mycobacterium tuberculosis (Mtb) is transmitted from person to person via airborne droplet nuclei. At the community level, Mtb transmission depends on the exposure venue, infectiousness of the tuberculosis (TB) index case and the susceptibility of the index case's social network. People living with HIV infection are at high risk of TB, yet the factors associated with TB transmission within communities with high rates of TB and HIV are largely undocumented. The primary aim of the Kopanyo study is to better understand the demographic, clinical, social and geospatial factors associated with TB and multidrug-resistant TB transmission in 2 communities in Botswana, a country where 60% of all patients with TB are also infected with HIV. This manuscript describes the methods used in the Kopanyo study. Methods and analysis The study will be conducted in greater Gaborone, which has high rates of HIV and a mobile population; and in Ghanzi, a rural community with lower prevalence of HIV infection and home to the native San population. Kopanyo aims to enrol all persons diagnosed with TB during a 4-year study period. From each participant, sputum will be cultured, and for all Mtb isolates, molecular genotyping (24-locus mycobacterial interspersed repetitive units-variable number of tandem repeats) will be performed. Patients with matching genotype results will be considered members of a genotype cluster, a proxy for recent transmission. Demographic, behavioural, clinical and social information will be collected by interview. Participant residence, work place, healthcare facilities visited and social gathering venues will be geocoded. We will assess relationships between these factors and cluster involvement to better plan interventions for reducing TB transmission. Ethics Ethical approval from the Independent Review Boards at the University of Pennsylvania, US Centers for Disease Control and Prevention, Botswana Ministry of Health and University of Botswana has been

  20. Typing methods used in the molecular epidemiology of microbial pathogens: a how-to guide.

    PubMed

    Ranjbar, Reza; Karami, Ali; Farshad, Shohreh; Giammanco, Giovanni M; Mammina, Caterina

    2014-01-01

    Microbial typing is often employed to determine the source and routes of infections, confirm or rule out outbreaks, trace cross-transmission of healthcare-associated pathogens, recognize virulent strains and evaluate the effectiveness of control measures. Conventional microbial typing methods have occasionally been useful in describing the epidemiology of infectious diseases. However, these methods are generally considered too variable, labour intensive and time-consuming to be of practical value in epidemiological investigations. Moreover, these approaches have proved to be insufficiently discriminatory and poorly reproducible. DNA-based typing methods rely on the analysis of the genetic material of a microorganism. In recent years, several methods have been introduced and developed for investigation of the molecular epidemiology of microbial pathogens. Each of them has advantages and limitations that make them useful in some studies and restrictive in others. The choice of a molecular typing method therefore will depend on the skill level and resources of the laboratory and the aim and scale of the investigation. This study reviews the most popular DNA-based molecular typing methods used in the epidemiology of bacterial pathogens together with their advantages and limitations. PMID:24531166

  1. Proceedings of The Second International Molecular Pathological Epidemiology (MPE) Meeting

    PubMed Central

    Ogino, Shuji; Campbell, Peter T.; Nishihara, Reiko; Phipps, Amanda I.; Beck, Andrew H.; Sherman, Mark E.; Chan, Andrew T.; Troester, Melissa A.; Bass, Adam J.; Fitzgerald, Kathryn C.; Irizarry, Rafael A.; Kelsey, Karl T.; Nan, Hongmei; Peters, Ulrike; Poole, Elizabeth M.; Qian, Zhi Rong; Tamimi, Rulla M.; Tchetgen Tchetgen, Eric J.; Tworoger, Shelley S.; Zhang, Xuehong; Giovannucci, Edward L.; van den Brandt, Piet A.; Rosner, Bernard A.; Wang, Molin; Chatterjee, Nilanjan; Begg, Colin B.

    2015-01-01

    Disease classification system increasingly incorporates information on pathogenic mechanisms to predict clinical outcomes and response to therapy and intervention. Technological advancements to interrogate omics (genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, interactomics, etc.) provide widely-open opportunities in population-based research. Molecular pathological epidemiology (MPE) represents integrative science of molecular pathology and epidemiology. This unified paradigm requires multidisciplinary collaboration between pathology, epidemiology, biostatistics, bioinformatics, and computational biology. Integration of these fields enables better understanding of etiologic heterogeneity, disease continuum, causal inference, and the impact of environment, diet, lifestyle, host factors (including genetics and immunity), and their interactions on disease evolution. Hence, the Second International MPE Meeting was held in Boston in December 2014, with aims to: (1) develop conceptual and practical frameworks; (2) cultivate and expand opportunities; (3) address challenges; and (4) initiate the effort of specifying guidelines for MPE. The meeting mainly consisted of presentations of method developments and recent data in various malignant neoplasms and tumors (breast, prostate, ovarian and colorectal cancers, renal cell carcinoma, lymphoma, and leukemia), followed by open discussion sessions on challenges and future plans. In particular, we recognized need for efforts to further develop statistical methodologies. This meeting provided an unprecedented opportunity for interdisciplinary collaboration, consistent with the purposes of the BD2K (Big Data to Knowledge), GAME-ON (Genetic Associations and Mechanisms in Oncology), and Precision Medicine Initiatives of the U.S.A. National Institute of Health. The MPE Meeting Series can help advance transdisciplinary population science, and optimize training and education systems for 21st century

  2. Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria.

    PubMed

    Jagielski, Tomasz; Minias, Alina; van Ingen, Jakko; Rastogi, Nalin; Brzostek, Anna; Żaczek, Anna; Dziadek, Jarosław

    2016-04-01

    Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed. PMID:26912567

  3. Concordance and discordance of sequence survey methods for molecular epidemiology

    PubMed Central

    Hasan, Nur A.; Cebula, Thomas A.; Colwell, Rita R.; Robison, Richard A.; Johnson, W. Evan; Crandall, Keith A.

    2015-01-01

    The post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. However, there are a number of molecular approaches to survey pathogen diversity, and the impact of these different approaches on parameter estimation and inference are not entirely clear. We sequenced whole genomes of bacterial pathogens, Burkholderia pseudomallei, Yersinia pestis, and Brucella spp. (60 new genomes), and combined them with 55 genomes from GenBank to address how different molecular survey approaches (whole genomes, SNPs, and MLST) impact downstream inferences on molecular evolutionary parameters, evolutionary relationships, and trait character associations. We selected isolates for sequencing to represent temporal, geographic origin, and host range variability. We found that substitution rate estimates vary widely among approaches, and that SNP and genomic datasets yielded different but strongly supported phylogenies. MLST yielded poorly supported phylogenies, especially in our low diversity dataset, i.e., Y. pestis. Trait associations showed that B. pseudomallei and Y. pestis phylogenies are significantly associated with geography, irrespective of the molecular survey approach used, while Brucella spp. phylogeny appears to be strongly associated with geography and host origin. We contrast inferences made among monomorphic (clonal) and non-monomorphic bacteria, and between intra- and inter-specific datasets. We also discuss our results in light of underlying assumptions of different approaches. PMID:25737810

  4. Epidemiology and molecular biology of gastrointestinal stromal tumors (GISTs): a population-based study in the South of Switzerland, 1999-2005.

    PubMed

    Mazzola, Paola; Spitale, Alessandra; Banfi, Sara; Mazzucchelli, Luca; Frattini, Milo; Bordoni, Andrea

    2008-11-01

    Introduction. Gastrointestinal stromal tumors (GISTs) are characterized at the molecular level by c-kit or PDGFRA oncogene mutations. Although GISTs raised major interest in past decades, population-based studies are still rare. Materials and Methods. All GISTs diagnosed in Southern Switzerland (1999-2005) were identified using Ticino Cancer Registry and analysed for c-kit and PDGFRA mutations. Clinical and molecular features were studied. Results. Annual incidence of GISTs was 1.47 cases/100,000 inhabitants (median age: 64 years; median size: 6.0 cm). Most GISTs arose in the stomach (60.5%). The malignancy risk was very-low/low in 47% of patients. DNA sequences showed a gene alteration in either c-kit or PDGFRA genes in 72.5% of patients. Mutations occurred mostly in c-kit exon 11 (60%). No mutations in c-kit exons 13 or 17 were found. An equal number of alterations in exons 12 and 18, and no mutations in exon 14 were observed in the PDGFRA gene. Discussion. This is the first comprehensive population-based study of GISTs incidence and molecular biology characterization in Central Europe. Our incidence data showed higher age-standardized rates compared to other European countries. The gene mutation spectrum differed when compared to the literature. This is relevant to improve the molecular profile knowledge based on Cancer Registry data. PMID:18785120

  5. Principles of study design in environmental epidemiology.

    PubMed Central

    Morgenstern, H; Thomas, D

    1993-01-01

    This paper discusses the principles of study design and related methodologic issues in environmental epidemiology. Emphasis is given to studies aimed at evaluating causal hypotheses regarding exposures to suspected health hazards. Following background sections on the quantitative objectives and methods of population-based research, we present the major types of observational designs used in environmental epidemiology: first, the three basic designs involving the individual as the unit of analysis (i.e., cohort, cross-sectional, and case-control studies) and a brief discussion of genetic studies for assessing gene-environment interactions; second, various ecologic designs involving the group or region as the unit of analysis. Ecologic designs are given special emphasis in this paper because of our lack of resources or inability to accurately measure environmental exposures in large numbers of individuals. The paper concludes with a section highlighting current design issues in environmental epidemiology and several recommendations for future work. PMID:8206038

  6. Molecular Epidemiology of Rotavirus in Cats in the United Kingdom

    PubMed Central

    Iturriza-Gómara, M.; Dove, W.; Sandrasegaram, M.; Nakagomi, T.; Nakagomi, O.; Cunliffe, N.; Radford, A. D.; Morgan, K. L.

    2014-01-01

    Rotaviruses are leading causes of gastroenteritis in the young of many species. Molecular epidemiological studies in children suggest that interspecies transmission contributes to rotavirus strain diversity in people. However, population-based studies of rotaviruses in animals are few. We investigated the prevalence, risk factors for infection, and genetic diversity of rotavirus A in a cross-sectional survey of cats housed within 25 rescue catteries across the United Kingdom. Morning litter tray fecal samples were collected during the winter and summer in 2012 from all pens containing kittens and a random sample of those housing adult cats. Group A rotavirus RNA was detected by real-time reverse transcription-PCR, and positive samples were G and P genotyped using nested VP4 and VP7 PCR assays. A total of 1,727 fecal samples were collected from 1,105 pens. Overall, the prevalence of rotavirus was 3.0% (95% confidence interval [CI], 1.2 to 4.9%). Thirteen out of 25 (52%; 95% CI, 31.3 to 72.2%) centers housed at least one rotavirus-positive cat. The prevalence of rotavirus was associated with season (odds ratio, 14.8 [95% CI, 1.1 to 200.4]; P = 0.04) but not age or diarrhea. It was higher during the summer (4.7%; 95% CI, 1.2 to 8.3%) than in winter (0.8%; 95% CI, 0.2 to 1.5%). Asymptomatic epidemics of infection were detected in two centers. G genotypes were characterized for 19 (33.3%) of the 57 rotavirus-positive samples and P genotypes for 36 (59.7%). Two rotavirus genotypes were identified, G3P[9] and G6P[9]. This is the first population-based study of rotavirus in cats and the first report of feline G6P[9], which questions the previous belief that G6P[9] in people is of bovine origin. PMID:25411173

  7. Molecular epidemiology of Vibrio nigripulchritudo, a pathogen of cultured penaeid shrimp (Litopenaeus stylirostris) in New Caledonia.

    PubMed

    Goarant, Cyrille; Reynaud, Yann; Ansquer, Dominique; de Decker, Sophie; Saulnier, Denis; le Roux, Frédérique

    2006-11-01

    A collection of 57 isolates of Vibrio nigripulchritudo from either diseased or healthy shrimp and from shrimp farms environment was studied in order to gain a better understanding of the epidemiology of this pathogen, notably isolated from two distinct shrimp disease complexes. Molecular typing using two different techniques, arbitrarily primed PCR (AP-PCR) and multi-locus sequence typing (MLST), studied together with experimental pathology data allowed a relevant epidemiological insight into this possibly emerging pathogen. Additionally, results obtained with the two molecular typing techniques were congruent and allowed discriminating the strains associated with the "Summer Syndrome" from strains isolated from other contexts, especially the other shrimp vibriosis "Syndrome 93". These results highlight that the "Summer Syndrome" is most probably caused by an emergent clonal pathogen that therefore deserves surveillance and that AP-PCR can satisfactorily be used for that purpose. PMID:16413158

  8. Lung cancer molecular epidemiology in China: recent trends

    PubMed Central

    2014-01-01

    Lung cancer is both the most common diagnosed cancer and the leading cause of cancer related deaths in China. During the past three decades, the incidence and mortality of lung cancer in China are increasing rapidly. According to data from National Central Cancer Registry (NCCR) in 2010, the crude incidence of lung cancer in China was 46.08 per 100,000 population (61.86 per 100,000 men and 29.54 per 100,000 women), with an estimated over 600,000 new diagnosed lung cancer patients (416,333 males and 189,613 females). Meanwhile, the crude mortality of lung cancer in China was 37.00 per 100,000 population (50.04 per 100,000 men and 23.33 per 100,000 women). Consistent with the change in developed countries, adenocarcinoma has become the most predominant histological subtype of lung cancer in China. For the majority advanced non-small-cell lung cancer (NSCLC) patients, especially patients with adenocarcinoma, targeted therapy became increasing important in the treatment. Chinese researcher have done a lot work in terms of lung cancer molecular epidemiology, therefore, in this review, we further summarized the epidemiology of driver genes in NSCLC, hoping to help clinicians to better screen certain driver genes in China for treatment decisions. PMID:25806311

  9. Molecular epidemiology of childhood neuronal ceroid-lipofuscinosis in Italy

    PubMed Central

    2013-01-01

    Background To review the descriptive epidemiological data on neuronal ceroid lipofuscinoses (NCLs) in Italy, identify the spectrum of mutations in the causative genes, and analyze possible genotype-phenotype relations. Methods A cohort of NCL patients was recruited through CLNet, a nationwide network of child neurology units. Diagnosis was based on clinical and pathological criteria following ultrastructural investigation of peripheral tissues. Molecular confirmation was obtained during the diagnostic procedure or, when possible, retrospectively. Results One hundred eighty-three NCL patients from 156 families were recruited between 1966 and 2010; 124 of these patients (from 88 families) were tested for known NCL genes, with 9.7% of the patients in this sample having not a genetic diagnosis. Late infantile onset NCL (LINCL) accounted for 75.8% of molecularly confirmed cases, the most frequent form being secondary to mutations in CLN2 (23.5%). Juvenile onset NCL patients accounted for 17.7% of this cohort, a smaller proportion than found in other European countries. Gene mutations predicted severe protein alterations in 65.5% of the CLN2 and 78.6% of the CLN7 cases. An incidence rate of 0.98/100,000 live births was found in 69 NCL patients born between 1992 and 2004, predicting 5 new cases a year. Prevalence was 1.2/1,000,000. Conclusions Descriptive epidemiology data indicate a lower incidence of NCLs in Italy as compared to other European countries. A relatively high number of private mutations affecting all NCL genes might explain the genetic heterogeneity. Specific gene mutations were associated with severe clinical courses in selected NCL forms only. PMID:23374165

  10. Clinical and molecular epidemiology of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in a long-term study from Japan.

    PubMed

    Chong, Y; Yakushiji, H; Ito, Y; Kamimura, T

    2011-01-01

    The detection rates of extended-spectrum β-lactamase (ESBL)-producing bacteria in Japan are very low (∼5%) compared with those obtained worldwide. Further, the current trend of these bacteria in Japan is not known, and few studies with longitudinal observations have been reported. To obtain epidemiologic data on ESBL-producing bacteria, their genotypic features, and their antibiotic resistance patterns in Japan, we analyzed bacterial isolates from hospitalized patients at our institution over the 7-year period from 2003 to 2009. Of 2,304 isolates, 202 (8.8%) were found to be ESBL producers, including Escherichia coli, Klebsiella pneumonia, and Proteus mirabilis. The detection rates of the ESBL-producing isolates gradually increased and reached 17.1% and 10.5% for the E. coli and K. pneumoniae strains, respectively, in 2009. Genotyping analysis showed that ∼90% of the ESBL-producing isolates carried the CTX-M genotype, in which the CTX-M-9 group was predominant, although the CTX-M-2 group is considered to be the main genotype in Japan; further, many of the strains produced multiple β-lactamases. The detection rates of ESBL-producing bacteria may tend to be high within a limited region in Japan. A countrywide survey is required to understand the trend for ESBL-producing bacteria at the national level. In addition, our findings suggest that the genotypes of the detected ESBL producers are similar to those exhibiting a successful nosocomial spread worldwide. PMID:20859753

  11. IMPROVING EXPOSURE ASSESSMENT IN DBP EPIDEMIOLOGIC STUDIES

    EPA Science Inventory

    In 1997, an EPA expert panel was convened to evaluate epidemiologic studies of adverse reproductive or developmental outcomes that may be associated with drinking water DBPs. The panel recommended that further efforts be made in an existing cohort study, headed by Dr. Waller and ...

  12. 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

  13. Molecular epidemiology of mastitis pathogens of dairy cattle and comparative relevance to humans.

    PubMed

    Zadoks, Ruth N; Middleton, John R; McDougall, Scott; Katholm, Jorgen; Schukken, Ynte H

    2011-12-01

    Mastitis, inflammation of the mammary gland, can be caused by a wide range of organisms, including gram-negative and gram-positive bacteria, mycoplasmas and algae. Many microbial species that are common causes of bovine mastitis, such as Escherichia coli, Klebsiella pneumoniae, Streptococcus agalactiae and Staphylococcus aureus also occur as commensals or pathogens of humans whereas other causative species, such as Streptococcus uberis, Streptococcus dysgalactiae subsp. dysgalactiae or Staphylococcus chromogenes, are almost exclusively found in animals. A wide range of molecular typing methods have been used in the past two decades to investigate the epidemiology of bovine mastitis at the subspecies level. These include comparative typing methods that are based on electrophoretic banding patterns, library typing methods that are based on the sequence of selected genes, virulence gene arrays and whole genome sequencing projects. The strain distribution of mastitis pathogens has been investigated within individual animals and across animals, herds, countries and host species, with consideration of the mammary gland, other animal or human body sites, and environmental sources. Molecular epidemiological studies have contributed considerably to our understanding of sources, transmission routes, and prognosis for many bovine mastitis pathogens and to our understanding of mechanisms of host-adaptation and disease causation. In this review, we summarize knowledge gleaned from two decades of molecular epidemiological studies of mastitis pathogens in dairy cattle and discuss aspects of comparative relevance to human medicine. PMID:21968538

  14. 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

  15. Molecular epidemiology and phylogeny of Nipah virus infection: A mini review.

    PubMed

    Angeletti, Silvia; Lo Presti, Alessandra; Cella, Eleonora; Ciccozzi, Massimo

    2016-07-01

    Nipah virus (NiV) is a member of the genus Henipavirus of the family Paramyxoviridae, characterized by high pathogenicity and endemic in South Asia. It is classified as a Biosafety Level-4 (BSL-4) agent. The case-fatality varies from 40% to 70% depending on the severity of the disease and on the availability of adequate healthcare facilities. At present no antiviral drugs are available for NiV disease and the treatment is just supportive. Phylogenetic and evolutionary analyses can be used to help in understanding the epidemiology and the temporal origin of this virus. This review provides an overview of evolutionary studies performed on Nipah viruses circulating in different countries. Thirty phylogenetic studies have been published from 2000 to 2015 years, searching on pub-med using the key words 'Nipah virus AND phylogeny' and twenty-eight molecular epidemiological studies from 2006 to 2015 have been performed, typing the key words 'Nipah virus AND molecular epidemiology'. Overall data from the published study demonstrated as phylogenetic and evolutionary analysis represent promising tools to evidence NiV epidemics, to study their origin and evolution and finally to act with effective preventive measure. PMID:27393089

  16. Strain Typing Methods and Molecular Epidemiology of Pneumocystis Pneumonia

    PubMed Central

    Roux, Patricia; Nevez, Gilles; Hauser, Philippe M.; Kovacs, Joseph A.; Unnasch, Thomas R.; Lundgren, Bettina

    2004-01-01

    Pneumocystis pneumonia (PCP) caused by the opportunistic fungal agent Pneumocystis jirovecii (formerly P. carinii) continues to cause illness and death in HIV-infected patients. In the absence of a culture system to isolate and maintain live organisms, efforts to type and characterize the organism have relied on polymerase chain reaction–based approaches. Studies using these methods have improved understanding of PCP epidemiology, shedding light on sources of infection, transmission patterns, and potential emergence of antimicrobial resistance. One concern, however, is the lack of guidance regarding the appropriateness of different methods and standardization of these methods, which would facilitate comparing results reported by different laboratories. PMID:15504257

  17. [Molecular epidemiology of imported malaria in Italy: the use of genetic markers and in vitro sensitivity test in a study of chloroquine resistance in Plasmodium falciparum].

    PubMed

    Menegon, Michela; Sannella, Anna Rosa; Severini, Carlo; Paglia, Maria Grazia; Matteelli, Alberto; Caramello, Pietro; Severini, Francesco; Taramelli, Donatella; Majori, Giancarlo

    2006-01-01

    The emergence of Plasmodium falciparum drug-resistance, especially chloroquine resistance, represents one of the main obstacles to the control of malaria. Several studies have shown that in P. falciparum the mechanism of chloroquine resistance is linked to specific point mutations in the pfcrt gene of the parasite. In the present study we have analyzed 120 Italian imported malaria cases to evaluate the prevalence of 76T and 220S mutantions in the pfcrt gene. Moreover, the correlation between the presence of pfcrt point mutations and in vitro chloroquine resistance has been evaluated on 25 plasmodial isolates. The results showed a high prevalence of the pfcrt point mutations in isolates analyzed and a significant association between point mutations and in vitro chloroquine resistance. Molecular screening on imported malaria cases can be a useful tool to be employed in surveillance activity and also in monitoring the development and spread of drug resistance in endemic areas. PMID:17033142

  18. Colorectal Cancer Epidemiology in the Nurses’ Health Study

    PubMed Central

    Lee, Dong Hoon; Giovannucci, Edward L.

    2016-01-01

    Objectives. To review the contribution of the Nurses’ Health Study (NHS) to identifying risk and protective factors for colorectal adenomas and colorectal cancer (CRC). Methods. We performed a narrative review of the publications using the NHS between 1976 and 2016. Results. Existing epidemiological studies using the NHS have reported that red and processed meat, alcohol, smoking, and obesity were associated with an increased risk of CRC, whereas folate, calcium, vitamin D, aspirin, and physical activity were associated with decreased risk of CRC. Moreover, modifiable factors, such as physical activity, vitamin D, folate, insulin and insulin-like growth factor binding protein-1, and diet quality, were identified to be associated with survival among CRC patients. In recent years, molecular pathological epidemiological studies have been actively conducted and have shown refined results by molecular subtypes of CRC. Conclusions. The NHS has provided new insights into colorectal adenomas, CRC etiology, and pathogenic mechanisms. With its unique strengths, the NHS should continue to contribute to the field of CRC epidemiology and play a major role in public health. PMID:27459444

  19. Molecular epidemiology of isolates of the Cryptococcus neoformans species complex from Spain.

    PubMed

    Frasés, Susana; Ferrer, Consuelo; Sánchez, Manuel; Colom-Valiente, María Francisca

    2009-06-30

    To study genetic diversity of Cryptococcus neoformans species complex in Spain, 97 isolates of the yeast recovered from human, animal and environmental samples have been analysed using three molecular epidemiological techniques. One of these, URA5 gene fragment length polymorphism (RFLP) analysis, has been previously described as a molecular epidemiology tool. Thus, standard profiles and reference strains have been defined for it. In addition, 5S rDNA/IGS RFLP and [GACA](4) microsatellite PCR fingerprinting were also used. Our results show five of the previously defined URA5 genotypes with a high frequency (33%) of the VNI type, which is in concordance with other studies. The high presence of VNIII pattern (28.9%) among our strains is remarkable and could be a specific feature of the isolates from our country. 5S rDNA/IGS RFLP showed a low intra-species discriminative power. Three different molecular profiles (S1-3), which showed a good correlation with the different species, varieties and genotypes, were obtained. [GACA](4) microsatellite PCR-fingerprinting analysis showed a high variability of patterns among the studied strains. Molecular profiles represented in a dendrogram clustered strains in four main groups related with the source of the yeast and also in concordance with some of the described genotypes (VNI-IV and VGI). PMID:19631160

  20. Examination of Different Exposure Metrics in an Epidemiological Study

    EPA Science Inventory

    Epidemiological studies of air pollution have traditionally relied upon measurements of ambient concentration from central-site monitoring stations as surrogates of population exposures. However, depending on the epidemiological study design, this approach may introduce exposure...

  1. Delta hepatitis: molecular biology and clinical and epidemiological features.

    PubMed Central

    Polish, L B; Gallagher, M; Fields, H A; Hadler, S C

    1993-01-01

    Hepatitis delta virus, discovered in 1977, requires the help of hepatitis B virus to replicate in hepatocytes and is an important cause of acute, fulminant, and chronic liver disease in many regions of the world. Because of the helper function of hepatitis delta virus, infection with it occurs either as a coinfection with hepatitis B or as a superinfection of a carrier of hepatitis B surface antigen. Although the mechanisms of transmission are similar to those of hepatitis B virus, the patterns of transmission of delta virus vary widely around the world. In regions of the world in which hepatitis delta virus infection is not endemic, the disease is confined to groups at high risk of acquiring hepatitis B infection and high-risk hepatitis B carriers. Because of the propensity of this viral infection to cause fulminant as well as chronic liver disease, continued incursion of hepatitis delta virus into areas of the world where persistent hepatitis B infection is endemic will have serious implications. Prevention depends on the widespread use of hepatitis B vaccine. This review focuses on the molecular biology and the clinical and epidemiologic features of this important viral infection. PMID:8358704

  2. Resistance to Tospoviruses in Vegetable Crops: Epidemiological and Molecular Aspects.

    PubMed

    Turina, Massimo; Kormelink, Richard; Resende, Renato O

    2016-08-01

    During the past three decades, the economic impact of tospoviruses has increased, causing high yield losses in a variety of crops and ornamentals. Owing to the difficulty in combating thrips vectors with insecticides, the best way to limit/prevent tospovirus-induced diseases involves a management strategy that includes virus resistance. This review briefly presents current tospovirus taxonomy, diversity, molecular biology, and cytopathology as an introduction to a more extensive description of the two main resistance genes employed against tospoviruses: the Sw5 gene in tomato and the Tsw in pepper. Natural and experimental resistance-breaking (RB) isolates allowed the identification of the viral avirulence protein triggering each of the two resistance gene products; epidemiology of RB isolates is discussed to reinforce the need for allelic variants and the need to search for new/alternative resistance genes. Ongoing efforts for alternative resistance strategies are described not only for Tomato spotted wilt virus (TSWV) in pepper and tomato but also for other vegetable crops heavily impacted by tospoviruses. PMID:27296139

  3. Spoligotyping for molecular epidemiology of the Mycobacterium tuberculosis complex.

    PubMed

    Driscoll, Jeffrey R

    2009-01-01

    Spacer oligonucleotide typing, or spoligotyping, is a rapid, polymerase chain reaction (PCR)-based method for genotyping strains of the Mycobacterium tuberculosis complex (MTB). Spoligotyping data can be represented in absolute terms (digitally), and the results can be readily shared among laboratories, thereby enabling the creation of large international databases. Since the spoligotype assay was standardized more than 10 yr ago, tens of thousands of isolates have been analyzed, giving a global picture of MTB strain diversity. The method is highly reproducible and has been developed into a high-throughput assay for large molecular epidemiology projects. In the United States, spoligotyping is employed on nearly all newly identified culture-positive cases of tuberculosis as part of a national genotyping program. The strengths of this method include its low cost, its digital data results, the good correlation of its results with other genetics markers, its fair level of overall differentiation of strains, its high-throughput capacity, and its ability to provide species information. However, the method's weaknesses include the inability of spoligotyping to differentiate well within large strain families such as the Beijing family, the potential for convergent evolution of patterns, the limited success in improving the assay through expansion, and the difficulty in obtaining the specialized membranes and instrumentation. PMID:19521871

  4. Psoriasis and comorbidities. Epidemiological studies.

    PubMed

    Egeberg, Alexander

    2016-02-01

    Psoriasis is a prevalent chronic inflammatory disease whose exact aetiology is not fully understood, but both genetic and environmental factors have been implicated in the onset and progression of the disease. At the skin level, psoriasis is characterized by localized or widespread thick raised silvery-white scaling and pruritic plaques and studies have shown that psoriasis negatively affects patients' quality of life, and depression occurs more often in patients with psoriasis. However, data have shown that psoriasis is a systemic disease which affects the joints, vasculature, and other tissues as well. Indeed, approximately one-third of patients with psoriasis develop psoriatic arthritis, and patients with severe psoriasis have a shortened life expectancy. Although our knowledge of the pathogenesis of psoriasis has advanced significantly in the past decade, as have the pharmacological treatment options which are now available, several important knowledge gaps remain. Many of the proinflammatory mediators involved in psoriasis have also been implicated in some central nervous system (CNS) diseases. However, studies on associations between psoriasis and CNS diseases are scarce. Based on nationwide registry data from the entire Danish population, the present thesis examined the associations between psoriasis and certain CNS diseases. The specific objectives of this work were to investigate the independent impact of depression on the risk of cardiovascular disease (CVD) in patients with psoriasis, the relationship between psoriasis and uveitis, and the risk of incident multiple sclerosis (MS) following the onset of psoriasis, respectively. The main results were a significantly increased risk of myocardial infarction, stroke, and CVD death in patients with psoriasis during stages of acute depression. Moreover, we found a bidirectional relationship between psoriasis and uveitis, where the occurrence of either disease significantly increased the risk of the other

  5. Molecular Epidemiological and Antibiotic Susceptibility Characterization of Brucella Isolates from Humans in Sicily, Italy▿

    PubMed Central

    Marianelli, Cinzia; Graziani, Caterina; Santangelo, Carmela; Xibilia, Maria Teresa; Imbriani, Alida; Amato, Rosa; Neri, Domenico; Cuccia, Mario; Rinnone, Sebastiano; Di Marco, Vincenzo; Ciuchini, Franco

    2007-01-01

    Brucellosis is a serious problem in Sicily. Brucella melitensis was identified as the species most frequently isolated in humans in Italy. No data, however, are available about the molecular epidemiological characterization of Brucella isolates from humans. We have conducted this study to molecularly characterize clinical isolates of Brucella spp. and to evaluate their antimicrobial susceptibilities. Twenty Brucella isolates were studied. Differential growth characteristics and DNA polymorphisms such as the restriction patterns of the PCR-amplified omp2a and omp2b genes, rpoB nucleotide sequencing, and multiple-locus variable-number tandem repeat analysis of 16 loci (MLVA-16) were used to characterize the strains. In vitro antibiotic susceptibility was determined by the E-test method on two different agar media, and the results were compared. All isolates were identified as B. melitensis biovar 3. rpoB nucleotide sequence analysis allowed the identification of two different genotypes of B. melitensis biovar 3. On the other hand, the MLVA-16 typing assay recognized 17 distinct genotypes. All isolates were sensitive to all tested antibiotics (rifampin, doxycycline, ciprofloxacin, ceftriaxone, and trimethoprim-sulfamethoxazole), and the Mueller-Hinton agar plate is recommended for antibiotic susceptibility testing by the E-test method. Our findings identify B. melitensis biovar 3 as the etiological agent isolated in Sicily and encourage the use of both molecular methods, and in particular of the MLVA-16 assay, in epidemiological trace-back analysis. This study represents the first epidemiological data from molecular typing of Brucella strains circulating in Italy and, in particular, in eastern Sicily. PMID:17634297

  6. ADHD in the Arab World: A Review of Epidemiologic Studies

    ERIC Educational Resources Information Center

    Farah, Lynn G.; Fayyad, John A.; Eapen, Valsamma; Cassir,Youmna; Salamoun, Mariana M.; Tabet, Caroline C.; Mneimneh, Zeina N.; Karam, Elie G.

    2009-01-01

    Objective: Epidemiological studies on psychiatric disorders are quite rare in the Arab World. This article reviews epidemiological studies on ADHD in all the Arab countries. Method: All epidemiological studies on ADHD conducted from 1966 through th present were reviewed. Samples were drawn from the general community, primary care clinical…

  7. Molecular epidemiology of Mannheimia haemolytica and Mannheimia glucosida associated with ovine mastitis.

    PubMed

    Omaleki, Lida; Browning, Glenn F; Allen, Joanne L; Barber, Stuart R

    2012-07-01

    While Mannheimia haemolytica and Mannheimia glucosida have been recognized as causes of intramammary infection in sheep, there has been no investigation of the epidemiology of the strains involved. Pulsed field gel electrophoresis was used to study the molecular epidemiology of isolates of these 2 species associated with ovine mastitis. Ten distinct strains were recognized among 12 M. haemolytica isolates, and 7 distinct strains among 13 M. glucosida isolates. The results demonstrate a high diversity of isolates with the ability to cause ovine mastitis. However, the presence of some identical isolates may suggest the possibility of horizontal transmission of these species in some flocks, possibly through lamb sucking, and/or differences in the capacity of some isolates to cause mastitis in sheep. PMID:22621951

  8. 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…

  9. Epidemiologic studies based on the Chernobyl accident

    SciTech Connect

    Beebe, G.

    1996-12-31

    There are great opportunities in the post-Chernobyl experience for significant epidemiologic research, perhaps even more in the area of disaster research than in the area of the human health effects of ionizing radiation. But the potential opportunity for learning the effects of radioiodine on the thyroid is very great and has aroused widespread national and international investigative interest. The opportunities for significant epidemiologic research are, however, severely limited currently by the worsening economic situation in Belarus and Ukraine, where the greatest exposure occurred, and by the lack of personnel trained in appropriate methods of study, the lack of modern equipment, the lack of supplies, the poor communication facilities, and the difficulties of accurate dose estimation. the disadvantages may or may not outweigh the obvious advantages of large numbers, the extensive direct thyroidal measurements made shortly after the accident in 1986, the magnitude of the releases of radioiodine, and the retention of the former Soviet system of universal medical care. Both the European Commission (EC) and the World Health Organization (WHO) have been working actively to strengthen the infrastructure of Russia, Belarus, and Ukraine. New scientific knowledge has yet to emerge from the extensive epidemiologic work but information of considerable public health significance has begun to accumulate. The bulk of the thyroid cancer has been shown to be valid by international pathology review; both EC and WHO representatives have declared the increase in thyroid cancer among children to have been caused in large part by Chernobyl. No increase in leukemia has been seen in the general population. The WHO pilot studies have shown no evidence of an increase in psychologic or neurologic complications among those exposed in utero. Ongoing epidemiologic work can be described by review of the inventory that the WHO has begun to maintain and publish. 20 refs., 7 tabs.

  10. [Global and historical development of the IMETAF (International Molecular Epidemiology Task Force) in Mexico].

    PubMed

    Gorodezky, C

    1997-01-01

    IMETAF or International Molecular Epidemiology Task Force was created upon the enthusiasm of Janice Dorman, molecular epidemiologist at Pittsburgh University. Also, she was in charge of the WHO type I Diabetes world project called DIAMOND. As a result of this project done with Mexican scientists. The Scientific Committee of IMETAF was formed on July 28, 1993. The activities began. A national infrastructure survey was done to analyze the epidemiology and molecular biology capabilities; a directory of scientist in epidemiology and molecular biology was elaborated; a theoric and practical course on molecular epidemiology was organized during 1996 and a second one will be held in 1997; and a series of Workshops were done: cancer and leukemias; bacterial diseases; trypanosomiosis and leishmaniosis and viral diseases. The results of these academic activities were brought to the National Academy of Medicine to a 2 days workshop and to an International Symposium called Projection of molecular epidemiology in medicine, held on April 17, 1996. The papers are published in this number. The goal of IMETAF will continue promoting transfer of technology, stimulating formal training in molecular epidemiology and helping getting funds for collaborative projects. PMID:9504097

  11. Metro system in Guangzhou as a hazardous reservoir of methicillin-resistant Staphylococci: findings from a point-prevalence molecular epidemiologic study

    PubMed Central

    Peng, Yang; Ou, Qianting; Lin, Dongxin; Xu, Ping; Li, Ying; Ye, Xiaohua; Zhou, Junli; Yao, Zhenjiang

    2015-01-01

    Staphylococci are common causes of healthcare-associated and community-associated infections. However, limited data are available on the prevalence, phenotypes and molecular characteristics of Staphylococci in metro system around the world. 320 surface samples were collected from the Guangzhou metro system to isolate and characterize Staphylococci strains. Of the samples, 75.6% (242/320) were contaminated with Staphylococci. The Staphylococci isolates, especially the methicillin resistant isolates, were resistance to most of the antibiotics, with 79.8% (193/242) classified as multidrug resistant (MDR) strains. 8 strains of methicillin-resistant Staphylococcus aureus (MRSA) carried a range of staphylococcal cassette chromosome mec (SCCmec) types [I (1), II (3), III (2) and NT (2)]. Staphylococcus aureus isolates were classified into several ST types and showed possible cross transmissions of strains from various sources. All MRSA strains were positive for the qac gene, and only one methicillin-susceptible Staphylococci aureus (MSSA) strain was positive for the Panton-Valentine leukocidin (PVL) genes. This study demonstrated that environmental surfaces in the Guangzhou metro system may be a hazardous reservoir for transmission of Staphylococci to passengers. The resistance to antibiotics and disinfectants observed among isolates was also noteworthy. PMID:26513750

  12. Molecular Epidemiology of Norovirus in Outbreaks of Gastroenteritis in Southwest Germany from 2001 to 2004

    PubMed Central

    Ike, Anthony C.; Brockmann, Stefan O.; Hartelt, Kathrin; Marschang, Rachel E.; Contzen, Matthias; Oehme, Rainer M.

    2006-01-01

    The identification and molecular epidemiology of norovirus in outbreaks of gastroenteritis were studied during a 3-year period in Germany. Specimens (n = 316) from 159 nonbacterial gastroenteritis outbreaks from March 2001 to June 2004 were analyzed for the presence of noroviruses by reverse transcriptase PCR. Outbreaks were most frequent in elderly people's homes and care centers (43%), followed by hospitals (24%). Molecular analyses of strains from 148 outbreaks showed that there were up to 12 genotypes involved in the outbreaks. Genogroup II noroviruses were responsible for 95% of the outbreaks. Cocirculation of more than one strain in the same outbreak and cocirculation of genogroup I and II strains in the same place were observed. Genogroup II4 (Grimsby-like) was the most prevalent strain, accounting for 48% and 67% of the outbreaks in 2002 and 2003, respectively. The genogroup IIb (Castell/Suria) genotype was observed in all the years of the study. Epidemiological and molecular data indicated that there was a major shift of the predominant strain that coincided with the appearance of a new variant of genogroup II4 in 2002. By the application of reverse transcriptase PCR, this study has demonstrated the importance and dynamism of noroviruses in Germany. PMID:16597849

  13. An integrative analysis of foot-and-mouth disease virus carriers in Vietnam achieved through targeted surveillance and molecular epidemiology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A multidisciplinary, molecular and conventional epidemiological approach was applied to an investigation of endemic foot-and-mouth disease in Vietnam. Within the study space, it was found that 22.3 percent of sampled ruminants had previously been infected with FMD virus (FMDV) and that 2.4 percent w...

  14. Molecular epidemiology of clonal diploids: a quick overview and a short DIY (do it yourself) notice.

    PubMed

    De Meeûs, Thierry; Lehmann, Laurent; Balloux, François

    2006-03-01

    In this short review we report the basic notions needed for understanding the population genetics of clonal diploids. We focus on the consequences of clonality on the distribution of genetic diversity within individuals, between individuals and between populations. We then summarise how to detect clonality in mainly sexual populations, conversely, how to detect sexuality in mainly clonal populations and also how genetic differentiation between populations is affected by clonality in diploids. This information is then used for building recipes on how to analyse and interpret genetic polymorphism data in molecular epidemiology studies of clonal diploids. PMID:16290062

  15. Development and perspective of current Brazilian studies on the epidemiology of childhood leukemia.

    PubMed

    Pombo de Oliveira, Maria S; Koifman, Sergio; Vasconcelos, Gisele M; Emerenciano, Mariana; de Oliveira Novaes, Cristiane

    2009-01-01

    In this concise report, we describe the history and evolution of childhood acute leukemia studies in Brazil, and the application if key biomarkers for clinical trials and epidemiological studies over the past 8 years. Highlights of each ongoing study are summarized. A Brazilian network integrating hospitals and scientific institutions from all country regions has been established. This organization is made possible through informatics and computer networking, and the standardization of pathological reviews including immunophenotyping and molecular characterization of childhood leukemias. The unique characteristics of the Brazilian population combined with a large clinical and epidemiologic framework for patient ascertainment has enabled large-scale epidemiological studies on childhood leukemia in Brazil. PMID:19064327

  16. Use of in-house studies of molecular epidemiology and full species identification for controlling spread of vancomycin-resistant Enterococcus faecalis isolates.

    PubMed Central

    Bodnar, U R; Noskin, G A; Suriano, T; Cooper, I; Reisberg, B E; Peterson, L R

    1996-01-01

    Infection with multidrug-resistant (MDR) organisms is a major clinical challenge, and few, if any, therapeutic options remain available. Increasingly, infection control measures have taken on greater importance in preventing the nosocomial transmission of MDR organisms. During December 1994 and January 1995, we identified a cluster of vancomycin-resistant Enterococcus faecalis isolates involving 16 patients situated in different areas of our university-affiliated teaching hospital. Initial review of laboratory requisition forms for the patients' locations revealed no common association, suggesting that the occurrence was not due to horizontal spread. However, using genomic DNA extraction, restriction enzyme analysis, and gel electrophoresis, we found that 12 patients were infected with isolates originating from a single clone, 2 other patients were infected with isolates from a different clone, and the remaining 2 patients were infected with unique strains. Because the typing data suggested nosocomial spread, chart review was undertaken to determine a possible common exposure source. With three exceptions, clonal isolates were linked to patient movement between surgical floors, intensive care units, and a rehabilitation unit. A detailed review of patient records revealing the association would not have been performed without realization of clonality. Thus, the data demonstrate the utility of genomic typing for epidemiological purposes. In turn, targeted infection control measures that halted the spread of the potentially lethal MDR pathogen were instituted. PMID:8862571

  17. The Molecular Epidemiology of Chronic Aflatoxin Driven Impaired Child Growth

    PubMed Central

    Turner, Paul Craig

    2013-01-01

    Aflatoxins are toxic secondary fungal metabolites that contaminate dietary staples in tropical regions; chronic high levels of exposure are common for many of the poorest populations. Observations in animals indicate that growth and/or food utilization are adversely affected by aflatoxins. This review highlights the development of validated exposure biomarkers and their use here to assess the role of aflatoxins in early life growth retardation. Aflatoxin exposure occurs in utero and continues in early infancy as weaning foods are introduced. Using aflatoxin-albumin exposure biomarkers, five major studies clearly demonstrate strong dose response relationships between exposure in utero and/or early infancy and growth retardation, identified by reduced birth weight and/or low HAZ and WAZ scores. The epidemiological studies include cross-sectional and longitudinal surveys, though aflatoxin reduction intervention studies are now required to further support these data and guide sustainable options to reduce the burden of exposure. The use of aflatoxin exposure biomarkers was essential in understanding the observational data reviewed and will likely be a critical monitor of the effectiveness of interventions to restrict aflatoxin exposure. Given that an estimated 4.5 billion individuals live in regions at risk of dietary contamination the public health concern cannot be over stated. PMID:24455429

  18. Molecular epidemiology of measles in India, 2005-2010.

    PubMed

    Wairagkar, Niteen; Chowdhury, Deepika; Vaidya, Sunil; Sikchi, Sarika; Shaikh, Naseem; Hungund, Laxman; Tomar, R S; Biswas, D; Yadav, K; Mahanta, J; Das, V N R; Yergolkar, Prasanna; Gunasekaran, P; Raja, D; Jadi, R; Ramamurty, Nalini; Mishra, A C

    2011-07-01

    Measles is a childhood disease that causes great morbidity and mortality in India and worldwide. Because measles surveillance in India is in its infancy, there is a paucity of countrywide data on circulating Measles virus genotypes. This study was conducted in 21 of 28 States and 2 of 7 Union Territories of India by MeaslesNetIndia, a national network of 27 centers and sentinel practitioners. MeaslesNetIndia investigated 52 measles outbreaks in geographically representative areas from 2005 through June 2010. All outbreaks were serologically confirmed by detection of antimeasles virus immunoglobulin M (IgM) antibodies in serum or oral fluid samples. Molecular studies, using World Health Organization (WHO)-recommended protocols obtained 203 N-gene, 40 H-gene, and 4 M-gene sequences during this period. Measles genotypes D4, D7, and D8 were found to be circulating in various parts of India during the study period. Further phylogenetic analysis revealed 4 lineages of Indian D8 genotypes: D8a, D8b, D8c, and D8d. This study generated a large, countrywide sequence database that can form the baseline for future molecular studies on measles virus transmission pathways in India. This study has created support and capabilities for countrywide measles molecular surveillance that must be carried forward. PMID:21666192

  19. Molecular epidemiology of cryptosporidiosis in cattle and other food animals [Spanish][Epidemiología molecular de cryptosporidiosis en el ganado vacuno y en otros animales de abasto

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular epidemiology of cryptosporidiosis in cattle and other food animals Cryptosporidium is an enteric protozoan parasite that infects a wide range of vertebrate hosts. Cryptosporidial infection is known now as one of the most common causes of diarrhea in humans and livestock. Worldwide prevale...

  20. Molecular Epidemiology of Mycobacterium tuberculosis Complex in Singapore, 2006-2012

    PubMed Central

    Win, Wah; Chee, Cynthia Bin-Eng; Hsu, Li Yang; Mak, Estelle; Earnest, Arul; Ong, Marcus Eng-Hock; Cutter, Jeffery; Wang, Yee Tang

    2013-01-01

    Background Tuberculosis remains common in Singapore, increasing in incidence since 2008. We attempted to determine the molecular epidemiology of Mycobacterium tuberculosis complex (MTC) isolates locally, identifying major circulating genotypes and obtaining a glimpse of transmission dynamics. Methodology Non-duplicate MTC isolates archived between 2006 and 2012 at the larger clinical tuberculosis laboratory in Singapore were sampled for spoligotyping and MIRU-VNTR typing, with case data obtained from the Singapore Tuberculosis Elimination Program registry database. Isolates between 2008 and 2012 were selected because of either multidrug-resistance or potential epidemiological linkage, whereas earlier isolates were randomly selected. Separate analyses were performed for the early (2006-2007) and later (2008-2012) study phases in view of potential selection bias. Principal Findings A total of 1,612 MTC isolates were typed, constituting 13.1% of all culture-positive tuberculosis cases during this period. Multidrug-resistance was present in 91 (5.6%) isolates – higher than the national prevalence in view of selection bias. The majority of isolates belonged to the Beijing (45.8%) and EAI (22.8%) lineages. There were 347 (30.7%) and 133 (27.5%) cases clustered by combined spoligotyping and MIRU-VNTR typing from the earlier and later phases respectively. Patients within these clusters tended to be of Chinese ethnicity, Singapore resident, and have isolates belonging to the Beijing lineage. A review of prior contact investigation results for all patients with clustered isolates failed to reveal epidemiological links for the majority, suggesting either unknown transmission networks or inadequate specificity of the molecular typing methods in a country with a moderate incidence of tuberculosis. Conclusion Our work demonstrates that Singapore has a large and heterogeneous distribution of MTC strains, and with possible cross-transmission over the past few years based on our

  1. Combining Radiation Epidemiology With Molecular Biology-Changing From Health Risk Estimates to Therapeutic Intervention.

    PubMed

    Abend, Michael; Port, Matthias

    2016-08-01

    The authors herein summarize six presentations dedicated to the key session "molecular radiation epidemiology" of the ConRad meeting 2015. These presentations were chosen in order to highlight the promise when combining conventional radiation epidemiology with molecular biology. Conventional radiation epidemiology uses dose estimates for risk predictions on health. However, combined with molecular biology, dose-dependent bioindicators of effect hold the promise to improve clinical diagnostics and to provide target molecules for potential therapeutic intervention. One out of the six presentations exemplified the use of radiation-induced molecular changes as biomarkers of exposure by measuring stabile chromosomal translocations. The remaining five presentations focused on molecular changes used as bioindicators of the effect. These bioindicators of the effect could be used for diagnostic purposes on colon cancers (genomic instability), thyroid cancer (CLIP2), or head and neck squamous cell cancers. Therapeutic implications of gene expression changes were examined in Chernobyl thyroid cancer victims and Mayak workers. PMID:27356062

  2. Genetic characterisation and molecular epidemiology of Ascaris spp. from humans and pigs in Brazil.

    PubMed

    Iñiguez, Alena M; Leles, Daniela; Jaeger, Lauren H; Carvalho-Costa, Filipe A; Araújo, Adauto

    2012-10-01

    The molecular epidemiology of Ascaris spp. of human and pig origin has been studied as a means to assess the potential of pigs as reservoirs for human ascariasis. In this study, human (H) and pig (P) Ascaris spp. haplotypes from two Brazilian regions were characterised based on two mitochondrial genes, nad1 and cox1. The results show six haplotypes of the cox1 gene, with two haplotypes (H9P9 and P3) corresponding to haplotypes previously characterised in China. Because P3 was found in humans in this study, it was designated as H14P3. Furthermore, five new Ascaris spp. nad1 haplotypes from humans (H12-H16) and five from pigs (P16-P20) were observed, with one being highly frequent and present in both hosts, here designated as H12P17. Phylogenetic and network analysis demonstrated that the molecular epidemiology of Ascaris spp. in Brazil is driven by the globally distributed haplotypes cox1 H14P3 and nad1 H12P17. In conclusion, in this study genetic characterisation of Ascaris spp. showed that humans and pigs share common haplotypes that are also present in two widely separated geographical regions of Brazil. PMID:22944771

  3. Clinical, Epidemiologic, Histopathologic and Molecular Features of an Unexplained Dermopathy

    PubMed Central

    Pearson, Michele L.; Selby, Joseph V.; Katz, Kenneth A.; Cantrell, Virginia; Braden, Christopher R.; Parise, Monica E.; Paddock, Christopher D.; Lewin-Smith, Michael R.; Kalasinsky, Victor F.; Goldstein, Felicia C.; Hightower, Allen W.; Papier, Arthur; Lewis, Brian; Motipara, Sarita; Eberhard, Mark L.

    2012-01-01

    Background Morgellons is a poorly characterized constellation of symptoms, with the primary manifestations involving the skin. We conducted an investigation of this unexplained dermopathy to characterize the clinical and epidemiologic features and explore potential etiologies. Methods A descriptive study was conducted among persons at least 13 years of age and enrolled in Kaiser Permanente Northern California (KPNC) during 2006–2008. A case was defined as the self-reported emergence of fibers or materials from the skin accompanied by skin lesions and/or disturbing skin sensations. We collected detailed epidemiologic data, performed clinical evaluations and geospatial analyses and analyzed materials collected from participants' skin. Results We identified 115 case-patients. The prevalence was 3.65 (95% CI = 2.98, 4.40) cases per 100,000 enrollees. There was no clustering of cases within the 13-county KPNC catchment area (p = .113). Case-patients had a median age of 52 years (range: 17–93) and were primarily female (77%) and Caucasian (77%). Multi-system complaints were common; 70% reported chronic fatigue and 54% rated their overall health as fair or poor with mean Physical Component Scores and Mental Component Scores of 36.63 (SD = 12.9) and 35.45 (SD = 12.89), respectively. Cognitive deficits were detected in 59% of case-patients and 63% had evidence of clinically significant somatic complaints; 50% had drugs detected in hair samples and 78% reported exposure to solvents. Solar elastosis was the most common histopathologic abnormality (51% of biopsies); skin lesions were most consistent with arthropod bites or chronic excoriations. No parasites or mycobacteria were detected. Most materials collected from participants' skin were composed of cellulose, likely of cotton origin. Conclusions This unexplained dermopathy was rare among this population of Northern California residents, but associated with significantly reduced health-related quality of

  4. The genomic Echinococcus microsatellite EmsB sequences: from a molecular marker to the epidemiological tool.

    PubMed

    Knapp, J; Bart, J M; Maillard, S; Gottstein, B; Piarroux, R

    2010-03-01

    In the field of molecular and epidemiological parasitology, characterization of fast evolving genetic markers appears as an important challenge to consider the diversity and genetic structure of parasites. The study of respective populations can help us to understand their adaptive strategies to survive and perpetuate the species within different host populations, all trying to resist infection. In the past, the relative monomorphic features of Echinococcus multilocularis, the causative agent of alveolar echinococcosis and a severe human parasitic disease, did not stimulate studies dealing with the genetic variability of Echinococcus species or respective populations. A recently developed, characterized and validated original multilocus microsatellite, named EmsB, tandemly repeated in the genome, offered an additional opportunity for this line of investigation. We have compiled in this review new insights brought by this molecular tracker on the transmission activity of Echinococcus among different hosts and at different geographical scales. PMID:20025824

  5. Epidemiological transition of colorectal cancer in developing countries: Environmental factors, molecular pathways, and opportunities for prevention

    PubMed Central

    Bishehsari, Faraz; Mahdavinia, Mahboobeh; Vacca, Michele; Malekzadeh, Reza; Mariani-Costantini, Renato

    2014-01-01

    Colorectal cancer (CRC) is one of the leading causes of cancer and cancer-related mortality worldwide. The disease has been traditionally a major health problem in industrial countries, however the CRC rates are increasing in the developing countries that are undergoing economic growth. Several environmental risk factors, mainly changes in diet and life style, have been suggested to underlie the rise of CRC in these populations. Diet and lifestyle impinge on nuclear receptors, on the intestinal microbiota and on crucial molecular pathways that are implicated in intestinal carcinogenesis. In this respect, the epidemiological transition in several regions of the world offers a unique opportunity to better understand CRC carcinogenesis by studying the disease phenotypes and their environmental and molecular associations in different populations. The data from these studies may have important implications for the global prevention and treatment of CRC. PMID:24876728

  6. [UNIFICATION OF THE MOLECULAR EPIDEMIOLOGICAL RESEARCH OF THE TICK-BORNE ENCEPHALITIS].

    PubMed

    Kovalev, S Y; Mukhacheva, T A

    2016-01-01

    Molecular genetic techniques and approaches in epidemiological studies were breakthrough in the understanding of the laws, ways, and mechanisms of the spread of the pathogens. However, lack of standard methods makes it difficult to compare results obtained by different scientific groups. In this work we propose to choose one fragment of the TBEV genome as a genetic marker whose sequencing would be both obligatory and sufficient for the molecular epidemiological studies. The best candidate for this purpose may be a fragment of the gene E of 454 nucleotides in length. The deduced amino acid sequence of this fragment was a basis for a new approach for the TBEV differentiation with clusteron being a structural unit (Kovalev and Mukhacheva, 2013). The clusteron approach was proved to be informative for studying the genetic structure of the TBEV-Sib population in the Middle Urals. TBE foci were shown to be unique in both quantitative and qualitative composition of the clusterons. The greatest clusteron diversity in the south of the Middle Urals, through the Trans-Siberian way, may reflect the history of the colonization, closely associated with the roads between Siberia and the European part of Russia. The age of three clusterons did not exceed 50 years, which may indicate an ongoing evolutionary process taking place in the TBEV-Sib populations. In turn, their spatial distribution indicates the crucial role of human factors in the spread of the TBEV (Kovalev & Mukhacheva, 2014). The clusteron approach provides formalization of ideas about the structure of the viral populations and could be used not only by researchers but also by epidemiological surveillance services. Unification of the studies of the TBEV on the basis of a standard genetic marker would consolidate the efforts of researchers from different regions of Russia and other countries. PMID:27451502

  7. Molecular epidemiology, phylogeny and evolution of the filarial nematode Wuchereria bancrofti.

    PubMed

    Small, Scott T; Tisch, Daniel J; Zimmerman, Peter A

    2014-12-01

    of data for diseases like malaria and HIV, there is a scarcity of this data for filarial nematodes. With the falling cost of genome sequencing, research on filarial nematodes could benefit from the addition of population genetics statistics and phylogenetics especially in dealing with elimination programs. A comprehensive review focusing on population genetics of filarial nematode does not yet exist. Here our goal is to provide a current overview of the molecular epidemiology of W. bancrofti (Wb) the primary causative agent of LF. We begin by reviewing studies utilizing molecular typing techniques with specific focus on genomic and population datasets. Next, we used whole mitochondrial genome data to construct a phylogeny and examine the evolutionary history of the Onchocercidae. Then, we provide a perspective to aid in understanding how population genetic techniques translate to modern epidemiology. Finally, we introduce the concept of genomic epidemiology and provide some examples that will aid in future studies of Wb. PMID:25176600

  8. An outbreak of infections caused by extensively drug-resistant Klebsiella pneumoniae strains during a short period of time in a Chinese teaching hospital: epidemiology study and molecular characteristics.

    PubMed

    Zhou, Tieli; Zhang, Yapei; Li, Meimei; Yu, Xiao; Sun, Yao; Xu, Jiru

    2015-07-01

    In this study, we comprehensively described the clinical risk factors, outcome, epidemiology, and molecular basis associated with an outbreak of extensively drug-resistant KPC-2-producing Klebsiella pneumoniae involving 15 patients in a teaching hospital from May 1 to June 27, 2013. Most of the patients were elderly and received long-term hospital treatment, and 40.0% (6/15) of them were dead. All strains carried bla(KPC-2), rmtB, bla(CTX-M-65), bla(SHV-11), oqxA, oqxB, and aac(6')-Ib-cr and even harbored additional other resistance genes, such as armA, bla(CTX-M-1), bla(TEM-1). bla(KPC-2), rmtB, and bla(CTX-M-65) were located on the same ~54.2-kb plasmid, and conjugation experiments further proved the cotransferable characteristic. Alterations of outer membrane proteins were confirmed by sodium dodecyl sulfate--olyacrylamide gelelectrophoresis and sequencing, which can lead to a drastic change in the permeability of cells. All isolates belonged to the clone complex 258, spreading rapidly across the world. Our study demonstrated that a high degree of awareness and surveillance of those drug resistance determinants is urgently needed. PMID:25865067

  9. Molecular approaches for a better understanding of the epidemiology and population genetics of Leishmania.

    PubMed

    Schönian, G; Kuhls, K; Mauricio, I L

    2011-04-01

    Molecular approaches are being used increasingly for epidemiological studies of visceral and cutaneous leishmaniases. Several molecular markers resolving genetic differences between Leishmania parasites at species and strain levels have been developed to address key epidemiological and population genetic questions. The current gold standard, multilocus enzyme typing (MLEE), needs cultured parasites and lacks discriminatory power. PCR assays identifying species directly with clinical samples have proven useful in numerous field studies. Multilocus sequence typing (MLST) is potentially the most powerful phylogenetic approach and will, most probably, replace MLEE in the future. Multilocus microsatellite typing (MLMT) is able to discriminate below the zymodeme level and seems to be the best candidate for becoming the gold standard for distinction of strains. Population genetic studies by MLMT revealed geographical and hierarchic population structure in L. tropica, L. major and the L. donovani complex. The existence of hybrids and gene flow between Leishmania populations suggests that sexual recombination is more frequent than previously thought. However, typing and analytical tools need to be further improved. Accessible databases should be created and sustained for integrating data obtained by different researchers. This would allow for global analyses and help to avoid biases in analyses due to small sample sizes. PMID:21078222

  10. Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees

    PubMed Central

    Kenah, Eben; Britton, Tom; Halloran, M. Elizabeth; Longini, Ira M.

    2016-01-01

    Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks. However, transmission trees from one outbreak do not generalize to future outbreaks. Reconstruction of transmission trees is most useful to public health if it leads to generalizable scientific insights about disease transmission. In a survival analysis framework, estimation of transmission parameters is based on sums or averages over the possible transmission trees. A phylogeny can increase the precision of these estimates by providing partial information about who infected whom. The leaves of the phylogeny represent sampled pathogens, which have known hosts. The interior nodes represent common ancestors of sampled pathogens, which have unknown hosts. Starting from assumptions about disease biology and epidemiologic study design, we prove that there is a one-to-one correspondence between the possible assignments of interior node hosts and the transmission trees simultaneously consistent with the phylogeny and the epidemiologic data on person, place, and time. We develop algorithms to enumerate these transmission trees and show these can be used to calculate likelihoods that incorporate both epidemiologic data and a phylogeny. A simulation study confirms that this leads to more efficient estimates of hazard ratios for infectiousness and baseline hazards of infectious contact, and we use these methods to analyze data from a foot-and-mouth disease virus outbreak in the United Kingdom in 2001. These results demonstrate the importance of data on individuals who escape infection, which is often overlooked. The combination of survival analysis and algorithms linking phylogenies to transmission trees is a rigorous but flexible statistical foundation for molecular infectious disease epidemiology. PMID:27070316

  11. Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees.

    PubMed

    Kenah, Eben; Britton, Tom; Halloran, M Elizabeth; Longini, Ira M

    2016-04-01

    Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks. However, transmission trees from one outbreak do not generalize to future outbreaks. Reconstruction of transmission trees is most useful to public health if it leads to generalizable scientific insights about disease transmission. In a survival analysis framework, estimation of transmission parameters is based on sums or averages over the possible transmission trees. A phylogeny can increase the precision of these estimates by providing partial information about who infected whom. The leaves of the phylogeny represent sampled pathogens, which have known hosts. The interior nodes represent common ancestors of sampled pathogens, which have unknown hosts. Starting from assumptions about disease biology and epidemiologic study design, we prove that there is a one-to-one correspondence between the possible assignments of interior node hosts and the transmission trees simultaneously consistent with the phylogeny and the epidemiologic data on person, place, and time. We develop algorithms to enumerate these transmission trees and show these can be used to calculate likelihoods that incorporate both epidemiologic data and a phylogeny. A simulation study confirms that this leads to more efficient estimates of hazard ratios for infectiousness and baseline hazards of infectious contact, and we use these methods to analyze data from a foot-and-mouth disease virus outbreak in the United Kingdom in 2001. These results demonstrate the importance of data on individuals who escape infection, which is often overlooked. The combination of survival analysis and algorithms linking phylogenies to transmission trees is a rigorous but flexible statistical foundation for molecular infectious disease epidemiology. PMID:27070316

  12. Molecular epidemiology of Campylobacter jejuni in a geographically isolated country with a uniquely structured poultry industry.

    PubMed

    Müllner, Petra; Collins-Emerson, Julie M; Midwinter, Anne C; Carter, Philip; Spencer, Simon E F; van der Logt, Peter; Hathaway, Steve; French, Nigel P

    2010-04-01

    In New Zealand the number of campylobacteriosis notifications increased markedly between 2000 and 2007. Notably, this country's poultry supply is different than that of many developed countries as the fresh and frozen poultry available at retail are exclusively of domestic origin. To examine the possible link between human cases and poultry, a sentinel surveillance site was established to study the molecular epidemiology of Campylobacter jejuni over a 3-year period from 2005 to 2008 using multilocus sequence typing. Studies showed that 60.1 to 81.4% of retail poultry carcasses from the major suppliers were contaminated with C. jejuni. Differences were detected in the probability and level of contamination and the relative frequency of genotypes for individual poultry suppliers and humans. Some carcasses were contaminated with isolates belonging to more than one sequence type (ST), and there was evidence of both ubiquitous and supplier-associated strains, an epidemiological pattern not recognized yet in other countries. The common poultry STs were also common in human clinical cases, providing evidence that poultry is a major contributor to human infection. Both internationally rare genotypes, such as ST-3069 and ST-474, and common genotypes, such as ST-45 and ST-48, were identified in this study. The dominant human sequence type in New Zealand, ST-474, was found almost exclusively in isolates from one poultry supplier, which provided evidence that C. jejuni has a distinctive molecular epidemiology in this country. These results may be due in part to New Zealand's geographical isolation and its uniquely structured poultry industry. PMID:20154115

  13. First insight into the molecular epidemiology of Mycobacterium tuberculosis in Santa Catarina, southern Brazil.

    PubMed

    Nogueira, Christiane Lourenço; Prim, Rodrigo Ivan; Senna, Simone Gonçalves; Rovaris, Darcita Büerger; Maurici, Rosemeri; Rossetti, Maria Lúcia; Couvin, David; Rastogi, Nalin; Bazzo, Maria Luiza

    2016-03-01

    Molecular epidemiology of Mycobacterium tuberculosis is useful for understanding disease transmission dynamics, and to establish strategic measures for TB control and prevention. The aim of this study was to analyze clinical, epidemiological and molecular characteristics of MTBC clinical isolates from Santa Catarina state, southern Brazil. During one-year period, 406 clinical isolates of MTBC were collected from Central Laboratory of Public Health and typed by spoligotyping. Demographic and clinical data were collected from the Brazilian National Mandatory Disease Reporting System. The majority of cases occurred in highest population densities regions and about 50% had some condition associated with TB. Among all isolates, 5.7% were MDR, which showed association with drug addiction. LAM was the most predominant lineage with 47.5%, followed by the T superfamily with 25.9% and Haarlem with 12.3%. The MST showed two major groups: the first was formed mainly by the LAM lineage and the second was mainly formed by the T and Haarlem lineages. Others lineages were distributed in peripheral positions. This study provides the first insight into the population structure of M. tuberculosis in SC State. Spoligotyping and other genotyping analyses are important to establish strategic measures for TB control and prevention. PMID:26980497

  14. Apocalypse...now? Molecular epidemiology, predictive genetic tests, and social communication of genetic contents.

    PubMed

    Castiel, L D

    1999-01-01

    The author analyzes the underlying theoretical aspects in the construction of the molecular watershed of epidemiology and the concept of genetic risk, focusing on issues raised by contemporary reality: new technologies, globalization, proliferation of communications strategies, and the dilution of identity matrices. He discusses problems pertaining to the establishment of such new interdisciplinary fields as molecular epidemiology and molecular genetics. Finally, he analyzes the repercussions of the social communication of genetic content, especially as related to predictive genetic tests and cloning of animals, based on triumphal, deterministic metaphors sustaining beliefs relating to the existence and supremacy of concepts such as 'purity', 'essence', and 'unification' of rational, integrated 'I's/egos'. PMID:10089550

  15. Molecular epidemiology of Cryptosporidium and Giardia in cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cryptosporidium spp. and Giardia duodenalis are enteric protozoan parasites that infect a wide range of vertebrate hosts including humans. Infections with both parasites are known as one of the most common causes of diarrhea in humans and livestock. The epidemiology of cryptosporidiosis and giardias...

  16. Malignant catarrhal fever: understanding molecular diagnostics in context of epidemiology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Malignant catarrhal fever (MCF) is a frequently fatal disease, primarily of ruminants, caused by a group of gammaherpesviruses. Due to complexities of pathogenesis and epidemiology in various species which are either clinically-susceptible or reservoir hosts, veterinary clinicians face significant ...

  17. Report of the second international symposium on molecular epidemiology in childhood leukaemia and embryonal tumours, Rio de Janeiro, Brazil.

    PubMed

    Pombo de Oliveira, M S; Ferman, S; de Camargo, B

    2008-01-01

    The recent International Symposium on Molecular epidemiology in Embryonal Tumours and Paediatric Leukaemia was held on 4-6 March 2008 in Rio de Janeiro, Brazil. It proved a very productive meeting in which studies relating to genetics, therapeutical trials, identification of risk factors in acute leukaemia neuroblastoma and Wilms' tumours were presented. Over 120 participants gathered for three days of fruitful discussions, including representatives of paediatrics, haematology, laboratory, epidemiology and pathology. Debates were held about strategies of applications of important biomarkers for clinical trials. Highlights of each of the scientific presentations are summarized below. PMID:22275972

  18. Molecular epidemiology of Haemophilus influenzae type b in the Gambia.

    PubMed Central

    Bijlmer, H A; van Alphen, L; Geelen-van den Broek, L; Greenwood, B M; Valkenburg, H A; Dankert, J

    1992-01-01

    One hundred two invasive and 64 noninvasive isolates of Haemophilus influenzae were collected in the course of a 2-year prospective field study on the epidemiology of H. influenzae meningitis in The Gambia. The isolates were serotyped, biotyped, and subtyped by outer membrane protein (OMP) profile analysis (OMP subtyping). H. influenzae meningitis was found to be caused by serotype b (95%). In invasive disease, serotype a, although present in the throat of healthy children, caused only occasionally (5.9%) disease. The distribution of biotypes of H. influenzae appeared to be very similar to that found outside The Gambia. A distinct pattern of OMP subtypes, different from other parts of the world, is prevalent in H. influenzae type b (Hib) in The Gambia. OMP subtypes 2, 4, 5, 8, and 9 were observed to be predominant. These subtypes, except subtype 2, have not been described. L subtypes (subtypes 2, 4, and 8) were associated with invasive disease, whereas non-L subtypes (subtypes 5 and 9) were found more often in healthy carriers (P less than 0.001). A significant difference in geographical distribution was found in subtypes of noninvasive Hib strains (P less than 0.05). We conclude that in The Gambia H. influenzae invasive disease is caused mainly by type b strains with a limited number of OMP subtypes, which are different from the subtypes found elsewhere in the world. These data are important for the surveillance of Hib disease in developing countries and are baseline data for a Hib polyribosyl-ribitolphosphate-conjugated vaccine trial in The Gambia. Alternative Hib OMP vaccines should include a set of representative OMPs. Images PMID:1537907

  19. Molecular epidemiology of measles virus in Italy, 2002–2007

    PubMed Central

    2012-01-01

    Background The European Regional Office of the World Health Organization (WHO/Europe) developed a strategic approach to halt the indigenous transmission of measles in its 53 Member States by 2015. In view of the goal of measles elimination, it is of great importance to assess the circulation of wild-type measles virus (MV). Genetic analysis is indispensable to understand the epidemiology of measles. Methods Urine and saliva samples were collected between May 2002 and December 2007, in order to find the origins and routes of wild type measles virus circulation. RT-PCR was performed on a total of 414 clinical samples of patients from different Italian regions. The results confirmed the genome presence in 199 samples, out of which 179 were sequenced. The sequences were genotyped by comparing the fragment coding for the carboxyl terminus of the nucleoprotein (450 nucleotides) with that one of the WHO reference strains. Results From the year 2002 to the year 2007 phylogenetic analysis of measles sequences showed a predominant circulation of the D7 genotype in the Italian territory for the years 2002–2004. This genotype was replaced by D4 and B3 genotypes in the biennium 2006–2007. During the same period C2, A, D5 and D8 genotypes were also detected. Conclusions Genetic characterization of wild-type MV provides a means to study the transmission pathways of the virus, and is an essential component of laboratory-based surveillance. Knowledge of currently circulating measles virus genotype in Italy will help in monitoring the success of the measles elimination programme and will contribute to evaluate the effectiveness of future vaccination campaigns. PMID:23173726

  20. Impact of immigration on HIV-1 molecular epidemiology in West Africa, Maghreb and Southern Europe.

    PubMed

    Miri, Lamia; Wakrim, Lahcen; Kassar, Hassène; Hemminki, Kari; Khyatti, Meriem

    2014-01-01

    There is global concern about the relation between international migration and the course of the AIDS epidemic. Maghreb is a North African region, which lies between sub-Saharan Africa and Europe. It has been turned recently into a region of immigration, since there are more and more flows of West African migrants hoping to reach European countries. Here we provide an overview on HIV-1 molecular epidemiology particularly in West African countries, Maghreb (Morocco, Algeria, Tunisia) and southern European countries (Spain, France, and Italy). The studies conducted in several countries of the region revealed different features of HIV-1 molecular epidemiology, especially for the distribution of viral subtypes and for transmitted drug resistance profiles. Furthermore, migration from West Africa to Europe seems to be a potential source of non-B subtype mobility to Maghreb and eventually to southern Europe, where HIV-1 non-B variants significantly increased in the last 10 to 15 years. As genetic differences between subtypes might impact the drug resistance pathways, it is important to provide continuous surveillance programs for the early detection of new variants spreading in the population before they become more prevalent, and to identify resistance profiles in different infected populations, especially migrants. PMID:24802562

  1. Phylogeography and molecular epidemiology of hepatitis C virus genotype 2 in Africa.

    PubMed

    Markov, Peter V; Pepin, Jacques; Frost, Eric; Deslandes, Sylvie; Labbé, Annie-Claude; Pybus, Oliver G

    2009-09-01

    Understanding the origin and nature of hepatitis C virus (HCV) genetic diversity is critical for improving treatment and vaccine design, and such diversity is the sole source of information about the virus' epidemic history prior to its identification 20 years ago. In this paper, we study the molecular epidemiology of HCV genotype 2 in its region of endemic origin, west and central Africa. Our analysis includes 56 new and highly diverse HCV isolates sampled from infected individuals in Guinea-Bissau. By combining phylogenetic, geographical and epidemiological information, we find a previously unappreciated geographical structure in the diversity of HCV genotype 2, pointing to a history of eastwards spatial spread from the west African coast to Cameroon that took place over several centuries. Molecular clock analysis dates the common ancestor of HCV in Guinea-Bissau to 1470 (1414-1582). The phylogenetic position of isolates from Madagascar and Martinique suggests a role for the historical slave trade in the global dissemination of HCV and of the epidemic subtypes 2a and 2c. Coalescent-based estimates of epidemic growth indicate a rapid 20th-century spread of HCV genotype 2 in Cameroon that is absent in Guinea-Bissau. We discuss this contrast in the context of possible parenteral HCV exposure during public-health campaigns undertaken during the colonial era. PMID:19474244

  2. [RET/PTC Gene Rearrangements in the Sporadic and Radiogenic Thyroid Tumors: Molecular Genetics, Radiobiology and Molecular Epidemiology].

    PubMed

    Ushenkova, L N; Koterov, A N; Biryukov, A P

    2015-01-01

    A review of molecular genetic, radiobiological and molecular epidemiological studies of gene (chromosome) rearrangements RET/PTC in the cells of the thyroid gland as well as the laws in relation to radiation exposure in vitro, in vivo and human populations identified with them are submitted. The data on the c-RET gene and its chimeric constructs with the gene-donors (RET/PTC rearrangements) are considered. The information about the history of the RET/PTC discovery, their types, carcinogenic potential and specificity both to tumor and non-tumor thyroid disease especially for papillary thyroid carcinoma are provided. The data (seven studies) on the induction of RET/PTC after irradiation of tumor and normal thyroid cells in vitro and mice are reviewed. The mechanisms of RET/PTC induction may be associated with DNA double strand breaks and oxidative stress. Some information (three publications) about the possibility of RET/PTC induction by low doses of radiation with low LET (to 0.1 Gy) is given and it is concluded that their potential evidentiary is generally weak. The achievements in the molecular epidemiology of RET/PTC frequency for exposed and unexposed cohorts are stated. At the same time it is noted that, despite the vast array. of data accumulated from 30 countries of the world and more than 20 years of research, the formed provisions are weakly confirmed statistically and have no base corresponding to the canons of evidence-based medicine. The possibility of use of the RET/PTC presence or their frequencies as markers of the papillary thyroid carcinomas and, specifically, their radiogenic forms, is considered. In the first case the answer may be positive, while in the second, the situation is characterized by uncertainty. Based to the above mentioned we came to a conclusion about the need of a pooled or meta-analysis of the totality of the published data. PMID:26310016

  3. Environmental pollutants and breast cancer: epidemiologic studies.

    PubMed

    Brody, Julia Green; Moysich, Kirsten B; Humblet, Olivier; Attfield, Kathleen R; Beehler, Gregory P; Rudel, Ruthann A

    2007-06-15

    Laboratory research has shown that numerous environmental pollutants cause mammary gland tumors in animals; are hormonally active, specifically mimicking estrogen, which is a breast cancer risk factor; or affect susceptibility of the mammary gland to carcinogenesis. An assessment of epidemiologic research on these pollutants identified in toxicologic studies can guide future research and exposure reduction aimed at prevention. The PubMed database was searched for relevant literature and systematic critical reviews were entered in a database available at URL: www.silentspring.org/sciencereview and URL: www.komen.org/environment (accessed April 10, 2007). Based on a relatively small number of studies, the evidence to date generally supports an association between breast cancer and polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) in conjunction with certain genetic polymorphisms involved in carcinogen activation and steroid hormone metabolism. Evidence regarding dioxins and organic solvents is sparse and methodologically limited but suggestive of an association. Methodologic problems include inadequate exposure assessment, a lack of access to highly exposed and unexposed populations, and a lack of preclinical markers to identify associations that may be obscured by disease latency. Among chemicals identified in toxicologic research as relevant to breast cancer, many have not been investigated in humans. The development of better exposure assessment methods is needed to fill this gap. In the interim, weaknesses in the epidemiologic literature argue for greater reliance on toxicologic studies to develop national policies to reduce chemical exposures that may be associated with breast cancer. Substantial research progress in the last 5 years suggests that the investigation of environmental pollutants will lead to strategies to reduce breast cancer risk. PMID:17503436

  4. NASA Remote Sensing Data for Epidemiological Studies

    NASA Technical Reports Server (NTRS)

    Maynard, Nancy G.; Vicente, G. A.

    2002-01-01

    In response to the need for improved observations of environmental factors to better understand the links between human health and the environment, NASA has established a new program to significantly improve the utilization of NASA's diverse array of data, information, and observations of the Earth for health applications. This initiative, lead by Goddard Space Flight Center (GSFC) has the following goals: (1) To encourage interdisciplinary research on the relationships between environmental parameters (e.g., rainfall, vegetation) and health, (2) Develop practical early warning systems, (3) Create a unique system for the exchange of Earth science and health data, (4) Provide an investigator field support system for customers and partners, (5) Facilitate a system for observation, identification, and surveillance of parameters relevant to environment and health issues. The NASA Environment and Health Program is conducting several interdisciplinary projects to examine applications of remote sensing data and information to a variety of health issues, including studies on malaria, Rift Valley Fever, St. Louis Encephalitis, Dengue Fever, Ebola, African Dust and health, meningitis, asthma, and filariasis. In addition, the NASA program is creating a user-friendly data system to help provide the public health community with easy and timely access to space-based environmental data for epidemiological studies. This NASA data system is being designed to bring land, atmosphere, water and ocean satellite data/products to users not familiar with satellite data/products, but who are knowledgeable in the Geographic Information Systems (GIS) environment. This paper discusses the most recent results of the interdisciplinary environment-health research projects and provides an analysis of the usefulness of the satellite data to epidemiological studies. In addition, there will be a summary of presently-available NASA Earth science data and a description of how it may be obtained.

  5. Molecular epidemiology of Theileria parva in the field.

    PubMed

    Geysen, D; Bishop, R; Skilton, R; Dolan, T T; Morzaria, S

    1999-09-01

    Molecular tools based on seminested RFLP-PCR techniques to characterize field parasites in bloodspots dried on filter paper permitted investigation of the extent and the dynamics of diversity of Theileria parva populations in the field. Parallel molecular studies explored the long-term genome stability of various isolates by probing Southern blots of EcoRI digested total genomic DNA with four different reference nucleic acid probes. Three polymorphic single copy loci encoding for antigen genes were developed for seminested PCR detection in order to apply them for a multilocus approach in population genetic studies. Seven alleles were identified for the polymorphic immunodominant molecule (PIM) locus by using restriction enzymes, and 4 alleles each for the p150 and p104 loci. A simple DNA extraction method gave good results in amplifying these loci from carrier animals using samples of blood dried on filter papers. Results from probing Southern blots of cultures taken at sequential timepoints indicate relative genome stability in T. parva in comparison to other parasitic protozoa such as Plasmodium. Comparatively homogeneous profiles in sympatric isolates from Zambia were identified using all four probes and PCR amplified products which contrasted with the variety found amongst Kenyan stocks. Preliminary characterization of T. parva field samples from the Southern Province of Zambia strongly suggest clonal expansion of one of the components of a non-Zambian trivalent vaccine used on a limited scale in the Province from 1985 until 1992. PMID:10540308

  6. alpha-Thalassaemia in Tunisia: some epidemiological and molecular data.

    PubMed

    Siala, H; Ouali, F; Messaoud, T; Bibi, A; Fattoum, S

    2008-12-01

    Unlike the other haemoglobinopathies, few researches have been published concerning alpha-thalassaemia in Tunisia. The aim of the present work is to acquire further data concerning alpha-thalassaemia prevalence and molecular defects spectrum in Tunisia, by collecting and studying several kinds of samples carrying alpha-thalassaemia. The first survey conducted on 529 cord blood samples using cellulose acetate electrophoresis, have displayed the prevalence of 7.38% Hb Bart's carriers at birth. Molecular analyses were conducted by PCR and DNA sequencing on 20 families' cases from the above survey carrying the Hb Bart's at birth and on 10 Hb H diseased patients. The results showed six alpha-globin gene molecular defects and were responsible for alpha-thalassaemia: -alpha(3.7), - -(MedI), alpha(TSaudi), alpha(2)(cd23GAG->Stop), Hb Greone Hart: alpha(1)(119CCT->TCT) corresponding to 11 genotypes out of which two are responsible for Hb H disease (- -(Med)/-alpha(3.7)) and (alpha(TSaudi)alpha/alpha(TSaudi)alpha) and a newly described polymorphism: alpha+6C->G. The geographical repartition of alpha-thal carriers showed that the -alpha3.7 deletion is distributed all over the country, respectively the alpha(HphI) and alpha(TSaudi) seem to be more frequent in the central region of the northeast region. The haematological and clinical data showed a moderate phenotype with a late age of diagnosis for Hb H disease. This work had permitted, in addition to an overview on alpha-thalassaemia in the country, the optimization of protocols for alpha-thalassaemia detection in our lab, allowing further investigations concerning phenotype-genotype correlation in sickle cell disease or beta-thalassaemia. PMID:19147907

  7. 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. PMID:27102715

  8. Integration of molecular pathology, epidemiology and social science for global precision medicine.

    PubMed

    Nishi, Akihiro; Milner, Danny A; Giovannucci, Edward L; Nishihara, Reiko; Tan, Andy S; Kawachi, Ichiro; Ogino, Shuji

    2016-01-01

    The precision medicine concept and the unique disease principle imply that each patient has unique pathogenic processes resulting from heterogeneous cellular genetic and epigenetic alterations and interactions between cells (including immune cells) and exposures, including dietary, environmental, microbial and lifestyle factors. As a core method field in population health science and medicine, epidemiology is a growing scientific discipline that can analyze disease risk factors and develop statistical methodologies to maximize utilization of big data on populations and disease pathology. The evolving transdisciplinary field of molecular pathological epidemiology (MPE) can advance biomedical and health research by linking exposures to molecular pathologic signatures, enhancing causal inference and identifying potential biomarkers for clinical impact. The MPE approach can be applied to any diseases, although it has been most commonly used in neoplastic diseases (including breast, lung and colorectal cancers) because of availability of various molecular diagnostic tests. However, use of state-of-the-art genomic, epigenomic and other omic technologies and expensive drugs in modern healthcare systems increases racial, ethnic and socioeconomic disparities. To address this, we propose to integrate molecular pathology, epidemiology and social science. Social epidemiology integrates the latter two fields. The integrative social MPE model can embrace sociology, economics and precision medicine, address global health disparities and inequalities, and elucidate biological effects of social environments, behaviors and networks. We foresee advancements of molecular medicine, including molecular diagnostics, biomedical imaging and targeted therapeutics, which should benefit individuals in a global population, by means of an interdisciplinary approach of integrative MPE and social health science. PMID:26636627

  9. A multicentre study of meticillin-resistant Staphylococcus aureus in acute bacterial skin and skin-structure infections in China: susceptibility to ceftaroline and molecular epidemiology.

    PubMed

    Zhang, Hui; Xiao, Meng; Kong, Fanrong; O'Sullivan, Matthew V N; Mao, Lei-Li; Zhao, Hao-Ran; Zhao, Ying; Wang, He; Xu, Ying-Chun

    2015-04-01

    Ceftaroline is a novel cephalosporin with activity against Gram-positive organisms, including meticillin-resistant Staphylococcus aureus (MRSA). The objective of this study was to investigate the susceptibility to ceftaroline of hospital-associated MRSA (HA-MRSA) isolates causing acute bacterial skin and skin-structure infections (ABSSSIs) in China and to examine their relationship by genotyping. A total of 251 HA-MRSA isolates causing ABSSSIs were collected from a multicentre study involving 56 hospitals in 38 large cities across 26 provinces in mainland China. All isolates were characterised by multilocus sequence typing (MLST), staphylococcal cassette chromosome mec (SCCmec) typing, spa typing and detection of the Panton-Valentine leukocidin locus (lukS-PV and lukF-PV). Minimum inhibitory concentrations (MICs) of 14 antimicrobial agents, including ceftaroline, were determined by broth microdilution and were interpreted using Clinical and Laboratory Standards Institute breakpoints. The ceftaroline MIC50 and MIC90 values (MICs that inhibit 50% and 90% of the isolates, respectively) were 1 μg/mL and 2 μg/mL, respectively; 33.5% (n=84) of the isolates studied were ceftaroline-non-susceptible, with MICs of 2 μg/mL, but no isolate exhibited ceftaroline resistance (MIC>2 μg/mL). All of the ceftaroline-non-susceptible isolates belonged to the predominant HA-MRSA clones: 95.2% (n=80) from MLST clonal complex 8 (CC8), with the remaining 4.8% (n=4) from CC5. The high rate of non-susceptibility to ceftaroline amongst HA-MRSA causing ABSSSIs in China is concerning. PMID:25649348

  10. A Longitudinal Study Simultaneously Exploring the Carriage of APEC Virulence Associated Genes and the Molecular Epidemiology of Faecal and Systemic E. coli in Commercial Broiler Chickens

    PubMed Central

    Kemmett, Kirsty; Humphrey, Tom; Rushton, Steven; Close, Andrew; Wigley, Paul; Williams, Nicola J.

    2013-01-01

    Colibacillosis is an economically important syndromic disease of poultry caused by extra-intestinal avian pathogenic Escherichia coli (APEC) but the pathotype remains poorly defined. Combinations of virulence-associated genes (VAGs) have aided APEC identification. The intestinal microbiota is a potential APEC reservoir. Broiler chickens are selectively bred for fast, uniform growth. Here we simultaneously investigate intestinal E. coli VAG carriage in apparently healthy birds and characterise systemic E. coli from diseased broiler chickens from the same flocks. Four flocks were sampled longitudinally from chick placement until slaughter. Phylogrouping, macro-restriction pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) were performed on an isolate subset from one flock to investigate the population structure of faecal and systemic E. coli. Early in production, VAG carriage among chick intestinal E. coli populations was diverse (average Simpson's D value  = 0.73); 24.05% of intestinal E. coli (n = 160) from 1 day old chicks were carrying ≥5 VAGs. Generalised Linear models demonstrated VAG prevalence in potential APEC populations declined with age; 1% of E. coli carrying ≥5 VAGs at slaughter and demonstrated high strain diversity. A variety of VAG profiles and high strain diversity were observed among systemic E. coli. Thirty three new MLST sequence types were identified among 50 isolates and a new sequence type representing 22.2% (ST-2999) of the systemic population was found, differing from the pre-defined pathogenic ST-117 at a single locus. For the first time, this study takes a longitudinal approach to unravelling the APEC paradigm. Our findings, supported by other studies, highlight the difficulty in defining the APEC pathotype. Here we report a high genetic diversity among systemic E. coli between and within diseased broilers, harbouring diverse VAG profiles rather than single and/or highly related pathogenic clones

  11. BioCAST/IFCT-1002: epidemiological and molecular features of lung cancer in never-smokers.

    PubMed

    Couraud, Sébastien; Souquet, Pierre-Jean; Paris, Christophe; Dô, Pascal; Doubre, Hélène; Pichon, Eric; Dixmier, Adrien; Monnet, Isabelle; Etienne-Mastroianni, Bénédicte; Vincent, Michel; Trédaniel, Jean; Perrichon, Marielle; Foucher, Pascal; Coudert, Bruno; Moro-Sibilot, Denis; Dansin, Eric; Labonne, Stéphanie; Missy, Pascale; Morin, Franck; Blanché, Hélène; Zalcman, Gérard

    2015-05-01

    Lung cancer in never-smokers (LCINS) (fewer than 100 cigarettes in lifetime) is considered as a distinct entity and harbours an original molecular profile. However, the epidemiological and molecular features of LCINS in Europe remain poorly understood. All consecutive newly diagnosed LCINS patients were included in this prospective observational study by 75 participating centres during a 14-month period. Each patient completed a detailed questionnaire about risk factor exposure. Biomarker and pathological analyses were also collected. We report the main descriptive overall results with a focus on sex differences. 384 patients were included: 65 men and 319 women. 66% had been exposed to passive smoking (significantly higher among women). Definite exposure to main occupational carcinogens was significantly higher in men (35% versus 8% in women). A targetable molecular alteration was found in 73% of patients (without any significant sex difference): EGFR in 51%, ALK in 8%, KRAS in 6%, HER2 in 3%, BRAF in 3%, PI3KCA in less than 1%, and multiple in 2%. We present the largest and most comprehensive LCINS analysis in a European population. Physicians should track occupational exposure in men (35%), and a somatic molecular alteration in both sexes (73%). PMID:25657019

  12. Epidemiological study of cauda equina syndrome

    PubMed Central

    Fuso, Fernando Augusto Freitas; Dias, André Luiz Natálio; Letaif, Olavo Biraghi; Cristante, Alexandre Fogaça; Marcon, Raphael Martus; de Barros, Tarcísio Eloy Pessoa

    2013-01-01

    OBJECTIVE : The primary purpose of this study was to determine the characteristics and outcomes of the patients admitted at our clinics diagnosed with cauda equina syndrome (CES). Secondarily, this study will serve as a basis for other comparative studies aiming at a better understanding of this condition and its epidemiology. METHODS : We conducted a retrospective study by reviewing the medical records of patients diagnosed with CES and neurogenic bladder between 2005 and 2011. The following variables were analyzed: gender, age, etiology, topographic level of the lesion, time between disease onset and diagnosis, presence of neurogenic bladder, time between diagnosis and surgery, neurological damage and neurogenic bladder persistence. RESULTS : Considering that CES is a rare condition, we were not able to establish statistic correlation between the analyzed variables and the outcomes of the disease. However, this study brought to light the inadequacy of our public health system in treating that kind of patient. CONCLUSION : The study shows that despite the well-defined basis for managing CES, we noted a greater number of patients with sequels caused by this condition, than is seen in the literature. The delayed diagnosis and, consequently, delayed treatment, were the main causes for the results observed. Level of Evidence IV, Case Series. PMID:24453661

  13. Molecular Testing for Clinical Diagnosis and Epidemiological Investigations of Intestinal Parasitic Infections

    PubMed Central

    Stensvold, C. Rune

    2014-01-01

    SUMMARY Over the past few decades, nucleic acid-based methods have been developed for the diagnosis of intestinal parasitic infections. Advantages of nucleic acid-based methods are numerous; typically, these include increased sensitivity and specificity and simpler standardization of diagnostic procedures. DNA samples can also be stored and used for genetic characterization and molecular typing, providing a valuable tool for surveys and surveillance studies. A variety of technologies have been applied, and some specific and general pitfalls and limitations have been identified. This review provides an overview of the multitude of methods that have been reported for the detection of intestinal parasites and offers some guidance in applying these methods in the clinical laboratory and in epidemiological studies. PMID:24696439

  14. Antimicrobial resistance and molecular epidemiology of streptococci from bovine mastitis.

    PubMed

    Rato, Márcia G; Bexiga, Ricardo; Florindo, Carlos; Cavaco, Lina M; Vilela, Cristina L; Santos-Sanches, Ilda

    2013-01-25

    Streptococcus agalactiae (Group B Streptococcus, GBS), Streptococcus dysgalactiae subsp. dysgalactiae (Group C Streptococcus, GCS) and Streptococcus uberis are relevant mastitis pathogens, a highly prevalent and costly disease in dairy industry due to antibiotherapy and loss in milk production. The aims of this study were the evaluation of antimicrobial drug resistance patterns, particularly important for streptococcal mastitis control and the identification of strain molecular features. Antimicrobial resistance was assessed by disk diffusion against amoxicillin-clavulanic acid, cefazolin, cefoperazone, pirlimycin-PRL, rifaximin, streptomycin, chloramphenicol, erythromycin-ERY, gentamicin, tetracycline-TET and vancomycin. Genotypic relationships were identified using pulsed-field gel electrophoresis (PFGE), macrolide and/or tetracycline resistance gene profiling, GBS capsular typing, GBS virulence gene profiling and GBS and S. uberis multi locus sequence typing (MLST). The majority of the isolates were susceptible to all drugs except to aminoglycoside, macrolide, lincosamide and tetracycline. Close to half of the TET resistant isolates have tetO and tetK and almost all ERY-PRL resistant isolates have ermB. A high degree of intra-species polymorphism was found for GCS. The GBS belonged to ST-2, -554, -61, -23 lineages and five new molecular serotypes and human GBS insertion sequences in the cpsE gene were found. Also, GBS of serotype V with scpB and lmb seem to be related with GBS isolates of human origin (same ST-2 and similar PFGE). Overall our results suggested that different therapeutic programs may have been implemented in the different farms and that in most cases clones were herd-specific. PMID:22964008

  15. Mandibular Fractures in Iraq: An Epidemiological Study

    PubMed Central

    Bede, Salwan

    2014-01-01

    The purpose of this study was to evaluate the epidemiological characteristics of the mandibular fractures relating to gender, age, the etiology of injury, and the rendered treatment modalities and complications. The data of the patients who sustained mandibular fractures were retrieved and were analyzed retrospectively, and based on these data a descriptive analysis was conducted. A total of 112 patients were included in this study; the most common cause was road traffic accidents (RTAs) followed by assaults and missile injuries. The most frequently involved age group was 11 to 20 years, treatment modalities included conservative, closed reduction and indirect fixation, and open reduction and internal fixation (ORIF) in 11.6, 79.5, and 8.9% of the cases, respectively. Most of the major complications were injury related. This study showed RTAs to be the most frequent cause followed by assaults, it also showed that a high percentage of assault victims were females mainly of low socioeconomic status. Another distinguishing feature in this study was the high incidence of missile injuries in the form of bullets and blasts. Closed reduction still has an important role in the treatment of fractures of mandible especially when the necessary equipments for ORIF are not readily available. A higher complication rate was observed in patients diagnosed with multiple and comminuted fractures as well as those caused by violence in the form of missile and assault injuries. PMID:25709754

  16. Data sources: use in the epidemiologic study of medical devices.

    PubMed

    Torrence, Mary E

    2002-05-01

    Medical device epidemiology is the study of the prevalence and incidence of use, effectiveness, and adverse events associated with medical devices in a population. The identification of large data sources with medical device data provides a large population for epidemiologic studies. Two challenges in medical device epidemiology are the ability to find data on the specific device and the exposure of a patient to that device. This paper identifies data sources both from the govenment and from the private sector that can be used for epidemiologic studies of medical devices and, to a limited degree, studies of medical devices in women. Each source provides data for different types of devices and in differing specificity. The paper also discusses briefly the strengths and weaknesses of each data source. More data sources are needed to enhance the study of medical device epidemiology. Additional efforts and focus are needed to enhance the ability to study medical devices in women. PMID:12071476

  17. Clinical and Molecular Epidemiology of Haemophilus influenzae Causing Invasive Disease in Adult Patients

    PubMed Central

    Puig, Carmen; Grau, Imma; Tubau, Fe; Calatayud, Laura; Pallares, Roman; Liñares, Josefina

    2014-01-01

    Objectives The epidemiology of invasive Haemophilus influenzae (Hi) has changed since the introduction of the Hi type b (Hib) vaccine. The aim of this study was to analyze the clinical and molecular epidemiology of Hi invasive disease in adults. Methods Clinical data of the 82 patients with Hi invasive infections were analyzed. Antimicrobial susceptibility, serotyping, and genotyping were studied (2008–2013). Results Men accounted for 63.4% of patients (whose mean age was 64.3 years). The most frequent comorbidities were immunosuppressive therapy (34.1%), malignancy (31.7%), diabetes, and COPD (both 22%). The 30-day mortality rate was 20.7%. The majority of the strains (84.3%) were nontypeable (NTHi) and serotype f was the most prevalent serotype in the capsulated strains. The highest antimicrobial resistance was for cotrimoxazole (27.1%) and ampicillin (14.3%). Twenty-three isolates (32.9%) had amino acid changes in the PBP3 involved in resistance. Capsulated strains were clonal and belonged to clonal complexes 6 (serotype b), 124 (serotype f), and 18 (serotype e), whereas NTHi were genetically diverse. Conclusions Invasive Hi disease occurred mainly in elderly and those with underlying conditions, and it was associated with a high mortality rate. NTHi were the most common cause of invasive disease and showed high genetic diversity. PMID:25379704

  18. DESIGN OF EXPOSURE MEASUREMENTS FOR EPIDEMIOLOGIC STUDIES

    EPA Science Inventory

    This presentation will describe the following items: (1) London daily air pollution and deaths that demonstrate how time series epidemiology can indicate that air pollution caused death; (2) Sophisticated statistical models required to establish this relationship for lower pollut...

  19. Molecular Epidemiology of Entamoeba: First Description of Entamoeba moshkovskii in a Rural Area from Central Colombia

    PubMed Central

    León, Cielo M.; Fonseca, Jairo; Reyes, Patricia; Moncada, Ligia; Olivera, Mario J.

    2015-01-01

    Background Entamoeba histolytica, E. dispar and E. moshkovskii are the most frequent species described in human infection where E. histolytica is the only true pathogen. The epidemiology of this infection is complex due to the absence of a routine exam that allows a correct discrimination of the Entamoeba species complex. Therefore, molecular methods appear as the unique epidemiological tool to accomplish the species discrimination. Herein, we conducted a cross-sectional study to determine the frequency of Entamoeba species infections in a group of asymptomatic individuals from a rural area in central Colombia. Methodology/Principal Findings A total of 181 fecal samples from asymptomatic children under 16 years old from the hamlet La Vírgen, Cundinamarca (Colombia) that voluntarily accepted to participate in the study were collected. The fecal samples were examined by light microscopy and DNA-extracted, subsequently submitted to molecular discrimination of E. dispar/E. histolytica/E. moshkovskii infection based on a multiplex PCR assay targeting the 18S rRNA fragment. To confirm the species description, twenty samples were randomly submitted to DNA sequencing of the aforementioned fragment. By direct microscopic examination, frequency of the complex E. histolytica/E. dispar/E. moshkovskii was 18.8% (34/181). PCR showed a frequency of 49.1% (89/181), discriminated as 23.2% (42/181) that were positive for E. dispar, 25.4% (46/181) for E. moshkovskii and 0.55% (1/ 181) for E. histolytica. Also, mixed infections were detected between E. dispar and E. moshkovskii at 4.42% (8/181) of the samples. Molecular barcoding confirmed the diagnosis depicted by the multiplex PCR assay. Conclusions/Significance This is the first description of E. moshkovskii in Colombia and the second report in South-America to our knowledge. Our results suggest the need to unravel the true epidemiology of Entamoeba infections around the world, including the real pathogenic role that E

  20. Molecular epidemiology of Cryptosporidium in HIV/AIDS patients in Malaysia.

    PubMed

    Asma, I; Sim, B L H; Brent, R D; Johari, S; Yvonne Lim, A L

    2015-06-01

    Cryptosporidiosis is a particular concern in immunocompromised individuals where symptoms may be severe. The aim of this study was to examine the epidemiological and molecular characteristics of Cryptosporidium infections in HIV/AIDS patients in Malaysia in order to identify risk factors and facilitate control measures. A modified Ziehl-Neelsen acid fast staining method was used to test for the presence of Cryptosporidium oocysts in the stools of 346 HIV/AIDS patients in Malaysia. Standard coproscopical methods were used to identify infections with other protozoan or helminths parasites. To identify the species of Cryptosporidium, DNA was extracted and nested-PCR was used to amplify a portion of the SSU rRNA gene. A total of 43 (12.4%) HIV-infected patients were found to be infected with Cryptosporidium spp. Of the 43 Cryptosporidium-positive HIV patients, 10 (23.3%) also harboured other protozoa, and 15 (34.9%) had both protozoa and helminths. The highest rates of cryptosporidiosis were found in adult males of Malay background, intravenous drug users, and those with low CD4 T cell counts (i.e., < 200 cells/mm3). Most were asymptomatic and had concurrent opportunistic infections mainly with Mycobacterium tuberculosis. DNA sequence analysis of 32 Cryptosporidium isolates identified C. parvum (84.3%), C. hominis (6.3%), C. meleagridis (6.3%), and C. felis (3.1%). The results of the present study revealed a high prevalence of Cryptosporidium infection in hospitalized HIV/AIDS patients. The results also confirmed the potential significance of zoonotic transmission of C. parvum in HIV infected patients, as it was the predominant species found in this study. However, these patients were found to be susceptible to a wide range of Cryptosporidium species. Epidemiological and molecular characterization of Cryptosporidium isolates provides clinicians and researchers with further information regarding the origin of the infection, and may enhance treatment and control

  1. The epidemiology and molecular characterization of methicillin-resistant staphylococci sampled from a healthy Jordanian population.

    PubMed

    Al-Bakri, A G; Al-Hadithi, H; Kasabri, V; Othman, G; Kriegeskorte, A; Becker, K

    2013-11-01

    The prevalence of natural carriage and molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative staphylococci (MR-CoNS) isolates in a Jordanian community were investigated. The MRSA nasal carriage rate in 227 healthy volunteers was 7·5% and the majority (81%) of MRSA harboured the resistance element SCCmec type IVe and were of a novel spa type t9519 (76%); other significant spa gene types were t223 (14·7%) and t044 (5·9%). All MRSA isolates were susceptible to other classes of antibiotics, and tested positive for at least three virulence factor encoding genes, but only two harboured the pvl gene. MR-CoNS carriage was 54·2% and these isolates were characterized by single, double and untypable SCCmec elements, with Staphylococcus epidermidis SCCmec type IVa predominating. Of eight subjects with nasal co-colonization of MR-CoNS + MRSA, three shared SCCmec type IV in both groups of organisms. This is the first report of methicillin-resistant staphylococci carriage in a Jordanian community and its findings are important for epidemiological study and infection control measures of these organisms. PMID:23340022

  2. Epidemiology and molecular characterization of hepatitis B virus in Luanda, Angola.

    PubMed

    Valente, Fatima; Lago, Barbara Vieira do; Castro, Carlos Augusto Velasco de; Almeida, Adilson José de; Gomes, Selma A; Soares, Caroline Cordeiro

    2010-12-01

    An estimated 360 million people are infected with hepatitis B virus (HBV) worldwide. Among these, 65 million live in Africa. Despite the high levels of hepatitis B in Africa, HBV epidemiology is still poorly documented in most African countries. In this work, the epidemiological and molecular characteristics of HBV infection were evaluated among the staff, visitors and adult patients (n = 508) of a public hospital in Luanda, Angola. The overall prevalence of hepatitis B core antibody (anti-HBc) and hepatitis B surface antigen was 79.7% and 15.1%, respectively. HBV infection was higher in males and was more prevalent in individuals younger than 50 years old. HBV-DNA was detected in 100% of HBV "e" antigen-positive serum samples and in 49% of anti-hepatitis Be antibody-positive samples. Thirty-five out of the 40 HBV genotypes belonged to genotype E. Circulation of genotypes A (4 samples) and D (1 sample) was also observed. The present study demonstrates that HBV infection is endemic in Luanda, which has a predominance of genotype E. This genotype is only sporadically found outside of Africa and is thought to have emerged in Africa at a time when the trans-Atlantic slave trade had stopped. PMID:21225192

  3. A cautionary note on fecal sampling and molecular epidemiology in predatory wild great apes.

    PubMed

    De Nys, Hélène Marie; Madinda, Nadège Freda; Merkel, Kevin; Robbins, Martha; Boesch, Christophe; Leendertz, Fabian Hubertus; Calvignac-Spencer, Sébastien

    2015-08-01

    Fecal samples are an important source of information on parasites (viruses, prokaryotes, or eukaryotes) infecting wild great apes. Molecular analysis of fecal samples has already been used for deciphering the origins of major human pathogens such as HIV-1 or Plasmodium falciparum. However, for apes that hunt (chimpanzees and bonobos), detection of parasite nucleic acids may reflect either true infection of the host of interest or ingestion of an infected prey, for example, another non-human primate. To determine the potential magnitude of this issue, we estimated the prevalence of prey DNA in fecal samples obtained from two wild chimpanzee communities. We observed values >15%, which are higher than or close to the fecal detection rates of many great ape parasites. Contamination of fecal samples with parasite DNA from dietary origin may therefore occasionally impact non-invasive epidemiological studies. This problem can be addressed (at least partially) by monitoring the presence of prey DNA. PMID:26031302

  4. A molecular epidemiological survey of Babesia, Hepatozoon, Ehrlichia and Anaplasma infections of dogs in Japan.

    PubMed

    Kubo, Shotaro; Tateno, Morihiro; Ichikawa, Yasuaki; Endo, Yasuyuki

    2015-10-01

    Tick-borne diseases are often encountered in canine clinical practice. In the present study, a molecular epidemiological survey of dogs in Japan was conducted to understand the prevalence and geographical distribution of Babesia spp., Hepatozoon spp., Ehrlichia spp. and Anaplasma spp. Pathogen-derived DNA in blood samples obtained from 722 dogs with a history of exposure to ticks and/or fleas was examined by PCR. The prevalence of Babesia gibsoni, Babesia odocoilei-like species, Hepatozoon canis and Ehrlichia spp./Anaplasma spp. was 2.4% (16/722), 0.1% (1/722), 2.5% (18/722) and 1.5% (11/722), respectively. While B. gibsoni and Ehrlichia spp./Anaplasma spp. were detected in the western part of Japan, H. canis was detected in Tohoku area in addition to western and central parts of Japan. PMID:25947226

  5. 40 CFR 159.170 - Human epidemiological and exposure studies.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Human epidemiological and exposure... Information § 159.170 Human epidemiological and exposure studies. Information must be submitted which concerns... that a correlation may exist between exposure to a pesticide and observed adverse effects in...

  6. EPIDEMIOLOGIC STUDIES OF DISINFECTANTS AND DISINFECTANT BY-PRODUCTS

    EPA Science Inventory

    This article provides a review of the epidemiologic evidence for human health effects that may be associated with the disinfection of drinking water. An epidemiologic study attempts to link human health effects with exposure to a specific agent (e.g., DBCM), agents (e.g., THMs or...

  7. 40 CFR 159.170 - Human epidemiological and exposure studies.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Human epidemiological and exposure... Information § 159.170 Human epidemiological and exposure studies. Information must be submitted which concerns... that a correlation may exist between exposure to a pesticide and observed adverse effects in...

  8. 40 CFR 159.170 - Human epidemiological and exposure studies.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Human epidemiological and exposure... Information § 159.170 Human epidemiological and exposure studies. Information must be submitted which concerns... that a correlation may exist between exposure to a pesticide and observed adverse effects in...

  9. Time series regression studies in environmental epidemiology

    PubMed Central

    Bhaskaran, Krishnan; Gasparrini, Antonio; Hajat, Shakoor; Smeeth, Liam; Armstrong, Ben

    2013-01-01

    Time series regression studies have been widely used in environmental epidemiology, notably in investigating the short-term associations between exposures such as air pollution, weather variables or pollen, and health outcomes such as mortality, myocardial infarction or disease-specific hospital admissions. Typically, for both exposure and outcome, data are available at regular time intervals (e.g. daily pollution levels and daily mortality counts) and the aim is to explore short-term associations between them. In this article, we describe the general features of time series data, and we outline the analysis process, beginning with descriptive analysis, then focusing on issues in time series regression that differ from other regression methods: modelling short-term fluctuations in the presence of seasonal and long-term patterns, dealing with time varying confounding factors and modelling delayed (‘lagged’) associations between exposure and outcome. We finish with advice on model checking and sensitivity analysis, and some common extensions to the basic model. PMID:23760528

  10. Time series regression studies in environmental epidemiology.

    PubMed

    Bhaskaran, Krishnan; Gasparrini, Antonio; Hajat, Shakoor; Smeeth, Liam; Armstrong, Ben

    2013-08-01

    Time series regression studies have been widely used in environmental epidemiology, notably in investigating the short-term associations between exposures such as air pollution, weather variables or pollen, and health outcomes such as mortality, myocardial infarction or disease-specific hospital admissions. Typically, for both exposure and outcome, data are available at regular time intervals (e.g. daily pollution levels and daily mortality counts) and the aim is to explore short-term associations between them. In this article, we describe the general features of time series data, and we outline the analysis process, beginning with descriptive analysis, then focusing on issues in time series regression that differ from other regression methods: modelling short-term fluctuations in the presence of seasonal and long-term patterns, dealing with time varying confounding factors and modelling delayed ('lagged') associations between exposure and outcome. We finish with advice on model checking and sensitivity analysis, and some common extensions to the basic model. PMID:23760528

  11. Overview of molecular typing methods for outbreak detection and epidemiological surveillance.

    PubMed

    Sabat, A J; Budimir, A; Nashev, D; Sá-Leão, R; van Dijl, J m; Laurent, F; Grundmann, H; Friedrich, A W

    2013-01-01

    Typing methods for discriminating different bacterial isolates of the same species are essential epidemiological tools in infection prevention and control. Traditional typing systems based on phenotypes, such as serotype, biotype, phage-type, or antibiogram, have been used for many years. However, more recent methods that examine the relatedness of isolates at a molecular level have revolutionised our ability to differentiate among bacterial types and subtypes. Importantly, the development of molecular methods has provided new tools for enhanced surveillance and outbreak detection. This has resulted in better implementation of rational infection control programmes and efficient allocation of resources across Europe. The emergence of benchtop sequencers using next generation sequencing technology makes bacterial whole genome sequencing (WGS) feasible even in small research and clinical laboratories. WGS has already been used for the characterisation of bacterial isolates in several large outbreaks in Europe and, in the near future, is likely to replace currently used typing methodologies due to its ultimate resolution. However, WGS is still too laborious and time-consuming to obtain useful data in routine surveillance. Also, a largely unresolved question is how genome sequences must be examined for epidemiological characterisation. In the coming years, the lessons learnt from currently used molecular methods will allow us to condense the WGS data into epidemiologically useful information. On this basis, we have reviewed current and new molecular typing methods for outbreak detection and epidemiological surveillance of bacterial pathogens in clinical practice, aiming to give an overview of their specific advantages and disadvantages. PMID:23369389

  12. The Molecular Epidemiology and Genetic Environment of Carbapenemases Detected in Africa.

    PubMed

    Sekyere, John Osei; Govinden, Usha; Essack, Sabiha

    2016-01-01

    Research articles describing carbapenemases and their genetic environments in Gram-negative bacteria were reviewed to determine the molecular epidemiology of carbapenemases in Africa. The emergence of resistance to the carbapenems, the last resort antibiotic for difficult to treat bacterial infections, affords clinicians few therapeutic options, with a resulting increase in morbidities, mortalities, and healthcare costs. However, the molecular epidemiology of carbapenemases throughout Africa is less described. Research articles and conference proceedings describing the genetic environment and molecular epidemiology of carbapenemases in Africa were retrieved from Google Scholar, Scifinder, Pubmed, Web of Science, and Science Direct databases. Predominant carbapenemase genes so far described in Africa include the blaOXA-48 type, blaIMP, blaVIM, and blaNDM in Acinetobacter baumannii, Klebsiella pneumoniae, Enterobacter cloacae, Citrobacter spp., and Escherichia coli carried on various plasmid types and sizes, transposons, and integrons. Class D and class B carbapenemases, mainly prevalent in A. baumannii, K. pneumoniae, E. cloacae, Citrobacter spp., and E. coli were the commonest carbapenemases. Carbapenemases are mainly reported in North and South Africa as under-resourced laboratories, lack of awareness and funding preclude the detection and reporting of carbapenemase-mediated resistance. Consequently, the true molecular epidemiology of carbapenemases and their genetic environment in Africa is still unknown. PMID:26161476

  13. Preferential Glutathione Conjugation of a Reverse Diol Epoxide Compared to a Bay Region Diol Epoxide of Phenanthrene in Human Hepatocytes: Relevance to Molecular Epidemiology Studies of Glutathione-S-Transferase Polymorphisms and Cancer

    PubMed Central

    Hecht, Stephen S.; Berg, Jeannette Zinggeler; Hochalter, J. Bradley

    2009-01-01

    Bay region diol epoxides are recognized ultimate carcinogens of polycyclic aromatic hydrocarbons (PAH), and in vitro studies have demonstrated that they can be detoxified by conjugation with glutathione, leading to the widely investigated hypothesis that individuals with low activity forms of glutathione-S-transferases are at higher risk of PAH induced cancer, a hypothesis that has found at most weak support in molecular epidemiology studies. A weakness in this hypothesis was that the mercapturic acids resulting from conjugation of PAH bay region diol epoxides had never been identified in human urine. We recently analyzed smokers’ urine for mercapturic acids derived from phenanthrene, the simplest PAH with a bay region. The only phenanthrene diol epoxide-derived mercapturic acid in smokers’ urine was produced from the reverse diol epoxide, anti-phenanthrene-3,4-diol-1,2-epoxide (11), not the bay region diol epoxide, anti-phenanthrene-1,2-diol-3,4-epoxide (10), which does not support the hypothesis noted above. In this study, we extended these results by examining the conjugation of phenanthrene metabolites with glutathione in human hepatocytes. We identified the mercapturic acid N-acetyl-S-(r-4,t-2,3-trihydroxy-1,2,3,4-tetrahydro-c-1-phenanthryl)-L-cysteine (14a), (0.33–35.9 pmol/mL at 10 µM 8, 24h incubation, N = 10) in all incubations with phenanthrene-3,4-diol (8) and the corresponding diol epoxide 11, but no mercapturic acids were detected in incubations with phenanthrene-1,2-diol (7) and only trace amounts were observed in incubations with the corresponding bay region diol epoxide 10. Taken together with our previous results, these studies clearly demonstrate that glutathione conjugation of a reverse diol epoxide of phenanthrene is favored over conjugation of a bay region diol epoxide. Since reverse diol epoxides of PAH are generally weakly or non-mutagenic/carcinogenic, these results, if generalizable to other PAH, do not support the widely held

  14. Molecular epidemiology in cancer risk assessment and prevention: recent progress and avenues for future research.

    PubMed Central

    Wogan, G N

    1992-01-01

    Molecular epidemiology is increasingly being applied in studies of cancer risks derived from exposure to environmental carcinogens of both endogenous and exogenous origins. Analytical methods have been developed that are capable of detecting and quantifying levels of covalent adducts of several important classes of carcinogens with cellular DNA and blood proteins. Methods of sufficient sensitivity and specificity to detect ambient levels of exposure are in current use. These are being used in studies related to tobacco use (polycyclic aromatic hydrocarbons, aromatic amines, tobacco-specific nitrosamines); dietary exposures (aflatoxins, N-nitrosamines, heterocyclic amines); medicinal exposures (cisplatin, alkylating agents, 8-methoxypsoralen, ultraviolet photoproducts); occupational exposures (aromatic amines, polycyclic aromatic hydrocarbons, oxides of ethylene and styrene, and vinyl chloride); and oxidative damage (8-hydroxyguanine, thymine glycol). Methodologic improvements together with their expanded use in feasibility studies continue to produce results that support the validity of this approach for detecting and quantifying exposure to carcinogens. Genetic markers are also being used to detect early biological responses in efforts to link carcinogen exposure to initiating events in the carcinogenesis process. These include, in addition to traditional cytogenetic markers (e.g., chromosomal aberrations, sister chromatid exchange, micronuclei), other alterations in chromosomal structure such as restriction fragment length polymorphisms, loss of heterozygosity, and translocation markers. Specific genetic changes have recently been identified as critical molecular events in the initiation and development of many cancers. Important among these are activation of oncogenes, especially those of the ras family, and inactivation of tumor-suppressor genes (e.g., p53 and Rb) by point mutations and/or chromosomal deletions and other structural changes. Although some of

  15. Molecular epidemiology and diagnosis of Leishmania: what have we learnt from genome structure, dynamics and function?

    PubMed

    Dujardin, J C; Victoir, K; De Doncker, S; Guerbouj, S; Arévalo, J; Le Ray, D

    2002-04-01

    This paper reviews our exploration of the dynamics of the Leishmania genome and its contribution to epidemiology and diagnosis. We used as a model Peruvian populations of L. (Viannia) braziliensis and L. (V.) peruviana, 2 species very close phylogenetically, but phenotypically very different in biotope and pathology. We initially focused on karyotype analysis. Our data showed that chromosomes were subject to a fast rate of evolution, and were sensitive indicators of genetic drift. Therefore, molecular karyotyping appeared an adequate tool for monitoring (i) emergence of close species, (ii) ecogeographical differentiation at the intraspecific level, and (iii) strain 'fingerprinting'. Chromosome size variation was mostly due to the number of tandemly repeated genes (rDNA, mini-exon, gp63, and cysteine proteinase genes), and could involve the deletion of unique genes (L. (V.) braziliensis-specific gp63 families). Considering the importance of these genes in parasitism, their rearrangement might have functional implications: adaptation to different environments and pleomorphic pathogenicity. Our knowledge of genome structure and dynamics was used to develop new polymerase chain reaction (PCR) techniques. Amplification of gp63 genes followed by cleavage with restriction enzymes and study of restriction fragment length polymorphism (gp63 PCR-RFLP) allowed the discrimination of all species tested, even directly in biopsies with 95% sensitivity (compared with PCR amplification of kinetoplast deoxyribonucleic acid). At the intra-specific level, RFLP was also observed and corresponded to mutations in major immunogen domains of gp63. These seem to be under strong selection pressure, and the technique should facilitate addressing how the host's immune pressure may modulate parasite population structure. Altogether, gp63 PCR-RFLP represents a significant operational improvement over the other techniques for molecular epidemiology and diagnosis: it combines sensitivity

  16. Penicillium marneffei Infection and Recent Advances in the Epidemiology and Molecular Biology Aspects

    PubMed Central

    Vanittanakom, Nongnuch; Cooper, Chester R.; Fisher, Matthew C.; Sirisanthana, Thira

    2006-01-01

    Penicillium marneffei infection is an important emerging public health problem, especially among patients infected with human immunodeficiency virus in the areas of endemicity in southeast Asia, India, and China. Within these regions, P. marneffei infection is regarded as an AIDS-defining illness, and the severity of the disease depends on the immunological status of the infected individual. Early diagnosis by serologic and molecular assay-based methods have been developed and are proving to be important in diagnosing infection. The occurrence of natural reservoirs and the molecular epidemiology of P. marneffei have been studied; however, the natural history and mode of transmission of the organism remain unclear. Soil exposure, especially during the rainy season, has been suggested to be a critical risk factor. Using a highly discriminatory molecular technique, multilocus microsatellite typing, to characterize this fungus, several isolates from bamboo rats and humans were shown to share identical multilocus genotypes. These data suggest either that transmission of P. marneffei may occur from rodents to humans or that rodents and humans are coinfected from common environmental sources. These putative natural cycles of P. marneffei infection need further investigation. Studies on the fungal genetics of P. marneffei have been focused on the characterization of genetic determinants that may play important roles in asexual development, mycelial-to-yeast phase transition, and the expression of antigenic determinants. Molecular studies have identified several genes involved in germination, hyphal development, conidiogenesis, and yeast cell polarity. A number of functionally important genes, such as the malate synthase- and catalase-peroxidase protein-encoding genes, have been identified as being upregulated in the yeast phase. Future investigations pertaining to the roles of these genes in host-fungus interactions may provide the key knowledge to understanding the

  17. EPIDEMIOLOGY AND MOLECULAR TYPING OF BRUCELLA STRAINS CIRCULATING IN GEORGIA.

    PubMed

    Sidamonidze, K; Ramishvili, M; Kalandadze, I; Tsereteli, D; Nikolich, M P

    2015-10-01

    In 2009-2013, 851 cases of brucellosis were registered in Georgia. Most cases of brucellosis were found in eastern Georgia (91.3% of cases). Mainly men were infected with brucellosis (81.0%).The age group with the most frequent cases of brucellosis is 30-59 years (48.5%). Brucellosis is rarely found among children(0-4 years - 2.0%, 5-14 years - 8.0%). Brucellosis cases were linked to professional activity; mainly by farmers (33.0% of those infected) and shepherds (27.0%). Biotyping Brucella by microbiological methods alone has limitations, so molecular typing was implemented in this study to confirm species. Isolates from human blood and ruminant milk or blood were identified by a bacteriological algorithm and confirmed by real-time PCR (Brucella T1, Idaho Technology). Species identity was confirmed using the AMOS conventional PCR assay, which differentiates four human pathogenic species but cannot recognize certain biovars within them. This gap was addressed by using more universal species-specific Single Nucleotide Polymorphism (SNP) assays. Real-time PCR was used to confirm 86 Brucella strains (48 human, 38 animal isolates) obtained 2009-2011. AMOS PCR supported the biochemical test results for 53 B. melitensis and four B. abortus strains, but not for 29 suspected B. abortus human and animal isolates. SNP typing of all 86 isolates supported the AMOS PCR results but also confirmed the species of the 29 strains not amplified by AMOS PCR. In 2009-2013 years the prevalence of brucellosis was still high. Nowadays cases of brucellosis are higher in the western part of Georgia than in the 1991-2005 period by a factor of 2.62. Brucellosis continues to be mainly an infection in males, because men are mostly engaged in sheep and cattle care. Combined AMOS PCR and SNP typing in this study provided the first genetic confirmation that both B. abortus and B. melitensis are actively circulating in humans and animals in Georgia. PMID:26483376

  18. [Eco-epidemiology: towards epidemiology of complexity].

    PubMed

    Bizouarn, Philippe

    2016-05-01

    In order to solve public health problems posed by the epidemiology of risk factors centered on the individual and neglecting the causal processes linking the risk factors with the health outcomes, Mervyn Susser proposed a multilevel epidemiology called eco-epidemiology, addressing the interdependence of individuals and their connection with molecular, individual, societal, environmental levels of organization participating in the causal disease processes. The aim of this epidemiology is to integrate more than a level of organization in design, analysis and interpretation of health problems. After presenting the main criticisms of risk-factor epidemiology focused on the individual, we will try to show how eco-epidemiology and its development could help to understand the need for a broader and integrative epidemiology, in which studies designed to identify risk factors would be balanced by studies designed to answer other questions equally vital to public health. PMID:27225924

  19. An epidemiologic approach to studying heterocyclic amines.

    PubMed

    Sinha, Rashmi

    2002-09-30

    Diets containing substantial amounts of red meat may increase the risk of colorectal, pancreatic, breast, prostate, and renal cancer. The association with red meat intake may be due to a combination of factors, such as content of fat, protein, and iron, and/or meat preparation (e.g. cooking or preserving methods). Laboratory results have shown that meats cooked at high temperatures contain heterocyclic amines (HCAs) known to be mutagenic and carcinogenic in animals. Many older epidemiologic studies of colon cancer using surrogates for HCA exposure from meat (for example, doneness level, surface browning, frying, intake of gravy) have produced suggestive but inconsistent results. These discrepancies may have resulted in part from having used dietary questionnaires that combined meat-cooking practices in ways that made the intake of HCAs difficult to estimate. Thus, over the last decade we have taken a multidisciplinary approach to investigating whether the association with red meat intake can be explained by meat-cooking practices that produce mutagens/carcinogens. To estimate intake, a database for HCAs have been developed and used in conjunction with a validated meat-cooking food frequency questionnaire (FFQ). To develop biological markers of internal exposure, a metabolic study was conducted where subjects consumed controlled amounts of meat cooked at low and high temperatures. The role of meat type, cooking methods, doneness levels, and meat-cooking mutagens were examined in case-control studies of colorectal adenomas, lung, and breast cancers using both questionnaire information and biomarkers. In a case-control study of colorectal adenomas, an increased risk was associated with a high intake of red meat. Most of this risk was due to intake of red meat cooked until well/very well done and/or by high-temperature cooking techniques such as grilling. Linking the FFQ information to HCA database, the impact several HCAs on risk was evaluated. An increased risk was

  20. PRELIMINARY HEALTH BURDEN ANALYSIS FOR EPIDEMIOLOGIC RECREATIONAL WATER STUDY

    EPA Science Inventory

    Introduction: The National Epidemiological and Environmental Assessment of Recreational Water Study (NEEAR) offers a rare opportunity for researchers. The study's design involves the collection of health data before and after visiting the beach in conjunction with water quality...

  1. Design and analysis of metabolomics studies in epidemiologic research: a primer on -omic technologies.

    PubMed

    Tzoulaki, Ioanna; Ebbels, Timothy M D; Valdes, Ana; Elliott, Paul; Ioannidis, John P A

    2014-07-15

    Metabolomics is the field of "-omics" research concerned with the comprehensive characterization of the small low-molecular-weight metabolites in biological samples. In epidemiology, it represents an emerging technology and an unprecedented opportunity to measure environmental and other exposures with improved precision and far less measurement error than with standard epidemiologic methods. Advances in the application of metabolomics in large-scale epidemiologic research are now being realized through a combination of improved sample preparation and handling, automated laboratory and processing methods, and reduction in costs. The number of epidemiologic studies that use metabolic profiling is still limited, but it is fast gaining popularity in this area. In the present article, we present a roadmap for metabolomic analyses in epidemiologic studies and discuss the various challenges these data pose to large-scale studies. We discuss the steps of data preprocessing, univariate and multivariate data analysis, correction for multiplicity of comparisons with correlated data, and finally the steps of cross-validation and external validation. As data from metabolomic studies accumulate in epidemiology, there is a need for large-scale replication and synthesis of findings, increased availability of raw data, and a focus on good study design, all of which will highlight the potential clinical impact of metabolomics in this field. PMID:24966222

  2. Taxonomy and molecular epidemiology of Echinococcus granulosus sensu lato.

    PubMed

    Romig, T; Ebi, D; Wassermann, M

    2015-10-30

    Echinococcus granulosus, formerly regarded as a single species with a high genotypic and phenotypic diversity, is now recognised as an assemblage of cryptic species, which differ considerably in morphology, development, host specificity (including infectivity/pathogenicity for humans) and other aspects. This diversity is reflected in the mitochondrial and nuclear genomes and has led to the construction of phylogenetic trees and hypotheses on the origin and geographic dispersal of various taxa. Based on phenotypic characters and gene sequences, E. granulosus (sensu lato) has by now been subdivided into E. granulosus sensu stricto (including the formerly identified genotypic variants G1-3), Echinococcus felidis (the former 'lion strain'), Echinococcus equinus (the 'horse strain', genotype G4), Echinococcus ortleppi (the 'cattle strain', genotype G5) and Echinococcus canadensis. The latter species, as recognised here, shows the highest diversity and is composed of the 'camel strain', genotype G6, the 'pig strain', genotype G7, and two 'cervid strains', genotypes G8 and G10. There is debate whether the closely related G6 and G7 should be placed in a separate species, but more morphological and biological data are needed to support or reject this view. In this classification, the application of rules for zoological nomenclature led to the resurrection of old species names, which had before been synonymised with E. granulosus. This nomenclatural subdivision of the agents of cystic echinococcosis (CE) may appear inconvenient for practical applications, especially because molecular tools are needed for identification of the cyst stage, and because retrospective data on 'E. granulosus' are now difficult to interpret without examination of voucher specimens. However, the increased awareness for the diversity of CE agents - now emphasised by species names rather than genotype numbers - has led to a large number of recent studies on this issue and a rapid increase of knowledge

  3. Review of epidemiological studies on the occupational risk of tuberculosis in low-incidence areas.

    PubMed

    Seidler, Andreas; Nienhaus, Albert; Diel, Roland

    2005-01-01

    This review summarizes the epidemiological evidence for occupationally acquired tuberculosis and considers the implications for the prevention of tuberculosis. The relevant epidemiological studies were identified on the basis of the Medline data bank, starting with the year 1966. The evaluation of occupational groups with an elevated tuberculosis risk is exclusively based on epidemiologic studies of good or acceptable quality, applying clearly defined criteria of methodological quality. In summary, the available epidemiological evidence suggests that the risk of tuberculosis is elevated in the following occupational groups: hospital employees in wards with tuberculosis patients; nurses in hospitals; nurses attending HIV-positive or drug-addicted patients; pathology and laboratory workers; respiratory therapists and physiotherapists; physicians in internal medicine, anaesthesia, surgery and psychiatry; non-medical hospital personnel in housekeeping and transport work; funeral home employees, and prison employees. However, the epidemiological evidence is limited for all these occupations, with the exception of the nurses, because of the lack of methodologically adequate studies that have got the statistical power to differentiate between specific work tasks. There is a need for large population-based studies with precise definition of exposure, which should include molecular epidemiologic methods in the investigation of occupational risk factors of tuberculosis. PMID:16088290

  4. Molecular Epidemiology of Mycobacterium tuberculosis Isolates in 100 Patients With Tuberculosis Using Pulsed Field Gel Electrophoresis

    PubMed Central

    Pooideh, Mohammad; Jabbarzadeh, Ismail; Ranjbar, Reza; Saifi, Mahnaz

    2015-01-01

    Background: Tuberculosis (TB) is a widespread infectious disease. Today, TB has created a public health crisis in the world. Genotyping of Mycobacterium tuberculosis isolates is useful for surveying the dynamics of TB infection, identifying new outbreaks, and preventing the disease. Different molecular methods for clustering of M. tuberculosis isolates have been used. Objectives: During a one year study of genotyping, 100 M. tuberculosis isolates from patients referred to Pasteur Institute of Iran were collected and their genotyping was accomplished using pulsed field gel electrophoresis (PFGE) method. Materials and Methods: Identification of all M. tuberculosis isolates was accomplished using standard biochemical and species-specific polymerase chain reaction (PCR) methods. Antibiotic susceptibility tests were performed using proportional method. After preparing PFGE plaques for each isolate of M. tuberculosis, XbaI restriction enzyme was applied for genome digestion. Finally, the digested DNA fragments were separated on 1% agarose gel and analyzed with GelCompar II software. Results: Genotyping of the studied isolates in comparison with the molecular weight marker revealed two common types; pulsotype A with 71 isolates and one multidrug resistant mycobacterium (MDR) case, and pulsotype B including 29 isolates and three MDR cases. No correlation between the antibiotypes and pulsotypes was observed. Conclusions: Molecular epidemiology studies of infectious diseases have been useful when bacterial isolates have been clustered in a period of time and in different geographical regions with variable antibiotic resistance patterns. In spite of high geographical differences and different antibiotic resistant patterns, low genetic diversity among the studied TB isolates may refer to the low rate of mutations in XbaI restriction sites in the mycobacterial genome. We also identified three MDR isolates in low-incidence pulsotype B, which could be disseminated and is highly

  5. RETROSPECTIVE EPIDEMIOLOGICAL STUDY OF DISEASE ASSOCIATED WITH WASTEWATER UTILIZATION

    EPA Science Inventory

    A retrospective epidemiological study was carried out on the association between enteric disease incidence and wastewater utilization in 79 kibbutzim (cooperative agricultural settlements) in Israel having a population of 32,672. Medical records on disease incidence were collecte...

  6. DESIGN STRATEGIES FOR EPIDEMIOLOGIC STUDIES OF ENVIRONMENTAL IMPACTS ON HEALTH

    EPA Science Inventory

    The papers describes epidemiologic designs and methods in studies of health effects of air pollution, whose implications, however, can be extended to the detection of health effects of other environmental exposures. Recent advances in measurement technology for the assessment of ...

  7. The 20th century Danish facial cleft population--epidemiological and genetic-epidemiological studies.

    PubMed

    Christensen, K

    1999-03-01

    Since Dr. Fogh-Andersen's legendary 1942 thesis, the Danish facial cleft population has been one of the most extensively studied in terms of epidemiology and genetic-epidemiology. The etiology of cleft lip and/or palate (CLP) is still largely an enigma, and different results concerning environmental and genetic risk factors are obtained in different countries and regions. This may be due to etiological heterogeneity between settings. Therefore, an in-depth studied area with an ethnically homogeneous population, such as Denmark, has provided one of the best opportunities for progress in CLP etiological research. The present review summarizes epidemiological and genetic-epidemiological studies conducted in the 20th century Danish facial cleft population. Furthermore, analyses of sex differences, time trends and seasonality for more than 7000 CLP cases born in Denmark in the period 1936 to 1987 are presented. The review also points toward the excellent opportunities for continued etiological CLP research in Denmark in the 21st century using already established resources and an on-going prospective cohort study of 100,000 pregnant women. PMID:10213053

  8. Syndromic Surveillance of Infectious Diseases meets Molecular Epidemiology in a Workflow and Phylogeographic Application.

    PubMed

    Janies, Daniel; Witter, Zachary; Gibson, Christian; Kraft, Thomas; Senturk, Izzet F; Çatalyürek, Ümit

    2015-01-01

    Traditionally, epidemiologists have counted cases and groups of symptoms. Modeling on these data consists of predicting expansion or contraction in the number of cases over time in epidemic curves or compartment models. Geography is considered a variable when these data are presented in choropleth maps. These approaches have significant drawbacks if the cases counted are not accurately diagnosed. For example, most regional public health authorities count influenza like illnesses (ILI). Cases of these diseases are designated as ILI if the patient exhibits fever, respiratory symptoms, and perhaps gastrointestinal symptoms. Several molecular epidemiological studies have shown that there are many pathogens that cause these symptoms and the relative proportions of these pathogens change over time and space. One way to bridge the gap between syndromic and genetic surveillance of infectious diseases is to compare signals of symptoms to pathogens recorded in molecular databases. We present a web-based workflow application that uses chief complaints found in the public Twitter feed as a syndromic surveillance tool and connects outbreak signals in these data to pathogens historically known to circulate in the same area. For the pathogen(s) of interest, we provide Genbank links to metadata and sequences in a workflow for phylogeographic analysis and visualization. The visualizations provide information on the geographic traffic of the spread of the pathogens and places that are hubs for their transport. PMID:26262155

  9. Molecular Epidemiology and Characterization of Genotypes of Acinetobacter baumannii Isolates from Regions of South China.

    PubMed

    Ying, Jun; Lu, Junwan; Zong, Li; Li, Ailing; Pan, Ruowang; Cheng, Cong; Li, Kunpeng; Chen, Liqiang; Ying, Jianchao; Tou, Huifen; Zhu, Chuanxin; Xu, Teng; Yi, Huiguang; Li, Jinsong; Ni, Liyan; Xu, Zuyuan; Bao, Qiyu; Li, Peizhen

    2016-05-20

    The aim of this study was to analyze the molecular epidemiologic characteristics of Acinetobacter baumannii. A total of 398 isolates were collected in 7 regions of South China from January to June of 2012. Drug sensitivity was tested toward 15 commonly used antibiotics; thus, 146 multi-drug-resistant strains (resistant to more than 7 drugs) were identified, representing 36.7% of all isolates. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used for molecular subtyping. According to the PFGE results (with a cutoff of 70% similarity for the DNA electrophoretic bands), 146 strains were subdivided into 15 clusters, with cluster A being the largest (33.6%, distributed in all districts except Jiaxing). Cluster B was also widespread and included 14.4% of all strains. In addition, MLST results revealed 11 sequence types (ST), with ST208 being the most prevalent, followed by ST191 and ST729. Furthermore, 4 novel alleles and 6 novel STs were identified. Our results showed that multi-drug-resistant A. baumannii in South China shares the origin with other widespread strains in other countries. The nosocomial infections caused by A. baumannii have been severe in South China. Continuous monitoring and judicious antibiotic use are required. PMID:26166496

  10. Epidemiology and molecular virus characterization of reemerging rabies, South Africa.

    PubMed

    Cohen, Cheryl; Sartorius, Benn; Sabeta, Claude; Zulu, Gugulethu; Paweska, Janusz; Mogoswane, Mamokete; Sutton, Chris; Nel, Louis H; Swanepoel, Robert; Leman, Patricia A; Grobbelaar, Antoinette A; Dyason, Edwin; Blumberg, Lucille

    2007-12-01

    The incidence of dog rabies in Limpopo Province, South Africa, increased from 5 cases in 2004 to 100 in 2006. Human rabies had last been confirmed in 1981, but investigations instituted after an index case was recognized in February 2006 identified 21 confirmed, 4 probable, and 5 possible human cases between August 5, 2005, and December 31, 2006. Twelve of these case-patients were identified retrospectively because the diagnosis of rabies was not considered: 6 of these patients consulted a traditional healer, 6 had atypical manifestations with prominent abdominal symptoms, and 6 of 7 patients tested had elevated liver enzyme activity. Molecular genetic analysis indicated that outbreak virus strains were most closely related to recent canine strains from southern Zimbabwe. Delayed recognition of the human cases may have resulted from decreased clinical suspicion after many years of effective control of the disease and the occurrence of atypical clinical presentations. PMID:18258039

  11. Enteroviruses and Rhinoviruses: Molecular Epidemiology of the Most Influenza-Like Illness Associated Viruses in Senegal.

    PubMed

    Fall, Amary; Dia, Ndongo; Kébé, Ousmane; Sarr, Fatoumata Diene; Kiori, Davy E; Cissé, El Hadj Abdoul Khadir; Sy, Sara; Goudiaby, Deborah; Richard, Vincent; Diop, Ousmane Madiagne; Niang, Mbayame Ndiaye

    2016-08-01

    Different viruses have been identified as etiologic agents of respiratory tract infections, including severe cases. Among these, human rhinoviruses (HRVs) and human enteroviruses (HEVs) are recognized as leading causes. The present study describes the molecular epidemiology of HRVs and HEVs in Senegal over a 3-year surveillance period. From January 2012 to December 2014, nasopharyngeal and oropharyngeal swabs specimen were collected from patients with influenza-like illness (ILI). A real-time reverse transcription polymerase chain reaction was performed for HRV and HEV detection using the RV16 kit. Two regions were targeted for the molecular characterization of RVs: 5' untranslated region (5'UTR) and viral protein 4/viral protein 2 (VP4/VP2) transition region. For enteroviruses (EVs) phylogeny, VP1 gene was targeted. A total of 4,194 samples were collected. Children up to 5 years accounted for 52.9%. Among them, 1,415 (33.7%) were positive for HRV, 857 (20.4%) for HEV, and 437 cases of dual infections HRV/HEV. HRVs and HEVs were identified significantly in children aged 5 years or less. Only cough and vomiting signs were observed with significant association with viral infection. Both viruses co-circulated all year long with a marked increase of activity during rainy and cold period. All HRV types circulate in Senegal. HRV-A and C groups were the most common. HEV serotyping identified coxsackie B viruses (CBV) only. VP1 region revealed different CBV (CBV1, CBV2, CBV3, CBV4, and CBV5), echoviruses, coxsackieviruses A4-like strains and a poliovirus 2. The results suggest strong year-round respiratory picornavirus activity in children up to 5 years of age. Molecular studies identified a wide variety of RVs along with diverse EVs in samples from patients with ILI. PMID:27246444

  12. Molecular epidemiology and outcome of Helicobacter pylori infection in Thailand: a cultural cross roads.

    PubMed

    Vilaichone, Ratha-Korn; Mahachai, Varocha; Tumwasorn, Somying; Wu, Jeng-Yih; Graham, David Y; Yamaoka, Yoshio

    2004-10-01

    ABSTRACT Background. Thailand is at the cultural cross roads between East and South Asia. It has been suggested that this is also the region where the predominant Helicobacter pylori (H. pylori) genotype changes from East Asian to South Asian. Methods. We compared the molecular epidemiology and outcome of H. pylori infections among different ethnic groups in Thailand (Thai, Thai-Chinese and Chinese). H. pylori isolates were genotyped by polymerase chain reaction based on cagA, cag right end junction and vacA genotypes. Results. Ninety-eight isolates from 38 ethnic Thai, 20 ethnic Chinese and 40 Thai-Chinese were categorized into East Asian (45%), South/Central Asian (26%), Western (1%) or mixed type (29%). The East Asian genotype was the most common among Chinese (85%) and Thai-Chinese (55%) (p <.01 compared to ethnic Thai). The ethnicity of the mother among mixed Thai-Chinese marriages predicted the genotype of the child's H. pylori (e.g. when the mother was Chinese, 84% had East Asian type vs. 29% when the mother was Thai) (p <.001). Gastric cancer was common among ethnic Chinese with East Asian genotype (e.g. all Chinese with gastric cancer or peptic ulcer disease had East Asian genotype, whereas only 40% of Chinese with gastritis had this genotype). Conclusions. Immigration, intermarriage and the variety of H. pylori genotypes in Thailand suggest that Thailand is an ideal site for epidemiological studies attempting to relate H. pylori genotypes and host factors to outcome. Our data also support the hypothesis that the primary caretaker of the children is most likely the source of the infection. PMID:15361085

  13. Molecular Epidemiology of Plasmodium falciparum Malaria Outbreak, Tumbes, Peru, 2010–2012

    PubMed Central

    Okoth, Sheila Akinyi; Arrospide, Nancy; Gonzalez, Rommell V.; Sánchez, Juan F.; Macedo, Silvia; Conde, Silvia; Tapia, L. Lorena; Salas, Carola; Gamboa, Dionicia; Herrera, Yeni; Edgel, Kimberly A.; Udhayakumar, Venkatachalam; Lescano, Andrés G.

    2015-01-01

    During 2010–2012, an outbreak of 210 cases of malaria occurred in Tumbes, in the northern coast of Peru, where no Plasmodium falciparum malaria case had been reported since 2006. To identify the source of the parasite causing this outbreak, we conducted a molecular epidemiology investigation. Microsatellite typing showed an identical genotype in all 54 available isolates. This genotype was also identical to that of parasites isolated in 2010 in the Loreto region of the Peruvian Amazon and closely related to clonet B, a parasite lineage previously reported in the Amazon during 1998–2000. These findings are consistent with travel history of index case-patients. DNA sequencing revealed mutations in the Pfdhfr, Pfdhps, Pfcrt, and Pfmdr1 loci, which are strongly associated with resistance to chloroquine and sulfadoxine/pyrimethamine, and deletion of the Pfhrp2 gene. These results highlight the need for timely molecular epidemiology investigations to trace the parasite source during malaria reintroduction events. PMID:25897626

  14. Molecular epidemiology of Mycobacterium tuberculosis in the United States-Affiliated Pacific Islands.

    PubMed

    Bamrah, Sapna; Desmond, Edward; Ghosh, Smita; France, Anne Marie; Kammerer, J Steve; Cowan, Lauren S; Heetderks, Andrew; Forbes, Alstead; Moonan, Patrick K

    2014-01-01

    The United States-Affiliated Pacific Islands (USAPI) are part of the US National Tuberculosis (TB) Surveillance System and use laboratory services contracted through a cooperative agreement with the Centers for Disease Control and Prevention (CDC). In 2004, the CDC established the National Tuberculosis Genotyping Service, a system to genotype 1 isolate from each culture-confirmed case of TB. To describe the molecular epidemiology of TB in the region, we examined all Mycobacterium tuberculosis isolates submitted for genotyping from January 1, 2004, to December 31, 2008. Over this time period, the USAPI jurisdictions reported 1339 verified TB cases to the National Tuberculosis Surveillance System. Among 419 (31%) reported culture-confirmed TB cases, 352 (84%) had complete genotype results. Routine TB genotyping allowed, for the first time, an exploration of the molecular epidemiology of TB in the USAPI. PMID:23239749

  15. Epidemiological studies of plague in India

    PubMed Central

    Seal, S. C.

    1960-01-01

    Data from early in the twentieth century up to the present day indicate that Rattus rattus among rodents and Xenopsylla cheopis among fleas are the two most important elements in urban human plague infection in India, R. norvegicus playing a more minor role. The relative numbers of both these species have decreased in recent years in Bombay and Calcutta, while those of Bandicota bengalensis, which is less heavily parasitized by X. cheopis, have risen. This reduction in the numbers of the epidemiologically more important rodents and their fleas has been accompanied by a reduction in the number of human plague cases. PMID:20604076

  16. Conventional and molecular epidemiology of Tuberculosis in Manitoba

    PubMed Central

    Blackwood, Kym S; Al-Azem, Assaad; Elliott, Lawrence J; Hershfield, Earl S; Kabani, Amin M

    2003-01-01

    Background To describe the demographic and geographic distribution of tuberculosis (TB) in Manitoba, thus determining risk factors associated with clustering and higher incidence rates in distinct subpopulations. Methods Data from the Manitoba TB Registry was compiled to generate a database on 855 patients with tuberculosis and their contacts from 1992–1999. Recovered isolates of M. tuberculosis were typed by IS6110 restriction fragment length polymorphisms. Bivariate and multivariate logistic regression models were used to identify risk factors involved in clustering. Results A trend to clustering was observed among the Canadian-born treaty Aboriginal subgroup in contrast to the foreign-born. The dominant type, designated fingerprint type 1, accounts for 25.8% of total cases and 75.3% of treaty Aboriginal cases. Among type 1 patients residing in urban areas, 98.9% lived in Winnipeg. In rural areas, 92.8% lived on Aboriginal reserves. Statistical models revealed that significant risk factors for acquiring clustered tuberculosis are gender, age, ethnic origin and residence. Those at increased risk are: males (p < 0.05); those under age 65 (p < 0.01 for each age subgroup); treaty Aboriginals (p < 0.001), and those living on reserve land (p < 0.001). Conclusion Molecular typing of isolates in conjunction with contact tracing data supports the notion of the largest ongoing transmission of a single strain of TB within the treaty-status population of Canada recorded to date. This data demonstrates the necessity of continued surveillance of countries with low prevalence of the disease in order to determine and target high-risk populations for concentrated prevention and control measures. PMID:12917019

  17. Molecular Epidemiology of the Pertussis Epidemic in Washington State in 2012

    PubMed Central

    Bowden, Katherine E.; Williams, Margaret M.; Cassiday, Pamela K.; Milton, Andrea; Pawloski, Lucia; Harrison, Marsenia; Martin, Stacey W.; Meyer, Sarah; Qin, Xuan; DeBolt, Chas; Tasslimi, Azadeh; Syed, Nusrat; Sorrell, Ronald; Tran, Mike; Hiatt, Brian

    2014-01-01

    Although pertussis disease is vaccine preventable, Washington State experienced a substantial rise in pertussis incidence beginning in 2011. By June 2012, the reported cases reached 2,520 (37.5 cases per 100,000 residents), a 1,300% increase compared with the same period in 2011. We assessed the molecular epidemiology of this statewide epidemic using 240 isolates collected from case patients reported from 19 of 39 Washington counties during 2012 to 2013. The typing methods included pulsed-field gel electrophoresis (PFGE), multilocus variable number tandem repeat analysis (MLVA), multilocus sequence typing (MLST), and pertactin gene (prn) mutational analysis. Using the scheme PFGE-MLVA-MLST-prn mutations-Prn deficiency, the 240 isolates comprised 65 distinct typing profiles. Thirty-one PFGE types were found, with the most common types, CDC013 (n = 51), CDC237 (n = 44), and CDC002 (n = 42), accounting for 57% of them. Eleven MLVA types were observed, mainly comprising type 27 (n = 183, 76%). Seven MLST types were identified, with the majority of the isolates typing as prn2-ptxP3-ptxA1-fim3-1 (n = 157, 65%). Four different prn mutations accounted for the 76% of isolates exhibiting pertactin deficiency. PFGE provided the highest discriminatory power (D = 0.87) and was found to be a more powerful typing method than MLVA and MLST combined (D = 0.67). This study provides evidence for the continued predominance of MLVA 27 and prn2-ptxP3-ptxA1 alleles, along with the reemergence of the fim3-1 allele. Our results indicate that the Bordetella pertussis population causing this epidemic was diverse, with a few molecular types predominating. The PFGE, MLVA, and MLST profiles were consistent with the predominate types circulating in the United States and other countries. For prn, several mutations were present in multiple molecular types. PMID:25031439

  18. Molecular epidemiology and clinical spectrum of hereditary spastic paraplegia in the Japanese population based on comprehensive mutational analyses.

    PubMed

    Ishiura, Hiroyuki; Takahashi, Yuji; Hayashi, Toshihiro; Saito, Kayoko; Furuya, Hirokazu; Watanabe, Mitsunori; Murata, Miho; Suzuki, Mikiya; Sugiura, Akira; Sawai, Setsu; Shibuya, Kazumoto; Ueda, Naohisa; Ichikawa, Yaeko; Kanazawa, Ichiro; Goto, Jun; Tsuji, Shoji

    2014-03-01

    Hereditary spastic paraplegia (HSP) is one of the most genetically heterogeneous neurodegenerative disorders characterized by progressive spasticity and pyramidal weakness of lower limbs. Because >30 causative genes have been identified, screening of multiple genes is required for establishing molecular diagnosis of individual patients with HSP. To elucidate molecular epidemiology of HSP in the Japanese population, we have conducted mutational analyses of 16 causative genes of HSP (L1CAM, PLP1, ATL1, SPAST, CYP7B1, NIPA1, SPG7, KIAA0196, KIF5A, HSPD1, BSCL2, SPG11, SPG20, SPG21, REEP1 and ZFYVE27) using resequencing microarrays, array-based comparative genomic hybridization and Sanger sequencing. The mutational analysis of 129 Japanese patients revealed 49 mutations in 46 patients, 32 of which were novel. Molecular diagnosis was accomplished for 67.3% (33/49) of autosomal dominant HSP patients. Even among sporadic HSP patients, mutations were identified in 11.1% (7/63) of them. The present study elucidated the molecular epidemiology of HSP in the Japanese population and further broadened the mutational and clinical spectra of HSP. PMID:24451228

  19. Mycosis fungoides in Iranian population: an epidemiological and clinicopathological study.

    PubMed

    Fatemi Naeini, Farahnaz; Abtahi-Naeini, Bahareh; Sadeghiyan, Hamidreza; Nilforoushzadeh, Mohammad Ali; Najafian, Jamshid; Pourazizi, Mohsen

    2015-01-01

    Background. Mycosis fungoides (MF) is the most common subtype of cutaneous T-cell lymphoma. Extensive studies on Iranian MF patients are absent. The present study aimed to produce updated clinical information on Iranian MF patients. Methods. This was a retrospective, descriptive, single-center study, including all cases of MF seen in the Department of Dermatology, University Hospital of Isfahan, Iran, between 2003 and 2013. Data systematically recorded for each patient included clinical, biological, histological, and molecular findings. Results. Eighty-six patients with clinical and histologic diagnosis of MF were included in the study. Thirty-nine patients (45.3%) were male. Female predominance was observed in patients (male : female ratio is 1 : 1.2). Patients were between 7 and 84 years of age (median: 41). The interval from disease onset to diagnosis ranged from 0 to 55 years (median: 1 year). Eighteen cases (20.9%) had unusual variants of MF. The most common types included hypopigmented and poikilodermatous MF. Childhood cases of MF constituted 5.8% (5/86) of all patients. The early stages were seen in 82 cases (95.34%). Conclusion. The major differences in epidemiologic characteristics of MF in Iran are the lack of male predominance and the lower age of patients at the time of diagnosis. PMID:25694829

  20. Mycosis Fungoides in Iranian Population: An Epidemiological and Clinicopathological Study

    PubMed Central

    Fatemi Naeini, Farahnaz; Abtahi-Naeini, Bahareh; Sadeghiyan, Hamidreza; Nilforoushzadeh, Mohammad Ali; Najafian, Jamshid; Pourazizi, Mohsen

    2015-01-01

    Background. Mycosis fungoides (MF) is the most common subtype of cutaneous T-cell lymphoma. Extensive studies on Iranian MF patients are absent. The present study aimed to produce updated clinical information on Iranian MF patients. Methods. This was a retrospective, descriptive, single-center study, including all cases of MF seen in the Department of Dermatology, University Hospital of Isfahan, Iran, between 2003 and 2013. Data systematically recorded for each patient included clinical, biological, histological, and molecular findings. Results. Eighty-six patients with clinical and histologic diagnosis of MF were included in the study. Thirty-nine patients (45.3%) were male. Female predominance was observed in patients (male : female ratio is 1 : 1.2). Patients were between 7 and 84 years of age (median: 41). The interval from disease onset to diagnosis ranged from 0 to 55 years (median: 1 year). Eighteen cases (20.9%) had unusual variants of MF. The most common types included hypopigmented and poikilodermatous MF. Childhood cases of MF constituted 5.8% (5/86) of all patients. The early stages were seen in 82 cases (95.34%). Conclusion. The major differences in epidemiologic characteristics of MF in Iran are the lack of male predominance and the lower age of patients at the time of diagnosis. PMID:25694829

  1. An Exercise in Molecular Epidemiology: Human Rhinovirus Prevalence and Genetics

    ERIC Educational Resources Information Center

    Albright, Catherine J.; Hall, David J.

    2011-01-01

    Human rhinovirus (HRV) is one of the most common human respiratory pathogens and is responsible for the majority of upper respiratory illnesses. Recently, a phylogeny was constructed from all known American Type Culture Collection (ATCC) HRV sequences. From this study, three HRV classifications (HRVA, HRVB, and HRVC) were determined and techniques…

  2. Molecular epidemiology of cryptosporidiosis in cattle and other food animals

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cryptosporidium spp. is an enteric protozoan parasite that infects a wide range of vertebrate hosts including humans. Cryptosporidial infection is known now as one of the most common causes of diarrhea in humans and livestock. Worldwide prevalence studies indicate that livestock has a high prevalenc...

  3. Serotype Distribution, Antimicrobial Susceptibility, and Molecular Epidemiology of Streptococcus pneumoniae Isolated from Children in Shanghai, China

    PubMed Central

    Pan, Fen; Han, Lizhong; Huang, Weichun; Tang, Jin; Xiao, Shuzhen; Wang, Chun; Qin, Huihong; Zhang, Hong

    2015-01-01

    Objective Streptococcus pneumoniae is a common pathogenic cause of pediatric infections. This study investigated the serotype distribution, antimicrobial susceptibility, and molecular epidemiology of pneumococci before the introduction of conjugate vaccines in Shanghai, China. Methods A total of 284 clinical pneumococcal isolates (270, 5, 4,3, and 2 of which were isolated from sputum, bronchoalveolar lavage fluid, blood, cerebral spinal fluid, and ear secretions, respectively) from children less than 14 years of age who had not been vaccinated with a conjugate vaccine, were collected between January and December in 2013. All isolates were serotyped by multiplex polymerase chain reaction or quellung reactions and antimicrobial susceptibility testing was performed using the broth microdilution method. The molecular epidemiology of S.pneumoniae was analyzed by multilocus sequence typing (MLST). Results Among the 284 pneumococcal isolates, 19F (33.5%), 19A (14.1%), 23F (12.0%), and 6A (8.8%) were the most common serotypes and the coverage rates of the 7-, 10-, and 13-valent pneumococcal conjugate vaccines (PCV7, PCV10, and PCV13) were 58.6%, 59.4% and 85.1%, respectively. Antimicrobial susceptibility showed that the prevalence rates of S.pneumoniae resistance to penicillin were 11.3% (32/284). Approximately 88.0% (250/284) of the isolates exhibited multi-drug resistance. MLST analysis revealed a high level of diversity, with 65 sequence types (STs) among 267 isolates. Specifically, the four predominant STs were ST271 (24.3%, 65/267), ST320 (11.2%, 30/267), ST81 (9.7%, 26/267), and ST3173 (5.2%, 14/267), which were mainly associated with serotypes 19F, 19A, 23F, and 6A, respectively. Conclusions The prevalent serotypes among clinical isolates from children were 19F, 19A, 23F, and 6A and these isolates showed high resistance rates to β-lactams and macrolides. The Taiwan19F-14 clone played a predominant role in the dissemination of pneumococcal isolates in Shanghai

  4. Molecular epidemiology of KPC-2-producing Enterobacteriaceae (non-Klebsiella pneumoniae) isolated from Brazil.

    PubMed

    Tavares, Carolina Padilha; Pereira, Polyana Silva; Marques, Elizabeth de Andrade; Faria, Celio; de Souza, Maria da Penha Araújo Herkenhoff; de Almeida, Robmary; Alves, Carlene de Fátima Morais; Asensi, Marise Dutra; Carvalho-Assef, Ana Paula D'Alincourt

    2015-08-01

    In Brazil, since 2009, there has been an ever increasing widespread of the bla(KPC-2) gene, mainly in Klebsiella pneumoniae. This study aims to assess the molecular epidemiology and genetic background of this gene in Enterobacteriaceae (non-K. pneumoniae) species from 9 Brazilian states between 2009 and 2011. Three hundred eighty-seven isolates were analyzed exhibiting nonsusceptibility to carbapenems, in which the bla(KPC-2) gene was detected in 21.4%. By disk diffusion and E-test, these isolates exhibited high rates of resistance to most of the antimicrobials tested, including tigecycline (45.6% nonsusceptible) and polymyxin B (16.5%), the most resistant species being Enterobacter aerogenes and Enterobacter cloacae. We found great clonal diversity and a variety of bla(KPC-2)-carrying plasmids, all of them exhibiting a partial Tn4401 structure. Therefore, this study demonstrates the dissemination of KPC-2 in 9 Enterobacteriaceae species, including species that were not previously described such as Pantoea agglomerans and Providencia stuartii. PMID:25935630

  5. Molecular epidemiology of imported cases of leishmaniasis in Australia from 2008 to 2014.

    PubMed

    Roberts, Tamalee; Barratt, Joel; Sandaradura, Indy; Lee, Rogan; Harkness, John; Marriott, Deborah; Ellis, John; Stark, Damien

    2015-01-01

    Leishmaniasis is a vector borne disease caused by protozoa of the genus Leishmania. Human leishmaniasis is not endemic in Australia though imported cases are regularly encountered. This study aimed to provide an update on the molecular epidemiology of imported leishmaniasis in Australia. Of a total of 206 biopsies and bone marrow specimens submitted to St Vincent's Hospital Sydney for leishmaniasis diagnosis by PCR, 55 were found to be positive for Leishmania DNA. All PCR products were subjected to restriction fragment length polymorphism analysis for identification of the causative species. Five Leishmania species/species complexes were identified with Leishmania tropica being the most common (30/55). Travel or prior residence in a Leishmania endemic region was the most common route of acquisition with ~47% of patients having lived in or travelled to Afghanistan. Cutaneous leishmaniasis was the most common manifestation (94%) with only 3 cases of visceral leishmaniasis and no cases of mucocutaneous leishmaniasis encountered. This report indicates that imported leishmaniasis is becoming increasingly common in Australia due to an increase in global travel and immigration. As such, Australian clinicians must be made aware of this trend and consider leishmaniasis in patients with suspicious symptoms and a history of travel in endemic areas. This study also discusses the recent identification of a unique Leishmania species found in native kangaroos and a potential vector host which could create the opportunity for the establishment of a local transmission cycle within humans. PMID:25734905

  6. Molecular epidemiology and evolution of human enterovirus 71 and hand, foot and mouth disease.

    PubMed

    Zhifang, Liu; Juanjuan, Gui; Qihang, Hua; Changzheng, Dong

    2015-05-01

    Human enterovirus 71(EV71), one of the major pathogens of the hand, foot and mouth disease (HFMD), causes skin rashes in palms, feet and mouth ulcers and complication in the central nervous system such as aseptic meningitis and acute flaccid paralysis that may lead to death. EV71 infection has been reported to be associated with many outbreaks of HFMD worldwide, especially the great outbreaks that occurred in the Asia-Pacific region and caused numerous death since 1997. The studies of molecular epidemiology and evolution of EV71 are important for the prevention and control of HFMD since no vaccines and antiviral drugs have been developed except symptomatic treatment for HFMD. In this review, we summarize genotype classification, temporal and spatial distribution, evolutionary characteristics and modes of EV71 as well as typical EV71 epidemics. Further studies on EV71 and HFMD may lead to better understanding of pathological mechanisms of EV71, development of antiviral drugs and prevention and control of HFMD. PMID:25998430

  7. Molecular Epidemiology of Imported Cases of Leishmaniasis in Australia from 2008 to 2014

    PubMed Central

    Roberts, Tamalee; Barratt, Joel; Sandaradura, Indy; Lee, Rogan; Harkness, John; Marriott, Deborah; Ellis, John; Stark, Damien

    2015-01-01

    Leishmaniasis is a vector borne disease caused by protozoa of the genus Leishmania. Human leishmaniasis is not endemic in Australia though imported cases are regularly encountered. This study aimed to provide an update on the molecular epidemiology of imported leishmaniasis in Australia. Of a total of 206 biopsies and bone marrow specimens submitted to St Vincent’s Hospital Sydney for leishmaniasis diagnosis by PCR, 55 were found to be positive for Leishmania DNA. All PCR products were subjected to restriction fragment length polymorphism analysis for identification of the causative species. Five Leishmania species/species complexes were identified with Leishmania tropica being the most common (30/55). Travel or prior residence in a Leishmania endemic region was the most common route of acquisition with ~47% of patients having lived in or travelled to Afghanistan. Cutaneous leishmaniasis was the most common manifestation (94%) with only 3 cases of visceral leishmaniasis and no cases of mucocutaneous leishmaniasis encountered. This report indicates that imported leishmaniasis is becoming increasingly common in Australia due to an increase in global travel and immigration. As such, Australian clinicians must be made aware of this trend and consider leishmaniasis in patients with suspicious symptoms and a history of travel in endemic areas. This study also discusses the recent identification of a unique Leishmania species found in native kangaroos and a potential vector host which could create the opportunity for the establishment of a local transmission cycle within humans. PMID:25734905

  8. The evolving molecular epidemiology of HIV type 1 among injecting drug users (IDUs) in Malaysia.

    PubMed

    Tee, Kok Keng; Saw, Teik Leong; Pon, Chee Keong; Kamarulzaman, Adeeba; Ng, Kee Peng

    2005-12-01

    Earlier studies in the 1990s indicate that human immunodeficiency virus type 1 (HIV-1) subtype B has been the predominant subtype among injecting drug users (IDUs) in Malaysia. More recent studies performed between 2003 and 2004, however, show a high prevalence of unique CRF01_AE/B intersubtype recombinants among IDUs. To determine the subtype distribution among IDUs in Kuala Lumpur prior to the emergence of CRF01_AE/B intersubtype recombinants, the gag-pol or the reverse transcriptase gene was sequenced from IDUs who were diagnosed as HIV positive between 1993 and 2002. Subtype B was present at 50.0% followed by CRF01_AE/B recombinant at 41.7%, with more CRF01_AE/B recombinants detected between 2000 and 2002. All CRF01_AE/B recombinants shared similar recombination patterns. Interestingly, we found that this potential new candidate of circulating recombinant form (CRF) could have emerged as early as the mid-1990s. The results showed evidence of changing HIV-1 molecular epidemiology toward the predominance of CRF01_AE/B intersubtype recombinants among IDUs in Kuala Lumpur. PMID:16379608

  9. Field epidemiologic studies of populations exposed to waste dumps.

    PubMed

    Heath, C W

    1983-02-01

    Epidemiologic studies are required for assessing health risks related to toxic waste exposure. Since the settings in which such studies must be performed are extremely diverse, epidemiologic approaches must be versatile. For any particular study, three fundamental requirements are to assess what toxic materials are present, understand how human exposure may occur, and objectively measure possible biologic effects. In assessing links between exposure and disease, epidemiologists must be particularly aware of: expected disease frequencies in relation to the size of populations studied, implications of long or varied disease latencies for study design and competing causes of disease and associated confounding variables. These concepts are illustrated by discussion of epidemiologic studies related to the Love Canal toxic waste dump site in Niagara Falls, NY. PMID:6825633

  10. Molecular epidemiology of childhood leukemia with emphasis on chemical exposures

    SciTech Connect

    Buffler, P.A.; Smith, M.T.; Wood, S.; Reynolds, P.

    1996-12-31

    Developing markets in the Pacific Basin depend heavily on the production and export of consumer goods. The generation of hazardous waste as a by-product of industrial production can be linked to adverse health outcomes, such as childhood leukemia, in ways that are presently unknown. In California, exposures resulting from hazardous waste disposal are of concern in the etiology of childhood cancer. Approximately 63% of the 57 hazardous waste sites that the U.S. Environmental Protection Agency (USEPA) included in the national priority list under the Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) statute were in the six-county San Francisco Bay area. This area includes California`s Silicon Valley, where a disproportionate majority of these sites are located. Although only one study links hazardous waste disposal to childhood leukemia evidence is accumulating that in utero and maternal pesticide exposures as well as chemical exposures during childhood are important in the etiology of childhood leukemia. This study investigates whether children with leukemia have common genetic changes, whether children with genetic changes experience common chemical exposures, and whether the occurrences of these genetic changes correspond to the same temporal sequence as exposure. The purpose of this paper is to describe the study design and report on the status of research activity. 10 refs., 1 fig., 3 tabs.

  11. Molecular epidemiology of adenoviral keratoconjunctivitis in Saudi Arabia

    PubMed Central

    Omar, Nazri; Hammouda, Ehab; Akanuma, Masataka; Ohguchi, Takeshi; Ariga, Toshihide; Tagawa, Yoshitsugu; Kitaichi, Nobuyoshi; Ishida, Susumu; Aoki, Koki; Ishiko, Hiroaki; Ohno, Shigeaki

    2010-01-01

    Purpose Adenoviral keratoconjunctivitis is a major cause of ocular morbidity and may lead to visual loss. Adenovirus types 8, 19, and 37 may cause epidemic keratoconjunctivitis. The main objective of this study was to determine the types of adenoviruses causing keratoconjunctivitis in Saudi Arabia. Methods We conducted a non-interventional observational clinical study. Seventy three eyes from 65 patients who presented to The Eye Center in Riyadh, Saudi Arabia with clinical features of acute adenoviral keratoconjunctivitis were included. Each patient underwent complete clinical examination and features such as membranous reaction, conjunctival hemorrhage, subepithelial corneal infiltrates, and preauricular lymph node enlargement were recorded. Conjunctival swabs were obtained from patients with presumed acute viral conjunctivitis. Immunochromatography (IC) and restriction fragment length polymorphism polymerase chain reaction (PCR-RFLP) were performed on the conjunctival swabs obtained from each eye. Serotype identification was performed using direct sequencing technique. Results Forty-nine (67.1%) were adenovirus type 8, 8 (11.0%) were adenovirus type 3, 6 (8.2%) type 37, 5 (6.8%) were adenovirus type 4, and 2 (2.3%) type 19. The remaining 5 were types 14, 19, and 22. The prevalence of membranous conjunctivitis was highest (83%) among eyes with adenovirus type 37 while subepithelial corneal opacities were most commonly seen among eyes with adenovirus type 8 (47%). Immunochromatography tests were positive for adenovirus in 48 (65.7%) out of 73 eyes. Conclusions This study determined the types of adenoviruses causing keratoconjunctivitis at one center in Saudi Arabia. Direct sequencing techniques is an efficient, accurate, and rapid means of diagnosing adenoviral keratoconjunctivitis. The most common causes of adenoviral keratoconjunctivitis in Saudi Arabia were adenovirus types 8, 3, and 37. Membranous conjunctivitis and subepithelial opacities had the highest

  12. Study design in genetic epidemiology: theoretical and practical considerations.

    PubMed

    Whittemore, A S; Nelson, L M

    1999-01-01

    Recent advances in molecular genetics have created new opportunities and challenges for genetic epidemiologists. Here we review some of the issues that arise when designing a study involving the genetic epidemiology of chronic diseases of late onset, such as cancer. We discuss two considerations that influence the choice of design. The first consideration is the study's goals. We describe the goals of identifying new susceptibility genes for a disease, of estimating important characteristics of known genes, and of learning how to prevent the disease in the genetically susceptible. We indicate how these goals affect the choice of design and present some guidelines for choosing designs that effectively address them. The second consideration is the set of practical constraints to successfully conducting the research. These contraints include problems of potential selection bias, reduced response rates, problems particular to family registries, problems particular to the cultures of various ethnic groups, and ethical issues. We indicate how these constraints affect the choice of design and discuss ways to deal with them. PMID:10854488

  13. Maximizing DNA yield for epidemiologic studies: no more buffy coats?

    PubMed

    Gail, Mitchell H; Sheehy, Tim; Cosentino, Mark; Pee, David; Diaz-Mayoral, Norma A; Garcia-Closas, Montserrat; Caporaso, Neil E; Pitt, Karen; Ziegler, Regina G

    2013-10-01

    Some molecular analyses require microgram quantities of DNA, yet many epidemiologic studies preserve only the buffy coat. In Frederick, Maryland, in 2010, we estimated DNA yields from 5 mL of whole blood and from equivalent amounts of all-cell-pellet (ACP) fraction, buffy coat, and residual blood cells from fresh blood (n = 10 volunteers) and from both fresh and frozen blood (n = 10). We extracted DNA with the QIAamp DNA Blood Midi Kit (Qiagen Sciences, Germantown, Maryland) for silica spin column capture and measured double-stranded DNA. Yields from frozen blood fractions were not statistically significantly different from those obtained from fresh fractions. ACP fractions yielded 80.6% (95% confidence interval: 66, 97) of the yield of frozen whole blood and 99.3% (95% confidence interval: 86, 100) of the yield of fresh blood. Frozen buffy coat and residual blood cells each yielded only half as much DNA as frozen ACP, and the yields were more variable. Assuming that DNA yield and quality from frozen ACP are stable, we recommend freezing plasma and ACP. Not only does ACP yield twice as much DNA as buffy coat but it is easier to process, and its yield is less variable from person to person. Long-term stability studies are needed. If one wishes to separate buffy coat before freezing, one should also save the residual blood cell fraction, which contains just as much DNA. PMID:23857774

  14. Epidemiological study air disaster in Amsterdam (ESADA): study design

    PubMed Central

    Slottje, Pauline; Huizink, Anja C; Twisk, Jos WR; Witteveen, Anke B; van der Ploeg, Henk M; Bramsen, Inge; Smidt, Nynke; Bijlsma, Joost A; Bouter, Lex M; van Mechelen, Willem; Smid, Tjabe

    2005-01-01

    Background In 1992, a cargo aircraft crashed into apartment buildings in Amsterdam, killing 43 victims and destroying 266 apartments. In the aftermath there were speculations about the cause of the crash, potential exposures to hazardous materials due to the disaster and the health consequences. Starting in 2000, the Epidemiological Study Air Disaster in Amsterdam (ESADA) aimed to assess the long-term health effects of occupational exposure to this disaster on professional assistance workers. Methods/Design Epidemiological study among all the exposed professional fire-fighters and police officers who performed disaster-related task(s), and hangar workers who sorted the wreckage of the aircraft, as well as reference groups of their non-exposed colleagues who did not perform any disaster-related tasks. The study took place, on average, 8.5 years after the disaster. Questionnaires were used to assess details on occupational exposure to the disaster. Health measures comprised laboratory assessments in urine, blood and saliva, as well as self-reported current health measures, including health-related quality of life, and various physical and psychological symptoms. Discussion In this paper we describe and discuss the design of the ESADA. The ESADA will provide additional scientific knowledge on the long-term health effects of technological disasters on professional workers. PMID:15921536

  15. Molecular Epidemiology of Seal Parvovirus, 1988–2014

    PubMed Central

    Bodewes, Rogier; Hapsari, Rebriarina; Rubio García, Ana; Sánchez Contreras, Guillermo J.; van de Bildt, Marco W. G.; de Graaf, Miranda; Kuiken, Thijs; Osterhaus, Albert D. M. E.

    2014-01-01

    A novel parvovirus was discovered recently in the brain of a harbor seal (Phoca vitulina) with chronic meningo-encephalitis. Phylogenetic analysis of this virus indicated that it belongs to the genus Erythroparvovirus, to which also human parvovirus B19 belongs. In the present study, the prevalence, genetic diversity and clinical relevance of seal parvovirus (SePV) infections was evaluated in both harbor and grey seals (Halichoerus grypus) that lived in Northwestern European coastal waters from 1988 to 2014. To this end, serum and tissue samples collected from seals were tested for the presence of seal parvovirus DNA by real-time PCR and the sequences of the partial NS gene and the complete VP2 gene of positive samples were determined. Seal parvovirus DNA was detected in nine (8%) of the spleen tissues tested and in one (0.5%) of the serum samples tested, including samples collected from seals that died in 1988. Sequence analysis of the partial NS and complete VP2 genes of nine SePV revealed multiple sites with nucleotide substitutions but only one amino acid change in the VP2 gene. Estimated nucleotide substitution rates per year were 2.00×10−4 for the partial NS gene and 1.15×10−4 for the complete VP2 gene. Most samples containing SePV DNA were co-infected with phocine herpesvirus 1 or PDV, so no conclusions could be drawn about the clinical impact of SePV infection alone. The present study is one of the few in which the mutation rates of parvoviruses were evaluated over a period of more than 20 years, especially in a wildlife population, providing additional insights into the genetic diversity of parvoviruses. PMID:25390639

  16. Molecular epidemiology of seal parvovirus, 1988-2014.

    PubMed

    Bodewes, Rogier; Hapsari, Rebriarina; Rubio García, Ana; Sánchez Contreras, Guillermo J; van de Bildt, Marco W G; de Graaf, Miranda; Kuiken, Thijs; Osterhaus, Albert D M E

    2014-01-01

    A novel parvovirus was discovered recently in the brain of a harbor seal (Phoca vitulina) with chronic meningo-encephalitis. Phylogenetic analysis of this virus indicated that it belongs to the genus Erythroparvovirus, to which also human parvovirus B19 belongs. In the present study, the prevalence, genetic diversity and clinical relevance of seal parvovirus (SePV) infections was evaluated in both harbor and grey seals (Halichoerus grypus) that lived in Northwestern European coastal waters from 1988 to 2014. To this end, serum and tissue samples collected from seals were tested for the presence of seal parvovirus DNA by real-time PCR and the sequences of the partial NS gene and the complete VP2 gene of positive samples were determined. Seal parvovirus DNA was detected in nine (8%) of the spleen tissues tested and in one (0.5%) of the serum samples tested, including samples collected from seals that died in 1988. Sequence analysis of the partial NS and complete VP2 genes of nine SePV revealed multiple sites with nucleotide substitutions but only one amino acid change in the VP2 gene. Estimated nucleotide substitution rates per year were 2.00 × 10(-4) for the partial NS gene and 1.15 × 10(-4) for the complete VP2 gene. Most samples containing SePV DNA were co-infected with phocine herpesvirus 1 or PDV, so no conclusions could be drawn about the clinical impact of SePV infection alone. The present study is one of the few in which the mutation rates of parvoviruses were evaluated over a period of more than 20 years, especially in a wildlife population, providing additional insights into the genetic diversity of parvoviruses. PMID:25390639

  17. Broad-coverage molecular epidemiology of Orientia tsutsugamushi in Thailand.

    PubMed

    Wongprompitak, Patimaporn; Anukool, Wichittra; Wongsawat, Ekkarat; Silpasakorn, Saowalak; Duong, Veasna; Buchy, Philippe; Morand, Serge; Frutos, Roger; Ekpo, Pattama; Suputtamongkol, Yupin

    2013-04-01

    Orientia tsutsugamushi, an obligate intracellular bacterium closely related to the genus Rickettsia, is the causative agent of scrub typhus, a major cause of febrile illness in rural areas of Asia-Pacific region. Scrub typhus is transmitted by the bite of infected mites of the genus Leptotrombidium. The region of the 56-kDa TSA gene spanning from variable domain I (VDI) to variable domain IV (VDIV) was sequenced and used for genotyping 77 O. tsutsugamushi samples from human patients confirmed with scrub typhus from 2001 to 2003 and 2009 to 2010 in different regions of Thailand. These sequences were also compared to previously published 56-kDa TSA sequences. Only 4 genotypes out of 8 previously reported in Thailand were identified, i.e. Karp, JG-v, TA763 and Kato, respectively. Two strains were not associated with known genotypes but were closely related to Taiwanese strains. The Karp genotype was confirmed as the predominant clade. The JG-v and TA763 genotypes, in contrast to other studies, also were found. The genotype TA716 was not found, except for one strain previously described. PMID:21712103

  18. Molecular Epidemiology of Tuberculosis in Finland, 2008-2011

    PubMed Central

    Smit, Pieter Willem; Haanperä, Marjo; Rantala, Pirre; Couvin, David; Lyytikäinen, Outi; Rastogi, Nalin; Ruutu, Petri; Soini, Hanna

    2013-01-01

    In industrialized countries the majority of tuberculosis (TB) cases are linked to immigration. In Finland, most cases are still Finnish born but the number of foreign born cases is steadily increasing. In this 4-year population based study, the TB situation in Finland was characterized by a genotypic analysis of Mycobacterium tuberculosis isolates. A total of 1048 M. tuberculosis isolates (representing 99.4% of all culture positive cases) were analyzed by spoligotyping and MIRU. Spoligotype lineages belonging to the Euro-American family were predominant among the Finnish isolates, particularly T (n=346, 33.0%) and Haarlem (n=237, 22.6%) strains. The lineage signature was unknown for 130 (12.4%) isolates. Out of the 17 multi-drug resistant TB strains, 10 (58.8%) belonged to the Beijing lineage. In total, 23 new SIT designations were given and 51 orphan strains were found, of which 58 patterns were unique to Finland. Phylogeographical TB mapping as compared to neighboring countries showed that the population structure in Finland most closely resembled that observed in Sweden. By combining spoligotyping and MIRU results, 98 clusters comprising 355 isolates (33.9%) were found. Only 10 clusters contained both Finnish and foreign born cases. In conclusion, a large proportion of the M. tuberculosis isolates were from Finnish born elderly patients. Moreover, many previously unidentified spoligotype profiles and isolates belonging to unknown lineages were encountered. PMID:24386443

  19. [Molecular epidemiology of phlebovirus in four provinces in Morocco].

    PubMed

    Es-Sette, N; Ajaoud, M; Charrel, R N; Lemrani, M

    2016-08-01

    Sandflies are vectors of protozoa, viruses, and bacteria. To investigate the transmission of phleboviruses, a total of 8753 sandflies were collected in four foci of leishmania. A total of 16 distinct species were morphologically identified. Nested-PCR and cell culture screening for phleboviruses, using an assay targeting the polymerase gene, showed positive results for 19 pools of sandflies. Sequencing of the corresponding products confirmed the results and allowed identification of Toscana virus exclusively. Corresponding sandfly species originated from four different foci, and were different from those commonly reported in the literature. Sequence analysis shows that the Moroccan Toscana viruses belong to genotype B and appear close to the Toscana viruses isolated in France and Spain. This study reported the existence of the virus in the north, center and south of the country. The abundance and diversity of sandflies in Morocco, Mediterranean climate, would support the continuous circulation of Toscana virus in our country, posing a potential risk of emergence of these arboviruses. PMID:27193286

  20. Molecular Epidemiology of Oral Treponemes Associated with Periodontal Disease

    PubMed Central

    Moter, Annette; Hoenig, Carina; Choi, Bong-Kyu; Riep, Birgit; Göbel, Ulf B.

    1998-01-01

    Periodontitis, a disease responsible for tooth loss worldwide, is characterized by chronic inflammation of the periodontium, eventually leading to destruction of periodontal ligaments and supporting alveolar bone. Spirochetes, identified by dark-field microscopy as being the most predominant bacteria in advanced lesions, are thought to play a causative role. Various spirochetal morphotypes were observed, but most of these morphotypes are as yet uncultivable. To assess the role of these organisms we designed oligonucleotide probes for the identification of both cultivable and so far uncultivable spirochetes in periodontitis patients. Subgingival plaque specimens taken from diseased sites (n = 200) and healthy control sites (n = 44) from 53 patients with rapidly progressive periodontitis (RPP) were submitted to direct in situ hybridization or dot blot hybridization after prior amplification with eubacterial primers. Spirochetes were found in all patients, but their distributions varied considerably. Parallel use of oligonucleotide probes specific for cultivable or so far uncultivable treponemes suggested the presence of novel yet unknown organisms at a high frequency. These uncultivable treponemes were visualized by fluorescence in situ hybridization, and their morphologies, sizes, and numbers could be estimated. All RPP patients included in this study harbored oral treponemes that represent either novel species, e.g., Treponema maltophilum, or uncultivable phylotypes. Therefore, it is necessary to include these organisms in etiologic considerations and to strengthen efforts to cultivate these as yet uncultivable treponemes. PMID:9574713

  1. Molecular epidemiology of Cryptosporidium species in livestock in Ireland.

    PubMed

    Mirhashemi, Marzieh Ezzaty; Zintl, Annetta; Grant, Tim; Lucy, Frances; Mulcahy, Grace; De Waal, Theo

    2016-01-30

    Cryptosporidium is a protozoan that can cause gastro-intestinal illness with diarrhoea in a wide range of hosts. In fact some species of Cryptosporidium can infect the broad range of hosts. The current paper is focused to investigate monthly prevalence and diversity of Cryptosporidium spp. during the spring and early summer (March-June) in 2009 and 2010 in farms with no history of cryptosporidiosis. Animal samples were analyzed to elucidate the prevalence of Cryptosporidium in two regions, West and the East catchments in Ireland. Our investigation demonstrates the prevalence ranges from 14% to 26% an early summer peak (June) was observed. Based on the findings of this study Cryptosporidium ryanae (in cattle, horses), and Cryptosporidium bovis/xiaoi followed by Cryptosporidium parvum (in sheep) were found to be the predominant species in asymptomatic cases. The circulation of other Cryptosporidium species such as C. parvum, C. bovis, C. ubiquitum, C. andersoni and Cryptosporidium horse and pig genotypes in livestock was investigated. PMID:26801590

  2. Molecular epidemiology of human Blastocystis isolates in France.

    PubMed

    Souppart, Laetitia; Sanciu, Giovanna; Cian, Amandine; Wawrzyniak, Ivan; Delbac, Frederic; Capron, Monique; Dei-Cas, Eduardo; Boorom, Kenneth; Delhaes, Laurence; Viscogliosi, Eric

    2009-08-01

    Blastocystis sp. is the most common eukaryotic parasite in the intestinal tract of humans. Due to its strong impact in public health, in this study, we determined the frequency of different Blastocystis subtypes in patients in France. We hypothesized on the mode of transmission and tested a possible relationship between the subtype and symptomatic status. We obtained a total of 40 stool samples identified as positive for Blastocystis by microscopic examination of smears. Participants consisted of 25 symptomatic and 15 asymptomatic patients, for whom clinical and parasitological data were collected. For nested-polymerase chain reaction and genotyping, DNA was extracted directly from fecal samples or from fecal cultures. Morphological forms observed in fecal cultures were uncorrelated with symptomatic status. Genotyping using partial small subunit rRNA gene analysis identified a total of 43 Blastocystis isolates corresponding to 37 single infections and three mixed infections by two different subtypes. These 43 isolates belonged to five subtypes (1, 2, 3, 4, and 7) with predominance of subtype 3 (53.5%). Patient symptomatic status was uncorrelated with Blastocystis subtype. PMID:19290540

  3. Molecular epidemiology of HIV type 1 subtypes in Rwanda.

    PubMed

    Kemal, Kimdar S; Anastos, Kathryn; Weiser, Barbara; Ramirez, Christina M; Shi, Qiuhu; Burger, Harold

    2013-06-01

    HIV-1 infection is characterized by genetic diversity, with multiple subtypes and recombinant variants circulating, particularly in sub-Saharan Africa. During the Rwandan genocide, many women experienced multiple rapes and some became HIV-1 infected. We studied plasma and peripheral blood mononuclear cells (PBMCs) from 30 infected women comprising two exposure groups: those with numerous contacts, raped multiple times, and women with one lifetime sexual partner and no history of rape. Population-based sequences from gag, pol, and env genes were analyzed to determine HIV-1 subtypes and intersubtype recombination. Individual plasma-derived variants from 12 women were also analyzed. Subtype A was found in 24/30 (80%), intersubtype recombination (AC and AD) in 4/30 (13%), and subtypes C and D in 1/30 each. In two subjects, the pattern of HIV-1 recombination differed between plasma and PBMC-derived sequences. Intersubtype recombination was common, although there were no significant differences in subtype or recombination rates between exposure groups. PMID:23458210

  4. Use of oral fluid to examine the molecular epidemiology of varicella zoster virus in the United Kingdom and continental Europe.

    PubMed

    Quinlivan, Mark; Sengupta, Nitu; Papaevangelou, Vassiliki; Sauerbrei, Andreas; Grillner, Lena; Rousseva, Rossitsa; Hague, Rosie; Lutsar, Irja; Jogi, Piia; Leca, Ana; Grytchol, Ruth; Alain, Sophie; Breuer, Judith

    2013-02-15

    We investigated oral fluid (OF) as an alternative to sampling of rashes for varicella zoster virus (VZV) genotyping and further characterized VZV clade prevalence in the United Kingdom and Europe. VZV was detected in up to 91% of OF specimens. Paired OF and vesicle fluid samples contained identical VZV clades. While clades 1 and 3 were the most prevalent across the United Kingdom and Europe, in Western Europe, clade 5 viruses were circulating. Viruses from the same outbreak belonged to different clades, but no clade was associated with a severe-disease phenotype. OF is suitable and convenient for large-scale molecular epidemiological studies of VZV. PMID:23087434

  5. Molecular epidemiology in environmental health: the potential of tumor suppressor gene p53 as a biomarker.

    PubMed Central

    Semenza, J C; Weasel, L H

    1997-01-01

    One of the challenges in environmental health is to attribute a certain health effect to a specific environmental exposure and to establish a cause-effect relationship. Molecular epidemiology offers a new approach to addressing these challenges. Mutations in the tumor suppressor gene p53 can shed light on past environmental exposure, and carcinogenic agents and doses can be distinguished on the basis of mutational spectra and frequency. Mutations in p53 have successfully been used to establish links between dietary aflatoxin exposure and liver cancer, exposure to ultraviolet light and skin cancer, smoking and cancers of the lung and bladder, and vinyl chloride exposure and liver cancer. In lung cancer, carcinogens from tobacco smoke have been shown to form adducts with DNA. The location of these adducts correlates with those positions in the p53 gene that are mutated in lung cancer, confirming a direct etiologic link between exposure and disease. Recent investigations have also explored the use of p53 as a susceptibility marker for cancer. Furthermore, studies in genetic toxicology have taken advantage of animals transgenic for p53 to screen for carcinogens in vivo. In this review, we summarize recent developments in p53 biomarker research and illustrate applications to environmental health. PMID:9114284

  6. Molecular Epidemiology of Porcine Cytomegalovirus (PCMV) in Sichuan Province, China: 2010–2012

    PubMed Central

    Xu, Zhiwen; Zhou, Yuancheng

    2013-01-01

    Porcine cytomegalovirus (PCMV) is an immunosuppressive virus that mainly inhibits the immune function of the macrophage and T-cell lymphatic systems, and has caused huge economic losses to the porcine breeding industry. Molecular epidemiological investigation of PCMV is important for prevention and treatment, and this study is the first such investigation in Sichuan Province, Southwest China. A PCMV positive infection rate of 84.4% (865/1025) confirmed that PCMV is widely distributed in Sichuan Province. A phylogenetic tree was constructed based on the PCMV glycoprotein B gene (gB) nucleotide and amino acid sequences from 24 novel Sichuan isolates and 18 other PCMV gB sequences from Genbank. PCMV does not appear to have evolved into different serotypes, and two distinct sequence groups were identified (A and B). However, whether PCMV from this region has evolved into different genotypes requires further research. Analysis of the amino acid sequences confirmed the conservation of gB, but amino acid substitutions in the major epitope region have caused antigenic drift, which may have altered the immunogenicity of PCMV. PMID:23762243

  7. Molecular epidemiology of Shigella spp strains isolated in two different metropolitam areas of southeast Brazil

    PubMed Central

    Angelini, Michelle; Stehling, Eliana Guedes; Moretti, Maria Luiza; da Silveira, Wanderley Dias

    2009-01-01

    Shigella spp., the human pathogen responsible for shigellosis, is highly infectious even at low levels. The incidence rate of shigellosis varies with geographical distribution, location human development index, and age groups, being higher among children aged under 5 years. In Brazil, a few works indicate that shigellosis cases are underestimated, with S. flexneri and S. sonnei strains being the major agents responsible for the shigellosis cases. The present study used pulsed field gel electrophoresis (PFGE) to investigate the molecular epidemiology of 119 strains of S. sonnei and S. flexneri isolated from shigellosis cases that occurred in the metropolitan areas of Ribeirão Preto and Campinas Cities, São Paulo Sate, southeast Brazil. The results indicated (i) the existence of just a few strain clusters for both species, but with genotype variability with either a high speed of genetic change or constant introduction of several genotypes, considering the intense migration to these two metropolitan areas, and (ii) the prevalence of specific genotypes in each geographical area, which suggests the successful adaptation of some genotypes to the local environmental conditions. Our results indicate the need of more efficacious sanitary barriers to prevent Shigella spp. outbreaks and epidemics. PMID:24031415

  8. Recent advances and perspectives in molecular epidemiology of Taenia solium cysticercosis.

    PubMed

    Ito, Akira; Yanagida, Tetsuya; Nakao, Minoru

    2016-06-01

    Cysticercosis caused by accidental ingestion of eggs of Taenia solium is spreading all over the world through globalization and is one of the most neglected, neglected tropical diseases (NTDs) or neglected zoonotic diseases (NZDs). In the present study, the reason why T. solium cysticercosis has been neglected is discussed at first, and followed with an overview on the most recent advances and perspectives in molecular approaches for epidemiology of T. solium taeniasis/cysticercosis, since although taeniasis does not constitute recognized zoonoses, transmission and complete development are dependent on human definitive hosts. Main topics are discussions on (1) the two, Asian and Afro/American, genotypes of T. solium, (2) comparative analysis of mitochondrial (haploid) and nuclear (diploid) genes, and (3) the presence of hybrids of these two genotypes which indicates out-crossing of two genotypes in hermaphrodite tapeworms in Madagascar. Additional topics are on (4) the usefulness of phylogeographic analyses to discuss where the infection was acquired from, and (5) miscellaneous unsolved topics around these genetic diversity of T. solium. PMID:26112071

  9. 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. PMID:26246243

  10. Molecular epidemiology of PRRSV from China's Guangxi Province between 2007 and 2009.

    PubMed

    Zhang, Hong-Yun; Liang, Jing-Jing; Meng, Xian-Ming; Li, Hui; Yang, Jian; Su, Li-Juan; Zhang, Hong-Pu; Xie, Lin-Juan; He, Xiao-Xia; Li, Yan-Sheng; Yin, Shan; Li, Xiao-Quan; Li, Xiao-Ning; Luo, Ting Rong

    2013-02-01

    Porcine reproductive and respiratory syndrome (PRRS) is considered to be one of the most important infectious diseases affecting livestock. This study used gene sequence analysis of ORF5 and Nsp2 to determine the molecular epidemiology of PRRSV in different parts of the Guangxi province of China. These genes were selected due to their extensive variation within the genome. Out of 189 samples from animals suspected to have PRRS, 145 were PRRSV RNA positive. ORF5 and Nsp2 gene sequence analysis of 31 of these samples showed that all of the Guangxi isolates were of type 2. A phylogenetic tree analysis based on ORF5 showed that the Guangxi isolates were divided into two groups. Most of these were closely related to highly pathogenic strains, showing a 30 amino acid deletion at positions 481 and 533-561 of Nsp2, but an additional unique isolate (GXNN06) possessed a further four amino acid deletion at positions 485-488 of Nsp2. PMID:23007890

  11. Molecular epidemiology of Mycobacterium bovis isolates from free-ranging wildlife in South African game reserves.

    PubMed

    Michel, A L; Coetzee, M L; Keet, D F; Maré, L; Warren, R; Cooper, D; Bengis, R G; Kremer, K; van Helden, P

    2009-02-01

    Bovine tuberculosis is endemic in African buffalo and a number of other wildlife species in the Kruger National Park (KNP) and Hluhluwe-iMfolozi Park (HiP) in South Africa. It was thought that the infection had been introduced into the KNP ecosystem through direct contact between cattle and buffalo, a hypothesis which was confirmed in this study by IS6110 and PGRS restriction fragment length polymorphism (RFLP) typing. The molecular characterisation of 189 Mycobacterium bovis isolates from nine wildlife species in the HiP, including three smaller associated parks, and the Kruger National Park with adjacent areas showed that the respective epidemics were each caused by an infiltration of a single M. bovis genotype. The two M. bovis strains had different genetic profiles, as demonstrated by hybridisation with the IS6110 and PGRS RFLP probes, as well as with regard to evidence of evolutionary changes to the IS profile. While the M. bovis type in HiP was transmitted between buffaloes and to at least baboon, bushpig and lion without obvious genetic changes in the RFLP patterns, in the KNP a dominant strain was represented in 73% of the M. bovis isolates, whilst the remaining 27% were variants of this strain. No species-specific variants were observed, except for one IS6110 type which was found only in a group of five epidemiologically related greater kudu. This finding was attributed to species-specific behaviour patterns rather than an advanced host-pathogen interaction. PMID:18786785

  12. Molecular epidemiologic analysis of Vibrio cholerae O1 isolates by pulsed-field gel electrophoresis.

    PubMed Central

    Mahalingam, S; Cheong, Y M; Kan, S; Yassin, R M; Vadivelu, J; Pang, T

    1994-01-01

    Isolates of Vibrio cholerae O1 El Tor from two well-defined cholera outbreaks in Malaysia were analyzed by using pulsed-field gel electrophoresis (PFGE). Isolates from sporadic cases occurring during the same time period were also studied. Digestion of chromosomal DNA from these isolates of V. cholerae O1 with restriction endonucleases NotI (5'-GCGGCCGC-3') and SfiI (5'-GGCCNNNN-3'), followed by PFGE, produced restriction endonuclease analysis (REA) patterns consisting of 13 to 24 bands (ranging in size from 46 to 398 kbp). Analysis of the REA patterns generated by PFGE after digestion with NotI and SfiI suggested the clonal nature and close genetic identity of the isolates obtained during each of the two outbreaks (Dice coefficient, 0.93 to 1.0). Although they had very similar REA patterns, the two outbreak clones were not identical. Isolates of V. cholerae O1 from sporadic cases, on the other hand, appeared to be much more heterogeneous (five different REA patterns detected in the five isolates tested; Dice coefficient, 0.31 to 0.81) than those obtained during the two outbreaks. We conclude that PFGE of V. cholerae O1 chromosomal DNA digested with infrequently cutting restriction endonucleases is a useful method for molecular typing of V. cholerae isolates for epidemiological purposes. Images PMID:7883885

  13. Molecular epidemiologic typing systems of bacterial pathogens: current issues and perspectives.

    PubMed

    Struelens, M J

    1998-01-01

    The epidemiologic typing of bacterial pathogens can be applied to answer a number of different questions: in case of outbreak, what is the extent and mode of transmission of epidemic clone(s)? In case of long-term surveillance, what is the prevalence over time and the geographic spread of epidemic and endemic clones in the population? A number of molecular typing methods can be used to classify bacteria based on genomic diversity into groups of closely-related isolates (presumed to arise from a common ancestor in the same chain of transmission) and divergent, epidemiologically-unrelated isolates (arising from independent sources of infection). Ribotyping, IS-RFLP fingerprinting, macrorestriction analysis of chromosomal DNA and PCR-fingerprinting using arbitrary sequence or repeat element primers are useful methods for outbreak investigations and regional surveillance. Library typing systems based on multilocus sequence-based analysis and strain-specific probe hybridization schemes are in development for the international surveillance of major pathogens like Mycobacterium tuberculosis. Accurate epidemiological interpretation of data obtained with molecular typing systems still requires additional research on the evolution rate of polymorphic loci in bacterial pathogens. PMID:9830521

  14. Molecular epidemiology of environmental MRSA at an equine teaching hospital: introduction, circulation and maintenance

    PubMed Central

    2014-01-01

    The role that environmental contamination might play as a reservoir and a possible source of Methicillin-resistant Staphylococcus aureus (MRSA) for patients and personnel at equine veterinary hospitals remains undefined, as the environment has only been monitored during outbreaks or for short periods. Therefore, the objectives of this study were to determine the monthly presence, distribution, and characteristics of environmental MRSA at an equine hospital, and to establish patterns of contamination over time using molecular epidemiological analyses. For this purpose, a yearlong active MRSA surveillance was performed targeting the environment and incoming patients. Antimicrobial susceptibility testing, SCCmec typing, PFGE typing, and dendrographic analysis were used to characterize and analyze these isolates. Overall, 8.6% of the surfaces and 5.8% of the horses sampled were positive for MRSA. The most common contaminated surfaces were: computers, feed-water buckets, and surgery tables-mats. Ninety percent of the isolates carried SCCmec type IV, and 62.0% were classified as USA500. Molecular analysis showed that new pulsotypes were constantly introduced into the hospital throughout the year. However, maintenance of strains in the environment was also observed when unique clones were detected for 2 consecutive months on the same surfaces. Additionally, pulsotypes were circulating throughout several areas and different contact surfaces of the hospital. Based on these results, it is evident that MRSA is constantly introduced and frequently found in the equine hospital environment, and that some contact surfaces could act as “hot-spots”. These contaminated surfaces should be actively targeted for strict cleaning and disinfection as well as regular monitoring. PMID:24641543

  15. Molecular epidemiology of environmental MRSA at an equine teaching hospital: introduction, circulation and maintenance.

    PubMed

    van Balen, Joany; Mowery, Jade; Piraino-Sandoval, Micha; Nava-Hoet, Rocio C; Kohn, Catherine; Hoet, Armando E

    2014-01-01

    The role that environmental contamination might play as a reservoir and a possible source of Methicillin-resistant Staphylococcus aureus (MRSA) for patients and personnel at equine veterinary hospitals remains undefined, as the environment has only been monitored during outbreaks or for short periods. Therefore, the objectives of this study were to determine the monthly presence, distribution, and characteristics of environmental MRSA at an equine hospital, and to establish patterns of contamination over time using molecular epidemiological analyses. For this purpose, a yearlong active MRSA surveillance was performed targeting the environment and incoming patients. Antimicrobial susceptibility testing, SCCmec typing, PFGE typing, and dendrographic analysis were used to characterize and analyze these isolates. Overall, 8.6% of the surfaces and 5.8% of the horses sampled were positive for MRSA. The most common contaminated surfaces were: computers, feed-water buckets, and surgery tables-mats. Ninety percent of the isolates carried SCCmec type IV, and 62.0% were classified as USA500. Molecular analysis showed that new pulsotypes were constantly introduced into the hospital throughout the year. However, maintenance of strains in the environment was also observed when unique clones were detected for 2 consecutive months on the same surfaces. Additionally, pulsotypes were circulating throughout several areas and different contact surfaces of the hospital. Based on these results, it is evident that MRSA is constantly introduced and frequently found in the equine hospital environment, and that some contact surfaces could act as "hot-spots". These contaminated surfaces should be actively targeted for strict cleaning and disinfection as well as regular monitoring. PMID:24641543

  16. Spatial and Molecular Epidemiology of Giardia intestinalis Deep in the Amazon, Brazil

    PubMed Central

    Coronato Nunes, Beatriz; Pavan, Márcio G.; Jaeger, Lauren H.; Monteiro, Kerla J. L.; Xavier, Samanta C. C.; Monteiro, Fernando A.; Bóia, Márcio N.; Carvalho-Costa, Filipe A.

    2016-01-01

    Background Current control policies for intestinal parasitosis focuses on soil-transmitted helminths, being ineffective against Giardia intestinalis, a highly prevalent protozoon that impacts children’s nutritional status in developing countries. The objective of this study was to explore spatial and molecular epidemiology of Giardia intestinalis in children of Amerindian descent in the Brazilian Amazon. Methodology/Principal Findings A cross sectional survey was performed in the Brazilian Amazon with 433 children aged 1 to 14 years. Fecal samples were processed through parasitological techniques and molecular characterization. Prevalence of G. intestinalis infection was 16.9% (73/433), reaching 22.2% (35/158) among children aged 2–5 years, and a wide distribution throughout the city with some hot spots. Positivity-rate was similar among children living in distinct socioeconomic strata (48/280 [17.1%] and 19/116 [16.4%] below and above the poverty line, respectively). Sequencing of the β-giardin gene revealed 52.2% (n = 12) of assemblage A and 47.8% (n = 11) of assemblage B with high haplotype diversity for the latter. The isolates clustered into two well-supported G. intestinalis clades. A total of 38 haplotypes were obtained, with the following subassemblages distribution: 5.3% (n = 2) AII, 26.3% (n = 10) AIII, 7.9% (n = 3) BIII, and 60.5% (n = 23) new B genotypes not previously described. Conclusions/Significance Giardia intestinalis infection presents a high prevalence rate among Amerindian descended children living in Santa Isabel do Rio Negro/Amazon. The wide distribution observed in a small city suggests the presence of multiple sources of infection, which could be related to environmental contamination with feces, possibly of human and animal origin, highlighting the need of improving sanitation, safe water supply and access to diagnosis and adequate treatment of infections. PMID:27392098

  17. Phenotypic Characters and Molecular Epidemiology of Campylobacter Jejuni in East China.

    PubMed

    Zeng, Dexin; Zhang, Xiaoping; Xue, Feng; Wang, Yanhong; Jiang, Luyan; Jiang, Yuan

    2016-01-01

    In this study, we investigated the distribution, phenotypic and molecular typing characters of Campylobacter jejuni in domestic fowl, and livestock populations in East China, to provide some reference for researches on its molecular epidemiology. A total of 1250 samples were collected from different animal sources, and C. jejuni strains were then isolated and tested for antibiotic sensitivity. Antibiotics-resistance gene and pathogenic genes were detected by polymerase chain reaction. Phylogenic analysis on the C. jejuni strains was performed by multilocus sequence typing (MLST) method. The results showed that 108 out of the 1250 samples (mean 8.64%) were C. jejuni positive. These 108 C. jejuni strains were highly sensitive to antibiotics such as chloramphenicol, amoxicillin, amikacin, cefotaxime, and azithromycin, whereas they were highly resistant to antibiotics such as cefoperazone, cotrimoxazole, cefamandole, sulfamethoxazole, and cefradine. Pathogenicity related gene identification indicated that the mean carrying rate of adhesion related gene cadF and racR, flagellin gene flaA, toxin regulating gene cdtA, cdtB, cdtC, wlaN and virB11, heat shock proteins and transferring proteins related genes dnaJ and ceuE, CiaB and pldA were 92.45%, 38.69%, 73.58%, 71.70%, 52.83%, 96.23%, 12.26%, 1.89%, 0.94%, 65.09%, 39.62% and 9.43%, respectively. A total of 58.82% of these strains contained more than 6 pathogenicity-related genes. MLST typed 58 ST types from the 108 isolated C. jejuni strains, including 24 new types, and ST-21 was the major type, accounting for 39.3% of the total strains. PMID:26565657

  18. Impact of gastrointestinal parasitic nematodes of sheep, and the role of advanced molecular tools for exploring epidemiology and drug resistance - an Australian perspective

    PubMed Central

    2013-01-01

    Parasitic nematodes (roundworms) of small ruminants and other livestock have major economic impacts worldwide. Despite the impact of the diseases caused by these nematodes and the discovery of new therapeutic agents (anthelmintics), there has been relatively limited progress in the development of practical molecular tools to study the epidemiology of these nematodes. Specific diagnosis underpins parasite control, and the detection and monitoring of anthelmintic resistance in livestock parasites, presently a major concern around the world. The purpose of the present article is to provide a concise account of the biology and knowledge of the epidemiology of the gastrointestinal nematodes (order Strongylida), from an Australian perspective, and to emphasize the importance of utilizing advanced molecular tools for the specific diagnosis of nematode infections for refined investigations of parasite epidemiology and drug resistance detection in combination with conventional methods. It also gives a perspective on the possibility of harnessing genetic, genomic and bioinformatic technologies to better understand parasites and control parasitic diseases. PMID:23711194

  19. Epidemiological Study of Greek University Students' Mental Health

    ERIC Educational Resources Information Center

    Kounenou, Kalliope; Koutra, Aikaterini; Katsiadrami, Aristea; Diacogiannis, Georgios

    2011-01-01

    In the present study, 805 Greek students participated by filling in self-report questionnaires studying depression (Center for Epidemiological Studies Depression Scale), general health status (General Health Questionnaire), general psychopathology (Symptom Checklist-90-R), and personal demographic features. Some of the more prevalent findings…

  20. Anthrax in the Gambia: an epidemiological study

    PubMed Central

    Heyworth, B; Ropp, M E; Voos, U G; Meinel, H I; Darlow, H M

    1975-01-01

    Epidemiological data on 448 cases of human cutaneous anthrax from the Gambia showed that this particular strain of anthrax bacillus causes widespread morbidity and some mortality with, at the same time, subclinical infection. Analysis also showed that anthrax is not an occupationally related disease in the Gambia. The possibility of human-to-human spread, affecting all age groups and both sexes, by means of a communal toilet article was also shown. The fact that the strain is a good toxin producer but contains a weak antigen may have accounted for the repeated clinical infection and the fact that antibody titres were generally transient. Subclinical infection in animals was also found, particularly in sheep and goats, and also, with an unusually low mortality, in cows. Insect vectors were not excluded, but were unlikely. Vultures may spread the disease from village to village. Some possible public health and immunization procedures are discussed, with a view to containing this difficult problem in this part of west Africa. PMID:810213

  1. A review of the global prevalence, molecular epidemiology and economics of cystic echinococcosis in production animals.

    PubMed

    Cardona, Guillermo A; Carmena, David

    2013-02-18

    Cystic echinococcosis (CE) is an important and widespread zoonotic infection caused by the larval stages of taeniid cestodes of the genus Echinococcus. The disease represents a serious animal health concern in many rural areas of the world, causing important economic losses derived from decreased productivity and viscera condemnation in livestock species. In this review we aim to provide a comprehensive overview on recent research progress in the epidemiology of CE in production animals from a global perspective. Particular attention has been paid to the discussion of the extent and significance of recent molecular epidemiologic data. The financial burden associated to CE on the livestock industry has also been addressed. Data presented are expected to improve our current understanding of the parasite's geographical distribution, transmission, host range, immunogenicity, pathogenesis, and genotype frequencies. This information should be also valuable for the design and implementation of more efficient control strategies against CE. PMID:23084536

  2. Epidemiological studies are like cherries, one draws another.

    PubMed

    Lunet, Nuno

    2009-01-01

    The proverb "Words are like cherries", meaning that when you start talking subjects pop up and you end up with long conversations, just like cherries coming out of the plate in chains when you pick one, may also be applied to epidemiological research. A sequence of epidemiological studies, each being drawn from the previous, is presented as an example of how each investigation may raise new questions to be addressed in following studies. This description stresses the need for appropriate planning and the usefulness of pilot testing to depict inadequacies that can hardly be anticipated without field work. I intend to illustrate how epidemiological research can provide a deep approach to research questions, as long as findings are properly interpreted and suboptimal methodological options are taken into account in future investigations. PMID:19713008

  3. CRITICAL REVIEW OF EPIDEMIOLOGIC STUDIES RELATED TO INGESTED ASBESTOS

    EPA Science Inventory

    Thirteen epidemiologic studies of ingested asbestos conducted in five areas of the U.S. and Canada were reviewed and evaluated for the definitiveness and applicability regarding the development of ambient water quality standards. One or more studies found male or female associati...

  4. CHLORINE DIOXIDE WATER DISINFECTION: A PROSPECTIVE EPIDEMIOLOGY STUDY

    EPA Science Inventory

    An epidemiologic study of 198 persons exposed for 3 months to drinking water disinfected with chlorine dioxide was conducted in a rural village. A control population of 118 nonexposed persons was also studied. Pre-exposure hematologic and serum chemical parameters were compared w...

  5. IMPROVING EXPOSURE ASSESSMENT IN DISINFECTION BYPRODUCTS (DBP) EPIDEMIOLOGIC STUDIES

    EPA Science Inventory

    In 1997, an EPA expert panel was convened to evaluate epidemiologic studies of adverse reproductive or developmental outcomes that may be associated with drinking water DBPs. The panel recommended that further efforts be made in an existing cohort study, headed by Dr. Waller and ...

  6. Taxonomy, phylogeny and molecular epidemiology of Echinococcus multilocularis: From fundamental knowledge to health ecology.

    PubMed

    Knapp, Jenny; Gottstein, Bruno; Saarma, Urmas; Millon, Laurence

    2015-10-30

    Alveolar echinococcosis, caused by the tapeworm Echinococcus multilocularis, is one of the most severe parasitic diseases in humans and represents one of the 17 neglected diseases prioritised by the World Health Organisation (WHO) in 2012. Considering the major medical and veterinary importance of this parasite, the phylogeny of the genus Echinococcus is of considerable importance; yet, despite numerous efforts with both mitochondrial and nuclear data, it has remained unresolved. The genus is clearly complex, and this is one of the reasons for the incomplete understanding of its taxonomy. Although taxonomic studies have recognised E. multilocularis as a separate entity from the Echinococcus granulosus complex and other members of the genus, it would be premature to draw firm conclusions about the taxonomy of the genus before the phylogeny of the whole genus is fully resolved. The recent sequencing of E. multilocularis and E. granulosus genomes opens new possibilities for performing in-depth phylogenetic analyses. In addition, whole genome data provide the possibility of inferring phylogenies based on a large number of functional genes, i.e. genes that trace the evolutionary history of adaptation in E. multilocularis and other members of the genus. Moreover, genomic data open new avenues for studying the molecular epidemiology of E. multilocularis: genotyping studies with larger panels of genetic markers allow the genetic diversity and spatial dynamics of parasites to be evaluated with greater precision. There is an urgent need for international coordination of genotyping of E. multilocularis isolates from animals and human patients. This could be fundamental for a better understanding of the transmission of alveolar echinococcosis and for designing efficient healthcare strategies. PMID:26260408

  7. Molecular Epidemiological Characterization and Health Burden of Thalassemias in the Chaoshan Region, People's Republic of China.

    PubMed

    Zheng, Xiangbin; Lin, Min; Yang, Hui; Pan, Mei-Chen; Cai, Ying-Mu; Wu, Jiao-Ren; Lin, Fen; Zhan, Xiao-Fen; Luo, Zhao-Yun; Yang, Hui-Tian; Yang, Li-Ye

    2016-01-01

    Thalassemia is one of the most prevalent inherited disease in southern China. However, there have been only a few epidemiological studies of thalassemia in the Chaoshan region of Guangdong Province, People's Republic of China (PRC). A total of 6231 unrelated subjects in two main geographical cities of the Chaoshan region was analyzed for thalassemia. Seven hundred and thirty-six cases of suspected thalassemia carriers with microcytosis [mean corpuscular volume (MCV) <82.0 fL] were found by complete blood cell (CBC) count, and were tested by reverse dot-blot gene chip to reveal a total of 331 mutant chromosomes, including 278 α-thalassemia (α-thal) alleles and 53 β-thalassemia (β-thal) alleles. The most common α-thal mutations were the Southeast Asian (- -(SEA)), followed by the -α(3.7) (rightward) and -α(4.2) (leftward) deletions. The two most common β-thal mutations were HBB: c.316-197C>T and HBB: c.126_129delCTTT, accounting for 69.81% of the β-thal defects in the studied individuals. In addition, a rare mutation, Cap +1 (A>C) (HBB: c.-50A>C) was described for the first time in the Chaoshan region. Our results gave a heterozygote frequency of 5.31% for common α- and β-thal in the Chaoshan region, and also indicated a higher prevalence of thalassemia with a heterozygote frequency of 6.29% in Chaozhou, followed by Shantou (3.37%). This study provided a detailed prevalence and molecular characterization of thalassemia in the Chaoshan region, and will be valuable for developing a strategy for prevention of thalassemia and reducing excessive health care costs in this area. PMID:26865073

  8. Epidemiology, molecular virology and diagnostics of Schmallenberg virus, an emerging orthobunyavirus in Europe

    PubMed Central

    2013-01-01

    After the unexpected emergence of Bluetongue virus serotype 8 (BTV-8) in northern Europe in 2006, another arbovirus, Schmallenberg virus (SBV), emerged in Europe in 2011 causing a new economically important disease in ruminants. The virus, belonging to the Orthobunyavirus genus in the Bunyaviridae family, was first detected in Germany, in The Netherlands and in Belgium in 2011 and soon after in the United Kingdom, France, Italy, Luxembourg, Spain, Denmark and Switzerland. This review describes the current knowledge on the emergence, epidemiology, clinical signs, molecular virology and diagnosis of SBV infection. PMID:23675914

  9. Diagnosis of bovine-associated parapoxvirus infections in humans: molecular and epidemiological evidence.

    PubMed

    MacNeil, A; Lederman, E; Reynolds, M G; Ragade, N J; Talken, R; Friedman, D; Hall, W; Shwe, T; Li, Y; Zhao, H; Smith, S; Davidson, W; Hughes, C; Damon, I K

    2010-12-01

    Orf virus, pseudocowpox virus and bovine papular stomatitis virus, are parapoxviruses, associated with domestic ruminants, which are capable of causing cutaneous infections in humans. Owing to virtually identical appearances in humans, clinical differentiation of these viruses is difficult. We discuss three recent occurrences of parapoxvirus infection, involving contact with domestic bovine and use a combination of molecular and epidemiological data in the diagnosis. These cases underscore the utility of modern diagnostic tools, along with species-specific contact information in acquiring a definitive diagnosis, in the case of suspected parapoxvirus infection. PMID:20163577

  10. Standards for epidemiologic studies and surveillance of epilepsy.

    PubMed

    Thurman, David J; Beghi, Ettore; Begley, Charles E; Berg, Anne T; Buchhalter, Jeffrey R; Ding, Ding; Hesdorffer, Dale C; Hauser, W Allen; Kazis, Lewis; Kobau, Rosemarie; Kroner, Barbara; Labiner, David; Liow, Kore; Logroscino, Giancarlo; Medina, Marco T; Newton, Charles R; Parko, Karen; Paschal, Angelia; Preux, Pierre-Marie; Sander, Josemir W; Selassie, Anbesaw; Theodore, William; Tomson, Torbjörn; Wiebe, Samuel

    2011-09-01

    Worldwide, about 65 million people are estimated to have epilepsy. Epidemiologic studies are necessary to define the full public health burden of epilepsy; to set public health and health care priorities; to provide information needed for prevention, early detection, and treatment; to identify education and service needs; and to promote effective health care and support programs for people with epilepsy. However, different definitions and epidemiologic methods complicate the tasks of these studies and their interpretations and comparisons. The purpose of this document is to promote consistency in definitions and methods in an effort to enhance future population-based epidemiologic studies, facilitate comparison between populations, and encourage the collection of data useful for the promotion of public health. We discuss: (1) conceptual and operational definitions of epilepsy, (2) data resources and recommended data elements, and (3) methods and analyses appropriate for epidemiologic studies or the surveillance of epilepsy. Variations in these are considered, taking into account differing resource availability and needs among countries and differing purposes among studies. PMID:21899536

  11. Molecular epidemiologic research on the effects of environmental pollutants on the fetus.

    PubMed Central

    Perera, F P; Jedrychowski, W; Rauh, V; Whyatt, R M

    1999-01-01

    Evidence shows that fetuses and infants are more affected than adults by a variety of environmental toxicants because of differential exposure, physiologic immaturity, and a longer lifetime over which disease initiated in early life can develop. In this article we review data on the effects of in utero exposure to common environmental contaminants, including polycyclic aromatic hydrocarbons (PAH), particulate matter and environmental tobacco smoke (ETS). We then summarize results from our molecular epidemiologic study to assess risks from in utero exposures to ambient air pollution and ETS. This research study, conducted in Poland, used biomarkers to measure the internal and bioeffective dose of toxicants and individual susceptibility factors. The study included 160 mothers and 160 newborns. Ambient air pollution was significantly associated (p= 0.05) with the amount of PAH bound to DNA (PAH-DNA adducts) in both maternal and infant cord white blood cells (WBC). Newborns with elevated PAH-DNA adducts (greater than the median) had significantly decreased birth weight (p= 0.05), birth length (p= 0.02), and head circumference (p= 0.0005) compared to the newborns with lower adducts (n= 135). Maternal and infant cotinine levels were increased by active and passive cigarette smoke exposure of the mother (p= 0.01). An inverse correlation was seen between newborn plasma cotinine (nanograms per milliliter) and birth weight (p= 0.0001) and length (p= 0.003). Adducts were elevated in placental tissue and WBC of newborns who were heterozygous or homozygous for the cytochrome P4501A1 MspI restriction fragment length polymorphism (RFLP) compared to newborns without the RFLP. Levels of PAH-DNA and cotinine were higher in newborns than mothers. These results document that there is significant transplacental transfer of PAH and ETS constituents from mother to fetus; that PAH-DNA adduct levels in maternal and newborn WBC were increased with environmental exposure to PAH from ambient

  12. Epidemiology, clinical manifestations, and molecular typing of salmonella typhi isolated from patients with typhoid fever in Lebanon.

    PubMed

    Kanj, Souha S; Kanafani, Zeina A; Shehab, Marwa; Sidani, Nisreen; Baban, Tania; Baltajian, Kedak; Dakdouki, Ghenwa K; Zaatari, Mohamad; Araj, George F; Wakim, Rima Hanna; Dbaibo, Ghassan; Matar, Ghassan M

    2015-06-01

    The objective of this study was to examine the epidemiology and the clinical manifestations of typhoid fever as well as the susceptibility and strain relatedness of Salmonella typhi isolates in Lebanon from 2006 to 2007. A total of 120 patients with typhoid fever were initially identified from various areas of the country based on positive culture results for S. typhi from blood, urine, stools, bone marrow and/or positive serology. Clinical, microbiological and molecular analysis was performed on cases with complete data available. These results indicated that drinking water was an unlikely mode of transmission of the infection. Despite increasing reports of antimicrobial resistance among S. typhi isolates, the vast majority of these isolates were susceptible to various antibiotic agents, including ampicillin, cephalosporins, quinolones, and trimethoprim/sulfamethoxazole. Molecular analysis of the isolates revealed a predominance of one single genotype with no variation in distribution across the geographical regions. PMID:25922325

  13. Genetic subdivisions within Trypanosoma cruzi (Discrete Typing Units) and their relevance for molecular epidemiology and experimental evolution

    PubMed Central

    Tibayrenc, Michel

    2003-01-01

    Background This paper summarizes the main results obtained on Trypanosoma cruzi genetic diversity and population structure since this parasite became the theme of many genetic and molecular studies in the early seventies. Results T. cruzi exibits a paradigmatic pattern of long-term, clonal evolution, which has structured its natural populations into several discrete genetic subdivisions or "Discrete Typing Units" (DTU). Rare hybridization events are nevertheless detectable in natural populations and have been recently obtained in the laboratory. Conclusions The DTUs and natural clones of T. cruzi constitute relevant units for molecular epidemiology and experimental evolution. Experimental mating opens the way to an in-depth knowledge of this parasite's formal genetics. PMID:14613498

  14. 40 CFR 159.170 - Human epidemiological and exposure studies.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Human epidemiological and exposure studies. 159.170 Section 159.170 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... that a correlation may exist between exposure to a pesticide and observed adverse effects in...

  15. 40 CFR 159.170 - Human epidemiological and exposure studies.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Human epidemiological and exposure studies. 159.170 Section 159.170 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... that a correlation may exist between exposure to a pesticide and observed adverse effects in...

  16. Burkholderia cepacia complex in Serbian patients with cystic fibrosis: prevalence and molecular epidemiology.

    PubMed

    Vasiljevic, Z V; Novovic, K; Kojic, M; Minic, P; Sovtic, A; Djukic, S; Jovcic, B

    2016-08-01

    The Burkholderia cepacia complex (Bcc) organisms remain significant pathogens in patients with cystic fibrosis (CF). This study was performed to evaluate the prevalence, epidemiological characteristics, and presence of molecular markers associated with virulence and transmissibility of the Bcc strains in the National CF Centre in Belgrade, Serbia. The Bcc isolates collected during the four-year study period (2010-2013) were further examined by 16 s rRNA gene, pulsed-field gel electrophoresis of genomic DNA, multilocus sequence typing analysis, and phylogenetic analysis based on concatenated sequence of seven alleles. Fifty out of 184 patients (27.2 %) were colonized with two Bcc species, B. cenocepacia (n = 49) and B. stabilis (n = 1). Thirty-four patients (18.5 %) had chronic colonization. Typing methods revealed a high level of similarity among Bcc isolates, indicating a person-to-person transmission or acquisition from a common source. New sequence types (STs) were identified, and none of the STs with an international distribution were found. One centre-specific ST, B. cenocepacia ST856, was highly dominant and shared by 48/50 (96 %) patients colonized by Bcc. This clone was characterized by PCR positivity for both the B. cepacia epidemic strain marker and cable pilin, and showed close genetic relatedness to the epidemic strain CZ1 (ST32). These results indicate that the impact of Bcc on airway colonization in the Serbian CF population is high and virtually exclusively limited to a single clone of B. cenocepacia. The presence of a highly transmissible clone and probable patient-to-patient spread was observed. PMID:27177755

  17. Molecular epidemiology and genetic diversity of hepatitis B virus in Ethiopia.

    PubMed

    Hundie, Gadissa Bedada; Raj, V Stalin; Michael, Daniel Gebre; Pas, Suzan D; Osterhaus, Albert D M E; Koopmans, Marion P; Smits, Saskia L; Haagmans, Bart L

    2016-06-01

    Although hepatitis B virus (HBV) infection is hyperendemic in Ethiopia and constitutes a major public health problem, little is known about its genetic diversity, genotypes, and circulation. The aim of this study was to determine the molecular epidemiology and genetic diversity of HBV in Ethiopia, using 391 serum samples collected from HBsAg-positive blood donors living in five different geographic regions. The HBV S/pol gene was amplified, sequenced, and HBV genotypes, subgenotypes, serotypes, and major hydrophilic region (MHR) variants were determined. Phylogenetic analysis of 371 samples (95%) revealed the distribution of genotypes A (78%) and D (22%) in Ethiopia. Further phylogenetic analysis identified one subgenotype (A1) within genotype A, and 4 subgenotypes within genotype D (D1; 1.3%, D2; 55%, D4; 2.5%, and D6; 8.8%). Importantly, 24 isolates (30%) of genotype D formed a novel phylogenetic cluster, distinct from any known D subgenotypes, and two A/D recombinants. Analysis of predicted amino-acid sequences within the HBsAg revealed four serotypes: adw2 (79%), ayw1 (3.1%), ayw2 (7.8%), and ayw3 (11.6%). Subsequent examination of sequences showed that 51 HBV isolates (14%) had mutations in the MHR and 8 isolates (2.2%) in the reverse transcriptase known to confer antiviral resistance. This study provides the first description of HBV genetic diversity in Ethiopia with a predominance of subgenotypes A1 and D2, and also identified HBV isolates that could represent a novel subgenotype. Furthermore, a significant prevalence of HBsAg variants in Ethiopian population is revealed. J. Med. Virol. 88:1035-1043, 2016. © 2015 Wiley Periodicals, Inc. PMID:26629781

  18. 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. PMID:25558753

  19. Molecular epidemiology of simian immunodeficiency virus SIVsm in U.S. primate centers unravels the origin of SIVmac and SIVstm.

    PubMed

    Apetrei, Cristian; Kaur, Amitinder; Lerche, Nicholas W; Metzger, Michael; Pandrea, Ivona; Hardcastle, Johnny; Falkenstein, Shelley; Bohm, Rudolf; Koehler, Jeffrey; Traina-Dorge, Vicki; Williams, Tessa; Staprans, Silvija; Plauche, Gail; Veazey, Ronald S; McClure, Harold; Lackner, Andrew A; Gormus, Bobby; Robertson, David L; Marx, Preston A

    2005-07-01

    Retrospective molecular epidemiology was performed on samples from four sooty mangabey (SM) colonies in the United States to characterize simian immunodeficiency virus SIVsm diversity in SMs and to trace virus circulation among different primate centers (PCs) over the past 30 years. The following SIVsm sequences were collected from different monkeys: 55 SIVsm isolates from the Tulane PC sampled between 1984 and 2004, 10 SIVsm isolates from the Yerkes PC sampled in 2002, 7 SIVsm isolates from the New Iberia PC sampled between 1979 and 1986, and 8 SIVsm isolates from the California PC sampled between 1975 and 1977. PCR and sequencing were done to characterize the gag, pol, and env gp36 genes. Phylogenetic analyses were correlated with the epidemiological data. Our analysis identified nine different divergent phylogenetic lineages that cocirculated in these four SM colonies in the Unites States in the past 30 years. Lineages 1 to 5 have been identified previously. Two of the newly identified SIVsm lineages found in SMs are ancestral to SIVmac251/SIVmac239/SIVmne and SIVstm. We further identified the origin of these two macaque viruses in SMs from the California National Primate Research Center. The diversity of SIVsm isolates in PCs in the United States mirrors that of human immunodeficiency virus type 1 (HIV-1) group M subtypes and offers a model for the molecular epidemiology of HIV and a new approach to vaccine testing. The cocirculation of divergent SIVsm strains in PCs resulted in founder effects, superinfections, and recombinations. This large array of SIVsm strains showing the same magnitude of diversity as HIV-1 group M subtypes should be extremely useful for modeling the efficacy of vaccination strategies under the real-world conditions of HIV-1 diversity. The genetic variability of SIVsm strains among PCs may influence the diagnosis and monitoring of SIVsm infection and, consequently, may bias the results of pathogenesis studies. PMID:15994793

  20. A nationwide epidemiological study of testicular torsion in Korea.

    PubMed

    Lee, Sol Min; Huh, Jung-Sik; Baek, Minki; Yoo, Koo Han; Min, Gyeong Eun; Lee, Hyung-Lae; Lee, Dong-Gi

    2014-12-01

    Testicular torsion is a surgical emergency in the field of urology. Knowledge of the epidemiology and pathophysiology is significant to an urologist. However, the epidemiology of testicular torsion in Korea has not been studied. We performed a nationwide epidemiological study to improve knowledge of the epidemiology of testicular torsion. From 2006-2011, the Korean Urologic Association began the patient registry service. The annual number of patients with testicular torsion from 2006 to 2011 were 225, 250, 271, 277, 345, and 210, respectively. The overall incidence of testicular torsion in males was 1.1 per 100,000; However, the incidence in men less than 25 yr old was 2.9 per 100,000. Adolescents showed the highest incidence. Total testicular salvage rate was 75.7% in this survey. There was no geographic difference of testicular salvage rate. Minimizing the possibility of orchiectomy for testicular torsion is important to improve public awareness to expedite presentation and provider education to improve diagnosis and surgery. PMID:25469070

  1. Molecular Epidemiology of Oral Treponemes in Patients with Periodontitis and in Periodontitis-Resistant Subjects

    PubMed Central

    Moter, Annette; Riep, Birgit; Haban, Vesna; Heuner, Klaus; Siebert, Gerda; Berning, Moritz; Wyss, Chris; Ehmke, Benjamin; Flemmig, Thomas F.; Göbel, Ulf B.

    2006-01-01

    The etiologic role of oral treponemes in human periodontitis is still under debate. Although seen by dark-field microscopy in large numbers, their possible role is still unclear since they comprise some 60 different phylotypes, most of which are still uncultured. To determine their status as mere commensals or opportunistic pathogens, molecular epidemiological studies are required that include both cultured and as-yet-uncultured organisms. Here we present such data, comparing treponemal populations from chronic periodontitis (CP) or generalized aggressive periodontitis (GAP) patients. As a periodontitis-resistant (PR) control group, we included elderly volunteers with more than 20 natural teeth and no history of periodontal treatment and no or minimal clinical signs of periodontitis. Almost every treponemal phylotype was present in all three groups. For most treponemes, the proportion of subjects positive for a certain species or phylotype was higher in both periodontitis groups than in the PR group. This difference was pronounced for treponemes of the phylogenetic groups II and IV and for Treponema socranskii and Treponema lecithinolyticum. Between the periodontitis groups the only significant differences were seen for T. socranskii and T. lecithinolyticum, which were found more often in periodontal pockets of GAP patients than of CP patients. In contrast, no difference was found for Treponema denticola. Our findings, however, strengthen the hypothesis of treponemes being opportunistic pathogens. It appears that T. socranskii, T. lecithinolyticum and group II and IV treponemes may represent good indicators for periodontitis and suggest the value of the respective probes for microbiological diagnosis in periodontitis subjects. PMID:16954230

  2. Community-associated Staphylococcus aureus pneumonia among Greek children: epidemiology, molecular characteristics, treatment, and outcome.

    PubMed

    Doudoulakakis, A G; Bouras, D; Drougka, E; Kazantzi, M; Michos, A; Charisiadou, A; Spiliopoulou, I; Lebessi, E; Tsolia, M

    2016-07-01

    Staphylococcus aureus is an infrequent cause of community-associated (CA-SA) pneumonia in children. The aim of this study was to evaluate the clinical, epidemiological, microbiological, and molecular characteristics of CA-SA pneumonia among children hospitalized in two large tertiary care referral centers during an 8-year period. Cases of CA-SA pneumonia admitted between 2007 and 2014 were retrospectively examined through medical record review. Molecular investigation was performed for available strains; mecA, Panton-Valentine leukocidin (PVL) (lukS-lukF-PV), and fibronectin binding protein A (fnbA) genes were detected by polymerase chain reaction (PCR). Clones were assigned by agr groups, pulsed-field gel electrophoresis (PFGE), SCCmec, and multilocus sequencing typing (MLST). In total, 41 cases were recorded (boys, 61 %), with a median age of 4.3 months (range, 1-175). Methicillin-resistant S. aureus (MRSA) accounted for 31 cases (75.6 %). Complications included empyema (25/41, 61 %), pneumatoceles (7/41, 17 %), and lung abscess (1/41, 2.5 %). Intensive care unit (ICU) admission was required in 58.5 %. Two deaths occurred (4.9 %). Definitive therapy was based on vancomycin with or without other antibiotics (55.9 %), followed by clindamycin and linezolid (26.5 % each). All isolates were susceptible to vancomycin (MIC90 2 mg/L, range 1-2), teicoplanin, and linezolid, whereas 26.8 % were resistant to clindamycin. Among the 25 studied strains, 20 were mecA-positive (MRSA), carrying also the fnbA gene. Of these, 90 % belonged to the ST80-IV/agr3/PVL-positive clone. Methicillin-susceptible S. aureus (MSSA) strains showed polyclonality, 3/5 were PVL-positive, and 3/5 were fnbA-positive. MRSA and particularly the ST80-IV clone predominated among staphylococcal pneumonia cases in children. Treatment provided was effective in all but two patients, despite the relatively high minimum inhibitory concentration (MIC) of vancomycin and a high resistance to

  3. Sero-Molecular Epidemiology of Japanese Encephalitis in Zhejiang, an Eastern Province of China

    PubMed Central

    Yan, Ju-ying; Zhou, Jia-yue; Tang, Xue-wen; He, Han-qing; Xie, Rong-hui; Mao, Hai-yan; Zhang, Yan-jun; Xie, Shu-yun

    2016-01-01

    Background Sporadic Japanese encephalitis (JE) cases still have been reported in Zhejiang Province in recent years, and concerns about vaccine cross-protection and population-level immunity have been raised off and on within the public health sphere. Genotype I (GI) has replaced GIII as the dominant genotype in Asian countries during the past few decades, which caused considerable concerns about the potential change of epidemiology characteristics and the vaccine effectiveness. The aim of this study was to investigate the prevalence of JE neutralizing antibody and its waning antibody trend after live attenuated JE vaccine immunization. Additionally, this study analyzed the molecular characteristics of the E gene of Zhejiang Japanese encephalitis virus (JEV) strains, and established genetic relationships with other JEV strains. Methodology/Principal Findings A total of 570 serum specimens were sampled from community population aged from 0 to 92 years old in Xianju county of Zhejiang Province in 2013–2014. Microseroneutralization test results were analyzed to estimate the population immunity and to observe antibody dynamics in vaccinated children. E genes of 28 JEV strains isolated in Zhejiang Province were sequenced for phylogenetic tree construction and molecular characteristics analysis with other selected strains. Positive JE neutralizing antibody rates were higher in residents ≥35 years old (81%~98%) and lower in residents <35 years old (0~57%). 7 or 8 years after the 2nd live attenuated vaccine dose, the antibodies against for 4 different strains with microseroneutralization test were decreased by 55%~73% on seropositive rates and by 25%~38% on GMTs respectively. JEV strains isolated in recent years were all grouped into GI, while those isolated in the 1980s belonged to GIII. On important amino acid sites related to antigenicity, there was no divergence between the Zhejiang JE virus strains and the vaccine strain (SA14-14-2). Conclusion/Significances JE

  4. Molecular epidemiology of Acinetobacter baumannii in central intensive care unit in Kosova Teaching Hospital.

    PubMed

    Raka, Lul; Kalenć, Smilja; Bosnjak, Zrinka; Budimir, Ana; Katić, Stjepan; Sijak, Dubravko; Mulliqi-Osmani, Gjyle; Zoutman, Dick; Jaka, Arbëresha

    2009-12-01

    Infections caused by bacteria of genus Acinetobacter pose a significant health care challenge worldwide. Information on molecular epidemiological investigation of outbreaks caused by Acinetobacter species in Kosova is lacking. The present investigation was carried out to enlight molecular epidemiology of Acinetobacter baumannii in the Central Intensive Care Unit (CICU) of a University hospital in Kosova using pulse field gel electrophoresis (PFGE). During March - July 2006, A. baumannii was isolated from 30 patients, of whom 22 were infected and 8 were colonised. Twenty patients had ventilator-associated pneumonia, one patient had meningitis, and two had coinfection with bloodstream infection and surgical site infection. The most common diagnoses upon admission to the ICU were politrauma and cerebral hemorrhage. Bacterial isolates were most frequently recovered from endotracheal aspirate (86.7%). First isolation occurred, on average, on day 8 following admission (range 1-26 days). Genotype analysis of A. baumannii isolates identified nine distinct PFGE patterns, with predominance of PFGE clone E represented by isolates from 9 patients. Eight strains were resistant to carbapenems. The genetic relatedness of Acinetobacter baumannii was high, indicating cross-transmission within the ICU setting. These results emphasize the need for measures to prevent nosocomial transmission of A. baumannii in ICU. PMID:20464330

  5. [Diagnosis and molecular epidemiology of viral gastroenteritis in the past, present and future].

    PubMed

    Ushijima, Hiroshi

    2009-06-01

    Outline, history of research, diagnosis and molecular epidemiology of viral gastroenteritis were described. Rotavirus, adenovirus, norovirus, sapovirus, astrovirus, human parechovirus, Aichivirus, and human bocavirus are the major target viruses which cause acute gastroenteritis. The viruses were differentiated into genogroup, genotypes and subgenotypes/clusters/lineages. The changing of their genetic backgrounds was well recognized in different areas and years. Some reassortments or recombinations were observed not only between humans and humans but also between humans and animals. Viral gastroenteritis diseases were transmitted by food-borne and humans to humans contact. The environmental factors were also impacted on the infections. Recently, situation of the diseases in the natural ecosystem is becoming clearly. Diagnoses by immunological methods and gene technology are available for the known viruses. Further development of diagnosis and discovery of new viruses will be expected. Therefore, the research on molecular epidemiology is needed to be conducted continuously and then new findings will appear. We need to precede the research by using new techniques and we need to cope with the demand of society especially during acute gastroenteritis outbreak seasons. PMID:19927992

  6. International Biological Engagement Programs Facilitate Newcastle Disease Epidemiological Studies.

    PubMed

    Miller, Patti J; Dimitrov, Kiril M; Williams-Coplin, Dawn; Peterson, Melanie P; Pantin-Jackwood, Mary J; Swayne, David E; Suarez, David L; Afonso, Claudio L

    2015-01-01

    Infections of poultry species with virulent strains of Newcastle disease virus (NDV) cause Newcastle disease (ND), one of the most economically significant and devastating diseases for poultry producers worldwide. Biological engagement programs between the Southeast Poultry Research Laboratory (SEPRL) of the United States Department of Agriculture and laboratories from Russia, Pakistan, Ukraine, Kazakhstan, and Indonesia collectively have produced a better understanding of the genetic diversity and evolution of the viruses responsible for ND, which is crucial for the control of the disease. The data from Kazakhstan, Russia, and Ukraine identified possible migratory routes for birds that may carry both virulent NDV (vNDV) and NDV of low virulence into Europe. In addition, related NDV strains were isolated from wild birds in Ukraine and Nigeria, and from birds in continental USA, Alaska, Russia, and Japan, identifying wild birds as a possible mechanism of intercontinental spread of NDV of low virulence. More recently, the detection of new sub-genotypes of vNDV suggests that a new, fifth, panzootic of ND has already originated in Southeast Asia, extended to the Middle East, and is now entering into Eastern Europe. Despite expected challenges when multiple independent laboratories interact, many scientists from the collaborating countries have successfully been trained by SEPRL on molecular diagnostics, best laboratory practices, and critical biosecurity protocols, providing our partners the capacity to further train other employes and to identify locally the viruses that cause this OIE listed disease. These and other collaborations with partners in Mexico, Bulgaria, Israel, and Tanzania have allowed SEPRL scientists to engage in field studies, to elucidate more aspects of ND epidemiology in endemic countries, and to understand the challenges that the scientists and field veterinarians in these countries face on a daily basis. Finally, new viral characterization tools

  7. International Biological Engagement Programs Facilitate Newcastle Disease Epidemiological Studies

    PubMed Central

    Miller, Patti J.; Dimitrov, Kiril M.; Williams-Coplin, Dawn; Peterson, Melanie P.; Pantin-Jackwood, Mary J.; Swayne, David E.; Suarez, David L.; Afonso, Claudio L.

    2015-01-01

    Infections of poultry species with virulent strains of Newcastle disease virus (NDV) cause Newcastle disease (ND), one of the most economically significant and devastating diseases for poultry producers worldwide. Biological engagement programs between the Southeast Poultry Research Laboratory (SEPRL) of the United States Department of Agriculture and laboratories from Russia, Pakistan, Ukraine, Kazakhstan, and Indonesia collectively have produced a better understanding of the genetic diversity and evolution of the viruses responsible for ND, which is crucial for the control of the disease. The data from Kazakhstan, Russia, and Ukraine identified possible migratory routes for birds that may carry both virulent NDV (vNDV) and NDV of low virulence into Europe. In addition, related NDV strains were isolated from wild birds in Ukraine and Nigeria, and from birds in continental USA, Alaska, Russia, and Japan, identifying wild birds as a possible mechanism of intercontinental spread of NDV of low virulence. More recently, the detection of new sub-genotypes of vNDV suggests that a new, fifth, panzootic of ND has already originated in Southeast Asia, extended to the Middle East, and is now entering into Eastern Europe. Despite expected challenges when multiple independent laboratories interact, many scientists from the collaborating countries have successfully been trained by SEPRL on molecular diagnostics, best laboratory practices, and critical biosecurity protocols, providing our partners the capacity to further train other employes and to identify locally the viruses that cause this OIE listed disease. These and other collaborations with partners in Mexico, Bulgaria, Israel, and Tanzania have allowed SEPRL scientists to engage in field studies, to elucidate more aspects of ND epidemiology in endemic countries, and to understand the challenges that the scientists and field veterinarians in these countries face on a daily basis. Finally, new viral characterization tools

  8. [Ecological studies in environmental health: Beyond epidemiology].

    PubMed

    Blanco-Becerra, Luis C; Pinzón-Flórez, Carlos E; Idrovo, Álvaro J

    2015-08-01

    Ecological studies provide important and frequent sources of evidence of environmental health, since their unit of analysis is populations. This review summarizes the foundations of ecological studies with the premise that they can be performed using quantitative, qualitative or mixed methods. It presents the logic behind their design, their role in exploring causality, the variables and categories of analysis and the design principles and techniques used to collect data. Examples of ecological studies performed in Latin America are then presented, as well as some common methodological problems and options to address them. Lastly, the relevance of quantitative and qualitative ecological studies to environmental health as a way to overcome the dominance of conceptual and methodological individualism is highlighted, though ecological studies alone do not suffice for studying population health. PMID:26535754

  9. The Molecular Epidemiological Characteristics and Genetic Diversity of Salmonella Typhimurium in Guangdong, China, 2007–2011

    PubMed Central

    Huang, Yanhui; He, Dongmei; Li, Xiaocui; Liang, Zhaoming; Ke, Changwen

    2014-01-01

    Background Salmonella enterica serovar Typhimurium is the most important serovar associated with human salmonellosis worldwide. Here we aimed to explore the molecular epidemiology and genetic characteristics of this serovar in Guangdong, China. Methodology We evaluated the molecular epidemiology and genetic characteristics of 294 endemic Salmonella Typhimurium clinical isolates which were collected from 1977 to 2011 in Guangdong, China, and compared them with a global set of isolates of this serovar using epidemiological data and Multilocus Sequence Typing (MLST) analysis. Principal Finding The 294 isolates were assigned to 13 Sequencing types (STs) by MLST, of which ST34 and ST19 were the most common in Guangdong. All the STs were further assigned to two eBurst Groups, eBG1 and eBG138. The eBG1 was the major group endemic in Guangdong. Nucleotide and amino acid variability were comparable for all seven MLST loci. Tajima’s D test suggested positive selection in hisD and thrA genes (p<0.01), but positive selection was rejected for the five other genes (p>0.05). In addition, The Tajima’s D test within each eBG using the global set of isolates showed positive selection in eBG1 and eBG138 (p<0.05), but was rejected in eBG243 (p>0.05). We also analyzed the phylogenetic structure of Salmonella Typhimurium from worldwide sources and found that certain STs are geographically restricted. ACSSuT was the predominant multidrug resistance pattern for this serovar. The resistant profiles ACSSuTTmNaG, ACSSuTTmNa and ACSuTTmNaG seem to be specific for ST34, and ASSuTNa for ST19. Conclusion Here we presented a genotypic characterization of Salmonella Typhimurium isolates using MLST and found two major STs are endemic in Guangdong. Our analyses indicate that genetic selection may have shaped the Salmonella Typhimurium populations. However, further evaluation with additional isolates from various sources will be essential to reveal the scope of the epidemiological characteristics

  10. Molecular epidemiology of bovine tuberculosis in wild animals in Spain: a first approach to risk factor analysis.

    PubMed

    Parra, A; Larrasa, J; García, A; Alonso, J M; de Mendoza, J Hermoso

    2005-10-31

    In human tuberculosis (Mycobacterium tuberculosis), molecular epidemiology has accurately indicated the risk factors involved in active transmission of the disease, by comparing individuals whose isolates belong to a cluster with patients whose strains are considered unique. Nevertheless, this application has not been used in bovine tuberculosis (Mycobacterium bovis). Our study describes the integration of epidemiological data into molecular classification data on M. bovis isolates. These were isolated from wild ungulates in Extremadura (western Spain) with the objective of detecting the risk factors linked to the association of strains in clades, which are indicators of the active spread of the disease. The molecular markers used were spoligotyping + VNTR typing (loci: VNTR 2165, VNTR 2461, VNTR 0577, VNTR 0580, VNTR 3192 VNTR 2163a and VNTR 2163b) on a population of 59 M. bovis strains isolated from deer (Cervus elaphus), 112 from wild boar (Sus scrofa), six from bovines, 28 from pigs and 2 from goats (n=207). Epidemiological variables included the animal species from which the strain was isolated, pathological condition of the host (incipient lesion, early and late generalisation), date of sampling (during or after the reproductive period) and hunting season. Bivariant analysis was used to establish the risk factors connected to the association of strains and later, the variables were evaluated by means of logistic regression. Molecular typing grouped a total of 131 strains (64.21%) in 28 clusters and 76 isolates shows unique profiles. The association of strains was connected to the appearance of macroscopic lesions during the reproductive period (O.R. 4.80; 95% CI 1.09-22.99, P<0.005), showing a possible higher transmission during the courting period. This happened mainly during the last hunting season analysed (2002-2003, O.R. 3.69; 95% CI 1.27-11.9, P<0.05), clashing with the time of higher prevalence of the disease in wild ungulates. Active spread was not

  11. Smile line and occlusion: An epidemiological study

    PubMed Central

    Harati, Mahsa; Mostofi, Shahbaz Naser; Jalalian, Ezzatollah; Rezvani, Gholamreza

    2013-01-01

    Background: The purpose of the present study was to discuss some new concepts of the desirable characteristics of smile tooth display. Due to the increasing application of cosmetic dental treatments, there is an increasing need for better understanding of the esthetic principles. Materials and Methods: In the present descriptive study, with 212 participants, included were patients with no history of orthodontic treatment, loss or prosthetic replacement of anterior teeth, extracted teeth, lips with asymmetry or a history of trauma. Chi-square test was used to determine possible significances in the relation of smile line to Angle occlusion class, overbite and overjet and arch form. A P level of <0.05 was set as to be significant. Results: Chi-square test indicated that there was a significant difference between the smile design and overbite, overjet and gender but no statistically significant association was found between the smile design and crossbite, molar Angle classification and arch form. Conclusion: Within the limitations of such studies, it might be concluded that there is a significant and important relation between some occlusal parameters and smile design, which must be considered. PMID:24379858

  12. Myasthenia gravis on the Dutch antilles: an epidemiological study.

    PubMed

    Holtsema, H; Mourik, J; Rico, R E; Falconi, J R; Kuks, J B; Oosterhuis, H J

    2000-12-01

    We carried out an epidemiological study on the prevalence and annual incidence of myasthenia gravis on tropical islands Curaçao and Aruba in the period 1980-1995. Twenty-one patients (seven men and 14 women) were identified. The point prevalence increased from 29 per million in 1980 to about 70 per million in 1990-1995; the annual incidence over the total period was 4.7 per million. The female:male ratio was 2:1; purely ocular cases (2/21) comprised 9.5% and thymomas (4/21), 19%. These data are in accordance with most other epidemiological studies in non-tropical areas. No other studies on myasthenia gravis in tropical areas have been reported. PMID:11154803

  13. Epidemiologic studies of Cyclospora cayetanensis in Guatemala.

    PubMed

    Bern, C; Hernandez, B; Lopez, M B; Arrowood, M J; de Mejia, M A; de Merida, A M; Hightower, A W; Venczel, L; Herwaldt, B L; Klein, R E

    1999-01-01

    In 1996 and 1997, cyclosporiasis outbreaks in North America were linked to eating Guatemalan raspberries. We conducted a study in health-care facilities and among raspberry farm workers, as well as a case-control study, to assess risk factors for the disease in Guatemala. From April 6, 1997, to March 19, 1998, 126 (2.3%) of 5, 552 surveillance specimens tested positive for Cyclospora; prevalence peaked in June (6.7%). Infection was most common among children 1.5 to 9 years old and among persons with gastroenteritis. Among 182 raspberry farm workers and family members monitored from April 6 to May 29, six had Cyclospora infection. In the case-control analysis, 62 (91%) of 68 persons with Cyclospora infection reported drinking untreated water in the 2 weeks before illness, compared with 88 (73%) of 120 controls (odds ratio [OR] 3.8, 95% confidence interval [CI] 1.4, 10.8 by univariate analysis). Other risk factors included water source, type of sewage drainage, ownership of chickens or other fowl, and contact with soil (among children younger than 2 years). PMID:10603209

  14. EPIDEMIOLOGICAL STUDY OF CHILDREN DIAPHYSEAL FEMORAL FRACTURES

    PubMed Central

    Hoffmann, Cassiano Ricardo; Traldi, Eduardo Franceschini; Posser, Alexandre

    2015-01-01

    Objective: To evaluate the personal, fracture, treatment and complication characteristics among patients with pediatric femoral shaft fractures attended at the pediatric orthopedic service of the Joana de Gusmão Children's Hospital. Methods: This was a retrospective cross-sectional study on a population consisting of patients with femoral shaft fractures, aged between birth and 14 years and 11 months, who were divided into four age groups. Information was obtained from medical records and was transferred to a survey questionnaire to present personal, fracture, treatment and complication variables. Results: The study population consisted of 96 patients. Their mean age was 6.8 years. The cases were predominantly among males, comprising closed fractures on the right side, in the middle third with a single line. Regarding fracture etiology, traffic accidents predominated overall in the sample. Most of the patients (74 to 77.1%) presented femoral fractures as their only injury. Conservative treatment predominated in the group younger than six years of age, and surgical treatment in the group aged 6 to 14 years and 11 months. The complications observed until bone union were: discrepancy, infection and movement limitation. The mean time taken for consolidation was 9.6 ± 2.4 weeks, varying with age. Conclusion: The features of these fractures were similar to those described in the literature and the treatment used showed good results. The Joana de Gusmão Children's Hospital has used the treatment proposed in the literature for pediatric femoral shaft fractures. PMID:27042619

  15. Trachoma in the Sudan. An epidemiological study.

    PubMed Central

    Salim, A R; Sheikh, H A

    1975-01-01

    The prevalence and distribution of trachoma in the Sudan has been studied. The morbidity rate of 83.2 per 1000 in the Northern Province decreases southwards until it reaches 0.94 in the extreme south (Equatoria Province). 2. In endemic areas infection starts very early--in the first year of life. 3. There is a marked difference between the prevalence of trachoma in towns and villages--71.3 per cent for the age group 1-4 years in villages, and 56.7 per cent for the same age group in the towns. This is probably due to better standards of living and hygiene in the towns. 4. Some relationship has been found between the rainfall, the relative humidity, and the incidence of trachoma, but this does not necessarily apply in other countries. 5. The factors that may explain the high prevalence of trachoma in the northern Sudan are: a. Mechanical trauma caused by frequent sandstorms. b. Irritation of the eyes by dust particles, leading to excessive watering and discharge, and rubbing with the fingers. c. The habit of frequent hand-shaking. d. Poor personal hygiene in pre-schoolchildren. e. Associated bacterial conjunctivitis. f. The presence of eye-seeking flies. PMID:1191619

  16. Molecular epidemiology of echoviruses 11 and 30 in Russia: different properties of genotypes within an enterovirus serotype.

    PubMed

    Yarmolskaya, Maria S; Shumilina, Elena Yu; Ivanova, Olga E; Drexler, Jan Felix; Lukashev, Alexander N

    2015-03-01

    Over 100 known enterovirus serotypes differ in their epidemiological and pathogenic properties. Much less is known about variation of these features on a sub-serotype level, such as genotypes. Echovirus 11 (E11) and E30 are amongst the most frequent causative agents of aseptic meningitis. We studied the molecular epidemiology of these pathogens to evaluate potential epidemiological and pathogenic dissimilarities of their genotypes. The complete VP1 genome region was sequenced for 97 E11 and 62 E30 isolates collected in Russia from 2008 to 2012, and they were studied in comparison with all 140 E11 and 432 E30 sequences available in GenBank. A geographic pattern of genotype prevalence was observed for both types. Russian E11 isolates belonged mainly to A genotype, which is common in Asia, and D5, which is predominant in Europe. For E30, genotype III by classification of Ke et al. (2011), also termed genotype a by Bailly et al. (2009), was endemic in Russia from 2003 to 2012, while it was not detected in Europe and North America during this time. The E30 genotypes VI-B, VI-G, and VI-H (e, f and h) were regularly introduced from different countries, became predominant and vanished after no more than 4years. In addition to geographic patterns, E11 genotypes also differed by isolation source. Genotype A2 viruses were significantly more often found in sewage, compared to genotype D5 that was isolated from both sewage and human samples. In addition, there was evidence of a different capacity for international transfers among E11 GtA subclusters. PMID:25562123

  17. GESDB: a platform of simulation resources for genetic epidemiology studies.

    PubMed

    Yao, Po-Ju; Chung, Ren-Hua

    2016-01-01

    Computer simulations are routinely conducted to evaluate new statistical methods, to compare the properties among different methods, and to mimic the observed data in genetic epidemiology studies. Conducting simulation studies can become a complicated task as several challenges can occur, such as the selection of an appropriate simulation tool and the specification of parameters in the simulation model. Although abundant simulated data have been generated for human genetic research, currently there is no public database designed specifically as a repository for these simulated data. With the lack of such a database, for similar studies, similar simulations may have been repeated, which resulted in redundant work. Thus, we created an online platform, the Genetic Epidemiology Simulation Database (GESDB), for simulation data sharing and discussion of simulation techniques for genetic epidemiology studies. GESDB consists of a database for storing simulation scripts, simulated data and documentation from published articles as well as a discussion forum, which provides a platform for discussion of the simulated data and exchanging simulation ideas. Moreover, summary statistics such as the simulation tools that are most commonly used and datasets that are most frequently downloaded are provided. The statistics will be informative for researchers to choose an appropriate simulation tool or select a common dataset for method comparisons. GESDB can be accessed at http://gesdb.nhri.org.twDatabase URL: http://gesdb.nhri.org.tw. PMID:27242038

  18. GESDB: a platform of simulation resources for genetic epidemiology studies

    PubMed Central

    Yao, Po-Ju; Chung, Ren-Hua

    2016-01-01

    Computer simulations are routinely conducted to evaluate new statistical methods, to compare the properties among different methods, and to mimic the observed data in genetic epidemiology studies. Conducting simulation studies can become a complicated task as several challenges can occur, such as the selection of an appropriate simulation tool and the specification of parameters in the simulation model. Although abundant simulated data have been generated for human genetic research, currently there is no public database designed specifically as a repository for these simulated data. With the lack of such a database, for similar studies, similar simulations may have been repeated, which resulted in redundant work. Thus, we created an online platform, the Genetic Epidemiology Simulation Database (GESDB), for simulation data sharing and discussion of simulation techniques for genetic epidemiology studies. GESDB consists of a database for storing simulation scripts, simulated data and documentation from published articles as well as a discussion forum, which provides a platform for discussion of the simulated data and exchanging simulation ideas. Moreover, summary statistics such as the simulation tools that are most commonly used and datasets that are most frequently downloaded are provided. The statistics will be informative for researchers to choose an appropriate simulation tool or select a common dataset for method comparisons. GESDB can be accessed at http://gesdb.nhri.org.tw. Database URL: http://gesdb.nhri.org.tw PMID:27242038

  19. Sequence Analysis of lip R: A Good Method for Molecular Epidemiology of Clinical Isolates of Mycobacterium tuberculosis.

    PubMed

    Saedi, Samaneh; Youssefi, Masoud; Safdari, Hadi; Soleimanpour, Saman; Marouzi, Parviz; Ghazvini, Kiarash

    2015-10-01

    Advances in DNA sequencing have greatly enhanced the molecular epidemiology studies. In order to assess evolutionary and phylogenetic relation of Mycobacterium tuberculosis isolates several gene targets were evaluated. In this study, appropriate fragments of 5 highly variable genes (rpsL, mprA, lipR, katG, and fgd1 genes) were sequenced. The sequence data were analyzed with neighbor-joining method using mega and Geneious software. The phylogenetic trees analyzes revealed that the discriminatory power of lipR is much stronger than that observed in the other genes. lipR could distinguish between more clinical isolates. Therefore, lipR is a promising target for sequence analyzes of M. tuberculosis. PMID:26063445

  20. Evaluation and comparison of molecular techniques for epidemiological typing of Salmonella enterica subsp. enterica serovar dublin.

    PubMed Central

    Liebisch, B; Schwarz, S

    1996-01-01

    A total of 28 unrelated isolates of the Salmonella enterica subsp. enterica serovar dublin (S. dublin) collected during a 6-year period, as well as four samples of the S. dublin live vaccine strain Bovisaloral and its prototype strain S. dublin 442/039, were investigated by different molecular typing methods for the following reasons: (i) to find the most discriminatory method for the epidemiological typing of isolates belonging to this Salmonella serovar and (ii) to evaluate these methods for their capacity to discriminate among the live vaccine strain Bovisaloral, its prototype strain S. dublin 442/039, and field isolates of the serovar dublin. Five different plasmid profiles were observed; a virulence plasmid of 76 kbp as identified by hybridization with an spvB-spvC gene probe was present in all isolates. The detection of 16S rRNA genes and that of IS200 elements proved to be unsuitable for the epidemiological typing of S. dublin; only one hybridization pattern could be observed with each of these methods. The results obtained from macrorestriction analysis strongly depended on the choice of restriction enzyme. While the enzyme NotI yielded the lowest discriminatory index among all enzymes tested, it was the only enzyme that allowed discrimination between the Bovisaloral vaccine strain and its prototype strain. In contrast to the enzymes XbaI and SpeI, which only differentiated among the S. dublin field isolates, XhoI as well as AvrII also produced restriction fragment patterns of the Bovisaloral strain and of its prototype strain that were not shared by any of the S. dublin field isolates. Macrorestriction analysis proved to be the most discriminatory method not only for the epidemiological typing of S. dublin field isolates but also for the identification of the S. dublin live vaccine strain Bovisaloral. PMID:8904430

  1. Assessing the first wave of epidemiological studies of nanomaterial workers

    PubMed Central

    Tsai, Candace S. J.; Pelclova, Daniela; Schubauer-Berigan, Mary K.; Schulte, Paul A.

    2015-01-01

    The results of early animal studies of engineered nanomaterials (ENMs) and air pollution epidemiology suggest that it is important to assess the health of ENM workers. Initial epidemiological studies of workers’ exposure to ENMs (<100 nm) are reviewed and characterized for their study designs, findings, and limitations. Of the 15 studies, 11 were cross-sectional, 4 were longitudinal (1 was both cross-sectional and longitudinal in design), and 1 was a descriptive pilot study. Generally, the studies used biologic markers as the dependent variables. All 11 cross-sectional studies showed a positive relationship between various biomarkers and ENM exposures. Three of the four longitudinal studies showed a negative relationship; the fourth showed positive findings after a 1-year follow-up. Each study considered exposure to ENMs as the independent variable. Exposure was assessed by mass concentration in 10 studies and by particle count in six studies. Six of them assessed both mass and particle concentrations. Some of the studies had limited exposure data because of inadequate exposure assessment. Generally, exposure levels were not very high in comparison to those in human inhalation chamber studies, but there were some exceptions. Most studies involved a small sample size, from 2 to 258 exposed workers. These studies represent the first wave of epidemiological studies of ENM workers. They are limited by small numbers of participants, inconsistent (and in some cases inadequate) exposure assessments, generally low exposures, and short intervals between exposure and effect. Still, these studies are a foundation for future work; they provide insight into where ENM workers are experiencing potentially adverse effects that might be related to ENM exposures. PMID:26635494

  2. Molecular Epidemiology of Enterovirus 71 Infection in the Central Region of Taiwan from 2002 to 2012

    PubMed Central

    Lin, Yu-Ting; Huang, Szu-Wei; Liu, Hsin-Fu; Wang, John; Chen, Yi-Ming Arthur

    2013-01-01

    Enterovirus 71 (EV71), a causative agent of hand, foot, and mouth disease can be classified into three genotypes and many subtypes. The objectives of this study were to conduct a molecular epidemiological study of EV71 in the central region of Taiwan from 2002–2012 and to test the hypothesis that whether the alternative appearance of different EV71 subtypes in Taiwan is due to transmission from neighboring countries or from re-emergence of pre-existing local strains. We selected 174 EV71 isolates and used reverse transcription-polymerase chain reaction to amplify their VP1 region for DNA sequencing. Phylogenetic analyses were conducted using Neighbor-Joining, Maximum Likelihood and Bayesian methods. We found that the major subtypes of EV71 in Taiwan were B4 for 2002 epidemic, C4 for 2004–2005 epidemic, B5 for 2008–2009 epidemic, C4 for 2010 epidemic and B5 for 2011–2012 epidemic. Phylogenetic analysis demonstrated that the 2002 and 2008 epidemics were associated with EV71 from Malaysia and Singapore; while both 2010 and 2011–2012 epidemics originated from different regions of mainland China including Shanghai, Henan, Xiamen and Gong-Dong. Furthermore, minor strains have been identified in each epidemic and some of them were correlated with the subsequent outbreaks. Therefore, the EV71 infection in Taiwan may originate from pre-existing minor strains or from other regions in Asia including mainland China. In addition, 101 EV71 isolates were selected for the detection of new recombinant strains using the nucleotide sequences spanning the VP1-2A-2B region. No new recombinant strain was found. Analysis of clinical manifestations showed that patients infected with C4 had significantly higher rates of pharyngeal vesicles or ulcers than patients infected with B5. This is the first study demonstrating that different EV 71 genotypes may have different clinical manifestations and the association of EV71 infections between Taiwan and mainland China. PMID:24391812

  3. Molecular epidemiology of rabies from Maranhão and surrounding states in the northeastern region of Brazil.

    PubMed

    Sato, G; Kobayashi, Y; Shoji, Y; Sato, T; Itou, T; Ito, F H; Santos, H P; Brito, C J C; Sakai, T

    2006-11-01

    Although many outbreaks of rabies have been reported in northern Brazil, few epidemiological studies of these outbreaks have been undertaken. In this study, molecular epidemiological analyses were performed using 41 rabies virus samples isolated in the Maranhão (MA), Pará (PA), and Tocantins (TO) states of northeastern Brazil. A 599-bp region of the glycoprotein (G) gene was first amplified from each sample by RT-PCR, then sequenced and subjected to phylogenetic analysis. A phylogenetic tree divided the 41 isolates into two clades: Clade I was associated with terrestrial carnivores and Clade II was associated with vampire bats. The Clade I isolates were further sub-divided into two groups. The first group was closer to carnivore isolates that predominate in central Brazil, whereas the second group more closely resembled wild fox isolates from the northeastern coastal state of Paraíba (PB). MA isolates of Clade II formed an entirely separate group. These results demonstrate that bat- and dog-transmitted rabies occur in northwestern Brazil. PMID:16773238

  4. Size distribution of airborne particles controls outcome of epidemiological studies.

    PubMed

    Harrison, Roy M; Giorio, Chiara; Beddows, David C S; Dall'Osto, Manuel

    2010-12-15

    Epidemiological studies typically using wide size range mass metrics (e.g. PM(10)) have demonstrated associations between airborne particulate matter and several adverse health outcomes. This approach ignores the fact that mass concentration may not correlate with regional lung dose, unlike the case of trace gases. When using measured particle size distributions as the basis for calculating regional lung dose, PM(10) mass concentration is found to be a good predictor of the mass dose in all regions of the lung, but is far less predictive of the surface area and particle number dose. On the other hand, measurements of particle number do not well predict mass dose, indicating that the chosen particle metric is likely to determine the health outcomes detectable by an epidemiological study. Consequently, epidemiological studies using mass metrics (PM(2.5) and PM(10)) may fail to recognise important health consequences of particulate matter exposure, leading to an underestimate of the public health consequences of particle exposure. PMID:21109288

  5. Identification and Molecular Epidemiology of Campylobacter coli Isolates from Human Gastroenteritis, Food, and Animal Sources by Amplified Fragment Length Polymorphism Analysis and Penner Serotyping

    PubMed Central

    Siemer, B. L.; Nielsen, E. M.; On, S. L. W.

    2005-01-01

    Campylobacter coli is an infrequently studied but important food-borne pathogen with a wide natural distribution. We investigated its molecular epidemiology by use of amplified fragment length polymorphism (AFLP)-based genotyping and Penner serotyping. Serotype reference strains and 177 Danish isolates of diverse origin identified by routine phenotyping as C. coli were examined. Molecular tools identified some 12% of field isolates as Campylobacter jejuni, emphasizing the need for improved identification methods in routine laboratories. Cluster analysis of AFLP profiles of 174 confirmed C. coli isolates revealed a difference in the distribution of isolates from pig and poultry (chicken, duck, turkey, and ostrich) species and indicated the various poultry species, but not pigs, to be likely sources of human C. coli infection. A poor correlation was observed between serotyping and AFLP profiling, suggesting that the former method has limited value in epidemiological studies of this species. PMID:15812025

  6. Molecular Epidemiology and Clinical Manifestations of Adenovirus Respiratory Infections in Taiwanese Children

    PubMed Central

    Wang, Ya-Fang; Shen, Fan-Ching; Wang, Shan-Li; Kuo, Pin-Hwa; Tsai, Huey-Pin; Liu, Ching-Chuan; Wang, Jen-Ren; Chi, Chia-Yu

    2016-01-01

    Abstract Human adenoviruses (HAdVs) are important causes of respiratory infections in children. They usually cause mild upper respiratory symptoms, but they can also produce severe pneumonia and other complications. The aims of this retrospective study were to better define the molecular epidemiology of respiratory adenoviruses circulating in Taiwanese children during 2002 and 2013, detect reinfections and co-infections, and characterize the clinical features and laboratory findings according to the causative genotypes. We collected a representative sample of 182 isolates of adenoviruses from 175 children during the 12-year study period. The most prevalent species was HAdV-B genotype 3 (HAdV-3) (92/182, 50.5%) followed by HAdV-C (HAdV-2) (38/182, 20.9%). A single outbreak of HAdV-E (6/182, 3.3%) was noted in 2007. The mean age of children with adenovirus infections was 3.7 ± 2.0 years, with a slight predominance of males (53.1%). Children with HAdV-B tended to be older, had more lower respiratory tract infections, gastrointestinal symptoms, and a higher rate of hospitalization than those with HAdV-C (P < 0.05). Adenovirus co-infections were noted in 25/175 (14.3%) of the children. The most frequent co-infections were with species B (HAdV-3) and C (HAdV-2) (14/25, 56.0%). Additional infections were noted in 23/175 (13.1%) of the children. Of these repeated infections, the initial isolates were always genotypes of HAdV-C. The second isolates were genotypes of HAdV-B or HAdV-E. The clinical features of the first HAdV-B infection and the reinfection of HAdV-B followed the HAdV-C were similar. In conclusion, HAdV-B, C, and E were the only adenovirus species that were isolated from children who were sufficiently ill with respiratory infections to require a visit to the hospital. Human adenovirus B (HAdV-3) accounted for half of these species. HAdV-B was more likely than other species to produce severe disease. The high incidence of adenovirus co-infection and

  7. Improving estimates of exposures for epidemiologic studies of plutonium workers.

    PubMed

    Ruttenber, A J; Schonbeck, M; McCrea, J; McClure, D; Martyny, J

    2001-01-01

    Epidemiologic studies of nuclear facilities usually focus on relations between cancer and doses from external penetrating radiation, and describe these exposures with little detail on measurement error and missing data. We demonstrate ways to document complex exposures to nuclear workers with data on external and internal exposures to ionizing radiation and toxic chemicals. We describe methods for assessing internal exposures to plutonium and external doses from neutrons; the use of a job exposure matrix for estimating chemical exposures; and methods for imputing missing data for exposures and doses. For plutonium workers at Rocky Flats, errors in estimating neutron doses resulted in underestimating the total external dose for production workers by about 16%. Estimates of systemic deposition do not correlate well with estimates of organ doses. Only a small percentage of workers had exposures to toxic chemicals, making epidemiologic assessments of risk difficult. PMID:11319050

  8. Multicollinearity in Regression Analyses Conducted in Epidemiologic Studies

    PubMed Central

    Vatcheva, Kristina P.; Lee, MinJae; McCormick, Joseph B.; Rahbar, Mohammad H.

    2016-01-01

    The adverse impact of ignoring multicollinearity on findings and data interpretation in regression analysis is very well documented in the statistical literature. The failure to identify and report multicollinearity could result in misleading interpretations of the results. A review of epidemiological literature in PubMed from January 2004 to December 2013, illustrated the need for a greater attention to identifying and minimizing the effect of multicollinearity in analysis of data from epidemiologic studies. We used simulated datasets and real life data from the Cameron County Hispanic Cohort to demonstrate the adverse effects of multicollinearity in the regression analysis and encourage researchers to consider the diagnostic for multicollinearity as one of the steps in regression analysis. PMID:27274911

  9. TIME-INTEGRATED EXPOSURE MEASURES TO IMPROVE THE PREDICTIVE POWER OF EXPOSURE CLASSIFICATION FOR EPIDEMIOLOGIC STUDIES

    EPA Science Inventory

    Accurate exposure classification tools are required to link exposure with health effects in epidemiological studies. Although long-term integrated exposure measurements are a critical component of exposure assessment, the ability to include these measurements into epidemiologic...

  10. Epidemiological-molecular evidence of metabolic reprogramming on proliferation, autophagy and cell signaling in pancreas cancer.

    PubMed

    Søreide, Kjetil; Sund, Malin

    2015-01-28

    Pancreatic cancer remains one of the deadliest human cancers with little progress made in survival over the past decades, and 5-year survival usually below 5%. Despite this dismal scenario, progresses have been made in understanding of the underlying tumor biology through among other definition of precursor lesions, delineation of molecular pathways, and advances in genome-wide technology. Further, exploring the relationship between epidemiological risk factors involving metabolic features to that of an altered cancer metabolism may provide the foundation for new therapies. Here we explore how nutrients and caloric intake may influence the KRAS-driven ductal carcinogenesis through mediators of metabolic stress, including autophagy in presence of TP53, advanced glycation end products (AGE) and the receptors (RAGE) and ligands (HMGB1), as well as glutamine pathways, among others. Effective understanding the cancer metabolism mechanisms in pancreatic cancer may propose new ways of prevention and treatment. PMID:24704294

  11. Molecular epidemiology identifies HIV transmission networks associated with younger age and heterosexual exposure among Korean individuals.

    PubMed

    Chin, Bum Sik; Chaillon, Antoine; Mehta, Sanjay R; Wertheim, Joel O; Kim, Gayeon; Shin, Hyoung-Shik; Smith, Davey M

    2016-10-01

    To evaluate if HIV transmission networks could be elucidated from data collected in a short time frame, 131 HIV-1 pol sequences were analyzed which were generated from treatment-naïve Korean individuals who were sequentially identified over 1 year. A transmission linkage was inferred when there was a genetic distance <1.5% and a total of 16 clusters, involving 39/131 (29.8%), were identified. Younger age and heterosexual exposure were independently related with clustering in the inferred network, which demonstrated that molecular epidemiology with currently generated data (i.e., drug resistance genotypes) can be used to identify local transmission networks, even over a short timeframe. J. Med. Virol. 88:1832-1835, 2016. © 2016 Wiley Periodicals, Inc. PMID:26990771

  12. 10 CFR 602.5 - Epidemiology and Other Health Studies Financial Assistance Program.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Epidemiology and Other Health Studies Financial Assistance Program. 602.5 Section 602.5 Energy DEPARTMENT OF ENERGY (CONTINUED) ASSISTANCE REGULATIONS EPIDEMIOLOGY AND OTHER HEALTH STUDIES FINANCIAL ASSISTANCE PROGRAM § 602.5 Epidemiology and Other Health...

  13. 10 CFR 602.5 - Epidemiology and Other Health Studies Financial Assistance Program.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 4 2013-01-01 2013-01-01 false Epidemiology and Other Health Studies Financial Assistance Program. 602.5 Section 602.5 Energy DEPARTMENT OF ENERGY (CONTINUED) ASSISTANCE REGULATIONS EPIDEMIOLOGY AND OTHER HEALTH STUDIES FINANCIAL ASSISTANCE PROGRAM § 602.5 Epidemiology and Other Health...

  14. 10 CFR 602.5 - Epidemiology and Other Health Studies Financial Assistance Program.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 4 2014-01-01 2014-01-01 false Epidemiology and Other Health Studies Financial Assistance Program. 602.5 Section 602.5 Energy DEPARTMENT OF ENERGY (CONTINUED) ASSISTANCE REGULATIONS EPIDEMIOLOGY AND OTHER HEALTH STUDIES FINANCIAL ASSISTANCE PROGRAM § 602.5 Epidemiology and Other Health...

  15. 10 CFR 602.5 - Epidemiology and Other Health Studies Financial Assistance Program.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 4 2011-01-01 2011-01-01 false Epidemiology and Other Health Studies Financial Assistance Program. 602.5 Section 602.5 Energy DEPARTMENT OF ENERGY (CONTINUED) ASSISTANCE REGULATIONS EPIDEMIOLOGY AND OTHER HEALTH STUDIES FINANCIAL ASSISTANCE PROGRAM § 602.5 Epidemiology and Other Health...

  16. 10 CFR 602.5 - Epidemiology and Other Health Studies Financial Assistance Program.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 4 2012-01-01 2012-01-01 false Epidemiology and Other Health Studies Financial Assistance Program. 602.5 Section 602.5 Energy DEPARTMENT OF ENERGY (CONTINUED) ASSISTANCE REGULATIONS EPIDEMIOLOGY AND OTHER HEALTH STUDIES FINANCIAL ASSISTANCE PROGRAM § 602.5 Epidemiology and Other Health...

  17. Molecular epidemiology of apparent outbreak of invasive aspergillosis in a hematology ward.

    PubMed Central

    Leenders, A; van Belkum, A; Janssen, S; de Marie, S; Kluytmans, J; Wielenga, J; Löwenberg, B; Verbrugh, H

    1996-01-01

    During a 2-month period, five patients suffering from invasive infections caused by Aspergillus flavus or Aspergillus fumigatus were identified in the Hematology Department of the University Hospital Dijkzigt (Rotterdam, The Netherlands). To study the epidemiological aspects of invasive aspergillosis, strains from these patients and from the hospital environment, isolated during extensive microbiological screening, were subjected to genotyping. A novel DNA extraction technique, involving freezing, grinding, and direct lysis in guanidium isothiocyanate-containing buffers of mycelial material, was applied. DNA isolation was followed by typing by random amplification of polymorphic DNA (RAPD) analysis. This showed that strains isolated from all patients infected with the same fungal species were genotypically distinct, thus providing evidence against the possibility of an ongoing, single-source nosocomial outbreak. Strains could also be differentiated from strains of geographically diverse origins. However, an A. flavus strain from one of the patients was also frequently encountered in the hospital environment. As all environmental strains were collected after this patient had been diagnosed with invasive disease, the epidemiological value of this observation could not be ascertained. Intensive investigations showed no single source of A. flavus or other aspergilli. RAPD genotyping proved that the outbreak of invasive aspergillosis in the hematology ward consisted of a series of unrelated events and was not due to a common source within the hospital. RAPD fingerprinting of aspergilli may greatly facilitate future investigations of the epidemiology of invasive disease caused by these pathogens. PMID:8789013

  18. Genetic and Molecular Epidemiological Characterization of a Novel Adenovirus in Antarctic Penguins Collected between 2008 and 2013.

    PubMed

    Lee, Sook-Young; Kim, Jeong-Hoon; Seo, Tae-Kun; No, Jin Sun; Kim, Hankyeom; Kim, Won-Keun; Choi, Han-Gu; Kang, Sung-Ho; Song, Jin-Won

    2016-01-01

    Antarctica is considered a relatively uncontaminated region with regard to the infectious diseases because of its extreme environment, and isolated geography. For the genetic characterization and molecular epidemiology of the newly found penguin adenovirus in Antarctica, entire genome sequencing and annual survey of penguin adenovirus were conducted. The entire genome sequences of penguin adenoviruses were completed for two Chinstrap penguins (Pygoscelis antarctica) and two Gentoo penguins (Pygoscelis papua). The whole genome lengths and G+C content of penguin adenoviruses were found to be 24,630-24,662 bp and 35.5-35.6%, respectively. Notably, the presence of putative sialidase gene was not identified in penguin adenoviruses by Rapid Amplification of cDNA Ends (RACE-PCR) as well as consensus specific PCR. The penguin adenoviruses were demonstrated to be a new species within the genus Siadenovirus, with a distance of 29.9-39.3% (amino acid, 32.1-47.9%) in DNA polymerase gene, and showed the closest relationship with turkey adenovirus 3 (TAdV-3) in phylogenetic analysis. During the 2008-2013 study period, the penguin adenoviruses were annually detected in 22 of 78 penguins (28.2%), and the molecular epidemiological study of the penguin adenovirus indicates a predominant infection in Chinstrap penguin population (12/30, 40%). Interestingly, the genome of penguin adenovirus could be detected in several internal samples, except the lymph node and brain. In conclusion, an analysis of the entire adenoviral genomes from Antarctic penguins was conducted, and the penguin adenoviruses, containing unique genetic character, were identified as a new species within the genus Siadenovirus. Moreover, it was annually detected in Antarctic penguins, suggesting its circulation within the penguin population. PMID:27309961

  19. Genetic and Molecular Epidemiological Characterization of a Novel Adenovirus in Antarctic Penguins Collected between 2008 and 2013

    PubMed Central

    Lee, Sook-Young; Kim, Jeong-Hoon; Seo, Tae-Kun; No, Jin Sun; Kim, Hankyeom; Kim, Won-keun; Choi, Han-Gu; Kang, Sung-Ho; Song, Jin-Won

    2016-01-01

    Antarctica is considered a relatively uncontaminated region with regard to the infectious diseases because of its extreme environment, and isolated geography. For the genetic characterization and molecular epidemiology of the newly found penguin adenovirus in Antarctica, entire genome sequencing and annual survey of penguin adenovirus were conducted. The entire genome sequences of penguin adenoviruses were completed for two Chinstrap penguins (Pygoscelis antarctica) and two Gentoo penguins (Pygoscelis papua). The whole genome lengths and G+C content of penguin adenoviruses were found to be 24,630–24,662 bp and 35.5–35.6%, respectively. Notably, the presence of putative sialidase gene was not identified in penguin adenoviruses by Rapid Amplification of cDNA Ends (RACE-PCR) as well as consensus specific PCR. The penguin adenoviruses were demonstrated to be a new species within the genus Siadenovirus, with a distance of 29.9–39.3% (amino acid, 32.1–47.9%) in DNA polymerase gene, and showed the closest relationship with turkey adenovirus 3 (TAdV-3) in phylogenetic analysis. During the 2008–2013 study period, the penguin adenoviruses were annually detected in 22 of 78 penguins (28.2%), and the molecular epidemiological study of the penguin adenovirus indicates a predominant infection in Chinstrap penguin population (12/30, 40%). Interestingly, the genome of penguin adenovirus could be detected in several internal samples, except the lymph node and brain. In conclusion, an analysis of the entire adenoviral genomes from Antarctic penguins was conducted, and the penguin adenoviruses, containing unique genetic character, were identified as a new species within the genus Siadenovirus. Moreover, it was annually detected in Antarctic penguins, suggesting its circulation within the penguin population. PMID:27309961

  20. Intragenomic Variation in the Internal Transcribed Spacer 1 Region of Dientamoeba fragilis as a Molecular Epidemiological Marker▿

    PubMed Central

    Bart, Aldert; van der Heijden, Harold M.; Greve, Sophie; Speijer, Dave; Landman, Wil J.; van Gool, Tom

    2008-01-01

    Dientamoeba fragilis is a parasite that has been recognized to be a causative agent of gastrointestinal symptoms. Because in most studies only some infected persons experience symptoms, it is possible that D. fragilis is a heterogeneous species with variants that display similar morphologies but different pathogenicities. The search for genetic variation in D. fragilis was based on the small-subunit rRNA gene, which was not found to be useful for molecular epidemiology. In this report, we describe the isolation and characterization of additional rRNA gene cluster sequences, the internal transcribed spacer 1 (ITS-1)-5.8S rRNA gene-ITS-2 region. For comparative purposes, we also isolated the ITS-1-5.8S rRNA gene-ITS-2 region of Histomonas meleagridis, a protozoan parasite of birds and a close relative of D. fragilis. This region was found to be highly variable, and 11 different alleles of the ITS-1 sequence could be identified. Variation in the ITS-1 region was found to be intragenomic, with up to four different alleles in a single isolate. So-called C profiles were produced from the ITS-1 repertoire of single isolates,. Analysis of the C profiles of isolates from nonrelated patients identified several clearly distinguishable strains of D. fragilis. Within families, it was shown that members can be infected with the same or different strains of D. fragilis. In conclusion, the ITS-1 region can serve as a molecular epidemiological tool for the subtyping of D. fragilis directly from feces. This may serve as a means of studying the transmission, geographical distribution, and relationships between strains and the pathogenicity of this parasite. PMID:18650356

  1. epiPATH: an information system for the storage and management of molecular epidemiology data from infectious pathogens

    PubMed Central

    Amadoz, Alicia; González-Candelas, Fernando

    2007-01-01

    Background Most research scientists working in the fields of molecular epidemiology, population and evolutionary genetics are confronted with the management of large volumes of data. Moreover, the data used in studies of infectious diseases are complex and usually derive from different institutions such as hospitals or laboratories. Since no public database scheme incorporating clinical and epidemiological information about patients and molecular information about pathogens is currently available, we have developed an information system, composed by a main database and a web-based interface, which integrates both types of data and satisfies requirements of good organization, simple accessibility, data security and multi-user support. Results From the moment a patient arrives to a hospital or health centre until the processing and analysis of molecular sequences obtained from infectious pathogens in the laboratory, lots of information is collected from different sources. We have divided the most relevant data into 12 conceptual modules around which we have organized the database schema. Our schema is very complete and it covers many aspects of sample sources, samples, laboratory processes, molecular sequences, phylogenetics results, clinical tests and results, clinical information, treatments, pathogens, transmissions, outbreaks and bibliographic information. Communication between end-users and the selected Relational Database Management System (RDMS) is carried out by default through a command-line window or through a user-friendly, web-based interface which provides access and management tools for the data. Conclusion epiPATH is an information system for managing clinical and molecular information from infectious diseases. It facilitates daily work related to infectious pathogens and sequences obtained from them. This software is intended for local installation in order to safeguard private data and provides advanced SQL-users the flexibility to adapt it to their

  2. METHODS STUDIES FOR THE NATIONAL CHILDREN'S STUDY: MOLECULARLY IMPRINTED POLYMERS

    EPA Science Inventory

    Accurate exposure classification tools are required to link exposure with health effects in epidemiological studies. Although long-term integrated exposure measurements are a critical component of exposure assessment, the ability to include these measurements into epidemiologic...

  3. Chapter 2. Fasciola, lymnaeids and human fascioliasis, with a global overview on disease transmission, epidemiology, evolutionary genetics, molecular epidemiology and control.

    PubMed

    Mas-Coma, Santiago; Valero, María Adela; Bargues, María Dolores

    2009-01-01

    Fascioliasis, caused by liver fluke species of the genus Fasciola, has always been well recognized because of its high veterinary impact but it has been among the most neglected diseases for decades with regard to human infection. However, the increasing importance of human fascioliasis worldwide has re-launched interest in fascioliasis. From the 1990s, many new concepts have been developed regarding human fascioliasis and these have furnished a new baseline for the human disease that is very different to a simple extrapolation from fascioliasis in livestock. Studies have shown that human fascioliasis presents marked heterogeneity, including different epidemiological situations and transmission patterns in different endemic areas. This heterogeneity, added to the present emergence/re-emergence of the disease both in humans and animals in many regions, confirms a worrying global scenario. The huge negative impact of fascioliasis on human communities demands rapid action. When analyzing how better to define control measures for endemic areas differing at such a level, it would be useful to have genetic markers that could distinguish each type of transmission pattern and epidemiological situation. Accordingly, this chapter covers aspects of aetiology, geographical distribution, epidemiology, transmission and control in order to obtain a solid baseline for the interpretation of future results. The origins and geographical spread of F. hepatica and F. gigantica in both the ruminant pre-domestication times and the livestock post-domestication period are analyzed. Paleontological, archaeological and historical records, as well as genetic data on recent dispersal of livestock species, are taken into account to establish an evolutionary framework for the two fasciolids across all continents. Emphasis is given to the distributional overlap of both species and the roles of transportation, transhumance and trade in the different overlap situations. Areas with only one Fasciola

  4. Contributions of occupational epidemiologic studies to radiation protection

    SciTech Connect

    Marks, S.

    1982-01-01

    Early evidence of health effects of occupational radiation exposure contributed importantly to the establishment of exposure standards, especially for internal emitters. Standards derived in this manner for radium body burdens and for air concentrations of radon and its daughters were especially influential. The body burden limits for plutonium and other bone-seeking radionuclides were based upon the radium standard. The exposure controls instituted as a consequence of those early limits have reduced the exposure of worker populations to the extent that the current, more sophisticated epidemiologic studies will probably not influence the revision of existing standards. The justification for conducting such studies is discussed.

  5. Application of Whole-Genome Sequencing for Bacterial Strain Typing in Molecular Epidemiology

    PubMed Central

    SenGupta, Dhruba J.; Cummings, Lisa A.; Land, Tyler A.; Hoogestraat, Daniel R.; Cookson, Brad T.

    2015-01-01

    Nosocomial infections pose a significant threat to patient health; however, the gold standard laboratory method for determining bacterial relatedness (pulsed-field gel electrophoresis [PFGE]) remains essentially unchanged 20 years after its introduction. Here, we explored bacterial whole-genome sequencing (WGS) as an alternative approach for molecular strain typing. We compared WGS to PFGE for investigating presumptive outbreaks involving three important pathogens: vancomycin-resistant Enterococcus faecium (n = 19), methicillin-resistant Staphylococcus aureus (n = 17), and Acinetobacter baumannii (n = 15). WGS was highly reproducible (average ≤ 0.39 differences between technical replicates), which enabled a functional, quantitative definition for determining clonality. Strain relatedness data determined by PFGE and WGS roughly correlated, but the resolution of WGS was superior (P = 5.6 × 10−8 to 0.016). Several discordant results were noted between the methods. A total of 28.9% of isolates which were indistinguishable by PFGE were nonclonal by WGS. For A. baumannii, a species known to undergo rapid horizontal gene transfer, 16.2% of isolate pairs considered nonidentical by PFGE were clonal by WGS. Sequencing whole bacterial genomes with single-nucleotide resolution demonstrates that PFGE is prone to false-positive and false-negative results and suggests the need for a new gold standard approach for molecular epidemiological strain typing. PMID:25631811

  6. Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology.

    PubMed

    Salipante, Stephen J; SenGupta, Dhruba J; Cummings, Lisa A; Land, Tyler A; Hoogestraat, Daniel R; Cookson, Brad T

    2015-04-01

    Nosocomial infections pose a significant threat to patient health; however, the gold standard laboratory method for determining bacterial relatedness (pulsed-field gel electrophoresis [PFGE]) remains essentially unchanged 20 years after its introduction. Here, we explored bacterial whole-genome sequencing (WGS) as an alternative approach for molecular strain typing. We compared WGS to PFGE for investigating presumptive outbreaks involving three important pathogens: vancomycin-resistant Enterococcus faecium (n=19), methicillin-resistant Staphylococcus aureus (n=17), and Acinetobacter baumannii (n=15). WGS was highly reproducible (average≤0.39 differences between technical replicates), which enabled a functional, quantitative definition for determining clonality. Strain relatedness data determined by PFGE and WGS roughly correlated, but the resolution of WGS was superior (P=5.6×10(-8) to 0.016). Several discordant results were noted between the methods. A total of 28.9% of isolates which were indistinguishable by PFGE were nonclonal by WGS. For A. baumannii, a species known to undergo rapid horizontal gene transfer, 16.2% of isolate pairs considered nonidentical by PFGE were clonal by WGS. Sequencing whole bacterial genomes with single-nucleotide resolution demonstrates that PFGE is prone to false-positive and false-negative results and suggests the need for a new gold standard approach for molecular epidemiological strain typing. PMID:25631811

  7. Molecular Epidemiology of Methicillin-Resistant Staphylococcus aureus Isolated from Australian Veterinarians

    PubMed Central

    Groves, Mitchell D.; Crouch, Bethany; Coombs, Geoffrey W.; Jordan, David; Pang, Stanley; Barton, Mary D.; Giffard, Phil

    2016-01-01

    This work investigated the molecular epidemiology and antimicrobial resistance of methicillin-resistant Staphylococcus aureus (MRSA) isolated from veterinarians in Australia in 2009. The collection (n = 44) was subjected to extensive molecular typing (MLST, spa, SCCmec, dru, PFGE, virulence and antimicrobial resistance genotyping) and antimicrobial resistance phenotyping by disk diffusion. MRSA was isolated from Australian veterinarians representing various occupational emphases. The isolate collection was dominated by MRSA strains belonging to clonal complex (CC) 8 and multilocus sequence type (ST) 22. CC8 MRSA (ST8-IV [2B], spa t064; and ST612-IV [2B], spa variable,) were strongly associated with equine practice veterinarians (OR = 17.5, 95% CI = 3.3–92.5, P < 0.001) and were often resistant to gentamicin and rifampicin. ST22-IV [2B], spa variable, were strongly associated with companion animal practice veterinarians (OR = 52.5, 95% CI = 5.2–532.7, P < 0.001) and were resistant to ciprofloxacin. A single pig practice veterinarian carried ST398-V [5C2], spa t1451. Equine practice and companion animal practice veterinarians frequently carried multiresistant-CC8 and ST22 MRSA, respectively, whereas only a single swine specialist carried MRSA ST398. The presence of these strains in veterinarians may be associated with specific antimicrobial administration practices in each animal species. PMID:26735694

  8. Antimicrobial susceptibility and molecular epidemiological analysis of clinical strains of Pseudomonas aeruginosa.

    PubMed

    Tsuchimochi, Noriko; Takuma, Takahiro; Shimono, Nobuyuki; Nagasaki, Yoji; Uchida, Yujiro; Harada, Mine

    2008-04-01

    Three hundred and seventy-one strains of Pseudomonas aeruginosa were isolated at the laboratory of Kyushu University Hospital in Japan from May 2002 through January 2003. Large proportions of isolated strains were resistant to carbapenems: 37.5% to imipenem, 21.3% to biapenem, and 18.3% to meropenem. A survey of injectable antibacterial agents used in our hospital during the corresponding period showed that carbapenems were most frequently used. Multidrug-resistant P. aeruginosa (MDRP) strains and metallo-beta-lactamase producing strains were isolated at frequencies of 1.6% (6 strains) and 0.81% (3 strains), respectively. By molecular epidemiological analysis, neither MDRP nor metallo-beta-lactamase producing strains were molecularly related, whereas some imipenem-resistant strains appeared to be epidemic strains, suggesting a possibility that they might spread by nosocomial infection. To control nosocomial infection, it is important to know a trend in drug-resistant P. aeruginosa and to prevent the spread of not only MDRP and metallo-beta-lactamase producing strains but also imipenem-resistant P. aeruginosa strains. PMID:18622671

  9. Molecular Epidemiology of Methicillin-Resistant Staphylococcus aureus Isolated from Australian Veterinarians.

    PubMed

    Groves, Mitchell D; Crouch, Bethany; Coombs, Geoffrey W; Jordan, David; Pang, Stanley; Barton, Mary D; Giffard, Phil; Abraham, Sam; Trott, Darren J

    2016-01-01

    This work investigated the molecular epidemiology and antimicrobial resistance of methicillin-resistant Staphylococcus aureus (MRSA) isolated from veterinarians in Australia in 2009. The collection (n = 44) was subjected to extensive molecular typing (MLST, spa, SCCmec, dru, PFGE, virulence and antimicrobial resistance genotyping) and antimicrobial resistance phenotyping by disk diffusion. MRSA was isolated from Australian veterinarians representing various occupational emphases. The isolate collection was dominated by MRSA strains belonging to clonal complex (CC) 8 and multilocus sequence type (ST) 22. CC8 MRSA (ST8-IV [2B], spa t064; and ST612-IV [2B], spa variable,) were strongly associated with equine practice veterinarians (OR = 17.5, 95% CI = 3.3-92.5, P < 0.001) and were often resistant to gentamicin and rifampicin. ST22-IV [2B], spa variable, were strongly associated with companion animal practice veterinarians (OR = 52.5, 95% CI = 5.2-532.7, P < 0.001) and were resistant to ciprofloxacin. A single pig practice veterinarian carried ST398-V [5C2], spa t1451. Equine practice and companion animal practice veterinarians frequently carried multiresistant-CC8 and ST22 MRSA, respectively, whereas only a single swine specialist carried MRSA ST398. The presence of these strains in veterinarians may be associated with specific antimicrobial administration practices in each animal species. PMID:26735694

  10. TCDD and cancer: A critical review of epidemiologic studies

    PubMed Central

    Boffetta, Paolo; Mundt, Kenneth A; Adami, Hans-Olov; Cole, Philip; Mandel, Jack S

    2011-01-01

    The authors reviewed the epidemiologic studies on exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and cancer risk, published since the last full-scale review made by the International Agency for Research on Cancer Monographs program in 1997. The update of a cohort of US herbicide producers generated negative results overall; the internal analysis provided evidence of an increased “all-cancer” risk in the highest exposure category, with a statistically significant exposure-response association in some of the many analyses performed.The update of a similar Dutch cohort did not confirm the previously observed association with TCDD exposure. The updated surveillance of the Seveso population provided evidence of increased all-cancer mortality 15-20 years after exposure among those living in the most contaminated area but might also reflect random variation, as overall excesses in the most recent follow-up were not observed. Corresponding data on cancer incidence offer little support to the mortality results. Updated results from cohort studies of Vietnam veterans potentially exposed to TCDD did not consistently suggest an increased risk of cancer. Results of additional, smaller studies of other occupational groups potentially exposed to TCDD, and of community-based case-control studies, did not provide consistent evidence of an increased cancer risk. In conclusion, recent epidemiological evidence falls far short of conclusively demonstrating a causal link between TCDD exposure and cancer risk in humans. The emphasis on results for overall cancer risk—rather than risk for specific neoplasms—is notjustified on epidemiologic grounds and is nota reason for ignoring the weaknesses of the available evidence. PMID:21718216

  11. Molecular Epidemiology of Mycobacterium leprae as Determined by Structure-Neighbor Clustering ▿ †

    PubMed Central

    Hall, Barry G.; Salipante, Stephen J.

    2010-01-01

    It has proven challenging to investigate the molecular epidemiology of Mycobacterium leprae, the causative agent of leprosy, due to difficulties with culturing of the organism and a lack of genetic heterogeneity between strains. Recently, a cost-effective panel of variable-number tandem-repeat (VNTR) markers has been developed. Use of this panel allows some of those limitations to be overcome and has allowed the genotyping of 475 M. leprae strains from six different countries. In the present report, we provide a comprehensive analysis of the relationships among the strains in order to investigate the patterns of transmission and migration of M. leprae. We find phylogenetic analysis to be inadequate and have developed an alternative method, structure-neighbor clustering, which assigns isolates with the most similar genotypes to the same groups and, subsequently, subgroups, without inferring how the strains descended from a common ancestor. We validate the approach by using simulated data and detecting expected epidemiological relationships from experimental data. Our results suggest that most M. leprae strains from a given country cluster together and that the occasional isolates assigned to different clusters are a consequence of migration. We found three genetically distinguishable populations among isolates from the Philippines, as well as evidence for the significant influx of strains to that nation from India. We also report that reference strain TN originated from the Philippines and not from India, as was previously believed. Lastly, analysis of isolates from the same families and villages suggests that most community infections originate from a common source or person-to-person transmission but that infection from independent sources does occur with measurable frequency. PMID:20351204

  12. Mining characteristics of epidemiological studies from Medline: a case study in obesity

    PubMed Central

    2014-01-01

    Background The health sciences literature incorporates a relatively large subset of epidemiological studies that focus on population-level findings, including various determinants, outcomes and correlations. Extracting structured information about those characteristics would be useful for more complete understanding of diseases and for meta-analyses and systematic reviews. Results We present an information extraction approach that enables users to identify key characteristics of epidemiological studies from MEDLINE abstracts. It extracts six types of epidemiological characteristic: design of the study, population that has been studied, exposure, outcome, covariates and effect size. We have developed a generic rule-based approach that has been designed according to semantic patterns observed in text, and tested it in the domain of obesity. Identified exposure, outcome and covariate concepts are clustered into health-related groups of interest. On a manually annotated test corpus of 60 epidemiological abstracts, the system achieved precision, recall and F-score between 79-100%, 80-100% and 82-96% respectively. We report the results of applying the method to a large scale epidemiological corpus related to obesity. Conclusions The experiments suggest that the proposed approach could identify key epidemiological characteristics associated with a complex clinical problem from related abstracts. When integrated over the literature, the extracted data can be used to provide a more complete picture of epidemiological efforts, and thus support understanding via meta-analysis and systematic reviews. PMID:24949194

  13. Critical review of epidemiologic studies related to ingested asbestos

    SciTech Connect

    Marsh, G.M.

    1983-11-01

    Thirteen epidemiologic studies of ingested asbestos conducted in five areas of the US and Canada were evaluated for the definitiveness and applicability regarding the development of ambient water quality standards. Associations between asbestos in water supplies and cancer mortality or incidence in humans were found in one or more studies dealing with neoplasms in the esophagus, stomach, small intestine, colon, rectum, gallbaldder, pancreas, peritoneum, lungs, pleura, prostate, kidneys, brain and thyroid as well as leukemia. However, no single study nor aggregate of studies existed that would establish risk levels from ingested asbestos. It is recommended that the integrated ecologic data to date be used to generate a rough priority of specific etiologic hypotheses that should be tested in the original settings or in independent study populations using studies designed at the more definitive individual level, such as case-control studies. 25 references, 7 tables.

  14. Molecular Epidemiology of Influenza A/H3N2 Viruses Circulating in Mexico from 2003 to 2012

    PubMed Central

    Escalera-Zamudio, Marina; Nelson, Martha I.; Cobián Güemes, Ana Georgina; López-Martínez, Irma; Cruz-Ortiz, Natividad; Iguala-Vidales, Miguel; García, Elvia Rodríguez; Barrera-Badillo, Gisela; Díaz-Quiñonez, Jose Alberto; López, Susana; Arias, Carlos F.; Isa, Pavel

    2014-01-01

    In this work, nineteen influenza A/H3N2 viruses isolated in Mexico between 2003 and 2012 were studied. Our findings show that different human A/H3N2 viral lineages co-circulate within a same season and can also persist locally in between different influenza seasons, increasing the chance for genetic reassortment events. A novel minor cluster was also identified, named here as Korea, that circulated worldwide during 2003. Frequently, phylogenetic characterization did not correlate with the determined antigenic identity, supporting the need for the use of molecular evolutionary tools additionally to antigenic data for the surveillance and characterization of viral diversity during each flu season. This work represents the first long-term molecular epidemiology study of influenza A/H3N2 viruses in Mexico based on the complete genomic sequences and contributes to the monitoring of evolutionary trends of A/H3N2 influenza viruses within North and Central America. PMID:25075517

  15. The epidemiology of vertebral fractures. European Vertebral Osteoporosis Study Group.

    PubMed

    Cooper, C; O'Neill, T; Silman, A

    1993-01-01

    Vertebral fractures are recognised as a hallmark of osteoporosis, yet little is known of their epidemiology. This deficiency limits accurate characterisation of the public health importance of osteoporosis. Assessment of the impact of vertebral fractures has been hampered by the absence of formal criteria for identifying fractures on a thoracolumbar radiograph. Initial methods relying upon subjective radiological assessments have given way to morphometric measurements of vertebral heights, with deformities defined according to various algorithms. These methods have been used in a series of studies performed in Rochester, MN, to determine the incidence, outcome, and time trends of vertebral deformities. The results suggest a prevalence rate of vertebral deformity of 25.3 per 100 Rochester women aged 50 years and over (95% CI, 22.3-28.2), with an estimated incidence of 17.8 per 1,000 person-years. The incidence of clinically diagnosed vertebral fractures among women in the same population was 5.3 per 1,000 person-years, suggesting that around 30% of such deformities in women receive clinical attention. Morphometric measurement on the radiographs of women with clinically diagnosed fractures revealed that 80% had grade 2 ( > 4 SD) deformities. Comparable data on the occurrence and health impact of vertebral deformities throughout Europe are urgently required. The European Vertebral Osteoporosis Study (EVOS) is a multicentre epidemiological study that aims to address this issue. It is designed as a radiographic prevalence study in 34 European centres.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8110529

  16. Drug data coding and analysis in epidemiologic studies.

    PubMed

    Pahor, M; Chrischilles, E A; Guralnik, J M; Brown, S L; Wallace, R B; Carbonin, P

    1994-08-01

    In epidemiologic studies that collect comprehensive information on medication use, the complexity of dealing with a large number of trade and generic names may limit the utilization of these data bases. This paper shows the specific advantage of using two coding systems, one to maximize efficiency of data entry, and the other to facilitate analysis by organizing the drug ingredients into hierarchical categories. The approach used by two large surveys, one in the USA and one in Italy, is described: the Established Populations for Epidemiologic Studies of the Elderly (EPESE) and the 'Gruppo Italiano di Farmacovigilanza nell' Anziano' (GIFA). To enter the medications into a computerized database, codes matching the drug product names are needed. In the EPESE the prescription and over the counter drug products are coded with the Drug Products Information Coding System (DPICS) and the Iowa Nonprescription Drug Products Information Coding System (INDPICS), respectively. The GIFA study uses the coding system of the Italian Ministry of Health (MINSAN), with a unique numeric code for each drug product available in Italy. To simplify the analytical process the drug entry codes are converted into hierarchical coding systems with unique codes for specific drug ingredients, chemical and therapeutic categories. The EPESE and GIFA drug data are coded with the Iowa Drug Information System (IDIS) ingredient codes, and the Anatomical Therapeutic and chemical (ATC) codes, respectively. Examples are provided that show coding of diuretics in these two studies and demonstrate the analytic advantages of these systems. PMID:7843344

  17. Molecular epidemiology of Newcastle disease virus isolates from vaccinated commercial poultry farms in non-epidemic areas of Japan

    PubMed Central

    2013-01-01

    Background Newcastle Disease (ND) is a highly contagious and economically devastating disease of poultry. At present, limited molecular epidemiological data are available regarding the causes of ND outbreaks in vaccinated commercial poultry farms. Knowing the genomic characteristics of Newcastle disease virus (NDV) infecting commercial poultry operations in spite of vaccination might give important insights on the infection dynamics of these viruses. In addition, molecular analyses at the subgenotype level and studies on the relationship of Japanese NDVs with other isolates from around the world are lacking. Therefore, in the present study, a molecular epidemiological investigation was conducted to characterize nine NDVs isolated from vaccinated commercial poultry flocks in five different Prefectures in non-epidemic areas of Japan between 1969 and 2002. Methods Nucleotide sequencing and phylogenetic studies were performed to characterize the complete fusion (F)-protein gene, 3-prime end of the nucleoprotein (NP)-gene and 5-prime end of the RNA dependent RNA polymerase (L)-gene. Sequence data were compared with 180 NDV strains from GenBank representing different NDV genotypes and subgenotypes from different regions of the world at different time periods. Deduced amino acids were analyzed for homologies, recombination and mutation. Recombination events were estimated using Recombination Detection Program (RDP) version 3.44. Phylogenetic trees were constructed to determine evolutionary relationships among strains. Results Mean death time (MDT: 48-56 hr), Intracerebral Pathogenicity Index (ICPI: 1.7-1.9) and deduced amino acid sequences of the F0 proteolytic cleavage site (112RRQKR116) revealed that all nine field isolates were velogenic. Phylogenetic analysis showed that these isolates could be classified into two genetic lineages and three sublineages namely genotypes VIa (lineage 4a), VId (lineage 4d) and VIId (lineage 5d). No recombination events were observed but

  18. The Air Force health study: an epidemiologic retrospective.

    PubMed

    Buffler, Patricia A; Ginevan, Michael E; Mandel, Jack S; Watkins, Deborah K

    2011-09-01

    In 1979, the U.S. Air Force announced that an epidemiologic study would be undertaken to determine whether the Air Force personnel involved in Operation Ranch Hand-the program responsible for herbicide spraying in Vietnam-had experienced adverse health effects as a result of that service. In January 1982 the Air Force Health Study (AFHS) protocol was approved and the 20 year matched cohort study consisting of independent mortality, morbidity and reproductive health components was initiated. This controversial study has been criticized regarding the study's potential scientific limitations as well as some of the administrative aspects of its conduct. Now, almost 30 years since the implementation of the AFHS and nearly a decade since the final follow up examinations, an appraisal of the study indicates that the results of the AFHS do not provide evidence of disease in the Ranch Hand veterans caused by their elevated levels of exposure to Agent Orange. PMID:21441038

  19. Genetic Epidemiology of Tuberculosis Susceptibility: Impact of Study Design

    PubMed Central

    Stein, Catherine M.

    2011-01-01

    Several candidate gene studies have provided evidence for a role of host genetics in susceptibility to tuberculosis (TB). However, the results of these studies have been very inconsistent, even within a study population. Here, we review the design of these studies from a genetic epidemiological perspective, illustrating important differences in phenotype definition in both cases and controls, consideration of latent M. tuberculosis infection versus active TB disease, population genetic factors such as population substructure and linkage disequilibrium, polymorphism selection, and potential global differences in M. tuberculosis strain. These considerable differences between studies should be accounted for when examining the current literature. Recommendations are made for future studies to further clarify the host genetics of TB. PMID:21283783

  20. Serum Biomarkers of (Anti)Oxidant Status for Epidemiological Studies

    PubMed Central

    Jansen, Eugène; Ruskovska, Tatjana

    2015-01-01

    In this review, we disclose a selection of serum/plasma biomarkers of (anti)oxidant status related to nutrition, which can be used for measurements in large-scale epidemiological studies. From personal experience, we have come to the following proposal of a set of biomarkers for nutritional intake, (anti)oxidant status, and redox status. We have selected the individual antioxidant vitamins E and A, and the carotenoids which can be measured in large series by HPLC. In addition, vitamin C was selected, which can be measured by an auto-analyzer or HPLC. As a biomarker for oxidative stress, the ROM assay (reactive oxygen metabolites) was selected; for the redox status, the total thiol assay; and for the total antioxidant status the BAP assay (biological antioxidant potential). All of these biomarkers can be measured in large quantities by an auto-analyzer. Critical points in biomarker validation with respect to blood sampling, storage conditions, and measurements are discussed. With the selected biomarkers, a good set is presented for use in the risk assessment between nutrition and (chronic) diseases in large-scale epidemiological studies. Examples of the successful application of these biomarkers in large international studies are presented. PMID:26580612

  1. MODELING AN IRRITANT GAS PLUME FOR EPIDEMIOLOGIC STUDY

    PubMed Central

    Jani, Dev D.; Reed, David; Feigley, Charles E.

    2015-01-01

    Plume dispersion modeling systems are often used in assessing human exposures to chemical hazards for epidemiologic study. We modeled the 2005 Graniteville, South Carolina, 54,915 kg railcar chlorine release using both the Areal Locations of Hazardous Atmospheres (ALOHA) and Hazard Prediction and Assessment Capability (HPAC) plume modeling systems. We estimated the release rate by an engineering analysis combining semi-quantitative observations and fundamental physical principles. The use of regional meteorological conditions was validated by comparing concentration estimates generated by two source-location weather data sets. The HPAC model estimated a chlorine plume with 20 ppm outdoor concentrations up to 7 km downwind and 0.25 km upwind/downgrade. A comparative analysis of our two models showed that HPAC was the best candidate for use as a model system on which epidemiologic studies could be based after further model validation. Further validation studies are needed before individual exposure estimates can be reliable and the chlorine plume more definitively modeled. PMID:25772143

  2. Epidemiology, clinical, immune, and molecular profiles of microsporidiosis and cryptosporidiosis among HIV/AIDS patients

    PubMed Central

    Wumba, Roger; Longo-Mbenza, Benjamin; Menotti, Jean; Mandina, Madone; Kintoki, Fabien; Situakibanza, Nani Hippolyte; Kakicha, Marie Kapepela; Zanga, Josue; Mbanzulu-Makola, Kennedy; Nseka, Tommy; Mukendi, Jean Pierre; Kendjo, Eric; Sala, Jean; Thellier, Marc

    2012-01-01

    Background The objective of this study was to determine the prevalence of intestinal parasites, with special emphasis on microsporidia and Cryptosporidium, as well as their association with human immunodeficiency virus (HIV) symptoms, risk factors, and other digestive parasites. We also wish to determine the molecular biology definitions of the species and genotypes of microsporidia and Cryptosporidium in HIV patients. Methods In this cross-sectional study, carried out in Kinshasa, Democratic Republic of the Congo, stool samples were collected from 242 HIV patients (87 men and 155 women) with referred symptoms and risk factors for opportunistic intestinal parasites. The analysis of feces specimen were performed using Ziehl–Neelsen stainings, real-time polymerase chain reaction (PCR), immunofluorescence indirect monoclonal antibody, nested PCR-restriction fragment length polymorphism, and PCR amplification and sequencing. Odds ratio (OR) and 95% confidence intervals were used to quantify the risk. Results Of the 242 HIV patients, 7.8%, 0.4%, 5.4%, 0.4%, 2%, 10.6%, and 2.8% had Enterocytozoon bieneusi, Encephalitozoon intestinalis, Cryptosporidium spp., Isospora belli, pathogenic intestinal protozoa, nonpathogenic intestinal protozoa, and helminths, respectively. We found five genotypes of E. bieneusi: two older, NIA1 and D, and three new, KIN1, KIN2, and KIN3. Only 0.4% and 1.6% had Cryptosporidium parvum and Cryptosporidium hominis, respectively. Of the patients, 36.4%, 34.3%, 31%, and 39% had asthenia, diarrhea, a CD4 count of <100 cells/mm3, and no antiretroviral therapy (ART), respectively. The majority of those with opportunistic intestinal parasites and C. hominis, and all with C. parvum and new E. bieneusi genotypes, had diarrhea, low CD4+ counts of <100 cells/mm3, and no ART. There was a significant association between Entamoeba coli, Kaposi sarcoma, herpes zoster, chronic diarrhea, and asthenia, and the presence of 28 cases with opportunistic intestinal

  3. 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).

  4. Epidemiologic study of ankle fractures in a tertiary hospital

    PubMed Central

    Sakaki, Marcos Hideyo; Matsumura, Bruno Akio Rodrigues; Dotta, Thiago De Angelis Guerra; Pontin, Pedro Augusto; dos Santos, Alexandre Leme Godoy; Fernandes, Tulio Diniz

    2014-01-01

    OBJECTIVES: To evaluate the epidemiology of ankle fractures surgically treated at the Instituto de Ortopedia e Traumatologia do Hospital das Clínicas da Universidade de São Paulo. METHODS: Medical records of patients admitted with foot and ankle fractures between 2006 and 2011 were revised. Seventy three ankle fractures that underwent surgical treatment were identified. The parameters analyzed included age, gender, injured side, AO and Gustilo & Anderson classification, associated injuries, exposure, need to urgent treatment, time to definitive treatment and early post-operative complications. Study design: retrospective epidemiological study. RESULTS: Male gender was predominant among subjects and the mean age was 27.5 years old. Thirty nine fractures resulted from traffic accidents and type B fracture according to AO classification was the most common. Twenty one were open fractures and 22 patients had associated injuries. The average time to definitive treatment was 6.5 days. Early post-operative complications were found in 21.3% of patients. CONCLUSIONS: Ankle fractures treated in a tertiary hospital of a large city in Brazil affect young people victims of high-energy accidents and present significant rates of associated injuries and post-operative complications. Level of Evidence IV, Cases Series. PMID:24868187

  5. Biologically based epidemiological studies of electric power and cancer.

    PubMed Central

    Stevens, R G

    1993-01-01

    As societies industrialize, the health profile of the population changes; in general, acute infectious disease declines and chronic disease increases. Use of electricity is a hallmark of the industrialization process, but there has been no suspicion that electricity could increase the risk of cancer. Recently, however, a number of epidemiologic studies have suggested that electromagnetic fields (EMF) may do just that. Although few cancer experiments have been done yet, there are a number of biological effects of EMF reported in the literature that might provide bases for designing cancer experiments and epidemiologic studies. These include effects of EMF on: a) DNA transcription and translation, b) calcium balance in cells, and c) pineal production of melatonin. Alterations in DNA transcription and translation could have pleiotropic effects. Disruption of calcium homeostasis has many implications including oncogene activation, promotional activity via protein kinases and ornithine decarboxylase (ODC), and increasing oxidative stress. Reduction of melatonin suggests a possible increased risk of cancers of hormone-dependent tissues such as breast and prostate. The idea that a cancer-causing agent must either be an initiator or a promoter should be discarded; indeed, the phenomenologic meaning of these two terms has become confused with imputed mechanistic necessity in recent years. Agents that affect division of normal cells or of fully transformed cells can play an important role in clinical cancer development quite apart from initiation or promotion.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8206047

  6. Optimal design for epidemiological studies subject to designed missingness.

    PubMed

    Morara, Michele; Ryan, Louise; Houseman, Andres; Strauss, Warren

    2007-12-01

    In large epidemiological studies, budgetary or logistical constraints will typically preclude study investigators from measuring all exposures, covariates and outcomes of interest on all study subjects. We develop a flexible theoretical framework that incorporates a number of familiar designs such as case control and cohort studies, as well as multistage sampling designs. Our framework also allows for designed missingness and includes the option for outcome dependent designs. Our formulation is based on maximum likelihood and generalizes well known results for inference with missing data to the multistage setting. A variety of techniques are applied to streamline the computation of the Hessian matrix for these designs, facilitating the development of an efficient software tool to implement a wide variety of designs. PMID:18080755

  7. [The mode of infection of tuberculosis--analysis using molecular epidemiologic methods].

    PubMed

    Abe, C

    1995-11-01

    In the 1950's, evidence showed that INH-resistant Mycobacterium tuberculosis organisms were attenuated in both virulence and pathogenicity in animals, and it was postulated that these bacilli might also be attenuated in their virulence to humans. Subsequent studies, however, indicated that all INH-resistant strains should not be considered as being attenuated in their virulence to humans. The general conclusion was that patients excreting INH-resistant organisms are somewhat less infectious to their contacts than patients excreting INH-susceptible organisms. Insertion sequences are suitable tools for the diagnosis and epidemiology of tuberculosis because of the highly variable copy number and variability of insertion sites in the chromosome. This variability allows the subtyping of M. tuberculosis strains by restriction fragment length polymorphism (RFLP) analysis. Patients with the same RFLP pattern constitute an epidemiologically linked cluster. Clustering indicates recent infection and rapid progression to clinical illness. Nearly one thirds of new cases of tuberculosis in San Francisco are the result of recent infection. In Thailand, tuberculosis has now emerged as the most common opportunistic disease associated with HIV infection. Cluster analysis showed the risk of progression to active tuberculosis among individuals infected with HIV. Ther have been numerous outbreaks of multidrug-resistant tuberculosis in the United States. Most of such outbreaks have primarily involved persons infected with HIV, who are thought to have been exposed to the strains in medical or correctional facilities. PMID:8656589

  8. Particulate matter and heart disease: Evidence from epidemiological studies

    SciTech Connect

    Peters, Annette . E-mail: peters@gsf.de

    2005-09-01

    The association between particulate matter and heart disease was noted in the mid-nineties of last century when the epidemiological evidence for an association between air pollution and hospital admissions due to cardiovascular disease accumulated and first hypotheses regarding the pathomechanism were formulated. Nowadays, epidemiological studies have demonstrated coherent associations between daily changes in concentrations of ambient particles and cardiovascular disease mortality, hospital admission, disease exacerbation in patients with cardiovascular disease and early physiological responses in healthy individuals consistent with a risk factor profile deterioration. In addition, evidence was found that annual average PM{sub 2.5} exposures are associated with increased risks for mortality caused by ischemic heart disease and dysrhythmia. Thereby, evidence is suggesting not only a short-term exacerbation of cardiovascular disease by ambient particle concentrations but also a potential role of particles in defining patients' vulnerability to acute coronary events. While this concept is consistent with the current understanding of the factors defining patients' vulnerability, the mechanisms and the time-scales on which the particle-induced vulnerability might operate are unknown.

  9. Molecular epidemiologic investigations of Mycoplasma gallisepticum conjunctivitis in songbirds by random amplified polymorphic DNA analyses.

    PubMed

    Ley, D H; Berkhoff, J E; Levisohn, S

    1997-01-01

    An ongoing outbreak of conjunctivitis in free-ranging house finches (Carpodacus mexicanus) began in 1994 in the eastern United States. Bacterial organisms identified as Mycoplasma gallisepticum (MG) were isolated from lesions of infected birds. MG was also isolated from a blue jay (Cyanocitta cristata) that contracted conjunctivitis after being housed in a cage previously occupied by house finches with conjunctivitis, and from free-ranging American goldfinches (Carduelis tristis) in North Carolina in 1996. To investigate the molecular epidemiology of this outbreak, we produced DNA fingerprints of MG isolates by random amplification of polymorphic DNA (RAPD). We compared MG isolates from songbirds examined from 1994 through 1996 in 11 states, representing three host species, with vaccine and reference strains and with contemporary MG isolates from commercial poultry. All MG isolates from songbirds had RAPD banding patterns identical to each other but different from other strains and isolates tested. These results indicate that the outbreak of MG in songbirds is caused by the same strain, which suggests a single source; the outbreak is not caused by the vaccine or reference strains analyzed; and MG infection has not been shared between songbirds and commercial poultry. PMID:9284386

  10. Molecular Epidemiology of Recent Belgian Isolates of Neisseria meningitidis Serogroup B

    PubMed Central

    Van Looveren, M.; Vandamme, P.; Hauchecorne, M.; Wijdooghe, M.; Carion, F.; Caugant, D. A.; Goossens, H.

    1998-01-01

    In Belgium an increase in the incidence of meningococcal disease has been noted since the early 1990s. Four hundred twenty clinical strains isolated during the period from 1990 to 1995, along with a set of 30 European reference strains, and 20 Dutch isolates were examined by random-primer and repetitive-motif-based PCR. A subset was investigated by multilocus enzyme electrophoresis and pulsed-field gel electrophoresis. The data were compared with results obtained by serotyping (M. Van Looveren, F. Carion, P. Vandamme, and H. Goossens, Clin. Microbiol. Infect. 4:224–228, 1998). Both phenotypic and molecular epidemiological data suggest that the lineage III of Neisseria meningitidis, first encountered in The Netherlands in about 1980, has been introduced in Belgium. The epidemic clone, as defined by oligonucleotide D8635-primed PCR, encompasses mainly phenotypes B:4:P1.4 and B:nontypeable:P1.4, but strains with several other phenotypes were also encountered. Therefore, serotyping alone would underestimate the prevalence of the epidemic clone. PMID:9738028

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

    PubMed Central

    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

    2015-01-01

    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. PMID:25859150

  12. Cryptosporidiosis in HIV/AIDS Patients in Kenya: Clinical Features, Epidemiology, Molecular Characterization and Antibody Responses

    PubMed Central

    Wanyiri, Jane W.; Kanyi, Henry; Maina, Samuel; Wang, David E.; Steen, Aaron; Ngugi, Paul; Kamau, Timothy; Waithera, Tabitha; O'Connor, Roberta; Gachuhi, Kimani; Wamae, Claire N.; Mwamburi, Mkaya; Ward, Honorine D.

    2014-01-01

    We investigated the epidemiological and clinical features of cryptosporidiosis, the molecular characteristics of infecting species and serum antibody responses to three Cryptosporidium-specific antigens in human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) patients in Kenya. Cryptosporidium was the most prevalent enteric pathogen and was identified in 56 of 164 (34%) of HIV/AIDS patients, including 25 of 70 (36%) with diarrhea and 31 of 94 (33%) without diarrhea. Diarrhea in patients exclusively infected with Cryptosporidium was significantly associated with the number of children per household, contact with animals, and water treatment. Cryptosporidium hominis was the most prevalent species and the most prevalent subtype family was Ib. Patients without diarrhea had significantly higher serum IgG levels to Chgp15, Chgp40 and Cp23, and higher fecal IgA levels to Chgp15 and Chgp40 than those with diarrhea suggesting that antibody responses to these antigens may be associated with protection from diarrhea and supporting further investigation of these antigens as vaccine candidates. PMID:24865675

  13. Molecular epidemiologic analysis of a Pneumocystis pneumonia outbreak among renal transplant patients.

    PubMed

    Urabe, N; Ishii, Y; Hyodo, Y; Aoki, K; Yoshizawa, S; Saga, T; Murayama, S Y; Sakai, K; Homma, S; Tateda, K

    2016-04-01

    Between 18 November and 3 December 2011, five renal transplant patients at the Department of Nephrology, Toho University Omori Medical Centre, Tokyo, were diagnosed with Pneumocystis pneumonia (PCP). We used molecular epidemiologic methods to determine whether the patients were infected with the same strain of Pneumocystis jirovecii. DNA extracted from the residual bronchoalveolar lavage fluid from the five outbreak cases and from another 20 cases of PCP between 2007 and 2014 were used for multilocus sequence typing to compare the genetic similarity of the P. jirovecii. DNA base sequencing by the Sanger method showed some regions where two bases overlapped and could not be defined. A next-generation sequencer was used to analyse the types and ratios of these overlapping bases. DNA base sequences of P. jirovecii in the bronchoalveolar lavage fluid from four of the five PCP patients in the 2011 outbreak and from another two renal transplant patients who developed PCP in 2013 were highly homologous. The Sanger method revealed 14 genomic regions where two differing DNA bases overlapped and could not be identified. Analyses of the overlapping bases by a next-generation sequencer revealed that the differing types of base were present in almost identical ratios. There is a strong possibility that the PCP outbreak at the Toho University Omori Medical Centre was caused by the same strain of P. jirovecii. Two different types of base present in some regions may be due to P. jirovecii's being a diploid species. PMID:26724988

  14. Population-Based Molecular Epidemiology of Leprosy in Cebu, Philippines ▿

    PubMed Central

    Sakamuri, Rama Murthy; Kimura, Miyako; Li, Wei; Kim, Hyun-Chul; Lee, Hyeyoung; Kiran, Madanahally D.; Black, William C.; Balagon, Marivic; Gelber, Robert; Cho, Sang-Nae; Brennan, Patrick J.; Vissa, Varalakshmi

    2009-01-01

    To address the persisting problem of leprosy in Cebu, Philippines, we compiled a database of more than 200 patients who attend an established referral skin clinic. We described the patient characteristics in conventional demographic parameters and also applied multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) and single nucleotide polymorphism (SNP) typing for Mycobacterium leprae in biopsied skin lesion samples. These combined approaches revealed that transmission is ongoing, with the affected including the young Cebuano population under 40 years of age in both crowded cities and rural areas of the island. The emergence of multicase families (MCF) is indicative of infection unconstrained by standard care measures. For the SNPs, we designed a low-cost PCR-restriction fragment length polymorphism typing method. MLVA in M. leprae was highly discriminatory in this population yet could retain broad groups, as defined by the more stable SNPs, implying temporal marker stability suitable for interpreting population structures and evolution. The majority of isolates belong to an Asian lineage (SNP type 1), and the rest belong to a putative postcolonial lineage (SNP type 3). Specific alleles at two VNTR loci, (GGT)5 and 21-3, were highly associated with SNP type 3 in this population. MLVA identified M. leprae genotype associations for patients with known epidemiological links such as in MCFs and in some villages. These methods provide a molecular database and a rational framework for targeted approaches to search and confirm leprosy transmission in various scenarios. PMID:19571027

  15. Molecular epidemiology of plasmid patterns in Shigella flexneri types 1-6.

    PubMed Central

    Gebre-Yohannes, A.; Drasar, B. S.

    1991-01-01

    A total of 123 drug-resistant and drug-sensitive Shigella flexneri types 1-6, and their Escherichia coli K12 transconjugants were used for plasmid profile analysis by agarose gel electrophoresis. Resistance factors (R-factors) were further characterized by incompatibility testing. The overall distribution of small plasmids in S. flexneri showed that a cryptic plasmid of about 4.6 Kb was found in all serotypes, and a plasmid of about 4.2 Kb was found in serotypes 1-4. Shigella flexneri types 2, 4 and 6 showed a 6.5 Kb plasmid which correlated with SSu-resistance. All S. flexneri serotypes harboured large plasmids of about 217 Kb. Plasmid profile analysis of S. flexneri in Ethiopia showed a high degree of uniformity within individual serotypes. However, there was a limited variability which, at times, could be useful for epidemiological investigation. Shigella flexneri serotypes 1-6 harboured resistance plasmids with diverse molecular weights but mostly belonging to incompatibility groups N and X. PMID:1936154

  16. Recruiting American Indian Women for a Genetic Epidemiology Study

    PubMed Central

    Nadeau, M.; Best, L.

    2010-01-01

    Due to previous negative experiences, some American Indian communities are distrustful of research in general and genetic research in particular. The Turtle Mountain Community College was awarded a National Institutes of Health (NIH) grant with 3 aims: (1) to study possible genetic influences on pre-eclampsia, (2) to encourage tribal college students to consider biomedical careers and (3) to develop the local research infrastructure. Retrospectively identified case (91) and control (188) participants were recruited into Phase I over a 3-year period and additional participants (71) were concurrently recruited from a prenatal clinic into a prospective case/control study, Phase II. This paper describes some of the challenges and solutions we encountered in the process of recruiting American Indian participants into a genetic epidemiologic study. PMID:20616521

  17. [French Guiana "papillonite" (lepidopterism). Clinical and epidemiological study].

    PubMed

    Ducombs, G; Lamy, M; Michel, M; Pradinaud, R; Jamet, P; Vincendeau, P; Maleville, J; Texier, L

    1983-01-01

    Clinical studies by Dr R. Pradinaud (Cayenne) has given prominence to the symptoms of "papillonite": its primary and secondary cutaneous lesions, their localisation and evolution as well as its accompanying symptoms such as respiratory pathology. Epidemiologic survey shows a parallelism between the occurrence of papillonite and the presence of the moth Hylesia urticans. The urticant apparatus of this moth was studied with the scanning electron microscope. "Arrow" (fléchettes) were found and they more or less resemble the urticant apparatus of Thaumetopoea pityocampa Schiff caterpillar. The mechanism of action has been studied in the animal and in humans. Extracts prepared from the "arrows" have been rested in vivo guinea-pigs (bleu Evans, Liacopoulos et al.). The findings seem to incriminate an histamino-liberation. PMID:6666924

  18. Human T-Cell Lymphotropic Virus Type 1 Subtype C Molecular Variants among Indigenous Australians: New Insights into the Molecular Epidemiology of HTLV-1 in Australo-Melanesia

    PubMed Central

    Afonso, Philippe V.; Gessain, Antoine

    2013-01-01

    Background HTLV-1 infection is endemic among people of Melanesian descent in Papua New Guinea, the Solomon Islands and Vanuatu. Molecular studies reveal that these Melanesian strains belong to the highly divergent HTLV-1c subtype. In Australia, HTLV-1 is also endemic among the Indigenous people of central Australia; however, the molecular epidemiology of HTLV-1 infection in this population remains poorly documented. Findings Studying a series of 23 HTLV-1 strains from Indigenous residents of central Australia, we analyzed coding (gag, pol, env, tax) and non-coding (LTR) genomic proviral regions. Four complete HTLV-1 proviral sequences were also characterized. Phylogenetic analyses implemented with both Neighbor-Joining and Maximum Likelihood methods revealed that all proviral strains belong to the HTLV-1c subtype with a high genetic diversity, which varied with the geographic origin of the infected individuals. Two distinct Australians clades were found, the first including strains derived from most patients whose origins are in the North, and the second comprising a majority of those from the South of central Australia. Time divergence estimation suggests that the speciation of these two Australian clades probably occurred 9,120 years ago (38,000–4,500). Conclusions The HTLV-1c subtype is endemic to central Australia where the Indigenous population is infected with diverse subtype c variants. At least two Australian clades exist, which cluster according to the geographic origin of the human hosts. These molecular variants are probably of very ancient origin. Further studies could provide new insights into the evolution and modes of dissemination of these retrovirus variants and the associated ancient migration events through which early human settlement of Australia and Melanesia was achieved. PMID:24086779

  19. Emergence of dengue virus 4 genotype II in Guangzhou, China, 2010: Survey and molecular epidemiology of one community outbreak

    PubMed Central

    2012-01-01

    Background The re-emergence of dengue virus 4 (DENV-4) has become a public health concern in South America, Southeast Asia and South Asia. However, it has not been known to have caused a local outbreak in China for the past 20 years. The purpose of this study was to elucidate the epidemiology of one local community outbreak caused by DENV-4 in Guangzhou city, China, in 2010; and to determine the molecular characteristics of the genotype II virus involved. Case presentations During September and October of 2010, one imported case, a Guangzhou resident who travelled back from Thailand, resulted in 18 secondary autochthonous cases in Guangzhou City, with an incidence rate of 5.53 per 10,000 residents. In indigenous cases, 14 serum samples tested positive for IgM against DENV and 7 for IgG from a total of 15 submitted serum samples, accompanied by 5 DENV-4 isolates. With identical envelope gene nucleotide sequences, the two isolates (D10168-GZ from the imported index case and Guangzhou 10660 from the first isolate in the autochthonous cases) were grouped into DENV-4 genotype II after comparison to 32 previous DENV-4 isolates from GenBank that originated from different areas. Conclusions Based on epidemiological and phylogenetic analyses, the outbreak, which was absent for 20 years after the DENV-4 genotype I outbreak in 1990, was confirmed as DENV-4 genotype II and initially traced to the imported index case, a Guangzhou resident who travelled back from Thailand. PMID:22497881

  20. The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia.

    PubMed

    Pham Thanh, Duy; Thompson, Corinne N; Rabaa, Maia A; Sona, Soeng; Sopheary, Sun; Kumar, Varun; Moore, Catrin; Tran Vu Thieu, Nga; Wijedoru, Lalith; Holt, Kathryn E; Wong, Vanessa; Pickard, Derek; Thwaites, Guy E; Day, Nicholas; Dougan, Gordon; Turner, Paul; Parry, Christopher M; Baker, Stephen

    2016-06-01

    Typhoid fever, caused by the bacterium Salmonella Typhi, is an endemic cause of febrile disease in Cambodia. The aim of this study was to better understand the epidemiology of pediatric typhoid fever in Cambodia. We accessed routine blood culture data from Angkor Hospital for Children (AHC) in Siem Reap province between 2007 and 2014, and performed whole genome sequencing (WGS) on the isolated bacteria to characterize the S. Typhi population. The resulting phylogenetic information was combined with conventional epidemiological approaches to investigate the spatiotemporal distribution of S. Typhi and population-level risk factors for reported disease. During the study period, there were 262 cases of typhoid within a 100 km radius of AHC, with a median patient age of 8.2 years (IQR: 5.1-11.5 years). The majority of infections occurred during the rainy season, and commune incidences as high as 11.36/1,000 in children aged <15 years were observed over the study period. A population-based risk factor analysis found that access to water within households and increasing distance from Tonle Sap Lake were protective. Spatial mapping and WGS provided additional resolution for these findings, and confirmed that proximity to the lake was associated with discrete spatiotemporal disease clusters. We confirmed the dominance of MDR H58 S. Typhi in this population, and found substantial evidence of diversification (at least seven sublineages) within this single lineage. We conclude that there is a substantial burden of pediatric typhoid fever in rural communes in Cambodia. Our data provide a platform for additional population-based typhoid fever studies in this location, and suggest that this would be a suitable setting in which to introduce a school-based vaccination programme with Vi conjugate vaccines. PMID:27331909

  1. The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia

    PubMed Central

    Rabaa, Maia A; Sona, Soeng; Sopheary, Sun; Kumar, Varun; Moore, Catrin; Tran Vu Thieu, Nga; Wijedoru, Lalith; Holt, Kathryn E.; Wong, Vanessa; Pickard, Derek; Thwaites, Guy E.; Day, Nicholas; Dougan, Gordon; Turner, Paul; Parry, Christopher M.; Baker, Stephen

    2016-01-01

    Typhoid fever, caused by the bacterium Salmonella Typhi, is an endemic cause of febrile disease in Cambodia. The aim of this study was to better understand the epidemiology of pediatric typhoid fever in Cambodia. We accessed routine blood culture data from Angkor Hospital for Children (AHC) in Siem Reap province between 2007 and 2014, and performed whole genome sequencing (WGS) on the isolated bacteria to characterize the S. Typhi population. The resulting phylogenetic information was combined with conventional epidemiological approaches to investigate the spatiotemporal distribution of S. Typhi and population-level risk factors for reported disease. During the study period, there were 262 cases of typhoid within a 100 km radius of AHC, with a median patient age of 8.2 years (IQR: 5.1–11.5 years). The majority of infections occurred during the rainy season, and commune incidences as high as 11.36/1,000 in children aged <15 years were observed over the study period. A population-based risk factor analysis found that access to water within households and increasing distance from Tonle Sap Lake were protective. Spatial mapping and WGS provided additional resolution for these findings, and confirmed that proximity to the lake was associated with discrete spatiotemporal disease clusters. We confirmed the dominance of MDR H58 S. Typhi in this population, and found substantial evidence of diversification (at least seven sublineages) within this single lineage. We conclude that there is a substantial burden of pediatric typhoid fever in rural communes in Cambodia. Our data provide a platform for additional population-based typhoid fever studies in this location, and suggest that this would be a suitable setting in which to introduce a school-based vaccination programme with Vi conjugate vaccines. PMID:27331909

  2. Epidemiologic studies of the human microbiome and cancer

    PubMed Central

    Vogtmann, Emily; Goedert, James J

    2016-01-01

    The human microbiome, which includes the collective genome of all bacteria, archaea, fungi, protists, and viruses found in and on the human body, is altered in many diseases and may substantially affect cancer risk. Previously detected associations of individual bacteria (e.g., Helicobacter pylori), periodontal disease, and inflammation with specific cancers have motivated studies considering the association between the human microbiome and cancer risk. This short review summarises microbiome research, focusing on published epidemiological associations with gastric, oesophageal, hepatobiliary, pancreatic, lung, colorectal, and other cancers. Large, prospective studies of the microbiome that employ multidisciplinary laboratory and analysis methods, as well as rigorous validation of case status, are likely to yield translational opportunities to reduce cancer morbidity and mortality by improving prevention, screening, and treatment. PMID:26730578

  3. [Alcohol and wine and cardiovascular diseases in epidemiologic studies].

    PubMed

    Sinkiewicz, Władysław; Weglarz, Magdalena

    2009-01-01

    Moderate alcohol intake is associated with lower risk of cardiovascular diseases. A large number of epidemiologic studies have demonstrated a U- or J-shaped relation between alcohol consumption and total mortality, coronary heart disease and ischemic stroke. The lowest risk occurs in those who drink one or two drinks per day. Many studies have dealt with the question if specific alcoholic beverage (vodka, beer, wine, liquor) might offer a greater protection. Red wine containing polyphenols is believed to possess exceptional cardioprotective properties, especially if consumed with meals. However, alcohol beverages should not be recommended to patients as a substitute for the well-proven, cardiovascular risk reducing alternatives such as low fat diet, exercise and pharmacotherapy. PMID:19739580

  4. Quality control for exposure assessment in epidemiological studies.

    PubMed

    Bornkessel, C; Blettner, M; Breckenkamp, J; Berg-Beckhoff, G

    2010-08-01

    In the framework of an epidemiological study, dosemeters were used for the assessment of radio frequency electromagnetic field exposure. To check the correct dosemeter's performance in terms of consistency of recorded field values over the entire study period, a quality control strategy was developed. In this paper, the concept of quality control and its results is described. From the 20 dosemeters used, 19 were very stable and reproducible, with deviations of a maximum of +/-1 dB compared with their initial state. One device was found to be faulty and its measurement data had to be excluded from the analysis. As a result of continuous quality control procedures, the confidence in the measurements obtained during the field work was strengthened significantly. PMID:20308051

  5. Hodgkin's disease: case control epidemiological study in Yorkshire.

    PubMed Central

    Bernard, S. M.; Cartwright, R. A.; Darwin, C. M.; Richards, I. D.; Roberts, B.; O'Brien, C.; Bird, C. C.

    1987-01-01

    This is the first report of a case-control epidemiological study on lymphomas and leukaemias occurring in Yorkshire during 1979-84. This paper deals with the results of the Hodgkin's disease analysis comprising 248 cases and 489 controls. The results indicate support for previous work with respect to small family size and past history of infectious mononucleosis. Positive observations made in a previous pilot study are also confirmed and extended with respect to associations with certain chronic skin lesions, dental anaesthesia and familial factors. Negative associations are described with respect to X-ray exposures and cigarette smoking. It is proposed that these results fit into a general hypothesis that these conditions are the result of interaction between infectious agents and altered immunity in those persons genetically predisposed. PMID:3814482

  6. How can epidemiological studies contribute to understanding autism spectrum disorders?

    PubMed

    Honda, Hideo

    2013-02-01

    More and more studies on the frequency of autism spectrum disorders (ASD) have been published recently, most of which show the increase in prevalence data. In this review, the author pointed out factors and parameters to be considered in analyzing frequency data, i.e., the enlargement of the concept of autism, prevalence and incidence, accuracy and precision in the initial screening, and the effect of the "vaccine debate". The proportion of high-functioning ASD has been growing higher and higher due to better recognition in the last few years, and the apparent increase might still be the tip of an iceberg. Future epidemiological studies should include themes on diversity of the longitudinal course and re-conceptualization of ASD by dimensional diagnosis. PMID:22766241

  7. Ultraviolet radiation and the eye: an epidemiologic study.

    PubMed Central

    Taylor, H R

    1989-01-01

    Circumstantial evidence from biochemical, animal, and epidemiologic studies suggests an association between exposure to UV-B radiation (290 nm to 320 nm) and cataract. Such an association had not been proven because it had not been possible to quantify ocular UV-B exposure of individuals or to reliably grade the type and severity of cataract in field studies. We undertook an epidemiologic survey of cataract among 838 watermen who work on the Chesapeake Bay. Their individual ocular UV-B exposure was quantified for each year of life over the age of 16, on the basis of a detailed occupational history combined with laboratory and field measurements of ocular UV-B exposure. Cataracts were graded by both type and severity through clinical and photographic means. SMD changes were ascertained by fundal photography. A general medical history was taken to discover potentially confounding factors. This study showed that people with cortical lens opacities had a 21% higher UV-B exposure at each year of life than people without these opacities. A doubling in lifetime UV-B exposure led to a 60% increase in the risk of cortical cataract, and those with a high annual UV-B exposure increased their risk of cortical cataract over threefold. Corneal changes, namely pterygium and CDK, were also strongly associated with high UV-B exposure. No association was found between nuclear lens opacities or macular degeneration and UV-B exposure. This study also indicated several simple, practical measures, such as wearing spectacles or a hat, that effectively protect the eye from UV-B exposure. Thus it is easily within the power of individuals to protect their eyes from excessive UV-B exposure and reduce their risk of cortical cataract. A program of public education in this area could be a cost-effective means of reducing this important disease. PMID:2562534

  8. Molecular epidemiology, evolution and phylogeny of Chikungunya virus: An updating review.

    PubMed

    Lo Presti, Alessandra; Cella, Eleonora; Angeletti, Silvia; Ciccozzi, Massimo

    2016-07-01

    Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus belonging to the Togaviridae family, causing a febrile illness associated with severe arthralgia and rash. In this review, we summarized a series of articles published from 2013 to 2016 concerning CHIKV epidemiology, phylogeny, vaccine and therapies, to give an update of our most recent article written in 2014 (Lo Presti et al.,2014). CHIKV infection was first reported in 1952 from Makonde plateaus and since this time caused many outbreaks worldwide, involving the Indian Ocean region, African countries, American continent and Italy. CHIKV infection is still underestimated and it is normally associated with clinical symptoms overlapping with dengue virus, recurring epidemics and mutations within the viral genome. These characteristics promote the geographical spread and the inability to control vector-mediated transmission of the virus. For these reasons, the majority of studies were aimed to describe outbreaks and to enhance knowledge on CHIKV biology, pathogenesis, infection treatment, and prevention. In this review, 16 studies on CHIKV phylogenetic and phylodinamics were considered, during the years 2013-2016. Phylogenetic and phylodinamic analysis are useful tools to investigate how the genealogy of a pathogen population is influenced by pathogen's demographic history, host immunological milieu and environmental/ecological factors. Phylogenetic tools were revealed important to reconstruct the geographic spread of CHIKV during the epidemics wave and to have information on the circulating strains of the virus, that are important for the prediction and control of the epidemics, as well as for vaccines and antiviral drugs development. In conclusion, this updating review can give a critical appraisal of the epidemiology, therapeutic and phylogenesis of CHIKV, reinforcing the need to monitor the geographic spread of virus and vectors. PMID:27085290

  9. Radiation epidemiology and recent paediatric computed tomography studies.

    PubMed

    Boice, J D

    2015-06-01

    Recent record-linkage studies of cancer risk following computed tomography (CT) procedures among children and adolescents under 21 years of age must be interpreted with caution. The reasons why the examinations were performed were not known, and the dosimetric approaches did not include individual dose reconstructions or account for the possibility for missed examinations. The recent report (2013) on children by the United Nations Scientific Committee on the Effects of Atomic Radiation concluded that the associations may have resulted from confounding by indication (also called 'reverse causation'), and not radiation exposure. The reported cancer associations may very well have been related to the patients' underlying health conditions that prompted the examinations. Reverse causation has been observed in other epidemiological investigations, such as a Swedish study of thyroid cancer risk following I-131 scintillation imaging scans, and in studies of brain cancer risk following Thorotrast for cerebral angiography. Epidemiological patterns reported in the CT studies were also inconsistent with the world's literature. For example, in a UK study, teenagers had a higher risk of brain tumour than young children; in an Australian study, cancers not previously linked to radiation were significantly elevated; and in a Taiwanese study, the risk of benign tumours decreased with age at the time of CT examination. In all studies, solid tumours appeared much earlier than previously reported. Remarkably, in the Australian study, brain cancer excesses were seen regardless of whether or not the CT was to the head, i.e. a significant excess was reported for CT examinations of the abdomen and extremities, which involved no radiation exposure to the brain. In the UK study, the significance of the 'leukaemia' finding was only because myelodysplastic syndrome was added to the category, and there was no significance for leukaemia alone. Without knowledge of why CT examinations were

  10. Bat Rabies in France: A 24-Year Retrospective Epidemiological Study

    PubMed Central

    Picard-Meyer, Evelyne; Robardet, Emmanuelle; Arthur, Laurent; Larcher, Gérald; Harbusch, Christine; Servat, Alexandre; Cliquet, Florence

    2014-01-01

    Since bat rabies surveillance was first implemented in France in 1989, 48 autochthonous rabies cases without human contamination have been reported using routine diagnosis methods. In this retrospective study, data on bats submitted for rabies testing were analysed in order to better understand the epidemiology of EBLV-1 in bats in France and to investigate some epidemiological trends. Of the 3176 bats submitted for rabies diagnosis from 1989 to 2013, 1.96% (48/2447 analysed) were diagnosed positive. Among the twelve recognised virus species within the Lyssavirus genus, two species were isolated in France. 47 positive bats were morphologically identified as Eptesicus serotinus and were shown to be infected by both the EBLV-1a and the EBLV-1b lineages. Isolation of BBLV in Myotis nattereri was reported once in the north-east of France in 2012. The phylogenetic characterisation of all 47 French EBLV-1 isolates sampled between 1989 and 2013 and the French BBLV sample against 21 referenced partial nucleoprotein sequences confirmed the low genetic diversity of EBLV-1 despite its extensive geographical range. Statistical analysis performed on the serotine bat data collected from 1989 to 2013 showed seasonal variation of rabies occurrence with a significantly higher proportion of positive samples detected during the autumn compared to the spring and the summer period (34% of positive bats detected in autumn, 15% in summer, 13% in spring and 12% in winter). In this study, we have provided the details of the geographical distribution of EBLV-1a in the south-west of France and the north-south division of EBLV-1b with its subdivisions into three phylogenetic groups: group B1 in the north-west, group B2 in the centre and group B3 in the north-east of France. PMID:24892287

  11. Pontiac fever: an operational definition for epidemiological studies

    PubMed Central

    Tossa, Paul; Deloge-Abarkan, Magali; Zmirou-Navier, Denis; Hartemann, Philippe; Mathieu, Laurence

    2006-01-01

    Background Pontiac fever is usually described in epidemic settings. Detection of Pontiac fever is a marker of an environmental contamination by Legionella and should thereby call for prevention measures in order to prevent outbreak of Legionnaire's disease. The objective of this study is to propose an operational definition of Pontiac fever that is amenable to epidemiological surveillance and investigation in a non epidemic setting. Methods A population of 560 elderly subjects residing in 25 nursing homes was followed during 4 months in order to assess the daily incidence of symptoms associated, in the literature, with Pontiac fever. The water and aerosol of one to 8 showers by nursing home were characterized combining conventional bacterial culture of Legionella and the Fluorescence In Situ Hybridization (FISH) technique that used oligonucleotides probes specific for Legionellaceae. A definition of Pontiac fever was devised based on clinical symptoms described in epidemic investigations and on their timing after the exposure event. The association between incidence of Pontiac fever and shower contamination levels was evaluated to test the relevance of this definition. Results The proposed definition of Pontiac fever associated the following criteria: occurrence of at least one symptom among headache, myalgia, fever and shivers, possibly associated with other 'minor' symptoms, within three days after a shower contaminated by Legionella, during a maximum of 8 days (minimum 2 days). 23 such cases occurred during the study (incidence rate: 0.125 cases per person-year [95% CI: 0.122–0.127]). A concentration of Legionella in water equal to or greater than 104.L-1 (FISH method) was associated with a significant increase of incidence of Pontiac fever (p = 0.04). Conclusion Once validated in other settings, the proposed definition of Pontiac fever might be used to develop epidemiological surveillance and help draw attention on sources of Legionella. PMID:16646972

  12. Comparative molecular epidemiology provides new insights into Zucchini yellow mosaic virus occurrence in France.

    PubMed

    Lecoq, H; Wipf-Scheibel, C; Nozeran, K; Millot, P; Desbiez, C

    2014-06-24

    Zucchini yellow mosaic virus (ZYMV, genus Potyvirus) causes important crop losses in cucurbits worldwide. In France, ZYMV epidemics are sporadic but occasionally very severe. This contrasts with Watermelon mosaic virus (WMV, genus Potyvirus) which causes regular and early epidemics. Factors influencing ZYMV epidemiology are still poorly understood. In order to gain new insights on the ecology and epidemiology of this virus, a 5-year multilocation trial was conducted in which ZYMV spread and populations were studied in each of the 20 plot/year combinations and compared with WMV. Search for ZYMV alternative hosts was conducted by testing weeds growing naturally around one plot and also by checking ZYMV natural infections in selected ornamental species. Although similar ZYMV populations were observed occasionally in the same plot in two successive years suggesting the occurrence of overwintering hosts nearby, only two Lamium amplexicaule plants were found to be infected by ZYMV of 3459 weed samples that were tested. The scarcity of ZYMV reservoirs contrasts with the frequent detection of WMV in the same samples. Since ZYMV and WMV have many aphid vectors in common and are transmitted with similar efficiencies, the differences observed in ZYMV and WMV reservoir abundances could be a major explanatory factor for the differences observed in the typology of ZYMV and WMV epidemics in France. Other potential ZYMV alternative hosts have been identified in ornamental species including begonia. Although possible in a few cases, exchanges of populations between different plots located from 500 m to 4 km apart seem uncommon. Therefore, the potential dissemination range of ZYMV by its aphid vectors seems to be rather limited in a fragmented landscape. PMID:24486486

  13. [Health examination in future at the era of low tuberculosis incidence--from contacts examination toward active epidemiological studies].

    PubMed

    Maeda, Hideo; Shirai, Chika

    2013-03-01

    test in Tokyo: Hideo MAEDA (Bureau of Social Welfare and Public Health, Tokyo Metropolitan Government). 2. Contact investigation of a tuberculosis outbreak: Kenichi MIYAMOTO (Takaido Community Health Center). We have experienced a TB outbreak in integrated junior and senior high school in Tokyo. Index patient was a student with persistent respiratory symptoms for six months before diagnosis of sputum smear-positive TB. Public health center started contact investigation immediately. QFT-positive rates were high in close contacts, especially in classmates. Additionally, a student outside of contact investigation was diagnosed as TB and considered to be infected from the first patient by VNTR analysis. Therefore, public health center expanded QFT-tests to all students and teachers in this school. Finally, 9 students and 2 teachers in this school were diagnosed as sputum smear-negative TB by contact investigation. 3. Utilization of molecular epidemiological procedure in contact investigation in Kyoto City: Masahiro ITO (Public Health Center of Kyoto City) Molecular epidemiological procedure using VNTR analysis has been used for contact investigation of tuberculosis since January 2011 in Kyoto City. One hundred forty four strains of Mycobacterium tuberculosis from patients with tuberculosis were investigated and 130 strains were fully analyzed. Fourteen clusters were found and the number of strains included in the cluster was ranged from two to 11. Epidemiological relationship between patients in one cluster was found, however, significant relationship in another clusters was not demonstrated. It was suggested that VNTR analysis is useful for molecular epidemiological analysis of tuberculosis. 4. The population based molecular epidemiological studies and QFT test in a contact examination: Riyo FUJIYAMA, Keisuke MATSUBAYASHI, Setsuko MIZUSHIRI, Junko HIGUCHIL Chika SHIRAI, Yuko KATAGAMI, Mieko CHIHARA, Akihiro IJICHI (Kobe City Public Health Center), Kentaro ARIKAWA, Noriko

  14. Identification of a predominant isolate of Mycobacterium tuberculosis using molecular and clinical epidemiology tools and in vitro cytokine responses

    PubMed Central

    Sharma, M Kaushal; Al-Azem, A; Wolfe, J; Hershfield, E; Kabani, A

    2003-01-01

    Background Tuberculosis (TB) surveillance programs in Canada have established that TB in Canada is becoming a disease of geographically and demographically distinct groups. In 1995, treaty status aboriginals from the province of Manitoba accounted for 46% of the disease burden of this sub-group in Canada. The TB incidence rates are dramatically high in certain reserves of Manitoba and are equivalent to rates in African countries. The objective of our study was to identify prevalent isolates of Mycobacterium tuberculosis in the patient population of Manitoba using molecular epidemiology tools, studying the patient demographics associated with the prevalent strain and studying the in vitro cytokine profiles post-infection with the predominant strain. Methods Molecular typing was performed on all isolates available between 1992 to1997. A clinical database was generated using patient information from Manitoba. THP-1 cells were infected using strains of M. tuberculosis and cytokine profiles were determined using immunoassays for cytokines IL-1β, IL-10, IL-12, IFN-γ and TNF-α. Results In Manitoba, 24% of the disease burden is due to a particular M. tuberculosis strain (Type1). The strain is common in patients of aboriginal decent and is responsible for at least 87% of these cases. Cytokine assays indicate that the Type1 strain induces comparatively lower titers of IL-1β, IFN-γ and TNF-α in infected THP-1 cells as compared to H37Ra and H37Rv strains. Conclusion In Manitoba, Type1 strain is predominant in TB patients. The majority of the cases infected with this particular strain are newly active with a high incidence of respiratory disease, positive chest radiographs and pulmonary cavities. In vitro secretion of IL-1β, IFN-γ and TNF-α is suppressed in Type1 infected culture samples when compared to H37Ra and H37Rv infected cells. PMID:12697047

  15. Cycloplegic refraction is the gold standard for epidemiological studies.

    PubMed

    Morgan, Ian G; Iribarren, Rafael; Fotouhi, Akbar; Grzybowski, Andrzej

    2015-09-01

    Many studies on children have shown that lack of cycloplegia is associated with slight overestimation of myopia and marked errors in estimates of the prevalence of emmetropia and hyperopia. Non-cycloplegic refraction is particularly problematic for studies of associations with risk factors. The consensus around the importance of cycloplegia in children left undefined at what age, if any, cycloplegia became unnecessary. It was often implicitly assumed that cycloplegia is not necessary beyond childhood or early adulthood, and thus, the protocol for the classical studies of refraction in older adults did not include cycloplegia. Now that population studies of refractive error are beginning to fill the gap between schoolchildren and older adults, whether cycloplegia is required for measuring refractive error in this age range, needs to be defined. Data from the Tehran Eye Study show that, without cycloplegia, there are errors in the estimation of myopia, emmetropia and hyperopia in the age range 20-50, just as in children. Similar results have been reported in an analysis of data from the Beaver Dam Offspring Eye Study. If the only important outcome measure of a particular study is the prevalence of myopia, then cycloplegia may not be crucial in some cases. But, without cycloplegia, measurements of other refractive categories as well as spherical equivalent are unreliable. In summary, the current evidence suggests that cycloplegic refraction should be considered as the gold standard for epidemiological studies of refraction, not only in children, but in adults up to the age of 50. PMID:25597549

  16. Molecular Epidemiological Investigation of Porcine kobuvirus and Its Coinfection Rate with PEDV and SaV in Northwest China

    PubMed Central

    Lan, Xi

    2016-01-01

    Porcine kobuvirus (PKV) has circulated throughout China in recent years. Although many studies have detected it throughout the world, its molecular epidemiology has not been characterized in northwest China. To understand its prevalence, 203 fecal samples were collected from different regions of Gansu Province and tested with reverse transcription-polymerase chain reaction. In this study, we tested these samples for PKV, porcine epidemic diarrhea virus (PEDV), and sapovirus and analyzed the amplified 2C gene fragments of PKV. Overall, 126 (62.1%) samples were positive for PKV. Of the 74 piglets samples among the 203 fecal samples, 65 (87.8%) were positive for PKV. PKV infection was often accompanied by PEDV, but the relationship between the two viruses must be confirmed. A phylogenetic analysis indicated that the PKV strains isolated from the same regions clustered on the same branches. This investigation shows that PKV infections are highly prevalent in pigs in northwest China, especially in piglets with symptoms of diarrhea. PMID:27294133

  17. Molecular Epidemiological Investigation of Porcine kobuvirus and Its Coinfection Rate with PEDV and SaV in Northwest China.

    PubMed

    Wang, Chen; Lan, Xi; Yang, Bin

    2016-01-01

    Porcine kobuvirus (PKV) has circulated throughout China in recent years. Although many studies have detected it throughout the world, its molecular epidemiology has not been characterized in northwest China. To understand its prevalence, 203 fecal samples were collected from different regions of Gansu Province and tested with reverse transcription-polymerase chain reaction. In this study, we tested these samples for PKV, porcine epidemic diarrhea virus (PEDV), and sapovirus and analyzed the amplified 2C gene fragments of PKV. Overall, 126 (62.1%) samples were positive for PKV. Of the 74 piglets samples among the 203 fecal samples, 65 (87.8%) were positive for PKV. PKV infection was often accompanied by PEDV, but the relationship between the two viruses must be confirmed. A phylogenetic analysis indicated that the PKV strains isolated from the same regions clustered on the same branches. This investigation shows that PKV infections are highly prevalent in pigs in northwest China, especially in piglets with symptoms of diarrhea. PMID:27294133

  18. Molecular epidemiology of canine picornavirus in Hong Kong and Dubai and proposal of a novel genus in Picornaviridae.

    PubMed

    Woo, Patrick C Y; Lau, Susanna K P; Choi, Garnet K Y; Huang, Yi; Sivakumar, Saritha; Tsoi, Hoi-Wah; Yip, Cyril C Y; Jose, Shanty V; Bai, Ru; Wong, Emily Y M; Joseph, Marina; Li, Tong; Wernery, Ulrich; Yuen, Kwok-Yung

    2016-07-01

    Previously, we reported the discovery of a novel canine picornavirus (CanPV) in the fecal sample of a dog. In this molecular epidemiology study, CanPV was detected in 15 (1.11%) of 1347 canine fecal samples from Hong Kong and one (0.76%) of 131 canine fecal samples from Dubai, with viral loads 1.06×10(3) to 6.64×10(6) copies/ml. Complete genome sequencing and phylogenetic analysis showed that CanPV was clustered with feline picornavirus (FePV), bat picornavirus (BatPV) 1 to 3, Ia io picornavirus 1 (IaioPV1) and bovine picornavirus (BoPV), and this cluster was most closely related to the genera Enterovirus and Sapelovirus. The Ka/Ks ratios of all the coding regions were <0.1. According to the definition of the Picornavirus Study Group of ICTV, CanPV, FePV, BatPV 1 to 3, IaioPV1 and BoPV should constitute a novel genus in Picornaviridae. BEAST analysis showed that this genus diverged from its most closely related genus, Sapelovirus, about 49 years ago. PMID:27051044

  19. Epidemiological characteristics and molecular typing of Salmonella enterica serovar Typhi during a waterborne outbreak in Eastern Anatolia.

    PubMed

    Bayram, Y; Güdücüoğlu, H; Otlu, B; Aypak, C; Gürsoy, N C; Uluç, H; Berktaş, M

    2011-07-01

    In this study, we aimed to study the molecular and epidemiological characteristics of Salmonella enterica serovar Typhi (S. Typhi) outbreak in Eastern Anatolia. Six hundred and thirty-seven patients from the same county with clinical diagnosis of typhoid fever were investigated with conventional methods from stool, urine and blood specimens. Antibiotic susceptibility tests and identifications were performed for positive specimens. Clonal relationships between the isolates were investigated using pulsed field gel electrophoresis (PFGE) method. A questionnaire was completed for the water consumption habits of patients. Of 91 culture positive specimens, 76 were blood, 13 were stool and 2 were urine. The isolates were resistant to ampicillin, ampicillin/sulbactam, chloramphenicol, cefuroxime, amikacin, gentamicin and trimethoprim-sulfamethoxazole. Although there was a single band difference in some isolates, PFGE results indicated that this was an outbreak caused by single strain according to the Tenover criteria. This outbreak thought to be associated with the consumption of tap water contaminated with sewage represents a breakdown of the basic public health and civil engineering infrastructure. Appropriate public health measures should be taken in order to avoid such outbreaks in the future. PMID:21929877

  20. Epidemiological characteristics and molecular typing of Salmonella enterica serovar Typhi during a waterborne outbreak in Eastern Anatolia

    PubMed Central

    BAYRAM, Y; GÜDÜCÜOĞLU, H; OTLU, B; AYPAK, C; GÜRSOY, N C; ULUÇ, H; BERKTAŞ, M

    2011-01-01

    In this study, we aimed to study the molecular and epidemiological characteristics of Salmonella enterica serovar Typhi (S. typhi) outbreak in Eastern Anatolia. Six hundred and thirty-seven patients from the same county with clinical diagnosis of typhoid fever were investigated with conventional methods from stool, urine and blood specimens. Antibiotic susceptibility tests and identifications were performed for positive specimens. Clonal relationships between the isolates were investigated using pulsed field gel electrophoresis (PFGE) method. A questionnaire was completed for the water consumption habits of patients. Of 91 culture positive specimens, 76 were blood, 13 were stool and 2 were urine. The isolates were resistant to ampicillin, ampicillin/sulbactam, chloramphenicol, cefuroxime, amikacin, gentamicin and trimethoprim–sulfamethoxazole. Although there was a single band difference in some isolates, PFGE results indicated that this was an outbreak caused by single strain according to the Tenover criteria. This outbreak thought to be associated with the consumption of tap water contaminated with sewage represents a breakdown of the basic public health and civil engineering infrastructure. Appropriate public health measures should be taken in order to avoid such outbreaks in the future. PMID:21929877

  1. Epidemiology and molecular genetics of colorectal cancer in iran: a review.

    PubMed

    Malekzadeh, Reza; Bishehsari, Faraz; Mahdavinia, Mahboobeh; Ansari, Reza

    2009-03-01

    Although the incidence of colorectal cancer in Iranian older age subjects is currently very low compared to Western population, the younger generation is experiencing an accelerated rate approaching the Western rates and the burden of disease will increase dramatically in near future. The high frequency of positive family history of colorectal cancer in Iranian patients indicates that a significant number of colorectal cancers in Iran arise in family members and relatives of colorectal cancer patients. It is clear that the familial clustering of colorectal cancer is more often seen in younger probands and cancer located in the right side of the colon. These epidemiologic findings call for a broader attempt to promote public awareness and screening strategies in those families with a member affected by colorectal cancer, especially at younger age or with proximal tumors. Based on our present understanding, the possibility of preventing or curing most colon and rectal cancers is now plausible. The molecular biology of colon cancer has been the subject of many researches and is better understood than those for any other solid cancer and have established an important example for cancer research. It is now clear that colorectal cancer develops as the result of genetic and epigenetic alterations that lead to malignant transformation of normal mucosa. In spite of these scientific progresses and the fact that screening can reduce the rate of death by detecting early cancer or premalignant polyps, the rate of screening is very low globally and negligible in Iran and many other developing countries which is due to cost, resistance by physicians, patients, and the healthcare system. In Iran screening should at least be started in family members at earlier age with colonoscopy as the preferred modality of screening method. PMID:19249887

  2. Acanthamoeba keratitis update-incidence, molecular epidemiology and new drugs for treatment.

    PubMed

    Seal, D V

    2003-11-01

    A reliable figure for the expected incidence of Acanthamoeba keratitis of one per 30000 contact lens wearers per year has now been obtained from a combination of three cohort and three Questionnaire Reporting Surveys; 88% of cases wore hydrogel lenses and 12% wore rigid lenses. This figure now provides a basis for the expected number of cases against which to judge either epidemic outbreaks or effects of prevention with disinfecting solutions, better hygiene, or the use of disposable lenses. Molecular biology of Acanthamoeba has advanced considerably in the last 10 years with new automated sequencing technology. This has allowed the construction of a genotype identification scheme with 13 different genotypes against which to compare clinical isolates for epidemiological investigations or pathogenicity markers. So far, only four genotypes have been associated with keratitis of which the majority have been T4 but T3, T6, and T11 have each caused individual cases. Each genotype is heterogenous and can be further subdivided by comparison of sequences of diagnostic fragments of 18S rDNA, riboprinting by PCR-RFLP of 18S rDNA, or by mitochondrial DNA RFLP. Drug therapy has been revolutionised with the introduction of the biguanides-chlorhexidine or polyhexamethylene biguanide-with most but not all infections quickly resolving. Failure can still occur occasionally and further research is needed on more effective combination chemotherapy. A number of guanidines have been identified in this paper that could be usefully pursued as part of combination chemotherapy along with the alkylphosphocholines. PMID:14631394

  3. Molecular epidemiology and genetic diversity of Blastocystis infection in humans in Italy.

    PubMed

    Mattiucci, S; Crisafi, B; Gabrielli, S; Paoletti, M; Cancrini, G

    2016-02-01

    In order to describe the molecular epidemiology of Blastocystis infection in Italy, 189 isolates, which had been collected during the years 2012-2014 from mildly symptomatic patients, or those affected by inflammatory bowel disease (IBD), irritable bowel syndrome (IBS) or chronic diarrhoea, or otherwise immunosuppressed, were subtyped by sequence analysis of the SSU rRNA gene (536 bp). Six subtypes (STs) were detected: ST1 (15·3%), ST2 (13·8%), ST3 (46·0%), ST4 (21·7%), ST6 (3·2%) and ST8 (0·5%). They clustered in distinct clades, as inferred from Bayesian inference phylogenetic and median joining network analyses. A high genetic differentiation was found at the inter-subtype level; it ranged from Jukes-Cantor (JC) distance = 0·02 (between ST1 and ST4) to JC = 0·11 (between ST6 and ST2). At the intra-ST level, a high genetic homogeneity was registered in ST4, whereas higher genetic variation was found in isolates corresponding to ST1 and ST2. Accordingly, high values of haplotype and nucleotide diversity were observed in ST1, ST2 and ST3. No association was found between patient gender and ST, whereas ST3 and ST1 were significantly more prevalent in patients aged 15-50 years. A significant occurrence of Blastocystis ST4 in patients suffering from IBS, IBD or chronic diarrhoea was observed; in addition, a slight significant association between ST1 and ST3 and IBS patients was found. Multiple correspondence analysis showed some significant contribution of different variables (subtypes, haplotypes, age) in the observed pattern of ordination of the 189 patients in the symptom categories. PMID:26194649

  4. Genotype Distribution and Molecular Epidemiology of Hepatitis C Virus in Hubei, Central China

    PubMed Central

    Peng, Jing; Lu, Yanjun; Liu, Weiyong; Zhu, Yaowu; Yan, Xiaoling; Xu, Jingxin; Wang, Xiong; Wang, Yue; Liu, Wei; Sun, Ziyong

    2015-01-01

    Background Little is known about the molecular epidemiology of hepatitis C virus (HCV) infection in Central China. Methodology/Principal Findings A total of 570 patients from Hubei Province in central China were enrolled. These patients were tested positive for HCV antibody prior to blood transfusion. Among them, 177 were characterized by partial NS5B and/or Core-E1 sequences and classified into five subtypes: 1b, 83.0% (147/177); 2a, 13.0% (23/177); 3b, 2.3% (4/177); 6a, 1.1% (2/177); 3a, 0.6% (1/177). Analysis of genotype-associated risk factors revealed that paid blood donation and transfusion before 1997 were strongly associated with subtypes 1b and 2a, while some subtype 2a cases were also found in individuals with high risk sexual behaviors; subtypes 3b, 6a, and 3a were detected only in intravenous drug users. Phylogeographic analyses based on the coalescent datasets demonstrated that 1b, 2a, 3b, and 6a were locally epidemic in Hubei Province. Among them, subtype 1b Hubei strains may have served as the origins of this subtype in China, and 2a and 3b Hubei strains may have descended from the northwest and southwest of China, respectively, while 6a Hubei strains may have been imported from the central south and southwest. Conclusion/Significance The results suggest that the migration patterns of HCV in Hubei are complex and variable among different subtypes. Implementation of mandatory HCV screening before donation has significantly decreased the incidence of transfusion-associated HCV infection since 1997. More attention should be paid to intravenous drug use and unsafe sexual contact, which may have become new risk factors for HCV infection in Hubei Province. PMID:26325070

  5. Molecular Epidemiology of Avian Leukosis Virus Subgroup J in Layer Flocks in China

    PubMed Central

    Gao, Yulong; Yun, Bingling; Qin, Liting; Pan, Wei; Qu, Yue; Liu, Zaisi; Wang, Yongqiang; Qi, Xiaole; Gao, Honglei

    2012-01-01

    Avian leukosis virus subgroup J (ALV-J) was first isolated from meat-type chickens in 1988. No field cases of ALV-J infection or tumors in layer chickens were observed worldwide until 2004. However, layer flocks in China have experienced outbreaks of this virus in recent years. The molecular epidemiology of ALV-J strains isolated from layer flocks was investigated. The env genes of 77.8% (21/27) of the ALV-J layer isolates with a high degree of genetic variation were significantly different from the env genes of the prototype strain of ALV-J (HPRS-103) and American and Chinese strains from meat-type chickens (designated ALV-J broiler isolates). A total of 205 nucleotides were deleted from the 3′ untranslated region of 89.5% (17/19) of the ALV-J layer isolates. Approximately 94.7% (16/17) of the layer isolates contained a complete E element of 146 to 149 residues. The U3 sequences of 84.2% (16/19) of the ALV-J layer isolates displayed less than 92.5% sequence homology to those of the ALV-J broiler isolates, although the transcriptional regulatory elements that are typical of avian retroviruses were highly conserved. Several unique nucleotide substitutions in the env gene, the U3 region, and the E element of most of the ALV-J layer isolates were detected. These results suggested that the env gene, E element, and U3 region in the ALV-J layer isolates have evolved rapidly and were significantly different from those of the ALV-J broiler isolates. These findings will contribute to a better understanding of the pathogenic mechanism of layer tumor diseases induced by ALV-J. PMID:22205787

  6. Surveillance of Canine Rabies in the Central African Republic: Impact on Human Health and Molecular Epidemiology

    PubMed Central

    Tricou, Vianney; Bouscaillou, Julie; Kamba Mebourou, Emmanuel; Koyanongo, Fidèle Dieudonné; Nakouné, Emmanuel; Kazanji, Mirdad

    2016-01-01

    Background Although rabies represents an important public health threat, it is still a neglected disease in Asia and Africa where it causes tens of thousands of deaths annually despite available human and animal vaccines. In the Central African Republic (CAR), an endemic country for rabies, this disease remains poorly investigated. Methods To evaluate the extent of the threat that rabies poses in the CAR, we analyzed data for 2012 from the National Reference Laboratory for Rabies, where laboratory confirmation was performed by immunofluorescence and PCR for both animal and human suspected cases, and data from the only anti-rabies dispensary of the country and only place where post-exposure prophylaxis (PEP) is available. Both are located in Bangui, the capital of the CAR. For positive samples, a portion of the N gene was amplified and sequenced to determine the molecular epidemiology of circulating strains. Results In 2012, 966 exposed persons visited the anti-rabies dispensary and 632 received a post-exposure rabies vaccination. More than 90% of the exposed persons were from Bangui and its suburbs and almost 60% of them were under 15-years of age. No rabies-related human death was confirmed. Of the 82 samples from suspected rabid dogs tested, 69 were confirmed positive. Most of the rabid dogs were owned although unvaccinated. There was a strong spatiotemporal correlation within Bangui and within the country between reported human exposures and detection of rabid dogs (P<0.001). Phylogenetic analysis indicated that three variants belonging to Africa I and II lineages actively circulated in 2012. Conclusions These data indicate that canine rabies was endemic in the CAR in 2012 and had a detrimental impact on human health as shown by the hundreds of exposed persons who received PEP. Implementation of effective public health interventions including mass dog vaccination and improvement of the surveillance and the access to PEP are urgently needed in this country. PMID

  7. Molecular Epidemiology of Clostridium difficile Infection in a Large Teaching Hospital in Thailand

    PubMed Central

    Ngamskulrungroj, Popchai; Sanmee, Sittinee; Pusathit, Papanin; Piewngam, Pipat; Elliott, Briony; Riley, Thomas V.; Kiratisin, Pattarachai

    2015-01-01

    Clostridium difficile infection (CDI) is a leading cause of healthcare-associated morbidity and mortality worldwide. In Thailand, CDI exhibits low recurrence and mortality and its molecular epidemiology is unknown. CDI surveillance was conducted in a tertiary facility (Siriraj Hospital, Bangkok). A total of 53 toxigenic C. difficile strains from Thai patients were analyzed by multi-locus sequence typing (MLST), PCR ribotyping, and pulse-field gel electrophoresis (PFGE). The mean age of the cohort was 64 years and 62.3% were female; 37.7% of patients were exposed to > two antibiotics prior to a diagnosis of CDI, with beta-lactams the most commonly used drug (56.3%). Metronidazole was used most commonly (77.5%; success rate 83.9%), and non-responders were treated with vancomycin (success rate 100%). None of the isolates carried binary toxin genes. Most isolates (98.2–100%) were susceptible to metronidazole, vancomycin, tigecycline and daptomycin. There were 11 sequence types (STs), 13 ribotypes (RTs) and four PFGE types. Six previously identified STs (ST12, ST13, ST14, ST33, ST41 and ST45) and five novel STs unique to Thailand (ST66, ST67, ST68, ST69 and ST70) were identified. PCR RTs UK 017 (ST45) (45.3%) and UK 014/020 (ST33) (24.5%) were the most common. High concordance was observed between the MLST and ribotyping results (p<0.001). C. difficile isolates from Thai patients were highly susceptible to standard antimicrobial agents. In conclusion, the five STs indicate the high genetic diversity and unique polymorphisms in Thailand. Moreover, the emergence of antimicrobial resistance to vancomycin warranted continuous surveillance to prevent further spread of the toxigenic C. difficile isolates. PMID:26000789

  8. Global trends in molecular epidemiology of HIV-1 during 2000–2007

    PubMed Central

    Hemelaar, Joris; Gouws, Eleanor; Ghys, Peter D.; Osmanov, Saladin

    2013-01-01

    Objective To estimate the global and regional distribution of HIV-1 subtypes and recombinants between 2000 and 2007. Design Country-specific HIV-1 molecular epidemiology data were combined with estimates of the number of HIV-infected people in each country. Method Cross-sectional HIV-1 subtyping data were collected from 65913 samples in 109 countries between 2000 and 2007. The distribution of HIV-1 subtypes in individual countries was weighted according to the number of HIV-infected people in each country to generate estimates of regional and global HIV-1 subtype distribution for the periods 2000–2003 and 2004–2007. Results Analysis of the global distribution of HIV-1 subtypes and recombinants in the two time periods indicated a broadly stable distribution of HIV-1 subtypes worldwide with a notable increase in the proportion of circulating recombinant forms (CRFs), a decrease in unique recombinant forms (URFs), and an overall increase in recombinants. In 2004–2007, subtype C accounted for nearly half (48%) of all global infections, followed by subtypes A (12%) and B (11%), CRF02_AG (8%), CRF01_AE (5%), subtype G (5%) and D(2%). Subtypes F, H, J and K together cause fewer than 1% of infections worldwide. Other CRFs and URFs are each responsible for 4% of global infections, bringing the combined total of worldwide CRFs to 16% and all recombinants (CRFs plus URFs) to 20%. Conclusions The global and regional distributions of individual subtypes and recombinants are broadly stable, although CRFs may play an increasing role in the HIV pandemic. The global diversity of HIV-1 poses a formidable challenge to HIV vaccine development. PMID:21297424

  9. Critical review of epidemiologic studies related to ingested asbestos.

    PubMed Central

    Marsh, G M

    1983-01-01

    Thirteen epidemiologic studies of ingested asbestos conducted in five areas of the United States and Canada were reviewed and evaluated for the definitiveness and applicability regarding the development of ambient water quality standards. One or more studies found male or female associations between asbestos in water supplies and cancer mortality (or incidence) due to neoplasms of the esophagus, stomach, small intestine, colon, rectum, gallbladder, pancreas, peritoneum, lungs, pleura, prostate, kidneys, brain, and thyroid, and also due to leukemia. Several methodologic weaknesses and limitations were found in each study, leading to the determination that no individual study or aggregation of studies exist that would establish risk levels from ingested asbestos. A binomial probability analysis of the eight independent studies suggested that, while the level of male-female agreement was generally low, the number of observed positive associations in males and females for neoplasms of the esophagus, stomach, pancreas, and prostate was unlikely to have been generated by chance factors alone, and thus, may have a biological basis related to ingested asbestos. Cancers of the small intestine and leukemia were implicated to a lesser degree in this analysis. The patterns of integrated findings for most gastrointestinal cancers were somewhat consistent with patterns observed among asbestos-exposed occupational groups, whereas the patterns found for pancreatic cancer, kidney cancer, and leukemia were not consistent.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:6662094

  10. Epidemiology and molecular characterisation of metallo-β-lactamase-producing Enterobacteriaceae in a university hospital Intensive Care Unit in Greece.

    PubMed

    Koratzanis, Evangelos; Souli, Maria; Galani, Irene; Chryssouli, Zoi; Armaganidis, Apostolos; Giamarellou, Helen

    2011-11-01

    The molecular epidemiology of VIM-producing Enterobacteriaceae isolated at the beginning of an epidemic in the Intensive Care Unit (ICU) of a university hospital in Athens, Greece, was studied. All Gram-negative organisms isolated from March 2004 to November 2005 positive for metallo-β-lactamase (MBL) production were submitted to polymerase chain reaction (PCR) and sequencing, to repetitive sequence-based PCR (Rep-PCR) for molecular typing, and to S1 nuclease digestion for plasmid DNA characterisation. Conjugation experiments and isoelectric focusing were performed to identify co-existing β-lactamases. Amongst 23 patients, 12 suffered one or more clinical infections. Eighty-two isolates representing one isolate per clone, source and ICU patient were studied, including Klebsiella pneumoniae (77), Enterobacter cloacae (2), Citrobacter freundii (1) and Pseudomonas aeruginosa (2). High clonal diversity was detected amongst the K. pneumoniae, with 10 distinct clones identified. Conjugation was successful in 54.5% of K. pneumoniae, and five different-sized plasmids were detected. All K. pneumoniae and both E. cloacae isolates shared the same bla(VIM-1)-containing class 1 integron structure also carrying aacA7, dhfrI and aadA1 gene cassettes. The C. freundii isolate carried a different integron that included bla(VIM-1) and aac(6')-IIc. Both P. aeruginosa isolates were positive for bla(VIM-2). It was not possible to identify specific clones with the potential to cause clinical infections. In conclusion, a multiclonal cluster of MBL-producers was responsible for the first cases of colonisation and/or infection in the ICU. A single integron structure, common in Greek hospitals, efficiently disseminated between clones and species, suggesting that the epidemic was mainly the result of successful horizontal transfer of mobile genetic material rather than the result of horizontal transfer of one or a few clones. PMID:21873034

  11. New Insights into the Molecular Epidemiology and Population Genetics of Schistosoma mansoni in Ugandan Pre-school Children and Mothers

    PubMed Central

    Betson, Martha; Sousa-Figueiredo, Jose C.; Kabatereine, Narcis B.; Stothard, J. Russell

    2013-01-01

    Significant numbers of pre-school children are infected with Schistosoma mansoni in sub-Saharan Africa and are likely to play a role in parasite transmission. However, they are currently excluded from control programmes. Molecular phylogenetic studies have provided insights into the evolutionary origins and transmission dynamics of S. mansoni, but there has been no research into schistosome molecular epidemiology in pre-school children. Here, we investigated the genetic diversity and population structure of S. mansoni in pre-school children and mothers living in lakeshore communities in Uganda and monitored for changes over time after praziquantel treatment. Parasites were sampled from children (<6 years) and mothers enrolled in the longitudinal Schistosomiasis Mothers and Infants Study at baseline and at 6-, 12- and 18-month follow-up surveys. 1347 parasites from 35 mothers and 45 children were genotyped by direct sequencing of the cytochrome c oxidase (cox1) gene. The cox1 region was highly diverse with over 230 unique sequences identified. Parasite populations were genetically differentiated between lakes and non-synonymous mutations were more diverse at Lake Victoria than Lake Albert. Surprisingly, parasite populations sampled from children showed a similar genetic diversity to those sampled from mothers, pointing towards a non-linear relationship between duration of exposure and accumulation of parasite diversity. The genetic diversity six months after praziquantel treatment was similar to pre-treatment diversity. Our results confirm the substantial genetic diversity of S. mansoni in East Africa and provide significant insights into transmission dynamics within young children and mothers, important information for schistosomiasis control programmes. PMID:24349589

  12. Molecular epidemiology of enterovirus B77 isolated from non polio acute flaccid paralytic patients in Pakistan during 2013.

    PubMed

    Angez, Mehar; Shaukat, Shahzad; Zahra, Rabaab; Khurshid, Adnan; Sharif, Salmaan; Alam, Muhammad Masroor; Zaidi, Syed Sohail Zahoor

    2015-01-01

    Human enteroviruses are associated with various clinical syndromes and severe neurological disorders. The aim of this study was to determine the molecular epidemiology of non polio enteroviruses and their correlation with acute flaccid paralysis (AFP) patients living in Khyber Pakhtunkhwa (KP) and Federally Administered Tribal Areas (FATA) of Pakistan. The stool samples collected from these patients were used for isolation of non polio enteroviruses (NPEVs). Out of 38 samples, 29 (76.3%) were successfully typed by microneutralization assay into eleven serotypes including echovirus (E)-3 (5.3%), E-7 (2.6%), E-11 (13.2%), E-12 (7.9%), E-13 (10.5%), E-20 (7.9%), E-27 (5.3%), E-29 (10.5%), E-30 (7.9%), E-33 (2.6%), coxsackievirus (CV) B5 (2.6%) and nine isolates (23.7%) remained untyped which were confirmed as NPEVs by real time RT-PCR. Complete VP1 genetic sequencing data characterized untypeable isolates into enterovirus B77 (EV-B77). Moreover, molecular phylogenetic analysis classified these viruses into two new genotypes having high genetic diversity (at least 17.7%) with prototype. This study provides valuable information on extensive genetic diversity of EV-B77 genotypes. Although, its association with neurological disorder has not yet been known but isolation of nine EV-B77 viruses from AFP cases highlights the fact that they may have a contributing role in the etiology of AFP. In addition, it is needed to establish enterovirus surveillance system and laboratory diagnostic facilities for early detection of NPEVs that may cause poliomyelitis like paralysis especially in the situation when we are at the verge of polio eradication. PMID:25433133

  13. Molecular photoionization studies

    SciTech Connect

    Dehmer, P.M.

    1983-01-01

    This program is concerned with the study of the electronic structure of small molecules and clusters of molecules. Of particular interest is the interaction of discrete electronic states with one another and with the various ionization and dissociation continua. Since the Second Annual Meeting of the DOE-OHER Program on The Physics and Chemistry of Energy-Related Atmospheric Pollutants in April 1981, significant progress has been made in the following areas: (1) the study of the electronic structure of dimers and small clusters of rare gas atoms using photoionization techniques; (2) similar studies on clusters of CO/sub 2/ molecules; (3) the study of electronic structure of rare gas dimers and trimers using photoelectron and photoelectron-photoion coincidence techniques; (4) the investigation of the relationship between Rydberg states in atoms, van der Waals molecules, and chemically-bonded molecules; (5) the extension of the study of photoabsorption, photoionization, and predissociation processes in H/sub 2/ to the unsymmetric isotope HD; (6) the study of photoelectron spectra of H/sub 2/ and C/sub 2/H/sub 2/; (7) a review of some of the aspects of dissociation processes in small molecules; and (8) the creation of a new program to study the spectra and dynamics of the photoionization processes in small molecules using the technique of multiphoton ionization followed by mass and electron energy analysis of the product ions and electrons. Some of the highlights of this work are reviewed.

  14. Overview of epidemiological studies on wine, health and mortality.

    PubMed

    Ruf, J C

    2003-01-01

    Numerous epidemiological studies have observed that moderate intake of alcohol including wine is associated with a lower risk of cardiovascular disease (CVD). However, according to several authors, moderate consumption of wine is more beneficial than that of beer or spirits. Some studies have shown that moderate consumption of wine can lower mortality from CVD and other causes. The link between drinking wine and total mortality risk (all causes combined) has been studied. The results of various prospective population studies show that intake of beer and spirits from abstention to light to moderate daily intake did not influence mortality, while wine seems to have a beneficial effect on all causes of mortality. Other studies have reached the same conclusion. In general, several authors have reported that in subjects consuming wine in moderation the risk of mortality from all causes is 20-30% lower than in abstainers. Grape wine appears to be the main alcoholic beverage that contains antioxidant phenolic substances known to inhibit oxidation of low-density lipoprotein and affect hemostasis and carcinogenesis. In conclusion, there are differences in the effects of wine, beer and spirits on health. These differences may not be significant in coronary heart disease. Only moderate wine consumption appears to have a beneficial effect on several types of cancer and on total mortality. PMID:15134372

  15. Parental occupation and childhood cancer: review of epidemiologic studies.

    PubMed Central

    Savitz, D A; Chen, J H

    1990-01-01

    Parental occupational exposures might affect childhood cancer in the offspring through genetic changes in the ovum or sperm or through transplacental carcinogenesis. The 24 published epidemiologic studies of this association have all used case-control designs, with controls generally selected from birth certificates or from general population sampling. Occupational exposures were inferred from job titles on birth certificates or through interviews. A large number of occupation-cancer associations have been reported, many of which were not addressed or not confirmed in other studies. Several associations have been found with consistency: paternal exposures in hydrocarbon-associated occupations, the petroleum and chemical industries, and especially paint exposures have been associated with brain cancer; paint exposures have also been linked to leukemias. Maternal exposures have received much less attention, but studies have yielded strongly suggestive results linking a variety of occupational exposures to leukemia and brain cancer. The primary limitations in this literature are the inaccuracy inherent in assigning exposure based on job title alone and imprecision due to limited study size. Although no etiologic associations have been firmly established by these studies, the public health concerns and suggestive data warrant continued research. PMID:2272330

  16. Epidemiology of Colonic Aberrant Crypt Foci: Review and Analysis of Existing Studies

    PubMed Central

    Stevens, Richard G.; Swede, Helen; Rosenberg, Daniel W.

    2007-01-01

    Since first described in a rodent model in 1987, aberrant crypt foci (ACF) in the colon have been shown to exhibit many of the molecular features of the more advanced colonic neoplasms including cancer. Therefore, they may be early lesions with potential for progression, and be valuable biomarkers for reduction of risk of colorectal cancer (CRC). For this review, we searched PubMed, and reference lists of recent publications, for studies which reported on associations of features of ACF in humans, such as number or size, with subject characteristics, such as age or family history of CRC. Over 150 papers have reported on ACF in humans. However, the vast majority of these publications are concerned with molecular and morphological features of biopsied lesions, and not their epidemiology. None of the epidemiological studies were of optimum design, primarily due to their absence of a well-defined subject sampling frame or method. Given their ‘first-generation’ nature, consistent findings were of increased ACF number with age and with synchronous advanced colonic neoplasia. One study reported a higher mean number of ACF in subjects with a family history of CRC than in those without. The strongest evidence on the ability of ACF to predict a diagnosis of CRC will be from prospective studies with baseline ACF assessment in a large sample of disease-free persons (many thousands) who are followed carefully for many years. In the interim, because ACF are asymptomatic, well-designed cross-sectional studies are feasible and will yield valuable information on the relation of ACF to the known risk factors for CRC. This information can then be used to improve the design of prospective studies, and of clinical intervention trials that use ACF as an intermediate endpoint. PMID:17182176

  17. Impact of Bisphenol A on the Cardiovascular System — Epidemiological and Experimental Evidence and Molecular Mechanisms

    PubMed Central

    Gao, Xiaoqian; Wang, Hong-Sheng

    2014-01-01

    Bisphenol A (BPA) is a ubiquitous plasticizing agent used in the manufacturing of polycarbonate plastics and epoxy resins. There is well-documented and broad human exposure to BPA. The potential risk that BPA poses to the human health has attracted much attention from regulatory agencies and the general public, and has been extensively studied. An emerging and rapidly growing area in the study of BPA’s toxicity is its impact on the cardiovascular (CV) system. Recent epidemiological studies have shown that higher urinary BPA concentration in humans is associated with various types of CV diseases, including angina, hypertension, heart attack and coronary and peripheral arterial disease. Experimental studies have demonstrated that acute BPA exposure promotes the development of arrhythmias in female rodent hearts. Chronic exposure to BPA has been shown to result in cardiac remodeling, atherosclerosis, and altered blood pressure in rodents. The underlying mechanisms may involve alteration of cardiac Ca2+ handling, ion channel inhibition/activation, oxidative stress, and genome/transcriptome modifications. In this review, we discuss these recent findings that point to the potential CV toxicity of BPA, and highlight the knowledge gaps in this growing research area. PMID:25153468

  18. [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. PMID:24923166

  19. 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. PMID:26684209

  20. Endometriosis and breast cancer: A survey of the epidemiological studies

    PubMed Central

    PONTIKAKI, A.; SIFAKIS, S.; SPANDIDOS, D. A.

    2016-01-01

    Endometriosis is a chronic gynecological disease with a wide spectrum of clinical manifestations that affects approximately 10% of women of reproductive age. Recent reviews have demonstrated the connection between endometriosis and breast cancer, which represents the most frequently diagnosed female cancer and the most common cause of cancer-related mortality among women worldwide. The aim of this study was to conduct a survey of available published epidemiological studies indicating the association between endometriosis and breast cancer, and simultaneously to categorize the results based on the strength of the association, with the intention of the critical evaluation of the existing data. We performed a rigorous search of the PubMed/Medline database, using the key words ‘endometriosis’ and ‘breast cancer’ for all studies published in the English language until September 2015. We found 4 retrospective cohort studies, 4 case-control studies and 3 case-cohort studies that demonstrated a notable risk for developing breast cancer among women with endometriosis. By contrast, we also found 5 case-control studies, 1 prospective cohort study, 1 case-cohort study and 1 cross-sectional study that demonstrated a negative association between endometriosis and breast cancer. In conclusion, as regards the clarification of a ‘robust’ or ‘weak’ association between endometriosis and breast cancer, no definite conclusions could be drawn, due to the limited number of studies and the limitations of each of these studies. New well-designed, prospective cohort or randomized control trials with long-term follow-up are warranted in order to provide evidence-based clinical recommendations for proper counseling, screening and treatment strategies for patients with endometriosis, and hence to improve public health. PMID:26870162

  1. Epidemiological study of fixed drug eruption in Pointe-Noire.

    PubMed

    Ognongo-Ibiaho, A N; Atanda, H L

    2012-11-01

    A prospective study was conducted over a 27 month period in order to determine the epidemiological profile of fixed drug eruption (FDE) observed during a dermatological consultation at Pointe-Noire. During the study period 54 out of 9,070 persons consulting (0.6%) suffered from clinically diagnosed FDE. The variables studied were: age, sex, medicine and point of sale. The average age of onset was 30 years. The frequency of onset was higher in males (38 patients) than in females (16 patients). The incriminated medicines were: the sulfamides (48 patients) including Cotrimoxazole (45 patients ) and Sulfadoxine and Pyremethamine (3 patients) Coartem(®) + Doliprane(®) (1 patient), Chloramphenicol(®) (1 patient), Amidol(®) (1 patient), Duocotexin(®) + Paracetamol(®) (1 patient), Surquina(®) (1 patient), Amodiaquine(®) (1 patient). The point of sale was illicit (peddlers, markets) for 44 patients; for 10 patients it was a lawful outlet (pharmacies). This study shows that cotrimoxazole bought at illicit points of sale is the main etiology of FDE in the department, confirming that these medicines are counterfeit. The involvement of dermatologists in the fight against the illicit sale of medicines should be made a priority. PMID:23210952

  2. Chapter 8. Tea and Cancer Prevention: Epidemiological Studies

    PubMed Central

    Yuan, Jian-Min; Sun, Canlan; Butler, Lesley M.

    2011-01-01

    Experimental studies have consistently shown the inhibitory activities of tea extracts on tumorigenesis in multiple model systems. Epidemiologic studies, however, have produced inconclusive results in humans. A comprehensive review was conducted to assess the current knowledge on tea consumption and risk of cancers in humans. In general, consumption of black tea was not associated with lower risk of cancer. High intake of green tea was consistently associated with reduced risk of upper gastrointestinal tract cancers after sufficient control for confounders. Limited data support a protective effect of green tea on lung and hepatocellular carcinogenesis. Although observational studies do not support a beneficial role of tea intake on prostate cancer risk, phase II clinical trials have demonstrated an inhibitory effect of green tea extract against the progression of prostate pre-malignant lesions. Green tea may exert beneficial effects against mammary carcinogenesis in premenopausal women and recurrence of breast cancer. There is no sufficient evidence that supports a protective role of tea intake on the development of cancers of the colorectum, pancreas, urinary tract, glioma, lymphoma, and leukemia. Future prospective observational studies with biomarkers of exposure and phase III clinical trials are required to provide definitive evidence for the hypothesized beneficial effect of tea consumption on cancer formation in humans. PMID:21419224

  3. DEVELOPMENT OF A BIOMARKERS DATABASE FOR THE NATIONAL CHILDREN'S STUDY, PROCEEDINGS TO BE PUBLISEHD FROM THE INTERNATIONAL CONFERENCE ON BIOMARKERS FOR TOXICOLOGY AND MOLECULAR EPIDEMIOLOGY, ATLANTA, GA, MARCH 15-17, 2004

    EPA Science Inventory

    The National Children's Study (NCS) is a federally-sponsored, longitudinal study of environmental influences on the health and development of children across the United States (www.nationalchildrensstudy.gov). Current plans are to study approximately 100,000 children and their f...

  4. Sequencing Strategies for Population and Cancer Epidemiology Studies (SeqSPACE) Webinar Series

    Cancer.gov

    The Sequencing Strategies for Population and Cancer Epidemiology Studies (SeqSPACE) Webinar Series provides an opportunity for our grantees and other interested individuals to share lessons learned and practical information regarding the application of next generation sequencing to cancer epidemiology studies.

  5. ESTIMATING RESIDENTIAL EXPOSURE TO DRINKING WATER ARSENIC IN INNER MONGOLIA, CHINA FOR EPIDEMIOLOGIC STUDIES

    EPA Science Inventory

    ESTIMATING RESIDENTIAL EXPOSURE TO DRINKING WATER ARSENIC IN INNER MONGOLIA, CHINA FOR EPIDEMIOLOGIC STUDIES

    Richard Kwok1, Pauline Mendola1 Zhixiong Ning2, Zhiyi Liu2 and Judy Mumford1

    1) Epidemiology and Biomarkers Branch, Human Studies Division, NHEERL, US EPA, R...

  6. Low-dose radiation epidemiology studies: status and issues.

    PubMed

    Shore, Roy E

    2009-11-01

    Although the Japanese atomic bomb study and radiotherapy studies have clearly documented cancer risks from high-dose radiation exposures, radiation risk assessment groups have long recognized that protracted or low exposures to low-linear energy transfer radiations are key radiation protection concerns because these are far more common than high-exposure scenarios. Epidemiologic studies of human populations with low-dose or low dose-rate exposures are one approach to addressing those concerns. A number of large studies of radiation workers (Chernobyl clean-up workers, U.S. and Chinese radiological technologists, and the 15-country worker study) or of persons exposed to environmental radiation at moderate to low levels (residents near Techa River, Semipalatinsk, Chernobyl, or nuclear facilities) have been conducted. A variety of studies of medical radiation exposures (multiple-fluoroscopy, diagnostic (131)I, scatter radiation doses from radiotherapy, etc.) also are of interest. Key results from these studies are summarized and compared with risk estimates from the Japanese atomic bomb study. Ideally, one would like the low-dose and low dose-rate studies to guide radiation risk estimation regarding the shape of the dose-response curve, DDREF (dose and dose-rate effectiveness factor), and risk at low doses. However, the degree to which low-dose studies can do so is subject to various limitations, especially those pertaining to dosimetric uncertainties and limited statistical power. The identification of individuals who are particularly susceptible to radiation cancer induction also is of high interest in terms of occupational and medical radiation protection. Several examples of studies of radiation-related cancer susceptibility are discussed, but none thus far have clearly identified radiation-susceptible genotypes. PMID:19820457

  7. Targeted Exon Sequencing Successfully Discovers Rare Causative Genes and Clarifies the Molecular Epidemiology of Japanese Deafness Patients

    PubMed Central

    Kamatani, Naoyuki; Usami, Shin-ichi

    2013-01-01

    Target exon resequencing using Massively Parallel DNA Sequencing (MPS) is a new powerful strategy to discover causative genes in rare Mendelian disorders such as deafness. We attempted to identify genomic variations responsible for deafness by massive sequencing of the exons of 112 target candidate genes. By the analysis of 216randomly selected Japanese deafness patients (120 early-onset and 96 late-detected), who had already been evaluated for common genes/mutations by Invader assay and of which 48 had already been diagnosed, we efficiently identified causative mutations and/or mutation candidates in 57 genes. Approximately 86.6% (187/216) of the patients had at least one mutation. Of the 187 patients, in 69 the etiology of the hearing loss was completely explained. To determine which genes have the greatest impact on deafness etiology, the number of mutations was counted, showing that those in GJB2 were exceptionally higher, followed by mutations in SLC26A4, USH2A, GPR98, MYO15A, COL4A5 and CDH23. The present data suggested that targeted exon sequencing of selected genes using the MPS technology followed by the appropriate filtering algorithm will be able to identify rare responsible genes including new candidate genes for individual patients with deafness, and improve molecular diagnosis. In addition, using a large number of patients, the present study clarified the molecular epidemiology of deafness in Japanese. GJB2 is the most prevalent causative gene, and the major (commonly found) gene mutations cause 30–40% of deafness while the remainder of hearing loss is the result of various rare genes/mutations that have been difficult to diagnose by the conventional one-by-one approach. In conclusion, target exon resequencing using MPS technology is a suitable method to discover common and rare causative genes for a highly heterogeneous monogenic disease like hearing loss. PMID:23967202

  8. [Program of studies on psychiatric epidemiology in Argentina. General report].

    PubMed

    Casullo, M M

    1980-12-01

    This paper is an outline of a wide program that is currently under development in the large territory of Argentina. The Director of the Program is Dr. Fernando Pagés Larraya; it is supported by the National Council of Scientific Researches (CONICET) and the National Board of Mental Health. The general purpose of the program is to study the prevalence of mental disorders in different ethnographic areas within the country. Epidemiology allows the forecasting of disease occurence. A research work this area may be qualified "effective" if it provides useful data for prevention programs. Therefore, it is necessary that researches and professional responsibles of Mental Health Governmental decissions work together. This rapprochment is being attempted in developing the Argentine research program. It has a cross-cultural approach. It can be called "a way of thinking" as opposed to a precise methodology. A considerable variety of research tools are being used, depending on the specific purposes and the characteristics of the ethnographic areas. One of the main difficulties in choosing a technique for "case-finding" is uncertainty about where to place the "cut-off point" between presence and absence of illness. In this program the Present State Examination (PSE) is used in population surveys of large urban centers. It is a semi-structured interview that has been extensively tested. In small rural communities, the work is done using "key-informants" and applying the snow-ball sample technique. One specific purpose of the research is the study of the modal personality structure in each ethnographic area, formulated in terms of the Holtzman Inkblot Test. The paper shows the relationships between purposes, research tools and responsible professionals. There is hardly time or surplus intellectual energy for polemic and alienation between clinicians and social scientists. Theories, methodologies, research data and prevention programs have not developed harmoniously. We need to

  9. An epidemiological study of dengue in Delhi, India.

    PubMed

    Vikram, Kumar; Nagpal, B N; Pande, Veena; Srivastava, Aruna; Saxena, Rekha; Anvikar, Anup; Das, Aparup; Singh, Himmat; Anushrita; Gupta, Sanjeev K; Tuli, N R; Telle, Olivier; Yadav, N K; Valecha, Neena; Paul, Richard

    2016-01-01

    Delhi, the capital of India, is an important metropolitan hub for major financial and sociocultural exchanges, offering challenging threats to current public health infrastructure. In recent past, an upsurge of dengue cases in Delhi posed a significant menace to the existing dengue control policies. To reform the control strategies and take timely intervention to prevent future epidemics, an epidemiological study on the proportion of both asymptomatic and symptomatic dengue infections in selected population was conducted. The aim of the study was to investigate and assess the epidemiology of dengue infection and to estimate the proportion of asymptomatic and symptomatic dengue infections in Delhi. In this study, around 50 confirmed dengue cases, a total of 2125 individuals as household and neighbourhood contacts, with or without dengue febrile illness, were finger pricked and serologically detected as dengue positive or negative using SD Duo Bioline Rapid Diagnostic Test (SD Inc, Korea) with NS1, IgM & IgG combo test, which detected dengue virus antigen and antibodies to dengue virus in human blood. Out of 2125 individuals, 768 (36.1%) individuals showed positive dengue test with past (25.5%), primary (1.88%) or secondary (8.8%) dengue infections. Higher percentage of IgG was found in age groups 15-24 years and 25-50 years (36% each). Infants (<1 year) presented higher incidence of new infections (22% of NS1+IgM positives) as compared to adults. Further analysis revealed that out of the 226 newly infected cases (including NS1 and IgM positives), 142 (63%) were asymptomatic and 84 (37%) were symptomatic, as per WHO guidelines. Our findings also suggest that out of the total population screened, 10.6% dengue infection was either primary or secondary. On the basis of these results, it may be hypothesized that there are large number of asymptomatic dengue infections in the community as compared to reported symptomatic cases in Delhi. For the effective control of dengue

  10. Exposure assessment in industry specific retrospective occupational epidemiology studies.

    PubMed Central

    Seixas, N S; Checkoway, H

    1995-01-01

    Quantitative estimation of exposure for occupational epidemiology studies has received increasing attention in recent years and, as a result, a body of methodological literature has begun to take form. This paper reviews the generic issues in the methodology of exposure assessment, particularly methods for quantitative retrospective assessment studies. A simple framework, termed an exposure data matrix (EDM), for defining and analysing exposure data is proposed and discussed in terms of the definition of matrix dimensions and scales. Several methods for estimation, interpolation, and extrapolation, ranging from subjective ratings to quantitative statistical modelling are presented and discussed. The various approaches to exposure assessment based on the EDM concept are illustrated with studies of lung disease among coal miners and other dust and chemically induced chronic occupational diseases. The advantages of validated statistical models are emphasised. The importance of analysis and control of errors in exposure assessments, and integration of the exposure assessment and exposure-response processes, especially for emerging occupational health issues, is emphasised. PMID:7489051

  11. Epidemiological Assessments of Skin Outcomes in the Nurses’ Health Studies

    PubMed Central

    Li, Wen-Qing; Cho, Eunyoung; Weinstock, Martin A.; Mashfiq, Hasan

    2016-01-01

    Objectives. To review the contribution of the Nurses’ Health Studies (NHSs) to identifying epidemiological factors associated with multiple skin diseases, including skin cancer, psoriasis, and other inflammatory and autoimmune skin diseases. Methods. We carried out a narrative review of NHS articles published between 1976 and 2016. Results. The NHSs have identified environmental and lifestyle factors related to psoriasis, supporting obesity and smoking as psoriasis risk factors; associations between psoriasis and diabetes, myocardial infarction, and Crohn’s disease, supporting psoriasis as a systemic disorder; and associations of pigmentary traits, ultraviolet radiation, and lifestyle factors such as citrus consumption with risk of skin cancer. Genetic studies have identified novel genetic loci for skin pigmentation (e.g., IRF4, SLC24A4, NID1, and EDNRB) and skin cancer (e.g., TET2 and HERC2-OCA2). Work continues on highly prevalent but less studied skin conditions such as rosacea, acne, and atopic dermatitis. The NHS results have influenced public health policies on indoor tanning devices. Conclusions. The NHSs have provided invaluable resources on skin disease population science and contributed to the etiological understanding of multiple skin disorders. PMID:27459457

  12. Interfacing anthropology and epidemiology: the Bedouin Arab Infant Feeding Study.

    PubMed

    Hundt, G A; Forman, M R

    1993-04-01

    This paper encapsulates a 10 year effort of multi-disciplinary research on the relationship between infant feeding, growth, and morbidity among the Negev Bedouin Arabs of Israel as they underwent a transition from semi-nomadism to urban settlement. The research team was multi-disciplinary including a nutritional epidemiologist and an anthropologist who both came to the study with previous experience in interdisciplinary work. The specific study objectives were (1) a description of infant feeding practices among Negev Bedouin Arab women at various stages of settlement, (2) an examination of the trend in these infant feeding practices, (3) a comparison of the extent to which different infant feeding practices are related to infant morbidity and growth after adjustment for exposure to social change and other covariates. The data collection took place in 1981-83 and the analysis from 1984-88. In this paper, two areas of the study are discussed in depth: the duration of exclusive breast feeding during the practice of the traditional postpartum 40 day rest period, and the development of a culture-specific scale of socioeconomic status. Through these examples, we highlight the use of ethnographic data and the merging of epidemiology and anthropology from hypothesis generation through data collection, data analysis and interpretation. PMID:8480241

  13. Study in molecular lasers

    NASA Astrophysics Data System (ADS)

    Burns, G.; Kutz, H. D.; Cohen, L. K.; Billard, T. C.

    1984-10-01

    A sensitive LIF system was constructed, using a Nd:YAG plus dye laser. The signal was accumulated and analyzed by employing a Tektronix R7912 transient Digitizer and a PDP-11 minicomputer. Reactivity of HF (v=5) was studied. Using the same equipment, a time-delayed photoemission from a trialkali photosensitive semiconductor was observed and results are now being examined. Using 3-D trajectory calculations a new computational observable, the relative nonequilibrium distribution (RNED) function at the steady state was determined for the Br + Ar reaction at 3500K. It is characterized by one adjustable parameter equal to 12, while the transition state theory prescribes that it should be infinitely large. RNED will be used to test and refine modern theories of reaction kinetics.

  14. Epidemiology and Molecular Characterization of Macrolide-Resistant Streptococcus pyogenes in Taiwan

    PubMed Central

    Huang, Chia-Ying; Lai, Jui-Fen; Huang, I-Wen; Chen, Pei-Chen; Wang, Hui-Ying; Shiau, Yih-Ru; Cheng, Ya-Wen; Hsieh, Li-Yun; Chang, Shan-Chwen

    2014-01-01

    Our multicenter nationwide surveillance data indicated that erythromycin (ERY) resistance among group A Streptococcus (GAS) isolates in Taiwan declined from 53.1% in 1998 and 2000 to 14.6% in 2002 and 2004 and 10.7% in 2006 to 2010 (P < 0.01). The present study aimed to assess the epidemiology of GAS in Taiwan and identify factors associated with ERY resistance. All 127 ERY-resistant (ERYr) isolates and 128 randomly selected ERY-susceptible (ERYs) isolates recovered from 1998 to 2010 were emm typed. ERYr isolates were also characterized by ERY resistance phenotype and mechanisms and pulsed-field gel electrophoresis (PFGE). Multilocus sequence typing was performed on selected ERYr isolates. The predominant emm types in ERYr isolates were emm22 (n = 33, 26.0%), emm12 (n = 24, 18.9%), emm4 (n = 21, 16.5%), and emm106 (n = 15, 11.8%). In ERYs isolates, emm12 (n = 27, 21.9%), emm1 (n = 18, 14.1%), emm106 (n = 16, 12.5%), and emm11 (n = 9, 7.1%) predominated. The most common ERY resistance phenotype was the M phenotype (resistant to macrolides) (70.9%), with all but one isolate carrying mef(A), followed by the constitutive macrolide-lincosamide-streptogramin B resistance (cMLSB) phenotype (26.8%), with isolates carrying erm(B) or erm(TR). ERYr isolates of the emm12-sequence type 36 (ST36) lineage with the cMLSB phenotype were mostly present before 2004, while those of the emm22-ST46 lineage with the M phenotype predominated in later years. Recovery from respiratory (throat swab) specimens was an independent factor associated with ERY resistance. emm1 and emm11 GAS isolates were significantly associated with ERYs, while emm22 was detected only in ERYr GAS. In addition, emm106 isolates were prevalent among the abscess/pus isolates, whereas emm12 isolates were strongly associated with a respiratory (throat) origin. In addition to identifying factors associated with ERY resistance in GAS, our study provides helpful information on the changing GAS epidemiology in Taiwan. PMID

  15. Clinical and Molecular Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit in the Decade following Implementation of an Active Detection and Isolation Program

    PubMed Central

    Nelson, Melissa U.; Bizzarro, Matthew J.; Baltimore, Robert S.; Dembry, Louise M.

    2015-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent source of infection in the neonatal intensive care unit (NICU), often associated with significant morbidity. Active detection and isolation (ADI) programs aim to reduce transmission. We describe a comprehensive analysis of the clinical and molecular epidemiology of MRSA in an NICU between 2003 and 2013, in the decade following the implementation of an MRSA ADI program. Molecular analyses included strain typing by pulsed-field gel electrophoresis, mec and accessory gene regulator group genotyping by multiplex PCR, and identification of toxin and potential virulence factor genes via PCR-based assays. Of 8,387 neonates, 115 (1.4%) had MRSA colonization and/or infection. The MRSA colonization rate declined significantly during the study period from 2.2 to 0.5/1,000 patient days (linear time, P = 0.0003; quadratic time, P = 0.006). There were 19 cases of MRSA infection (16.5%). Few epidemiologic or clinical differences were identified between MRSA-colonized and MRSA-infected infants. Thirty-one different strains of MRSA were identified with a shift from hospital-associated to combined hospital- and community-associated strains over time. Panton-Valentine leukocidin-positive USA300 strains caused 5 of the last 11 infections. Staphylococcal cassette chromosome mec (SCCmec) types II and IVa and agr groups 1 and 2 were most predominant. One isolate possessed the gene for toxic shock syndrome toxin; none had genes for exfoliative toxin A or B. These results highlight recent trends in MRSA colonization and infection and the corresponding changes in molecular epidemiology. Continued vigilance for this invasive pathogen remains critical, and specific attention to the unique host, the neonate, and the distinct environment, the NICU, is imperative. PMID:26019206

  16. Epidemiological studies of CHD and the evolution of preventive cardiology.

    PubMed

    Wong, Nathan D

    2014-05-01

    Cardiovascular diseases (CVDs) cause nearly one-third of all deaths worldwide. Coronary heart disease (CHD) accounts for the greatest proportion of CVDs, and risk factors such as hypertension, cigarette smoking, diabetes mellitus or elevated glucose level, elevated cholesterol levels, and obesity or being overweight are the top six causes of death globally. Ecological and population-based longitudinal studies, conducted globally or within individual countries, have established the role of traditional and novel risk factors and measures of subclinical disease in the prediction of CHD. Risk assessment with short-term or long-term risk prediction algorithms can help to identify individuals who would benefit most from risk-factor interventions. Evaluation of novel risk factors and screening for subclinical atherosclerosis can also help to identify individuals at highest cardiovascular risk. Prevention of CHD focuses on identifying and managing risk factors at both the population and individual levels through primordial, primary, and secondary prevention. Epidemiological studies have provided the hypotheses for subsequent clinical trials that have documented the efficacy of risk-factor interventions, which are the basis of preventive cardiology. Future research efforts will determine the screening and intervention strategies that have the greatest effect on CHD prevention. PMID:24663092

  17. An update of epidemiologic studies of plutonium workers.

    PubMed

    Voelz, G L; Wilkinson, G S; Acquavella, J F; Tietjen, G L; Brackbill, R N; Reyes, M; Wiggs, L D

    1983-01-01

    Retrospective and prospective epidemiologic studies are being conducted as part of a national survey of plutonium workers at four Department of Energy facilities (Los Alamos, NM; Rocky Flats, CO; Mound Laboratory, OH; and Savannah River, SC). A preliminary analysis of mortality was done for all white males who have worked at the Rocky Flats Plant during the period 1952-79. The 452 observed deaths were significantly fewer than the 831 expected for all causes. The 107 deaths due to all malignant neoplasms were also significantly fewer than the 167 expected from these diseases. Expected deaths were derived from age and calendar-specific death rates for U.S. white males. Deaths reported for benign and unspecified neoplasms numbered eight versus an expected two, a significant elevation. These tumors, all intracranial, are the subject of a case-control study to be reported later. Subdividing the cohort on the basis of plutonium exposures and external radiation exposures results in similar overall findings. The benign and unspecified neoplasms, however, were not significantly high in the plutonium-exposed group. PMID:6862925

  18. An Epidemiological Study of Neuropathic Pain Symptoms in Canadian Adults

    PubMed Central

    VanDenKerkhof, Elizabeth G.; Mann, Elizabeth G.; Torrance, Nicola; Smith, Blair H.; Johnson, Ana; Gilron, Ian

    2016-01-01

    The reported prevalence of neuropathic pain ranges from 6.9% to 10%; however the only Canadian study reported 17.9%. The objective of this study was to describe the epidemiology of neuropathic pain in Canada. A cross-sectional survey was conducted in a random sample of Canadian adults. The response rate was 21.1% (1504/7134). Likely or possible neuropathic pain was defined using a neuropathic pain-related diagnosis and a positive outcome on the Self-Report Leeds Assessment of Neuropathic Symptoms and Signs pain scale (S-LANSS) or the Douleur Neuropathique 4 (DN4) Questions. The prevalence of likely neuropathic pain was 1.9% (S-LANSS) and 3.4% (DN4) and that of possible neuropathic pain was 5.8% (S-LANSS) and 8.1% (DN4). Neuropathic pain was highest in economically disadvantaged males. There is a significant burden of neuropathic pain in Canada. The low response rate and a slightly older and less educated sample than the Canadian population may have led to an overestimate of neuropathic pain. Population prevalence varies by screening tool used, indicating more work is needed to develop reliable measures. Population level screening targeted towards high risk groups should improve the sensitivity and specificity of screening, while clinical examination of those with positive screening results will further refine the estimate of prevalence. PMID:27445636

  19. Biotyping of Serratia marcescens and its use in epidemiological studies.

    PubMed Central

    Grimont, P A; Grimont, F

    1978-01-01

    A Serratia marcescens biotyping system using eight carbon sources (benzoate, DL-carnitine, m-erythritol, 3-hydroxybenzoate, 4-hydroxybenzoate, lactose, D-quinate, and trigonelline), a tetrathionate reduction test, production of prodigiosin, and horse blood hemolysis was derived from a recent numerical taxonomic study (Grimont et al., J. Gen. Microbiol. 98:39-66, 1977). A total of 98.6% of 2,210 isolates from various sources could be assigned to 1 of 19 biotypes. Distribution and spread of 1,088 S. marcescens isolates throughout 13 clinical departments of Pellegrin Hospital (Bordeaux, France) were studied from 1968 through 1975. Except for one that colonized the intestinal tract of newborns, the six pigmented biotypes were seldom isolated. Each of the 13 nonpigmented biotypes showed a particular pattern of distribution and spread. The usefulness of S. marcescens biotyping was shown by relating several isolates recovered from patients and their inanimate environment and by pointing out the possible existence of infections or colonizations by two unrelated biotypes. S. marcescens strains isolated from the natural environment (water) are usually pigmented, and their biotypes are uncommon in hospitals. Biotyping can, therefore, be of help in epidemiological and ecological surveys. PMID:353073

  20. Cognition and Vascular Risk Factors: An Epidemiological Study

    PubMed Central

    Vicario, Augusto; Del Sueldo, Mildren; Fernández, Ruth A.; Enders, Julio; Zilberman, Judith; Cerezo, Gustavo H.

    2012-01-01

    We conducted an epidemiological approach to identify the negative impact of the vascular risk factors (such as hypertension, diabetes and hypercholesterolemia) over cognition. The interesting aspect of this study was that the survey was conducted in all age groups through a voluntary call (n = 1365; ≥18 years old, both sexes; age 49 ± 15 y, female 75.7%). Thus, we demonstrated that the use of a Minimum Cognitive Examination (MCE), a brief, simple, and easy managed neuropsychological evaluation, detected a greater number of people with cognitive decline surpassing to the Minimal Mental Statement Examination alone (14.5% of the participants showed MMSE ≤24, 34,6% showed dys-executive function, and 45,8% memory impairment. Out of the 4 studied RF, the only one that was not related to cognitive impairment was dyslipemia. Finally, we noted the importance of cognitive state early detection in all age groups, even in the youngest group. Acting in the middle of the life stages, we can prevent or delay the onset of a disease in adults, nowadays incurable: dementia. PMID:22988488

  1. Molecular Epidemiology of Streptococcus pneumoniae Isolates from Children with Recurrent Upper Respiratory Tract Infections

    PubMed Central

    Korona-Glowniak, Izabela; Maj, Maciej; Siwiec, Radosław; Niedzielski, Artur; Malm, Anna

    2016-01-01

    A total of 125 isolates were recovered from adenoids and/or nasopharynx of 170 children aged 2 to 5 from south-east Poland; they had undergone adenoidectomy for recurrent and/or persistent symptoms of upper respiratory tract infections. Pneumococcal isolates were analyzed by phenotyping (serotyping and antimicrobial resistance tests) and genotyping together with the clonality of the pneumococcal isolates based on resistance determinants, transposon distribution and multilocus sequence typing (MLST). Serotypes 19F, 6B and 23F constituted 44.8% of the isolates. Among all of the strains, 44.8% showed decreased susceptibility to penicillin and resistance to co-trimoxazole (52.8%), tetracycline (38.4%), erythromycin (53.6%), clindamycin (52.8%) and chloramphenicol (27.2%) was observed. Tn6002 was found in 34.8% of erythromycin-resistant isolates while composite Tn2010—in 16.7% of erm(B)-carrying isolates that harboured also mef(E) gene. Tn3872-related elements were detected in 27.3% of erythromycin-resistant strains. In the majority of chloramphenicol-resistant catpC194-carrying isolates (79.4%), ICESp23FST81-family elements were detected. The genotyping showed that pneumococcal population was very heterogeneous; 82 sequence types (STs) were identified, and the most frequent contributed to not more than 8% of the isolates. Nearly 44% STs were novel, each of them was recovered only from one child. Four STs belonged to one of the 43 worldwide spread resistant pneumococcal clones currently accepted by Pneumococcal Molecular Epidemiology Network (PMEN), i.e. Spain 9V-3, Spain 23F-1, Norway NT-42 and Poland 6B-20, accounting for 12 (16.7%) of the 75 nonususceptible isolates, and five STs were single-locus variants of PMEN resistant clones (England 14–9, Spain 9V-3, Spain 23F-1, Greece 21–30, Denmark 14–32), accounting 9 (12%) of nonsusceptible isolates. A few MDR clones belonging to 6B and 19F serotypes found among preschool children emphasizes rather the role of

  2. Molecular epidemiology of Escherichia coli producing extended-spectrum beta-lactamases isolated in Rome, Italy.

    PubMed

    Carattoli, Alessandra; García-Fernández, Aurora; Varesi, Paola; Fortini, Daniela; Gerardi, Serena; Penni, Adriano; Mancini, Carlo; Giordano, Alessandra

    2008-01-01

    Escherichia coli strains producing extended-spectrum beta-lactamases (ESBLs) are a major problem in many different hospitals worldwide, causing outbreaks as well as sporadic infections. The prevalence of Escherichia coli ESBL producers was analyzed in a surveillance study performed on the population attending the Policlinico Umberto I, the largest university hospital in Rome, Italy. We also investigated genotypes, pathogenicity islands, and plasmids in the ESBL-positive E. coli isolates as further markers that are useful in describing the epidemiology of the infections. In this survey, 163 nonreplicate isolates of Escherichia coli were isolated from patients from 86 different wards, and 28 were confirmed as ESBL producers. A high prevalence (26/28) of CTX-M-15 producers was observed within the bacterial population circulating in this hospital, and the dissemination of this genetic trait was associated with the spread of related strains; however, these do not have the characteristics of a single epidemic clone spreading. The dissemination was also linked to horizontal transfer among the prevalent E. coli genotypes of multireplicon plasmids showing FIA, FIB, and FII replicons in various combinations, which are well adapted to the E. coli species. The analysis of related bacteria suggests a probable interpatient transmission occurring in several wards, causing small outbreaks. PMID:17959756

  3. Molecular epidemiology of an outbreak of clinical mastitis in sheep caused by Mannheimia haemolytica.

    PubMed

    Omaleki, Lida; Browning, Glenn F; Allen, Joanne L; Markham, Philip F; Barber, Stuart R

    2016-08-15

    The aetiology and epidemiology of outbreaks of clinical mastitis in sheep under extensive pastoral conditions are incompletely understood. The objective of this study was to conduct a detailed investigation of a clinical mastitis outbreak that affected more than 10% of 230 at-risk ewes on a sheep and grain producing property in south east Australia during drought conditions in 2009. Milk samples were collected aseptically from all affected ewes and plated on sheep blood agar for bacterial identification. M. haemolytica was isolated from 80% of the samples that yielded cultivable microorganisms and thus was the main microorganism responsible for the outbreak. Analysis of the restriction endonuclease cleavage patterns of the isolates using pulsed field gel electrophoresis revealed some evidence of clonality, suggesting the possibility of horizontal transmission, but there was also considerable diversity between the clusters of closely related isolates. Multilocus sequence typing of the M. haemolytica isolates revealed most of the isolates belonged to ST1 with no association between the PFGE and MLST fingerprints of the isolates. Resistance to neomycin, streptomycin and sulphafurazole was detected in some of the isolates, but they were all susceptible to penicillin, ampicillin, ceftiofur, amoxycillin/clavulanic acid, ciprofloxacin, tetracycline, erythromycin and trimethoprim. This is the first published record of a comparison of the strains of M. haemolytica involved in a clinical mastitis outbreak in sheep and demonstrates the importance of this pathogen in sheep production systems, particularly during adverse climatic conditions and increased stocking rate. PMID:27374911

  4. Molecular epidemiology of rotavirus in four provinces of Angola before vaccine introduction.

    PubMed

    Esteves, Aida; Nordgren, Johan; Pereira, Joana; Fortes, Filomeno; Dimbu, Rafael; Saraiva, Nilton; Mendes, Cristina; Istrate, Claudia

    2016-09-01

    Angola is a sub-Saharan country in southern Africa highly affected by diarrhoeal disease with limited epidemiological data regarding etiologic agents. This study was performed during 2012-2013, prior to rotavirus vaccine introduction, with the objective to detect and characterize the rotavirus strains circulating in four provinces of the country: Huambo, Luanda, Zaire, and Cabinda. A high rotavirus detection rate (35%, 117/334) was observed. G1 was the most common G-genotype (83.6%), whereas P[8] (50.9%) followed by P[6] (38.8%) were the most common P-types. G1P[8] was identified as the predominant combination (50%), followed by the unusual G1P[6] (29.3%). Strains such G2P[4], G8P[6], G9P[6], and G12P[6] were also found in lower frequencies (5.2-1.7%). The P[6] strains did not cluster in the phylogenetic trees according to their geographic origin or even the corresponding G-genotype, suggesting a limited number of recent introductions and extensive reassortment events. Our results represent the first report on rotavirus genotype profiles in Angola, showing a wide circulation of the unusual genotype G1P[6], and underline the importance of RV surveillance after the vaccine introduction. J. Med. Virol. 88:1511-1520, 2016. © 2016 Wiley Periodicals, Inc. PMID:26946356

  5. Two Independent HIV Epidemics in Saint Petersburg, Russia Revealed by Molecular Epidemiology

    PubMed Central

    Dukhovlinova, Elena; Masharsky, Alexey; Toussova, Olga; Verevochkin, Sergei; Solovyeva, Tatiana; Meringof, Maria; Paintsil, Elijah; White, Edward; Barbour, Russell; Heimer, Robert

    2015-01-01

    Abstract The HIV epidemic in Russia, one of the world's fastest growing, has been concentrated mostly among people who inject drugs (PWID). We sought to explore the epidemiology of the epidemic in St. Petersburg by sampling from the highest risk groups of PWID and men who have sex with men (MSM) and use viral sequencing data to better understand the nature of the city's epidemic. Serological testing confirmed an HIV prevalence among PWID in excess of 40%. All but 1 of 110 PWID whose blood samples were tested for genetic diversity were infected by subtype A virus, specifically by the AFSU strain. The remaining person was infected with a CRF-06cpx recombinant. Analysis of pairwise genetic distance among all PWID studied revealed an average of 3.1% sequence divergence, suggesting clonal introduction of the AFSU strain and/or constraints on sequence divergence. The HIV prevalence was less than 10% among MSM. All 17 sequences from HIV-infected MSM were found to be a clade B virus with a much higher average sequence diversity of 15.7%. These findings suggest two independent epidemics with little overlap between the two highest at-risk populations, which will require different HIV prevention approaches. PMID:25417740

  6. Comparison of Mycotic Keratitis with Nonmycotic Keratitis: An Epidemiological Study

    PubMed Central

    Khater, Mohammad M.; Shehab, Nehal S.; El-Badry, Anwar S.

    2014-01-01

    Purpose. This work aims to study the problems encountered with and the different epidemiological features of patients with fungal keratitis. Patients and Methods. All cases with keratitis attending the Outpatient Clinic of Ophthalmology Department at Tanta University Hospital during three years from the first of January 2011 to the end of December 2013 were selected and carefully examined and cases with mycotic keratitis were further examined and investigated. Results. From 66303 attendants during this period with different complaints, there were 361 cases (0.54%) with mycotic keratitis and 473 cases (0.71%) of nonmycotic origin. Mycotic keratitis is common between 40 and 60 years, more in farmers (64%), families with large number and large crowding index, rural than urban residence, and patients with outdoor water sources and insanitary sewage disposal. Positive fungal cultures were obtained in 84.5% and were negative in 15.5% of cases in spite of their typical clinical findings for diagnosis and their improvement with antifungal therapy. Conclusion. Mycotic keratitis is more frequent in farmers, rural areas, outdoor water supply, insanitary sewage disposal, and patients preceded with organic trauma. Atypical clinical findings were found in some cases and not all cases improved with specific antifungal therapy. PMID:25548657

  7. Fatalities associated with farm tractor injuries: an epidemiologic study.

    PubMed

    Goodman, R A; Smith, J D; Sikes, R K; Rogers, D L; Mickey, J L

    1985-01-01

    Death certificates were used as a source of information to characterize fatalities associated with farm tractor injuries in Georgia for the period 1971-81. In this period, 202 tractor-associated fatalities occurred among residents of Georgia; 198 of these persons were males. The annual tractor-associated fatality rate for males based on the population of male farm residents was 23.6 per 100,000; rates of fatal injury increased with age for this population. Persons whose primary occupation was other than farming accounted for more than half of all tractor-associated deaths. Fatal injuries occurred throughout the year but predominantly during the planting and harvesting months. Injuries occurred throughout the day (7 a.m. to midnight), with a peak at 4 p.m. to 5 p.m. Most fatal injuries, 76 percent, resulted when tractors overturned. Fatalities were attributed to crushed chest, exsanguination, strangulation or asphyxia, drowning, and other injuries. Current safety standards for the operation of farm tractors are limited; rollover protective canopies are not required for farm owners or their family members. Descriptive epidemiologic information obtained from death certificates can be used to define injury determinants and to suggest approaches for the further study and prevention of specific types of injuries. PMID:3923543

  8. [Acute and overuse injuries in elite paracycling - an epidemiological study].

    PubMed

    Kromer, P; Röcker, K; Sommer, A; Baur, H; Konstantinidis, L; Gollhofer, A; Südkamp, N P; Hirschmüller, A

    2011-09-01

    Although paracycling is a growing discipline in high level competitive sports as well as in posttraumatic rehabilitation, epidemiological data of resulting injuries is still missing. Therefore, 19 athletes of the German national paracycling team were asked about their injuries during the 2008 season using a standardized questionnaire. Overall, 18 (94.7 %) of 19 athletes reported overuse injuries; most commonly localized at the back (83.3 %), neck/shoulder (77.8 %), knee (50 %), groin/buttock (50 %) and hands/wrists (38.9 %). Altogether, 18 accidents were registered, corresponding to an injury rate of 0,95 acute injuries per athlete per year (0,07 / 1000 km). The most common acute injuries were abrasions (69.2 %) and contusions (61.5 %), whereas fractures were stated only twice (11.8 %). The anatomical distribution of overuse injuries in disabled cyclists confirms the results of studies in able-bodied cycling, although the incidences in low-back pain and neck/shoulder pain is clearly higher in disabled cycling, as well as the rate of traumatic injuries. PMID:21922439

  9. Histopathologic reproducibility of thyroid disease in an epidemiologic study

    SciTech Connect

    Ron, E.; Griffel, B.; Liban, E.; Modan, B.

    1986-03-01

    An investigation of the long-term effects of childhood scalp irradiation demonstrated a significantly increased risk of thyroid tumors in the irradiated population. Because of the complexity of thyroid cancer diagnosis, a histopathologic slide review of 59 of the 68 patients (irradiated and nonirradiated) with thyroid disease was undertaken. The review revealed 90% agreement (kappa = +0.85, P less than 0.01) between the original and review diagnosis. Four of 27 cases previously diagnosed as malignant were reclassified as benign, yielding a cancer misdiagnosis rate of 14.8%. All four of the misdiagnosed cancers were of follicular or mixed papillary-follicular type. As a result of the histologic review, the ratio of malignant to benign tumors decreased from 2.55 to 1.75. Since disagreement in diagnosis was similar in the irradiated and nonirradiated groups, the relative risk of radiation-associated neoplasms did not change substantially. The histopathologic review shows that although there were some problems in diagnostic reproducibility, they were not statistically significant and did not alter our previous conclusions regarding radiation exposure. However, a 15% reduction in the number of malignancies might affect epidemiologic studies with an external comparison as well as geographic or temporal comparisons.

  10. Problem gambling and homelessness: results from an epidemiologic study.

    PubMed

    Nower, Lia; Eyrich-Garg, Karin M; Pollio, David E; North, Carol S

    2015-06-01

    The purpose of this study was to investigate the prevalence of gambling disorder and comorbid psychiatric disorders in a homeless population and identify features related to potential subtypes. At baseline, participants were administered a structured interview including socio-demographic sections of the National Comorbidity Study (NCS) interview; seven diagnostic sections of the Diagnostic Interview Schedule (DIS); the alcohol and drug abuse sections of the Composite International Diagnostic Interview-Substance Abuse Module (CIDI-SAM); and the Homeless Supplement to the DIS. At nine months post-baseline assessment, participants were administered additional NCS family history questions and the South Oaks Gambling Screen (SOGS). Participants were an epidemiologic sample of 275 predominately African-American homeless individuals, grouped as lifetime non-gamblers (n = 60), recreational gamblers (n = 152), and problem gamblers (n = 63), recruited on the street and through homeless shelters. Results indicate that lifetime rates of sub-clinical problem (46.2%) and disordered (12.0%) gambling were significantly higher than in the general population. Problem gamblers were more likely than non-problem gamblers to meet diagnostic criteria for antisocial personality disorder, post-traumatic stress disorder, bipolar disorder, and any psychiatric disorder, and more likely than non-gamblers to use illicit drugs or meet criteria for abuse/dependence for nicotine, alcohol, or any substance. This study provides evidence that problem gambling is a significant public health issue among the African-American homeless population. Homeless services should include assessment for problem gambling along with psychiatric disorders and referrals to resources and treatment programs. Future studies should explore the relationship of the onset and course of problem gambling and other psychiatric disorders with homelessness as well as racial differences in gambling patterns and problem severity

  11. Molecular epidemiology of lung cancer and geographic variations with special reference to EGFR mutations

    PubMed Central

    2014-01-01

    Lung cancer is a leading cause of cancer-related mortality in many countries. Although recent advances in targeted therapy against driver oncogenes have significantly improved patient outcome, cure of this disease is still exceptional. Although tobacco is a known cause of lung cancer, not all smokers develop lung cancer, and conversely many patients, especially Asian female patients with lung cancer, are lifetime never-smokers. Therefore, efforts to understand the basis for different susceptibilities to lung cancer among individuals with different genetic, biologic, ethnic, and social backgrounds are important to help develop effective preventive measures. Lung cancer in never-smokers has many different characteristics to lung cancer in smokers, such as adenocarcinoma predominance and high frequency of epidermal growth factor receptor (EGFR) mutation yet low number of genetic changes. Epidemiologic studies suggest that East Asians are more susceptible to smoking-unrelated lung cancer but less susceptible to smoking-related lung cancer compared with Caucasians. Mutations in the EGFR gene are more common in Asian females and never-smokers. Our case-control study suggests that EGFR mutation occurs independent of smoking, and that the apparent low frequency of EGFR mutations in smokers may be the result of dilution by smoking-related lung cancer. The frequencies of three EGFR gene polymorphisms associated with increased protein expression are significantly different between East Asians and Caucasians, favoring lower protein expression in East Asians. Although these may be associated with preferred expression of the EGFR mutant allele, it is difficult to explain the frequent EGFR mutation in Asian patients. Genome wide association studies (GWAS) revealed several loci related to lung cancer susceptibility. In the future, GWAS may identify loci that are specifically related to EGFR-targeted carcinogenesis, leading to identification of carcinogens that induce EGFR

  12. Molecular epidemiology of lung cancer and geographic variations with special reference to EGFR mutations.

    PubMed

    Mitsudomi, Tetsuya

    2014-08-01

    Lung cancer is a leading cause of cancer-related mortality in many countries. Although recent advances in targeted therapy against driver oncogenes have significantly improved patient outcome, cure of this disease is still exceptional. Although tobacco is a known cause of lung cancer, not all smokers develop lung cancer, and conversely many patients, especially Asian female patients with lung cancer, are lifetime never-smokers. Therefore, efforts to understand the basis for different susceptibilities to lung cancer among individuals with different genetic, biologic, ethnic, and social backgrounds are important to help develop effective preventive measures. Lung cancer in never-smokers has many different characteristics to lung cancer in smokers, such as adenocarcinoma predominance and high frequency of epidermal growth factor receptor (EGFR) mutation yet low number of genetic changes. Epidemiologic studies suggest that East Asians are more susceptible to smoking-unrelated lung cancer but less susceptible to smoking-related lung cancer compared with Caucasians. Mutations in the EGFR gene are more common in Asian females and never-smokers. Our case-control study suggests that EGFR mutation occurs independent of smoking, and that the apparent low frequency of EGFR mutations in smokers may be the result of dilution by smoking-related lung cancer. The frequencies of three EGFR gene polymorphisms associated with increased protein expression are significantly different between East Asians and Caucasians, favoring lower protein expression in East Asians. Although these may be associated with preferred expression of the EGFR mutant allele, it is difficult to explain the frequent EGFR mutation in Asian patients. Genome wide association studies (GWAS) revealed several loci related to lung cancer susceptibility. In the future, GWAS may identify loci that are specifically related to EGFR-targeted carcinogenesis, leading to identification of carcinogens that induce EGFR

  13. Molecular Epidemiology of Mycobacterium Tuberculosis Strains in the North-West and West of Iran

    PubMed Central

    Sahebi, L; Ansarin, K; Hoffner, S; Farajnia, S; Seyyedi, M; Khalili, M; Monfaredan, A

    2015-01-01

    Background: Identifying Mycobacterium tuberculosis (MTB) transmission type is a key step in the control of this disease. Aim: This study aimed to determine the path and transmission type of MTB and the insertion sequence IS6110 band number and verify their relationship to demographic and clinical risk factors. Subjects and Methods: In this cross-sectional study, 64 MTB patients from three border provinces of Iran were selected after full clinical history and physical evaluation design. The drug susceptibility testing was carried out using the standard proportion technique on sputum samples. Isolates tested with restriction fragment length polymorphism technique used IS6110. Results: Recent transmission of disease was 33/50 (66%) based on clustering rate. The IS6110 band number had a significant relationship with drug resistance detected in proportion method tested by univariate linear regression (P < 0.01). Furthermore, the IS6110 band number had association with Bacillus Calmette–Guérin vaccination history (P = 0.02), sex (P < 0.01), and purified protein derivative (PPD) reaction size (P < 0.01) tested by multiple analysis. The risk of recent transmission inferred from the clustering rate was significantly higher in patients from Western provinces compared to those from the North-West province (P = 0.048). However, age (P = 0.39), gender (P = 0.16), vaccination history (P = 0.57), drug susceptibility, and PPD (P < 0.6) were independent of clustering. The largest cluster of up to six subjects was found in the Western provinces. Conclusion: Recent MTB transmission was much more common in the West compared to the North-West of Iran. Large MTB clusters with strong epidemiological links may be reflective of a disease outbreak. Correlation noted between the IS6110 band number and vaccination history; PPD size and female gender necessitates further studies. PMID:26500790

  14. Serotypes, antimicrobial susceptibility, and molecular epidemiology of invasive and non-invasive Streptococcus pneumoniae isolates in paediatric patients after the introduction of 13-valent conjugate vaccine in a nationwide surveillance study conducted in Japan in 2012-2014.

    PubMed

    Nakano, Satoshi; Fujisawa, Takao; Ito, Yutaka; Chang, Bin; Suga, Shigeru; Noguchi, Taro; Yamamoto, Masaki; Matsumura, Yasufumi; Nagao, Miki; Takakura, Shunji; Ohnishi, Makoto; Ihara, Toshiaki; Ichiyama, Satoshi

    2016-01-01

    Pneumococcal infection in children is a major public health problem worldwide, including in Japan. The pneumococcal conjugate vaccine 7 (PCV7) was licensed for use in Japan in 2010 followed by PCV13 in 2013. This report includes the results of a nationwide surveillance of invasive pneumococcal disease (IPD) and non-IPD in paediatric patients from January 2012 to December 2014. We collected 343 isolates from 337 IPD patients and 286 isolates from 278 non-IPD patients. Of the IPD isolates, the most identified serotypes included 19A, 24F, and 15A. The prevalence of non-PCV13 serotype isolates increased significantly from 2012 to 2014 (51.6-71.4%, p=0.004). Serotypes 19A, 15A and 35B were highly non-susceptible to penicillin, and the rates of non-susceptible isolates from IPD patients to penicillin and cefotaxime significantly declined during the study period (p=0.029 and p=0.013, respectively). The non-susceptible rate to meropenem increased, particularly for serotype 15A. The IPD isolates comprised clonal complex (CC) 3111 (93.8% was serotype 19A) followed by CC2572 (81.5% was serotype 24F) and CC63 (97.1% was serotype 15A). CC3111, CC63 and CC156 (33.3% was serotype 23A, 28.6% was serotype 6B, and 14.3% was serotype 19A) were highly non-susceptible to penicillin. Of the non-IPD isolates, the most identified serotypes included 19A, 15A, and 3. In conclusion, the introduction of PCV7 and PCV13 resulted in increasing non-PCV13 serotypes and clones, including antimicrobial resistant serotypes 15A and CC63 (Sweden(15A)-25 clone). PMID:26602268

  15. Failure to initiate early insulin therapy – A risk factor for diabetic retinopathy in insulin users with Type 2 diabetes mellitus: Sankara Nethralaya-Diabetic Retinopathy Epidemiology and Molecular Genetics Study (SN-DREAMS, Report number 35)

    PubMed Central

    Gupta, Aditi; Delhiwala, Kushal S; Raman, Rajiv P G; Sharma, Tarun; Srinivasan, Sangeetha; Kulothungan, Vaitheeswaran

    2016-01-01

    Context: Insulin users have been reported to have a higher incidence of diabetic retinopathy (DR). Aim: The aim was to elucidate the factors associated with DR among insulin users, especially association between duration, prior to initiating insulin for Type 2 diabetes mellitus (DM) and developing DR. Materials and Methods: Retrospective cross-sectional observational study included 1414 subjects having Type 2 DM. Insulin users were defined as subjects using insulin for glycemic control, and insulin nonusers as those either not using any antidiabetic treatment or using diet control or oral medications. The duration before initiating insulin after diagnosis was calculated by subtracting the duration of insulin usage from the duration of DM. DR was clinically graded using Klein's classification. SPSS (version 9.0) was used for statistical analysis. Results: Insulin users had more incidence of DR (52.9% vs. 16.3%, P < 0.0001) and sight threatening DR (19.1% vs. 2.4%, P < 0.0001) in comparison to insulin nonusers. Among insulin users, longer duration of DM (odds ratio [OR] 1.12, 95% confidence interval [CI] 1.00–1.25, P = 0.044) and abdominal obesity (OR 1.15, 95% CI 1.02–1.29, P = 0.021) was associated with DR. The presence of DR was significantly associated with longer duration (≥5 years) prior to initiating insulin therapy, overall (38.0% vs. 62.0%, P = 0.013), and in subjects with suboptimal glycemic control (32.5% vs. 67.5%, P = 0.022). Conclusions: The presence of DR is significantly associated with longer duration of diabetes (>5 years) and sub-optimal glycemic control (glycosylated hemoglobin <7.0%). Among insulin users, abdominal obesity was found to be a significant predictor of DR; DR is associated with longer duration prior to initiating insulin therapy in Type 2 DM subjects with suboptimal glycemic control. PMID:27488152

  16. The clinical and molecular epidemiology of pre-transplant vancomycin-resistant enterococci colonization among liver transplant recipients.

    PubMed

    Banach, David B; Peaper, David R; Fortune, Brett E; Emre, Sukru; Dembry, Louise M

    2016-03-01

    Vancomycin-resistant enterococci (VRE) infections cause significant morbidity in liver transplant recipients. The epidemiology and impact of pre-transplant colonization with VRE among patients who undergo liver transplantation are poorly understood. We conducted an observational cohort study to identify risk factors and outcomes associated with pre-transplant VRE colonization and described the molecular diversity among VRE strains colonizing patients who undergo liver transplantation. Perirectal VRE surveillance cultures were performed prior to transplantation. Repetitive sequence-based polymerase chain reaction (rep-PCR) testing was used to identify clonality among VRE isolates. Of 61 patients who underwent pre-transplant VRE surveillance and subsequent liver transplantation, 27 (44%) were colonized with VRE. In multivariate analysis, pre-transplant VRE colonization was associated with central venous catheterization (OR 9.4, 95% confidence interval [CI]= 1.3-70.2, p = 0.03) and rifaximin use (OR 15.4, 95% CI 1.5-159.7, p = 0.02). Pre-transplant VRE colonization was associated with more hospital days post-transplant (26.6 vs. 16.1 d, p = 0.04). Of VRE-colonized patients analyzed with rep-PCR, 68% were colonized with the same strain as another patient in the cohort. Active surveillance identifies VRE-colonized patients who may benefit from targeted antimicrobial prophylaxis and enhanced infection prevention measures to prevent VRE spread. The relationship between rifaximin receipt and VRE colonization warrants further study. The identification of similar VRE isolates may suggest linked transmission during pre-transplant hospitalizations, which should be further investigated in prospective studies. PMID:26780305

  17. The Biomonitoring, Environmental Epidemiology, and Short-Lived Chemicals (BEES-C) Instrument for Assessing Study Quality

    EPA Science Inventory

    Environmental epidemiology studies can be an effective means to assess impacts on human health from exposure to environmental stressors. Exposure scenarios are often extremely complex and proper assessment is critical for interpreting epidemiological study results. Biomarkers are...

  18. Epidemiological studies on radiation carcinogenesis in human populations following acute exposure: nuclear explosions and medical radiation

    SciTech Connect

    Fabrikant, J.I.

    1982-08-01

    The present review provides an understanding of our current knowledge of the carcinogenic effect of low-dose radiation in man, and surveys the epidemiological studies of human populations exposed to nuclear explosions and medical radiation. Discussion centers on the contributions of quantitative epidemiology to present knowledge, the reliability of the dose-incidence data, and those relevant epidemiological studies that provide the most useful information for risk estimation of cancer-induction in man. Reference is made to dose-incidence relationships from laboratory animal experiments where they may obtain for problems and difficulties in extrapolation from data obtained at high doses to low doses, and from animal data to the human situation. The paper describes the methods of application of such epidemiological data for estimation of excess risk of radiation-induced cancer in exposed human populations, and discusses the strengths and limitations of epidemiology in guiding radiation protection philosophy and public health policy.

  19. An epidemiological study of RSV infection in the Gambia.

    PubMed Central

    Weber, Martin W.; Milligan, Paul; Sanneh, Mariama; Awemoyi, Agnes; Dakour, Raduwan; Schneider, Gisela; Palmer, Ayo; Jallow, Mariatou; Oparaogu, Anslem; Whittle, Hilton; Mulholland, E. Kim; Greenwood, Brian M.

    2002-01-01

    OBJECTIVE: To describe the epidemiology of respiratory syncytial virus (RSV) infection in a developing country. METHODS: The work was carried out in three hospitals for primary cases and in the community for secondary cases in the western region of the Gambia, West Africa. RSV infection was diagnosed by immunofluorescence of nasopharyngeal aspirate samples in children younger than two years admitted to hospital with acute lower respiratory infection (ALRI). Routine records of all children with ALRI were analysed, and the incidence rates of ALRI, severe RSV-associated respiratory illness and hypoxaemic RSV infections were compared. A community-based study was undertaken to identify secondary cases and to obtain information about spread of the virus. FINDINGS: 4799 children with ALRI who were younger than two years and lived in the study area were admitted to the study hospitals: 421 had severe RSV-associated respiratory illness; 55 of these were hypoxaemic. Between 1994 and 1996, the observed incidence rate for ALRI in 100 children younger than one year living close to hospital was 9.6 cases per year; for severe RSV-associated respiratory illness 0.83; and for hypoxaemic RSV-associated respiratory illness 0.089. The proportion of all ALRI admissions due to RSV was 19%. Overall, 41% of children younger than five years in compounds in which cases lived and 42% in control compounds had evidence of RSV infection during the surveillance period. CONCLUSION: RSV is an important cause of ALRI leading to hospital admission in the Gambia. Morbidity is considerable and efforts at prevention are worthwhile. PMID:12163920

  20. Descriptive Epidemiology of Somatising Tendency: Findings from the CUPID Study.

    PubMed

    Vargas-Prada, Sergio; Coggon, David; Ntani, Georgia; Walker-Bone, Karen; Palmer, Keith T; Felli, Vanda E; Harari, Raul; Barrero, Lope H; Felknor, Sarah A; Gimeno, David; Cattrell, Anna; Bonzini, Matteo; Solidaki, Eleni; Merisalu, Eda; Habib, Rima R; Sadeghian, Farideh; Kadir, M Masood; Warnakulasuriya, Sudath S P; Matsudaira, Ko; Nyantumbu, Busisiwe; Sim, Malcolm R; Harcombe, Helen; Cox, Ken; Sarquis, Leila M M; Marziale, Maria H; Harari, Florencia; Freire, Rocio; Harari, Natalia; Monroy, Magda V; Quintana, Leonardo A; Rojas, Marianela; Harris, E Clare; Serra, Consol; Martinez, J Miguel; Delclos, George; Benavides, Fernando G; Carugno, Michele; Ferrario, Marco M; Pesatori, Angela C; Chatzi, Leda; Bitsios, Panos; Kogevinas, Manolis; Oha, Kristel; Freimann, Tiina; Sadeghian, Ali; Peiris-John, Roshini J; Sathiakumar, Nalini; Wickremasinghe, A Rajitha; Yoshimura, Noriko; Kelsall, Helen L; Hoe, Victor C W; Urquhart, Donna M; Derrett, Sarah; McBride, David; Herbison, Peter; Gray, Andrew; Vega, Eduardo J Salazar

    2016-01-01

    Somatising tendency, defined as a predisposition to worry about common somatic symptoms, is importantly associated with various aspects of health and health-related behaviour, including musculoskeletal pain and associated disability. To explore its epidemiological characteristics, and how it can be specified most efficiently, we analysed data from an international longitudinal study. A baseline questionnaire, which included questions from the Brief Symptom Inventory about seven common symptoms, was completed by 12,072 participants aged 20-59 from 46 occupational groups in 18 countries (response rate 70%). The seven symptoms were all mutually associated (odds ratios for pairwise associations 3.4 to 9.3), and each contributed to a measure of somatising tendency that exhibited an exposure-response relationship both with multi-site pain (prevalence rate ratios up to six), and also with sickness absence for non-musculoskeletal reasons. In most participants, the level of somatising tendency was little changed when reassessed after a mean interval of 14 months (75% having a change of 0 or 1 in their symptom count), although the specific symptoms reported at follow-up often differed from those at baseline. Somatising tendency was more common in women than men, especially at older ages, and varied markedly across the 46 occupational groups studied, with higher rates in South and Central America. It was weakly associated with smoking, but not with level of education. Our study supports the use of questions from the Brief Symptom Inventory as a method for measuring somatising tendency, and suggests that in adults of working age, it is a fairly stable trait. PMID:27128094

  1. Descriptive Epidemiology of Somatising Tendency: Findings from the CUPID Study

    PubMed Central

    Vargas-Prada, Sergio; Coggon, David; Ntani, Georgia; Walker-Bone, Karen; Palmer, Keith T.; Felli, Vanda E.; Harari, Raul; Barrero, Lope H.; Felknor, Sarah A.; Gimeno, David; Cattrell, Anna; Bonzini, Matteo; Solidaki, Eleni; Merisalu, Eda; Habib, Rima R.; Sadeghian, Farideh; Kadir, M. Masood; Warnakulasuriya, Sudath S. P.; Matsudaira, Ko; Nyantumbu, Busisiwe; Sim, Malcolm R.; Harcombe, Helen; Cox, Ken; Sarquis, Leila M. M.; Marziale, Maria H.; Harari, Florencia; Freire, Rocio; Harari, Natalia; Monroy, Magda V.; Quintana, Leonardo A.; Rojas, Marianela; Harris, E. Clare; Serra, Consol; Martinez, J. Miguel; Delclos, George; Benavides, Fernando G.; Carugno, Michele; Ferrario, Marco M.; Pesatori, Angela C.; Chatzi, Leda; Bitsios, Panos; Kogevinas, Manolis; Oha, Kristel; Freimann, Tiina; Sadeghian, Ali; Peiris-John, Roshini J.; Sathiakumar, Nalini; Wickremasinghe, A. Rajitha; Yoshimura, Noriko; Kelsall, Helen L.; Hoe, Victor C. W.; Urquhart, Donna M.; Derrett, Sarah; McBride, David; Herbison, Peter; Gray, Andrew; Vega, Eduardo J. Salazar

    2016-01-01

    Somatising tendency, defined as a predisposition to worry about common somatic symptoms, is importantly associated with various aspects of health and health-related behaviour, including musculoskeletal pain and associated disability. To explore its epidemiological characteristics, and how it can be specified most efficiently, we analysed data from an international longitudinal study. A baseline questionnaire, which included questions from the Brief Symptom Inventory about seven common symptoms, was completed by 12,072 participants aged 20–59 from 46 occupational groups in 18 countries (response rate 70%). The seven symptoms were all mutually associated (odds ratios for pairwise associations 3.4 to 9.3), and each contributed to a measure of somatising tendency that exhibited an exposure-response relationship both with multi-site pain (prevalence rate ratios up to six), and also with sickness absence for non-musculoskeletal reasons. In most participants, the level of somatising tendency was little changed when reassessed after a mean interval of 14 months (75% having a change of 0 or 1 in their symptom count), although the specific symptoms reported at follow-up often differed from those at baseline. Somatising tendency was more common in women than men, especially at older ages, and varied markedly across the 46 occupational groups studied, with higher rates in South and Central America. It was weakly associated with smoking, but not with level of education. Our study supports the use of questions from the Brief Symptom Inventory as a method for measuring somatising tendency, and suggests that in adults of working age, it is a fairly stable trait. PMID:27128094

  2. Molecular Epidemiology of Streptococcus uberis Clinical Mastitis in Dairy Herds: Strain Heterogeneity and Transmission.

    PubMed

    Davies, P L; Leigh, J A; Bradley, A J; Archer, S C; Emes, R D; Green, M J

    2016-01-01

    Multilocus sequence typing was successfully completed on 494 isolates of Streptococcus uberis from clinical mastitis cases in a study of 52 commercial dairy herds over a 12-month period. In total, 195 sequence types (STs) were identified. S. uberis mastitis cases that occurred in different cows within the same herd and were attributed to a common ST were classified as potential transmission events (PTEs). Clinical cases attributed to 35 of the 195 STs identified in this study were classified PTE. PTEs were identified in 63% of the herds. PTE-associated cases, which include the first recorded occurrence of that ST in that herd (index case) and all persistent infections with that PTE ST, represented 40% of all the clinical mastitis cases and occurred in 63% of the herds. PTE-associated cases accounted for >50% of all S. uberis clinical mastitis cases in 33% of the herds. Nine STs (ST-5, -6, -20, -22, -24, -35, -233, -361, and -512), eight of which were grouped within a clonal complex (sharing at least four alleles), were statistically overrepresented (OVR STs). The findings indicate that 38% of all clinical mastitis cases and 63% of the PTEs attributed to S. uberis in dairy herds may be caused by the nine most prevalent strains. The findings suggest that a small subset of STs is disproportionally important in the epidemiology of S. uberis mastitis in the United Kingdom, with cow-to-cow transmission of S. uberis potentially occurring in the majority of herds in the United Kingdom, and may be the most important route of infection in many herds. PMID:26491180

  3. Molecular Epidemiology of Streptococcus uberis Clinical Mastitis in Dairy Herds: Strain Heterogeneity and Transmission

    PubMed Central

    Leigh, J. A.; Bradley, A. J.; Archer, S. C.; Emes, R. D.; Green, M. J.

    2015-01-01

    Multilocus sequence typing was successfully completed on 494 isolates of Streptococcus uberis from clinical mastitis cases in a study of 52 commercial dairy herds over a 12-month period. In total, 195 sequence types (STs) were identified. S. uberis mastitis cases that occurred in different cows within the same herd and were attributed to a common ST were classified as potential transmission events (PTEs). Clinical cases attributed to 35 of the 195 STs identified in this study were classified PTE. PTEs were identified in 63% of the herds. PTE-associated cases, which include the first recorded occurrence of that ST in that herd (index case) and all persistent infections with that PTE ST, represented 40% of all the clinical mastitis cases and occurred in 63% of the herds. PTE-associated cases accounted for >50% of all S. uberis clinical mastitis cases in 33% of the herds. Nine STs (ST-5, -6, -20, -22, -24, -35, -233, -361, and -512), eight of which were grouped within a clonal complex (sharing at least four alleles), were statistically overrepresented (OVR STs). The findings indicate that 38% of all clinical mastitis cases and 63% of the PTEs attributed to S. uberis in dairy herds may be caused by the nine most prevalent strains. The findings suggest that a small subset of STs is disproportionally important in the epidemiology of S. uberis mastitis in the United Kingdom, with cow-to-cow transmission of S. uberis potentially occurring in the majority of herds in the United Kingdom, and may be the most important route of infection in many herds. PMID:26491180

  4. FEASIBILITY OF MATCHING STUDY PARTICIPANT RESIDENCE WITH SPECIFIC WATER UTILITY TRIHALOMETHANE (THM) DATA IN EPIDEMIOLOGIC STUDIES

    EPA Science Inventory

    Many epidemiologic studies concerning by-products of water disinfection use utility monitoring data to estimate exposure. Use of such data requires linkage of residence location to a specific water utility and associated monitoring data during a given exposure period. The inabil...

  5. Antimicrobial Resistance and Molecular Epidemiology of Escherichia coli Causing Bloodstream Infections in Three Hospitals in Shanghai, China.

    PubMed

    Wang, Su; Zhao, Sheng-Yuan; Xiao, Shu-Zhen; Gu, Fei-Fei; Liu, Qing-Zhong; Tang, Jin; Guo, Xiao-Kui; Ni, Yu-Xing; Han, Li-Zhong

    2016-01-01

    Escherichia coli (E. coli) is one of the most frequent and lethal causes of bloodstream infections (BSIs). We carried out a retrospective multicenter study on antimicrobial resistance and phylogenetic background of clinical E. coli isolates recovered from bloodstream in three hospitals in Shanghai. E. coli isolates causing BSIs were consecutively collected between Sept 2013 and Sept 2014. Ninety isolates randomly selected (30 from each hospital) were enrolled in the study. Antimicrobial susceptibility testing was performed by disk diffusion. PCR was used to detect antimicrobial resistance genes coding for β-lactamases (TEM, CTX-M, OXA, etc.), carbapenemases (IMP, VIM, KPC, NDM-1 and OXA-48), and phylogenetic groups. eBURST was applied for analysis of multi-locus sequence typing (MLST). The resistance rates for penicillins, second-generation cephalosporins, fluoroquinolone and tetracyclines were high (>60%). Sixty-one of the 90 (67.8%) strains enrolled produced ESBLs and no carbapenemases were found. Molecular analysis showed that CTX-M-15 (25/61), CTX-M-14 (18/61) and CTX-M-55 (9/61) were the most common ESBLs. Phylogenetic group B2 predominated (43.3%) and exhibited the highest rates of ESBLs production. ST131 (20/90) was the most common sequence type and almost assigned to phylogenetic group B2 (19/20). The following sequence types were ST405 (8/90) and ST69 (5/90). Among 61 ESBL-producers isolates, B2 (26, 42.6%) and ST131 (18, 29.5%) were also the most common phylogenetic group and sequence type. Genetic diversity showed no evidence suggesting a spread of these antimicrobial resistant isolates in the three hospitals. In order to provide more comprehensive and reliable epidemiological information for preventing further dissemination, well-designed and continuous surveillance with more hospitals participating was important. PMID:26824702

  6. Antimicrobial Resistance and Molecular Epidemiology of Escherichia coli Causing Bloodstream Infections in Three Hospitals in Shanghai, China

    PubMed Central

    Xiao, Shu-Zhen; Gu, Fei-Fei; Liu, Qing-Zhong; Tang, Jin; Guo, Xiao-Kui; Ni, Yu-Xing; Han, Li-Zhong

    2016-01-01

    Escherichia coli (E. coli) is one of the most frequent and lethal causes of bloodstream infections (BSIs). We carried out a retrospective multicenter study on antimicrobial resistance and phylogenetic background of clinical E. coli isolates recovered from bloodstream in three hospitals in Shanghai. E. coli isolates causing BSIs were consecutively collected between Sept 2013 and Sept 2014. Ninety isolates randomly selected (30 from each hospital) were enrolled in the study. Antimicrobial susceptibility testing was performed by disk diffusion. PCR was used to detect antimicrobial resistance genes coding for β-lactamases (TEM, CTX-M, OXA, etc.), carbapenemases (IMP, VIM, KPC, NDM-1 and OXA-48), and phylogenetic groups. eBURST was applied for analysis of multi-locus sequence typing (MLST). The resistance rates for penicillins, second-generation cephalosporins, fluoroquinolone and tetracyclines were high (>60%). Sixty-one of the 90 (67.8%) strains enrolled produced ESBLs and no carbapenemases were found. Molecular analysis showed that CTX-M-15 (25/61), CTX-M-14 (18/61) and CTX-M-55 (9/61) were the most common ESBLs. Phylogenetic group B2 predominated (43.3%) and exhibited the highest rates of ESBLs production. ST131 (20/90) was the most common sequence type and almost assigned to phylogenetic group B2 (19/20). The following sequence types were ST405 (8/90) and ST69 (5/90). Among 61 ESBL-producers isolates, B2 (26, 42.6%) and ST131 (18, 29.5%) were also the most common phylogenetic group and sequence type. Genetic diversity showed no evidence suggesting a spread of these antimicrobial resistant isolates in the three hospitals. In order to provide more comprehensive and reliable epidemiological information for preventing further dissemination, well-designed and continuous surveillance with more hospitals participating was important. PMID:26824702

  7. New insights into the molecular epidemiology of Trichinella infection in domestic pigs, wild boars, and bears in Romania.

    PubMed

    Nicorescu, Isabela Madalina Dragoi; Ionita, Mariana; Ciupescu, Laurentiu; Buzatu, Cristian Vasile; Tanasuica, Rodica; Mitrea, Ioan Liviu

    2015-09-15

    Trichinellosis is a food-borne zoonosis caused by the parasitic nematode Trichinella, characterized by an extremely wide host range and geographical distribution. In Romania, it is recognized as one of the most serious zoonotic diseases. A cross-sectional study, covering all regions of Romania, was conducted in 2014 to investigate and update the prevalence of Trichinella infection among domestic pigs, wild boars, and bears. Additional, molecular identification of Trichinella species circulating among these animals was performed in order to establish the biogeography of Trichinella species within the seven geographical regions of Romania. For this, a total of 113,383 pigs raised in non-controlled housing conditions (backyards), 5596 hunted wild boars and 147 hunted bears were subjected to Trichinella analysis. The highest prevalence of Trichinella infections was found in bears (12.93%), followed by wild boars (1.66%) and domestic pigs (0.20%). Of 294 Trichinella isolates that tested positive by multiplex PCR, 219 (74.49%) were identified as Trichinella spiralis, 66 (22.45%) as Trichinella britovi, and 9 isolates (3.06%) as mixed infections of T. spiralis and T. britovi. T. spiralis was more prevalent in domestic pigs (165/228; 72.37%) than in game (63/228; 27.63%), while T. britovi showed a higher prevalence in game (50/75; 66.66%) than in domestic pigs (25/75; 33.33%). Moreover, the present study revealed a significant host- and area- related distribution of Trichinella species within the seven regions of Romania. Therefore, these findings are of epidemiological relevance, updating data on the prevalence and distribution of Trichinella species circulating among domestic and wild animals in South-Eastern Europe. PMID:26238657

  8. New Insights into Handling Missing Values in Environmental Epidemiological Studies