Science.gov

Sample records for molecular epidemiological study

  1. Molecular epidemiology: issues in study design and statistical analysis.

    PubMed

    Chia, K S; Shi, C Y; Lee, J; Seow, A; Lee, H P

    1996-01-01

    Traditional analytical epidemiology is directed at identifying the association between risk factors and occurrence of disease by using crude exposure data derived from questionnaires or clinical measures, and taking clinical disease as the end point. With the rapid development in molecular biology and laboratory methods, it is now possible to use biomarkers which are capable of identifying molecular events for epidemiologic research. This improved sensitivity enables us to develop a mechanistic understanding of disease causation: a step closer to the unravelling of the "black box" of traditional epidemiology. Biomarkers may be classified as internal indicators of exposure (biomarkers of exposure), indicators of preclinical adverse effect (biomarkers of effect) or indicators of an intrinsic or acquired susceptibility to disease (biomarkers of susceptibility). Biomarkers provide a better definition of exposure and disease status and consequently they could help to reduce misclassification bias in both exposure and disease, reduce the follow-up time in prospective studies, as well as identify possible interactions between risk factors on disease occurrence. However, a biomarker needs to be validated and its distribution in large populations described before it can be used profitably for aetiologic research. Also, the use of biomarkers in epidemiologic research raises other interesting epidemiological and statistical issues like confounding, effect modification and the analysis of repeated measurements. Molecular epidemiology is a multidisciplinary endeavour which comprises molecular biology, epidemiology and biostatistics. Clearly then, to carry out research in this field profitably, the molecular biologist, epidemiologist and biostatistician must acquire not only expertise in their respective fields, but also an integrated understanding of all three fields. The molecular biologist is not merely a laboratory bench worker; the epidemiologist, a field data-collector and

  2. A Molecular Epidemiologic Case-Case Study of Prostate Cancer

    DTIC Science & Technology

    2001-03-01

    AD__ _ _ _ Award Number: DAMD17-98-1-8471 TITLE: A Molecular Epidemiologic Case-Case Study of Prostate Cancer PRINCIPAL INVESTIGATOR: Sara S. Strom...Molecular Epidmeiologic Case-Case Study of Prostate DAMD17-98-1-8471 Cancer Susceptibility 6. AUTHOR(S) Sara S. Strom, Ph.D. Sue-Hwa Lin 7. PERFORMING...DISTRIBUTION CODE Approved for Public Release; Distribution Unlimited 13. ABSTRACT (Maximum 200 Words) Although prostate cancer is the most common cancer in

  3. [Molecular epidemiology studies on the immigrant population in Spain].

    PubMed

    González-Candelas, Fernando; Alma Bracho, María; Comas, Iñaki; d'Auria, Giuseppe; D Unková, Mária; García, Rodrigo; Gosalbes, María José; Isaac, Sandrine; Latorre, Amparo; López-Labrador, Francisco Xavier; Patiño Galindo, Juan Ángel; Palero, Ferran; Pérez-Brocal, Vicente; Pérez-Cobas, Ana Elena; Sánchez-Busó, Leonor; Silva, Francisco J; Vázquez-Castellanos, Jorge F; Moya, Andrés

    2014-01-01

    Molecular epidemiology is a new scientific discipline which allows to integrate information on the genetic variation of infectious pathogens with their diffusion in a population and its subgroups including, for instance, resistance mutations to antibiotics and antiretrovirals. We present the results of an analysis of scientific publications that analyze the health status of the immigrant population in Spain from a molecular epidemiology perspective. We reviewed original articles published in 1998-2014 with the keywords "molecular epidemiology", "molecular typing", "sequencing", "immigrant", and "Spain". From a total of 267 articles identified initially, only 50 passed through the established filters. Most of them (36) analyzed infections by Mycobacterium tuberculosis (3) and HIV (3), followed at a large distance by Staphylococcus aureus and hepatitis B virus. The main goal of these works was the typing of the pathogen and to determine the frequency of resistance mutations. Is difficult to generalize the conclusions from the analyzed articles because most of them have a purely descriptive and quite restricted scope, considering the type and size of the samples studied. Several studies are focused on the most likely origin for the strains or variants of the pathogen but others also reveal transmissions from the local to the immigrant populations.

  4. A molecular epidemiological study of rabies in Puerto Rico.

    PubMed

    Nadin-Davis, Susan A; Velez, Jafet; Malaga, Carlos; Wandeler, Alexander I

    2008-01-01

    The mongoose is the principal reservoir for rabies on the island of Puerto Rico. This report describes a molecular epidemiological study of representative rabies viruses recovered from the island in 1997. Two closely related but distinct variants circulating in regionally localised parts of the island were identified. The lack of a monophyletic relationship of these viruses suggests that two independent incursions of rabies onto the island have occurred. Both of these Puerto Rican variants were closely related to a variant, known as the north central skunk strain, currently circulating in North American skunk populations and all are members of the cosmopolitan rabies lineage spread during the colonial period. However, the Puerto Rican viruses are clearly distinct from those presently circulating in mongooses in Cuba and which are epidemiologically closely linked to the Mexican dog rabies virus. This study clearly establishes the distinct origins of the rabies viruses now circulating on these two Caribbean islands.

  5. First molecular epidemiological study of cutaneous leishmaniasis in Libya.

    PubMed

    Amro, Ahmad; Gashout, Aisha; Al-Dwibe, Hamida; Zahangir Alam, Mohammad; Annajar, Badereddin; Hamarsheh, Omar; Shubar, Hend; Schönian, Gabriele

    2012-01-01

    Cutaneous leishmaniasis (CL) is a major public health problem in Libya. The objective of this study was to investigate, for the first time, epidemiological features of CL outbreaks in Libya including molecular identification of parasites, the geographical distribution of cases and possible scenarios of parasite transmission. We studied 450 patients that came from 49 areas distributed in 12 districts in north-west Libya. The patients' ages ranged from 9 months to 87 years (median age 25 years); 54% of the cases were males. Skin scrapings spotted on glass slides were collected for molecular identification of causative agent. The ribosomal internal transcribed spacer 1 (ITS1) was amplified and subsequently characterized by restriction fragment length polymorphism (RFLP) analysis. In total, 195 samples were successfully identified of which 148 (75.9%) were Leishmania major, and 47 (24.1%) Leishmania tropica. CL cases infected with L. major were found in all CL areas whereas L. tropica cases came mainly from Al Jabal Al Gharbi (46.4%), Misrata (17.8%) and Tarhuna districts (10.7%). A trend of seasonality was noticed for the infections with L. major which showed a clear peak between November and January, but was less pronounced for infections by L. tropica. The first molecular study on CL in Libya revealed that the disease is caused by L. major and L. tropica and the epidemiological patterns in the different foci were the same as in other Mediterranean foci of CL.

  6. First Molecular Epidemiological Study of Cutaneous Leishmaniasis in Libya

    PubMed Central

    Amro, Ahmad; Gashout, Aisha; Al-Dwibe, Hamida; Zahangir Alam, Mohammad; Annajar, Badereddin; Hamarsheh, Omar; Shubar, Hend; Schönian, Gabriele

    2012-01-01

    Background Cutaneous leishmaniasis (CL) is a major public health problem in Libya. The objective of this study was to investigate, for the first time, epidemiological features of CL outbreaks in Libya including molecular identification of parasites, the geographical distribution of cases and possible scenarios of parasite transmission. Methodology/Principal Findings We studied 450 patients that came from 49 areas distributed in 12 districts in north-west Libya. The patients' ages ranged from 9 months to 87 years (median age 25 years); 54% of the cases were males. Skin scrapings spotted on glass slides were collected for molecular identification of causative agent. The ribosomal internal transcribed spacer 1 (ITS1) was amplified and subsequently characterized by restriction fragment length polymorphism (RFLP) analysis. In total, 195 samples were successfully identified of which 148 (75.9%) were Leishmania major, and 47 (24.1%) Leishmania tropica. CL cases infected with L. major were found in all CL areas whereas L. tropica cases came mainly from Al Jabal Al Gharbi (46.4%), Misrata (17.8%) and Tarhuna districts (10.7%). A trend of seasonality was noticed for the infections with L. major which showed a clear peak between November and January, but was less pronounced for infections by L. tropica. Conclusion The first molecular study on CL in Libya revealed that the disease is caused by L. major and L. tropica and the epidemiological patterns in the different foci were the same as in other Mediterranean foci of CL. PMID:22724036

  7. [Surveillance of hepatitis A by molecular epidemiologic studies].

    PubMed

    Stene-Johansen, K; Skaug, K; Blystad, H

    1999-10-20

    Hepatitis A virus was studied by molecular epidemiology in connection with an outbreak of hepatitis A associated with intravenous drug users (IVDU) in Norway. Hepatitis A virus was characterised by sequencing 114 of 1,242 notified cases of hepatitis A from January 1995 to July 1998. One hepatitis A variant (IVDU variant I) was detected among IVDU during an outbreak of hepatitis A, as well as among 19 out of 49 cases with no apparent association to this outbreak. During the autumn of 1997, a new variant (IVDU variant II) was detected in the IVDU communities. Genotyping of virus from imported cases associated with travel to endemic regions, revealed that they were distinct from the two other IVDU variants. Hepatitis A has disseminated among IVDU over years; this indicates that hepatitis A is endemic in these communities. At the turn of the year 1997/98, there was a smaller outbreak of hepatitis A among homosexual men in Oslo, distinguished by genotyping from the outbreaks in the IVDU communities. By molecular epidemiology we have been able to identify individual outbreaks of hepatitis A and distinguish them from the IVDU outbreak.

  8. Molecular Epidemiology of Foodborne Pathogens

    NASA Astrophysics Data System (ADS)

    Chen, Yi; Brown, Eric; Knabel, Stephen J.

    The purpose of this chapter is to describe the basic principles and advancements in the molecular epidemiology of foodborne pathogens. Epidemiology is the study of the distribution and determinants of infectious diseases and/or the dynamics of disease transmission. The goals of epidemiology include the identification of physical sources, routes of transmission of infectious agents, and distribution and relationships of different subgroups. Molecular epidemiology is the study of epidemiology at the molecular level. It has been defined as "a science that focuses on the contribution of potential genetic and environmental risk factors, identified at the molecular level, to the etiology, distribution and prevention of diseases within families and across populations".

  9. Molecular epidemiological approaches to study the epidemiology of tuberculosis in low-incidence settings receiving immigrants.

    PubMed

    Garzelli, Carlo; Rindi, Laura

    2012-06-01

    Although in most wealthy western countries the total incidence of tuberculosis (TB) steadily decreased in the last decades, the proportion of cases in immigrants from high-burden TB countries generally increased and to date a large proportion of all new active cases, often exceeding 50%, occurs among foreign-born individuals. In this context, molecular typing of Mycobacterium tuberculosis isolates has significantly contributed to understand the epidemiology of TB, allowing an objective evaluation of the dynamics and the risk of TB importation and transmission within low-incidence host countries. Many molecular studies have shown that a large part of active TB cases in immigrants yield unique, unclustered DNA fingerprints; this finding reflects reactivation of remote latent infections, rather than recent TB infections, and, at the same time, indicates a low rate of disease transmission within the host country. Some studies however express more concern on the basis of higher rates of transmission within the host country with foreign-born index cases. Molecular analysis of isolates also showed that TB infections in migrants may be acquired after arrival in the host country and that TB transmission between foreign-born and autochthonous individuals may occur in both directions. Molecular typing of isolates has been also profitably used to evaluate the diffusion of M. tuberculosis strain families across different geographic areas and human populations and to monitor the diffusion of threatening strains, such as Beijing and/or (multi)drug-resistant strains. To date, based on the contribution of molecular epidemiology, it is possible to adapt or design appropriate strategies for a rational control of TB in low-incidence countries.

  10. Molecular and epidemiological studies of Porcine rubulavirus infection - an overview.

    PubMed

    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.

  11. Analysis of the transcriptome in molecular epidemiology studies

    PubMed Central

    McHale, Cliona M.; Zhang, Luoping; Thomas, Reuben; smith, Martyn T.

    2016-01-01

    The human transcriptome is complex, comprising multiple transcript types, mostly in the form of non-coding RNA (ncRNA). The majority of ncRNA is of the long form (lncRNA, ≥200bp), which plays an important role in gene regulation through multiple mechanisms including epigenetics, chromatin modification, control of transcription factor binding, and regulation of alternative splicing. Both mRNA and ncRNA exhibit additional variability in the form of alternative splicing and RNA editing. All aspects of the human transcriptome can potentially be dysregulated by environmental exposures. Next-generation RNA sequencing (RNA-Seq) is the best available methodology to measure this although it has limitations, including experimental bias. The third phase of the MicroArray Quality Control Consortium project (MAQC-III), also called Sequencing Quality Control (SeQC), aims to address these limitations through standardization of experimental and bioinformatic methodologies. A limited number of toxicogenomic studies have been conducted to date using RNA-Seq. This review describes the complexity of the human transcriptome, the application of transcriptomics by RNA-Seq or microarray in molecular epidemiology studies, and limitations of these approaches including the type of cell or tissue analyzed, experimental variation, and confounding. By using good study designs with precise, individual exposure measurements, sufficient power and incorporation of phenotypic anchors, studies in human populations can identify biomarkers of exposure and/or early effect and elucidate mechanisms of action underlying associated diseases, even at low doses. Analysis of datasets at the pathway level can compensate for some of the limitations of RNA-Seq and, as more datasets become available, will increasingly elucidate the exposure-disease continuum. PMID:23907930

  12. [Molecular epidemiology in the epidemiological transition].

    PubMed

    Tapia-Conyer, R

    1997-01-01

    The epidemiological transition describes the changes in the health profile of populations where infectious diseases are substituted by chronic or non-communicable diseases. Even in industrialized countries, infectious diseases emerge as important public health problems and with a very important association with several type of neoplasm. Molecular epidemiology brings in new tools for the study of the epidemiological transition by discovering infectious agents as etiology of diseases, neither of both new. Much has been advanced in the understanding of the virulence and resistance mechanism of different strains, or improving the knowledge on transmission dynamics and dissemination pathways of infectious diseases. As to the non-communicable diseases, molecular epidemiology has enhanced the identification of endogenous risk factors link to alterations, molecular changes in genetic material, that will allow a more detail definition of risk and the identification of individual and groups at risk of several diseases. The potential impact of molecular epidemiology in other areas as environmental, lifestyles and nutritional areas are illustrated with several examples.

  13. Progress of epidemiological and molecular epidemiological studies on benzene in China.

    PubMed

    Li, Guilan; Yin, Songnian

    2006-09-01

    Benzene is an organic solvent that has been used in industry for about 100 years throughout the world. Since 1973, a series of toxicological and molecular epidemiological studies on benzene were conducted by researchers at the Chinese Academy of Preventive Medicine (CAPM) (1973-1986) and subsequently by a collaboration between the CAPM and the National Cancer Institute (NCI) in the United States that began in 1986, which was joined by investigators from the University of California at Berkeley, the University of North Carolina at Chapel Hill, and New York University. The findings demonstrated that the risk of leukemia and lymphoma among benzene-exposed workers was significantly increased, with elevated risks for leukemia present not only at higher exposure but also among workers exposed to under 10 ppm. Therefore, the benzene permissible level was decreased to 1.8 ppm (6 mg/m(3)) and benzene-induced leukemia is treated as an occupational cancer in China. The benzene permissible level is 1.0 in the United States and in several other developed countries and it has been suggested to be decreased to 0.5 ppm (ACGIH). A number of potential biomarkers are related to benzene exposure and poisoning. Some of these are benzene oxide-protein adducts, chromosome aberration of lymphocytes, and GPA mutations in erythrocytes, a decrease in B cell and CD4(-)T cell counts in peripheral blood, and altered expression of CXCL16, ZNF331, JUN, and PF4 in lymphocytes. Variation in multiple benzene metabolizing genes may be associated with risk of benzene hematotoxicity, including CYP2E1, MPO, NQO1, and GSTT1.

  14. 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

  15. A Molecular Epidemiologic Case-Case Study of Prostate Cancer

    DTIC Science & Technology

    2002-03-01

    Receptor Polymorphism and Prostate Cancer Risk 1 Sara S. Strom 2, Qiang Zhang, Yun Gu, Margaret R. Spitz, Peter T. Scardino 3, Christopher J. Logothetis...Taylor, J. A. Vitamin D receptor polymorphisms and prostate cancer. Molecular Carcinogenesis, 27: 18-23, 2000. 6. Ma, J., Stampfer , M. J., Gann, P. H...Margaret R. Spitz, Richard J. Babaian, Christopher Logothetis, Sara S. Strom, University of Texas M.D. Anderson Cancer Center, Houston, TX; The University

  16. Molecular and epidemiological study of Salmonella clinical isolates.

    PubMed Central

    Rivera, M J; Rivera, N; Castillo, J; Rubio, M C; Gómez-Lus, R

    1991-01-01

    A survey of Salmonella infections was carried out over a 1-year period in the rural community covered by the Hospital Reina Sofía (Tudela, Spain). The 255 strains that were collected were studied by serotyping, antimicrobial resistance, and plasmid profile analysis. The predominant serotype was S. enteritidis (85.90%), followed by S. typhimurium (7.06%) and S. virchow (2.36%). Only 7.84% of the strains were resistant to antimicrobial agents. The most common resistance was to beta-lactam antibiotics. This resistance was due to the presence of one of two types of beta-lactamases, TEM-1 or TEM-2. Resistance to kanamycin was associated with the synthesis of a 3'-O-phosphotransferase. The resistance to streptomycin and chloramphenicol was either not enzymatic or was due to a 3"-O-phosphotransferase and a chloramphenicol acetyltransferase, respectively. Analysis of total plasmid DNA content revealed the presence of plasmids in 96.08% of the isolates. According to their plasmid profile, the strains could be classified into different groups. The three main groups, which accounted for 50.19, 20.78, and 4.70% of the isolates, respectively, corresponded to the antimicrobial-susceptible S. enteritidis serotype. These results suggested that plasmid profile analysis in conjunction with antimicrobial resistance determination can be useful for subtyping resistant Salmonella isolates. Images PMID:2056061

  17. 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.

  18. Use of molecular epidemiology in veterinary practice.

    PubMed

    Zadoks, Ruth N; Schukken, Ynte H

    2006-03-01

    Molecular epidemiology is a relatively new branch of epidemiology that uses molecular biology methods to study health and disease in populations. This article gives an introduction to molecular epidemiologic terminology and methodology and its usefulness in large animal medicine and veterinary public health. Applications in source tracing and vaccine studies and insights into transmission dynamics, host specificity, and niche adaptation of infectious organisms are presented. Examples are drawn from a variety of diseases, organisms, and host species and range from the global level to the individual-animal level.

  19. 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

  20. Establishment and operation of a biorepository for molecular epidemiologic studies in Costa Rica.

    PubMed

    Cortés, Bernal; Schiffman, Mark; Herrero, Rolando; Hildesheim, Allan; Jiménez, Silvia; Shea, Katheryn; González, Paula; Porras, Carolina; Fallas, Greivin; Rodríguez, Ana Cecilia

    2010-04-01

    The Proyecto Epidemiológico Guanacaste (PEG) has conducted several large studies related to human papillomavirus (HPV) and cervical cancer in Guanacaste, Costa Rica in a long-standing collaboration with the U.S. National Cancer Institute. To improve molecular epidemiology efforts and save costs, we have gradually transferred technology to Costa Rica, culminating in state-of-the-art laboratories and a biorepository to support a phase III clinical trial investigating the efficacy of HPV 16/18 vaccine. Here, we describe the rationale and lessons learned in transferring molecular epidemiologic and biorepository technology to a developing country. At the outset of the PEG in the early 1990s, we shipped all specimens to repositories and laboratories in the United States, which created multiple problems. Since then, by intensive personal interactions between experts from the United States and Costa Rica, we have successfully transferred liquid-based cytology, HPV DNA testing and serology, chlamydia and gonorrhea testing, PCR-safe tissue processing, and viable cryopreservation. To accommodate the vaccine trial, a state-of-the-art repository opened in mid-2004. Approximately 15,000 to 50,000 samples are housed in the repository on any given day, and >500,000 specimens have been shipped, many using a custom-made dry shipper that permits exporting >20,000 specimens at a time. Quality control of shipments received by the NCI biorepository has revealed an error rate of <0.2%. Recently, the PEG repository has incorporated other activities; for example, large-scale aliquotting and long-term, cost-efficient storage of frozen specimens returned from the United States. Using Internet-based specimen tracking software has proven to be efficient even across borders. For long-standing collaborations, it makes sense to transfer the molecular epidemiology expertise toward the source of specimens. The successes of the PEG molecular epidemiology laboratories and biorepository prove that

  1. 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

  2. Molecular pathological epidemiology: new developing frontiers of big data science to study etiologies and pathogenesis.

    PubMed

    Hamada, Tsuyoshi; Keum, NaNa; Nishihara, Reiko; Ogino, Shuji

    2017-03-01

    Molecular pathological epidemiology (MPE) is an integrative field that utilizes molecular pathology to incorporate interpersonal heterogeneity of a disease process into epidemiology. In each individual, the development and progression of a disease are determined by a unique combination of exogenous and endogenous factors, resulting in different molecular and pathological subtypes of the disease. Based on "the unique disease principle," the primary aim of MPE is to uncover an interactive relationship between a specific environmental exposure and disease subtypes in determining disease incidence and mortality. This MPE approach can provide etiologic and pathogenic insights, potentially contributing to precision medicine for personalized prevention and treatment. Although breast, prostate, lung, and colorectal cancers have been among the most commonly studied diseases, the MPE approach can be used to study any disease. In addition to molecular features, host immune status and microbiome profile likely affect a disease process, and thus serve as informative biomarkers. As such, further integration of several disciplines into MPE has been achieved (e.g., pharmaco-MPE, immuno-MPE, and microbial MPE), to provide novel insights into underlying etiologic mechanisms. With the advent of high-throughput sequencing technologies, available genomic and epigenomic data have expanded dramatically. The MPE approach can also provide a specific risk estimate for each disease subgroup, thereby enhancing the impact of genome-wide association studies on public health. In this article, we present recent progress of MPE, and discuss the importance of accounting for the disease heterogeneity in the era of big-data health science and precision medicine.

  3. Measuring molecular biomarkers in epidemiologic studies: laboratory techniques and biospecimen considerations.

    PubMed

    Erickson, Heidi S

    2012-09-28

    The future of personalized medicine depends on the ability to efficiently and rapidly elucidate a reliable set of disease-specific molecular biomarkers. High-throughput molecular biomarker analysis methods have been developed to identify disease risk, diagnostic, prognostic, and therapeutic targets in human clinical samples. Currently, high throughput screening allows us to analyze thousands of markers from one sample or one marker from thousands of samples and will eventually allow us to analyze thousands of markers from thousands of samples. Unfortunately, the inherent nature of current high throughput methodologies, clinical specimens, and cost of analysis is often prohibitive for extensive high throughput biomarker analysis. This review summarizes the current state of high throughput biomarker screening of clinical specimens applicable to genetic epidemiology and longitudinal population-based studies with a focus on considerations related to biospecimens, laboratory techniques, and sample pooling. Copyright © 2012 John Wiley & Sons, Ltd.

  4. A pilot study on the application of statistical classification procedures to molecular epidemiological data.

    PubMed

    Schwender, Holger; Zucknick, Manuela; Ickstadt, Katja; Bolt, Hermann M

    2004-06-15

    The development of new statistical methods for use in molecular epidemiology comprises the building and application of appropriate classification rules. The aim of this study was to assess various classification methods that can potentially handle genetic interactions. A data set comprising genotypes at 25 single nucleotide polymorphic (SNP) loci from 518 breast cancer cases and 586 age-matched population-based controls from the GENICA study was used to built a classification rule with the discrimination methods SVM (support vector machine), CART (classification and regression tree), Bagging, Random Forest, LogitBoost and k nearest neighbours (kNN). A blind pilot analysis of the genotypic data set was a first approach to obtain an impression of the statistical structure of the data. Furthermore, this analysis was performed to explore classification methods that may be applied to molecular-epidemiological evaluation. The results showed that all blindly applied classification methods had a slightly smaller misclassification rate than a random classification. The findings, nevertheless, suggest that SNP data might be useful for the classification of individuals into categories of high or low risk of diseases.

  5. An Overview of Genetic Polymorphisms and Pancreatic Cancer Risk in Molecular Epidemiologic Studies

    PubMed Central

    Lin, Yingsong; Yagyu, Kiyoko; Egawa, Naoto; Ueno, Makoto; Mori, Mitsuru; Nakao, Haruhisa; Ishii, Hiroshi; Nakamura, Kozue; Wakai, Kenji; Hosono, Satoyo; Tamakoshi, Akiko; Kikuchi, Shogo

    2011-01-01

    Background Although pancreatic cancer has been extensively studied, few risk factors have been identified, and no validated biomarkers or screening tools exist for early detection in asymptomatic individuals. We present a broad overview of molecular epidemiologic studies that have addressed the relationship between pancreatic cancer risk and genetic polymorphisms in several candidate genes and suggest avenues for future research. Methods A comprehensive literature search was performed using the PubMed database. Results Overall, individual polymorphisms did not seem to confer great susceptibility to pancreatic cancer; however, interactions of polymorphisms in carcinogen-metabolizing genes, DNA repair genes, and folate-metabolizing genes with smoking, diet, and obesity were shown in some studies. The major problem with these studies is that, due to small sample sizes, they lack sufficient statistical power to explore gene–gene or gene–environment interactions. Another important challenge is that the measurement of environmental influence needs to be improved to better define gene–environment interaction. It is noteworthy that 2 recent genome-wide association studies of pancreatic cancer have reported that variants in ABO blood type and in 3 other chromosomal regions are associated with risk for this cancer, thus providing new insight into pancreatic cancer etiology. Conclusions As is the case in other complex diseases, common, low-risk variants in different genes may act collectively to confer susceptibility to pancreatic cancer in individuals with repeated environmental exposures, such as smoking and red meat intake. Clarification of gene–gene and gene–environmental interaction is therefore indispensable for future studies. To address these issues, a rigorously designed molecular epidemiologic study with a large sample is desirable. PMID:21071884

  6. First nationwide study regarding ceftriaxone resistance and molecular epidemiology of Neisseria gonorrhoeae in China.

    PubMed

    Chen, Shao-Chun; Yin, Yue-Ping; Dai, Xiu-Qin; Unemo, Magnus; Chen, Xiang-Sheng

    2016-01-01

    Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a major public health concern worldwide. This is the first nationwide study, performed within the China Gonococcal Antimicrobial Susceptibility Programme (China-GASP), regarding AMR, including ceftriaxone genetic resistance determinants, and molecular epidemiology of gonococci in China. Gonococcal isolates (n = 1257) from consecutive patients were collected at 11 sentinel sites distributed across China during 2012-13. Susceptibility to ceftriaxone, spectinomycin, ciprofloxacin and tetracycline was determined using the agar dilution method. Ceftriaxone resistance determinants penA and penB were examined using sequencing. N. gonorrhoeae multiantigen sequence typing (NG-MAST) was performed for molecular epidemiology. Among isolates, 0.2% were resistant to spectinomycin, 4.4% to ceftriaxone, 42.9% to tetracyclines (high-level resistance) and 99.8% to ciprofloxacin. Among 890 sequenced isolates, 16 (1.8%) possessed a penA mosaic allele; 4 of these isolates belonged to the MDR internationally spread NG-MAST genogroup G1407 (first description in China). Non-mosaic penA alleles with an A501T mutation and an A102D alteration in porB1b were statistically associated with decreased susceptibility/resistance to ceftriaxone. NG-MAST G10339, G1424 and G1053 were associated with decreased susceptibility/resistance to ceftriaxone. In China, ceftriaxone and spectinomycin can continue to be recommended for gonorrhoea treatment, with the possible exception of Hainan and Sichuan provinces where ceftriaxone resistance exceeded 5% and AMR surveillance needs to be strengthened. Molecular approaches including genotyping and AMR determinant analysis can be valuable to supplement and enhance conventional surveillance of gonococcal AMR in China. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections.

    PubMed

    Lam, Tommy Tsan-Yuk; Hon, Chung-Chau; Tang, Julian W

    2010-01-01

    Since DNA sequencing techniques first became available almost 30 years ago, the amount of nucleic acid sequence data has increased enormously. Phylogenetics, which is widely applied to compare and analyze such data, is particularly useful for the analysis of genes from rapidly evolving viruses. It has been used extensively to describe the molecular epidemiology and transmission of the human immunodeficiency virus (HIV), the origins and subsequent evolution of the severe acute respiratory syndrome (SARS)-associated coronavirus (SCoV), and, more recently, the evolving epidemiology of avian influenza as well as seasonal and pandemic human influenza viruses. Recent advances in phylogenetic methods can infer more in-depth information about the patterns of virus emergence, adding to the conventional approaches in viral epidemiology. Examples of this information include estimations (with confidence limits) of the actual time of the origin of a new viral strain or its emergence in a new species, viral recombination and reassortment events, the rate of population size change in a viral epidemic, and how the virus spreads and evolves within a specific population and geographical region. Such sequence-derived information obtained from the phylogenetic tree can assist in the design and implementation of public health and therapeutic interventions. However, application of many of these advanced phylogenetic methods are currently limited to specialized phylogeneticists and statisticians, mainly because of their mathematical basis and their dependence on the use of a large number of computer programs. This review attempts to bridge this gap by presenting conceptual, technical, and practical aspects of applying phylogenetic methods in studies of influenza, HIV, and SCoV. It aims to provide, with minimal mathematics and statistics, a practical overview of how phylogenetic methods can be incorporated into virological studies by clinical and laboratory specialists.

  8. Molecular epidemiological study of enteroviruses associated with encephalitis in children from India.

    PubMed

    Kumar, Arvind; Shukla, Deepti; Kumar, Rashmi; Idris, Mohammad Z; Misra, Usha K; Dhole, Tapan N

    2012-11-01

    Enteroviruses have been reported in encephalitis cases. However, clinical and epidemiological characteristics of enteroviruses in encephalitis are not fully established. We prospectively investigated 204 children with encephalitis over a period of 2 years (2009 to 2010) for enterovirus. Enterovirus was detected in 45 specimens (22.1%); of these, 40 were typed by seminested reverse transcription-PCR (RT-PCR) and sequencing of the VP1 gene. Molecular typing of enterovirus revealed the predominance of echovirus 21 associated with an epidemic during the rainy seasons of 2010 and the circulation of echovirus 1, coxsackievirus B1, enterovirus 75, enterovirus 76, coxsackievirus B5, and echovirus 19. The nucleotide divergence among echovirus 21 strains was 0 to 2% at the nucleotide level. This study suggests that enterovirus is an important cause of encephalitis in children from India. To our knowledge, this is the first report of echovirus 21 in encephalitis cases worldwide.

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

    USDA-ARS?s Scientific Manuscript database

    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 ...

  10. 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

  11. Relative abundance of Mycobacterium bovis molecular types in cattle: a simulation study of potential epidemiological drivers.

    PubMed

    Trewby, Hannah; Wright, David M; Skuce, Robin A; McCormick, Carl; Mallon, Thomas R; Presho, Eleanor L; Kao, Rowland R; Haydon, Daniel T; Biek, Roman

    2017-08-22

    The patterns of relative species abundance are commonly studied in ecology and epidemiology to provide insights into underlying dynamical processes. Molecular types (MVLA-types) of Mycobacterium bovis, the causal agent of bovine tuberculosis, are now routinely recorded in culture-confirmed bovine tuberculosis cases in Northern Ireland. In this study, we use ecological approaches and simulation modelling to investigate the distribution of relative abundances of MVLA-types and its potential drivers. We explore four biologically plausible hypotheses regarding the processes driving molecular type relative abundances: sampling and speciation; structuring of the pathogen population; historical changes in population size; and transmission heterogeneity (superspreading). Northern Irish herd-level MVLA-type surveillance shows a right-skewed distribution of MVLA-types, with a small number of types present at very high frequencies and the majority of types very rare. We demonstrate that this skew is too extreme to be accounted for by simple neutral ecological processes. Simulation results indicate that the process of MVLA-type speciation and the manner in which the MVLA-typing loci were chosen in Northern Ireland cannot account for the observed skew. Similarly, we find that pathogen population structure, assuming for example a reservoir of infection in a separate host, would drive the relative abundance distribution in the opposite direction to that observed, generating more even abundances of molecular types. However, we find that historical increases in bovine tuberculosis prevalence and/or transmission heterogeneity (superspreading) are both capable of generating the skewed MVLA-type distribution, consistent with findings of previous work examining the distribution of molecular types in human tuberculosis. Although the distribution of MVLA-type abundances does not fit classical neutral predictions, our simulations show that increases in pathogen population size and

  12. Molecular Epidemiology of Glanders, Pakistan

    PubMed Central

    Hornstra, Heidie; Pearson, Talima; Georgia, Shalamar; Liguori, Andrew; Dale, Julia; Price, Erin; O’Neill, Matthew; DeShazer, David; Muhammad, Ghulam; Saqib, Muhammad; Naureen, Abeera

    2009-01-01

    We collected epidemiologic and molecular data from Burkholderia mallei isolates from equines in Punjab, Pakistan from 1999 through 2007. We show that recent outbreaks are genetically distinct from available whole genome sequences and that these genotypes are persistent and ubiquitous in Punjab, probably due to human-mediated movement of equines. PMID:19961695

  13. Molecular epidemiological study of enteroviruses associated with encephalitis in children from Hangzhou, China.

    PubMed

    Wei, Li; Qiong, Zhang; Xiao-Ting, Shen; Yu-Jie, Liu; Jian-Hua, Mao; Qiang, Shu; Shi-Qiang, Shang

    2016-10-01

    Enterovirus (EV) has over 100 serotypes of species A-D, which can cause various symptoms in infants. Enterovirus encephalitis (EVE) is serve disease with high morbidity and mortality in children. To well define the epidemiology of EVE, we wanted to know more about EV and EV molecular typing by conducting this study in Hangzhou.Cerebrospinal fluid samples were collected from children with diagnosis of encephalitis. Meanwhile, one-step real-time RT-PCR was used for the detection of EV, and we also identified the serotypes of EV by using gene sequencing of VP1 or 5'UTR region.A total of 126 CSF specimens were tested and EV was detected in 26 specimens (20.6%). The molecular typing results showed different types of EV strains including Coxsackievirus B2, Coxsackievirus B3, Echovirus 5, Echovirus 16, Echovirus 18, Echovirus 30, and all EV isolates belonging to the human EV species B.According to the sequence of VP1 and 5'UTR region, E30 may be major cause of children's EVE in Hangzhou, China.

  14. Molecular epidemiological study of enteroviruses associated with encephalitis in children from Hangzhou, China

    PubMed Central

    Wei, Li; Qiong, Zhang; Xiao-ting, Shen; Yu-jie, Liu; Jian-hua, Mao; Qiang, Shu; Shi-qiang, Shang

    2016-01-01

    Abstract Enterovirus (EV) has over 100 serotypes of species A–D, which can cause various symptoms in infants. Enterovirus encephalitis (EVE) is serve disease with high morbidity and mortality in children. To well define the epidemiology of EVE, we wanted to know more about EV and EV molecular typing by conducting this study in Hangzhou. Cerebrospinal fluid samples were collected from children with diagnosis of encephalitis. Meanwhile, one-step real-time RT-PCR was used for the detection of EV, and we also identified the serotypes of EV by using gene sequencing of VP1 or 5′UTR region. A total of 126 CSF specimens were tested and EV was detected in 26 specimens (20.6%). The molecular typing results showed different types of EV strains including Coxsackievirus B2, Coxsackievirus B3, Echovirus 5, Echovirus 16, Echovirus 18, Echovirus 30, and all EV isolates belonging to the human EV species B. According to the sequence of VP1 and 5′UTR region, E30 may be major cause of children's EVE in Hangzhou, China. PMID:27749541

  15. Molecular epidemiology of Campylobacter jejuni infection in Israel-a nationwide study.

    PubMed

    Weinberger, M; Moran-Gilad, J; Rokney, A; Davidov, Y; Agmon, V; Peretz, C; Valinsky, L

    2016-12-01

    The incidence of Campylobacter infection in Israel, particularly among children <2 years of age, has risen over the last decade and became one of the highest among industrialized countries. This study explored the molecular epidemiology of Campylobacter jejuni in Israel over a decade (2003-2012) using multilocus sequence typing (MLST) combined with demographic metadata. Representative clinical isolates (438) from a large national repository together with selected veterinary isolates (74) were subject to MLST. The distribution of age groups, ethnicity and clinical source across various genotypes was evaluated using Poisson modelling. The 512 studied isolates were assigned 126 distinct sequence types (STs) (18.8% novel STs) grouped into 21 clonal complexes (CCs). Most human, poultry and bovine STs clustered together in the leading CCs. Three dominant STs (ST21, ST6608, ST4766) were detected only since 2006. Patients infected with the leading CCs were similarly distributed along densely populated areas. The frequency of blood isolates was higher in patients infected with CC353 (relative rate (RR)=2.0, 95% CI 1.03-3.9, adjusted p value (adj.p) 0.047) and CC42 (RR=4.4, 95% CI 1.7-11.6, adj.p 0.018) and lower with CC257 (RR=0.3, 95% CI 0.1-0.9, adj. p 0.047). The distribution of age groups and ethnicity also varied across the leading CCs. In conclusion, C. jejuni isolates in a national sample appeared highly diverse with a high proportion of new STs. Phylogenic analysis was compatible with poultry and cattle as possible food sources of clinical infection. Demographic characteristics of the infected patients coupled with strain invasiveness across different genotypes revealed a complex epidemiology of C. jejuni transmission in Israel. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

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

    PubMed

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

    2015-12-01

    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. 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. 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 literature. Improved and faster method of diagnosis employed here to

  18. Implementation of new tools in molecular epidemiology studies of Echinococcus granulosus sensu lato in South America.

    PubMed

    Avila, Héctor G; Santos, Guilherme B; Cucher, Marcela A; Macchiaroli, Natalia; Pérez, Matías G; Baldi, Germán; Jensen, Oscar; Pérez, Verónica; López, Raúl; Negro, Perla; Scialfa, Exequiel; Zaha, Arnaldo; Ferreira, Henrique B; Rosenzvit, Mara; Kamenetzky, Laura

    2017-06-01

    The aim of this work was to determine Echinococcus granulosus sensu lato species and genotypes in intermediate and definitive hosts and in human isolates from endemic regions of Argentina and Brazil including those where no molecular data is available by a combination of classical and alternative molecular tools. A total of 227 samples were isolated from humans, natural intermediate and definitive hosts. Amplification of cytochrome c oxidase subunit I gene fragment was performed and a combination of AluI digestion assay, High Resolution Melting analysis (HRM) assay and DNA sequencing was implemented for Echinococcus species/genotype determination. E. granulosus sensu stricto (G1) was found in sheep (n=35), cattle (n=67) and dogs (n=5); E. ortleppi (G5) in humans (n=3) and cattle (n=108); E. canadensis (G6) in humans (n=2) and E. canadensis (G7) in pigs (n=7). We reported for the first time the presence of E. ortleppi (G5) and E. canadensis (G6) in humans from San Juan and Catamarca Argentinean provinces and E. canadensis (G7) in pigs from Cordoba Argentinean province. In this work, we widened molecular epidemiology studies of E. granulosus s. l. in South America by analyzing several isolates from definitive and intermediate hosts, including humans from endemic regions were such information was scarce or unavailable. The presence of different species/genotypes in the same region and host species reinforce the need of rapid and specific techniques for accurate determination of Echinococcus species such as the ones proposed in this work.

  19. Impact of Laboratory Cross-Contamination on Molecular Epidemiology Studies of Tuberculosis

    PubMed Central

    Martínez, Miguel; de Viedma, Darío García; Alonso, María; Andrés, Sandra; Bouza, Emilio; Cabezas, Teresa; Cabeza, Isabel; Reyes, Armando; Sánchez-Yebra, Waldo; Rodríguez, Manuel; Sánchez, M. Isabel; Rogado, M. Cruz; Fernández, Rosa; Peñafiel, Teresa; Martínez, Juan; Barroso, Pilar; Lucerna, M. Ángeles; Diez, L. Felipe; Gutiérrez, Carmelo

    2006-01-01

    Laboratory cross-contamination by Mycobacterium tuberculosis is known to be responsible for the misdiagnosis of tuberculosis, but its impact on other contexts has not been analyzed. We present the findings of a molecular epidemiology analysis in which the recent transmission events identified by a genotyping reference center were overestimated as a result of unnoticed laboratory cross-contamination in the original diagnostic laboratories. PMID:16891518

  20. Epidemiology, molecular epidemiology and evolution of bovine respiratory syncytial virus.

    PubMed

    Sarmiento-Silva, Rosa Elena; Nakamura-Lopez, Yuko; Vaughan, Gilberto

    2012-11-30

    The bovine respiratory syncytial virus (BRSV) is an enveloped, negative sense, single-stranded RNA virus belonging to the pneumovirus genus within the family Paramyxoviridae. BRSV has been recognized as a major cause of respiratory disease in young calves since the early 1970s. The analysis of BRSV infection was originally hampered by its characteristic lability and poor growth in vitro. However, the advent of numerous immunological and molecular methods has facilitated the study of BRSV enormously. The knowledge gained from these studies has also provided the opportunity to develop safe, stable, attenuated virus vaccine candidates. Nonetheless, many aspects of the epidemiology, molecular epidemiology and evolution of the virus are still not fully understood. The natural course of infection is rather complex and further complicates diagnosis, treatment and the implementation of preventive measures aimed to control the disease. Therefore, understanding the mechanisms by which BRSV is able to establish infection is needed to prevent viral and disease spread. This review discusses important information regarding the epidemiology and molecular epidemiology of BRSV worldwide, and it highlights the importance of viral evolution in virus transmission.

  1. Molecular Epidemiological Study of Cutaneous Leishmaniasis in the Focus of Bushehr City, Southwestern Iran

    PubMed Central

    Yaghoobi-Ershadi, Mohammad Reza; Shahbazi, Farideh; Darvishi, Mohammad; Akhavan, Amir Ahmad; Jafari, Reza; Khajeian, Mohammad; Rassi, Yavar; Soleimani, Hassan; Shirzadi, Mohammad Reza; Hanafi-Bojd, Ahmad Ali; Darabi, Hossein; Arandian, Mohammad Hossein; Sanei-Dehkordi, Alireza; Heidari, Mansour

    2013-01-01

    Background Cutaneous leishmaniasis (CL) represents the most frequent vector borne parasitoses in Iran. The objective of this study was to determine the epidemiological features of CL including human infection and the reservoir host in the city of Bushehr, Bushehr Province, Iran during 2010–2011. Methods: Studies on human infection was carried out on 2962 school children aged 7–14 years old from 60 primary schools and among 400 households with a total population of 1568 in four infected districts of the city in December 2010. Serosity materials from patients on glass slides were collected for molecular identification of causative agent. Rodents were caught by Sherman traps and examined for identification of the parasite. Results: Prevalence of scars and ulcers among the inhabitants were 5.86% and 0.12% respectively. Molecular study indicated the presence of two coexisting species: Leishmania major and L. tropica among patients. The scar rate was 1.24% but no ulcers were seen among the students. Nineteen rodents were caught and identified as Tatera indica (47.4%) and Rattus norvegicus (52.6%). Specimens from 7 T. indica and 9 R. norvegicus were examined by two techniques, microscopic examination and nested-PCR. Out of 7 T. indica, 14.3% were infected with L. major and 42.9% with L. turanica by nested-PCR. Out of 9 R. norvegicus 22.2% were infected with L. turanica and 11.1% with L. gerbilli. Conclusion: Based on this survey L. major and L. tropica are the causative agents of the disease among patients and T. indica plays a predominant role in the dissemination of L. major in the city. PMID:24409436

  2. Molecular epidemiology study of Mycobacterium tuberculosis and its susceptibility to anti-tuberculosis drugs in Indonesia.

    PubMed

    Lisdawati, Vivi; Puspandari, Nelly; Rif'ati, Lutfah; Soekarno, Triyani; M, Melatiwati; K, Syamsidar; Ratnasari, Lies; Izzatun, Nur; Parwati, Ida

    2015-08-22

    Genotyping of Mycobacterium tuberculosis helps to understand the molecular epidemiology of tuberculosis and to address evolutionary questions about the disease spread. Certain genotypes also have implications for the spread of infection and treatment. Indonesia is a very diverse country with a population with multiple ethnicities and cultures and a history of many trade and tourism routes. This study describes the first attempt to map the molecular epidemiology of TB in the Indonesian archipelago. From 2008 to 2011, 404 clinical specimens from sputum-smear (SS+) TB patients, age ≥15 years, were collected from 16 TB referral primary health centers (PHC) in 16 provincial capitals in Indonesia. Susceptibility testing to first line drugs was conducted for 262 samples using the agar proportion method as per WHO guidelines. Spoligotyping was done on all samples. Ninety-three of the 404 samples (23 %) were from the Beijing family, making it the predominant family in the country. However, the geographic distribution of the family varied by region with 86/294 (29.3 %) in the western region, 6/72 (8.3 %) in the central region, and 2/72 (2.8 %) in the eastern region (p < 0.001). The predominant genotype in the central and eastern regions was from the East-African-Indian (EAI) family, comprising 15.3 % (11/72), and 26.3 % (10/38) of the isolates, respectively. Drug susceptibility to first-line anti-TB drugs was tested in 262 isolates. 162 (61.8 %) isolates were susceptible to all TB drugs, 70 (26.7 %) were mono-resistant 16 (6.1 %) were poly-resistant, and 14 (5.4 %) were multi-drug resistant (MDR). The proportion of Beijing family isolates in the susceptible, mono-resistant, poly-resistant, and MDR groups was 33/162 (20.4 %), 28/70 (40.0 %), 6/16 (37.5 %), and 3/14 (21.4 %), respectively. Overall, resistance of the Beijing family isolates to any of the first line TB drugs was significantly higher than non-Beijing families [37/71 (52.1 %) vs. 63/191 (33.0 %) (p-value = 0

  3. Web tools for molecular epidemiology of tuberculosis.

    PubMed

    Shabbeer, Amina; Ozcaglar, Cagri; Yener, Bülent; Bennett, Kristin P

    2012-06-01

    In this study we explore publicly available web tools designed to use molecular epidemiological data to extract information that can be employed for the effective tracking and control of tuberculosis (TB). The application of molecular methods for the epidemiology of TB complement traditional approaches used in public health. DNA fingerprinting methods are now routinely employed in TB surveillance programs and are primarily used to detect recent transmissions and in outbreak investigations. Here we present web tools that facilitate systematic analysis of Mycobacterium tuberculosis complex (MTBC) genotype information and provide a view of the genetic diversity in the MTBC population. These tools help answer questions about the characteristics of MTBC strains, such as their pathogenicity, virulence, immunogenicity, transmissibility, drug-resistance profiles and host-pathogen associativity. They provide an integrated platform for researchers to use molecular epidemiological data to address current challenges in the understanding of TB dynamics and the characteristics of MTBC.

  4. [Molecular epidemiological study of measles viruses isolated in Qinghai Province during 2000-2011].

    PubMed

    Fan, Li-Xia; Ba, Zhuo-Ma; Zhao, Sheng-Cang; Yi, Hu; Jiang, Shuang-Ying; Zhang, Yan; Wang, Hui-Ling; Xu, Wen-Bo

    2013-08-01

    To carry out the molecular epidemiological study of the wild-type measles virus isolated in Qinghai Province during 2000-2011, and provide a scientific basis for the measles elimination. Measles viruses were isolated using B95a cell line or Vero/SLAM cell line from throat swabs collected from suspected measles cases during measles outbreak and sporadic in 6 prefectures during 2000-2011. The fragment of 696 nucleotides of N gene carboxy terminal was amplified by using RT-PCR methods. The PCR products were sequenced and analyzed. The phylogenetic tree was conducted with the viruses isolated in viruses from other province. Total 19 measles viruses were isolated during 2000-2011 in Qinghai province and all belong to genotype H1a. The results of phylogenetic tree showed that viruses in 2000-2005 and in 2009-2011 were distributed in two different lineages, and it revealed that these strains belonged to at least 2 viral transmission chains and the viruses circulated during 2000-2005 were not detected after 2005. Genotype H1a was the predominant genotype circulated in Qinghai province during 2000-2011. Qinghai measles virus strains had not evolved independently, but coevolved with the measles virus strains in other provinces in mainland China. The variation of important amino acid sites of measles virus should be continuous monitored and provide the scientific strategy for the measles elimination.

  5. 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

  6. A national study of the molecular epidemiology of HIV-1 in Australia 2005-2012.

    PubMed

    Castley, Alison; Sawleshwarkar, Shailendra; Varma, Rick; Herring, Belinda; Thapa, Kiran; Dwyer, Dominic; Chibo, Doris; Nguyen, Nam; Hawke, Karen; Ratcliff, Rodney; Garsia, Roger; Kelleher, Anthony; Nolan, David

    2017-01-01

    Rates of new HIV-1 diagnoses are increasing in Australia, with evidence of an increasing proportion of non-B HIV-1 subtypes reflecting a growing impact of migration and travel. The present study aims to define HIV-1 subtype diversity patterns and investigate possible HIV-1 transmission networks within Australia. The Australian Molecular Epidemiology Network (AMEN) HIV collaborating sites in Western Australia, South Australia, Victoria, Queensland and western Sydney (New South Wales), provided baseline HIV-1 partial pol sequence, age and gender information for 4,873 patients who had genotypes performed during 2005-2012. HIV-1 phylogenetic analyses utilised MEGA V6, with a stringent classification of transmission pairs or clusters (bootstrap ≥98%, genetic distance ≤1.5% from at least one other sequence in the cluster). HIV-1 subtype B represented 74.5% of the 4,873 sequences (WA 59%, SA 68.4%, w-Syd 73.8%, Vic 75.6%, Qld 82.1%), with similar proportion of transmission pairs and clusters found in the B and non-B cohorts (23% vs 24.5% of sequences, p = 0.3). Significantly more subtype B clusters were comprised of ≥3 sequences compared with non-B clusters (45.0% vs 24.0%, p = 0.021) and significantly more subtype B pairs and clusters were male-only (88% compared to 53% CRF01_AE and 17% subtype C clusters). Factors associated with being in a cluster of any size included; being sequenced in a more recent time period (p<0.001), being younger (p<0.001), being male (p = 0.023) and having a B subtype (p = 0.02). Being in a larger cluster (>3) was associated with being sequenced in a more recent time period (p = 0.05) and being male (p = 0.008). This nationwide HIV-1 study of 4,873 patient sequences highlights the increased diversity of HIV-1 subtypes within the Australian epidemic, as well as differences in transmission networks associated with these HIV-1 subtypes. These findings provide epidemiological insights not readily available using standard surveillance methods

  7. Immunohistochemical expression of ERG in the molecular epidemiology of fatal prostate cancer study.

    PubMed

    Weinmann, Sheila; Van Den Eeden, Stephen K; Haque, Reina; Chen, Chuhe; Richert-Boe, Kathryn; Schwartzman, Jacob; Gao, Lina; Berry, Deborah L; Kallakury, Bhaskar V S; Alumkal, Joshi J

    2013-09-01

    Gene fusions between the ERG transcription factor and the androgen-regulated gene TMPRSS2 occur in a subset of prostate cancers and contribute to transformation of prostatic epithelial cells. Prior reports have used fluorescence in situ hybridization (FISH) or quantitative PCR (QPCR) to determine the presence of TMPRSS2-ERG fusions or ERG expression, respectively. Recently, several groups have reported on immunohistochemistry (IHC) to measure ERG expression, which is much more readily performed in clinical practice. However, the prior studies examining ERG expression by IHC had small sample sizes or they failed to clarify the association of ERG protein expression with important clinico-pathological features or prostate cancer-specific mortality. To address these deficits, we evaluated ERG expression by IHC in 208 radical prostatectomy samples from the Kaiser Permanente Molecular Epidemiology of Fatal Prostate Cancer (MEFPC) study, a case-control study of prostate cancer-specific mortality. Nuclear ERG expression was seen in neoplastic prostate epithelia in 49 of the samples (23.7%). ERG expression in tumor cells was associated with higher tumor stage (OR = 2.0, 95% confidence interval 1.0-4.0, P value = 0.04). ERG immunoreactivity was positively associated with prostate cancer-specific mortality, although the confidence interval was wide (OR = 1.9, 95% confidence interval 0.88-4.0, P value = 0.10). Our results demonstrate that ERG protein expression is readily quantifiable with an existing commercial antibody. Evaluating ERG protein expression may improve our ability to identify the subset of more aggressive, invasive prostate cancers. © 2013 Wiley Periodicals, Inc.

  8. Transmission of Mycobacterium tuberculosis in China: A Population-Based Molecular Epidemiologic Study

    PubMed Central

    Yang, Chongguang; Shen, Xin; Peng, Ying; Lan, Rushu; Zhao, Yuling; Long, Bo; Luo, Tao; Sun, Guomei; Li, Xia; Qiao, Ke; Gui, Xiaohong; Wu, Jie; Xu, Jiying; Li, Fabin; Li, Dingyue; Liu, Feiying; Shen, Mei; Hong, Jianjun; Mei, Jian; DeRiemer, Kathryn; Gao, Qian

    2015-01-01

    Background. Understanding the transmission of Mycobacterium tuberculosis is essential for the development of efficient tuberculosis control strategies. China has the second-largest tuberculosis burden in the world. Recent transmission and infection with M. tuberculosis, particularly drug-resistant strains, may account for many new tuberculosis cases. Methods. We performed a population-based molecular epidemiologic study of pulmonary tuberculosis in China during 1 July 2009 to 30 June 2012. We defined clusters as cases with identical variable number tandem repeat genotype patterns and identified the risk factors associated with clustering, by logistic regression. Relative transmission rates were estimated by the sputum smear status and drug susceptibility status of tuberculosis patients. Results. Among 2274 culture-positive tuberculosis patients with genotyped isolates, there were 705 (31.0%) tuberculosis patients in 287 clusters. Multidrug-resistant (MDR) tuberculosis (adjusted odds ratio [aOR], 1.86; 95% confidence interval [CI], 1.25–2.63) and infection with a Beijing family strain (aOR, 1.56; 95% CI, 1.23–2.96) were associated with clustering. Eighty-four of 280 (30.0%) clusters had a putative source case that was sputum smear negative, and 30.6% of their secondary cases were attributed to transmission by sputum smear–negative patients. The relative transmission rate for sputum smear negative compared with sputum smear–positive patients was 0.89 (95% CI, .68–1.10), and was 1.51 (95% CI, 1.00–2.24) for MDR tuberculosis vs drug-susceptible tuberculosis. Conclusions. Recent transmission of M. tuberculosis, including MDR strains, contributes substantially to tuberculosis disease in China. Sputum smear–negative cases were responsible for at least 30% of the secondary cases. Interventions to reduce the transmission of M. tuberculosis should be implemented in China. PMID:25829000

  9. A Large Cohort of Hemoglobin Variants in Thailand: Molecular Epidemiological Study and Diagnostic Consideration

    PubMed Central

    Srivorakun, Hataichanok; Singha, Kritsada; Fucharoen, Goonnapa; Sanchaisuriya, Kanokwan; Fucharoen, Supan

    2014-01-01

    Background Hemoglobin (Hb) variants are structurally inherited changes of globin chains. Accurate diagnoses of these variants are important for planning of appropriate management and genetic counseling. Since no epidemiological study has been conducted before, we have investigated frequencies, molecular and hematological features of Hb variants found in a large cohort of Thai subjects. Materials and Methods Study was conducted on 26,013 unrelated subjects, inhabiting in all geographical parts of Thailand over a period of 11 years from January 2002-December 2012. Hb analysis was done on high performance liquid chromatography (HPLC) or capillary electrophoresis (CE). Mutations causing Hb variants were identified using PCR and related techniques. Results Among 26,013 subjects investigated, 636 (2.4%) were found to carry Hb variants. Of these 636 subjects, 142 (22.4%) carried α-chain variants with 13 different mutations. The remaining included 451 (70.9%) cases with 16 β-chain variants, 37 (5.8%) cases with Hb Lepore (δβ-hybrid Hb) and 6 (0.9%) cases with a single δ-chain variant. The most common α-globin chain variant was the Hb Q-Thailand (α74GAC-CAC, Asp-His) which was found in 101 cases (15.8%). For β-globin chain variants, Hb Hope (β136GGT-GAT, Gly-Asp) and Hb Tak (β146+AC, Ter-Thr) are the two most common ones, found in 121 (19.0%) and 90 (14.2%) cases, respectively. Seven Hb variants have never been found in Thai population. Hb analysis profiles on HPLC or CE of these variants were illustrated to guide presumptive diagnostics. Conclusions Hb variants are common and heterogeneous in Thai population. With varieties of thalassemias and hemoglobinopathies in the population, interactions between them leading to complex syndromes are common and render their diagnoses difficult in routine practices. Knowledge of the spectrum, molecular basis, genotype-phenotype correlation and diagnostic features should prove useful for prevention and control of the diseases

  10. Use of molecular epidemiological techniques in a pilot study on workers exposed to chromium.

    PubMed Central

    Gao, M; Levy, L S; Faux, S P; Aw, T C; Braithwaite, R A; Brown, S S

    1994-01-01

    OBJECTIVES--Molecular epidemiological techniques, capable of detecting damage to DNA, were used to see if such damage occurred in the lymphocytes of a group of workers exposed to chromium. The two aims of this pilot study were to see if these new techniques might make useful biological monitoring tools for workers exposed to chromium and also, to help assess whether the current occupational exposure limit for chromium (VI) was sufficiently protective in this specific working situation. METHODS--Volunteer groups of 10 workers exposed to chromium and 10 non-exposed workers provided urine and blood samples towards the end of the working week. Chromium concentrations were measured in whole blood, plasma, lymphocytes, and urine. Lymphocytes were used to examine two forms of DNA damage in the two groups; these were the level of DNA strand breakage and, the production of 8-hydroxydeoxyguanosine. RESULTS--Chromium concentration in whole blood, plasma, and urine of workers exposed to chromium was significantly raised (P < 0.01) compared with non-exposed controls, but in isolated lymphocytes, there was only a modest but significant (P < 0.05) increase in chromium in the group exposed to chromium. There was no difference in the levels of DNA strand breaks or 8-hydroxydeoxyguanosine between the groups. Air monitoring for chromium was not undertaken but current levels for the group exposed to chromium were reported to be around 0.01 mg/m3, which is 20% of the current United Kingdom occupational exposure limit. CONCLUSIONS--We were unable to detect any damage in lymphocytic DNA due to exposure to chromium. This may have been due to the low chromium exposure (< 20% of the United Kingdom occupational exposure limit), the ability of plasma to detoxify chromium (VI) to chromium (III) before it reached the lymphocytes, or perhaps the insensitivity of the molecular techniques used. It is now important to test these and other such techniques on groups exposed to levels closer to the

  11. 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...

  12. 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...

  13. Molecular epidemiology of HIV: tracking AIDS pandemic.

    PubMed

    TakebE, Yutaka; Kusagawa, Shigeru; Motomura, Kazushi

    2004-04-01

    Human immunodeficiency virus (HIV) and acquired immunodeficiency syndrome (AIDS) epidemic is a global threat to maternal and child health, especially in developing countries. It is estimated that 800 000 children are infected and 580 000 children die of AIDS-related illnesses every year. Molecular epidemiology has been a useful tool in analyzing the origin of HIV and tracking the course of global HIV spread. This article provides an overview of recent advances in the field of molecular epidemiology of HIV across the world, and discuss the biological implications. Based on the near full-length or partial nucleotide sequence information, the phylogeny and recombinant structure of HIV strains are analyzed. Using genotype classification of HIV as a molecular marker, the origin and the genesis of HIV epidemic are investigated. The HIV-1 group M, a major HIV group responsible for current AIDS pandemic, began its expansion in human population approximately 70 years ago and diversified rapidly over time, now comprising a number of different subtypes and circulating recombinant forms (CRF). Of note, recent studies revealed that new recombinant strains are arising continually, becoming a powerful force in the spread of HIV-1 across the globe. Global dissemination of HIV is a dramatic and deadly example of recent genome emergence and expansion. Molecular epidemiological investigation is expected to provide information critical for prevention and future vaccine strategies.

  14. The integration of molecular tools into veterinary and spatial epidemiology.

    PubMed

    Muellner, Petra; Zadoks, Ruth N; Perez, Andres M; Spencer, Simon E F; Schukken, Ynte H; French, Nigel P

    2011-09-01

    At the interface of molecular biology and epidemiology, the emerging discipline of molecular epidemiology offers unique opportunities to advance the study of diseases through the investigation of infectious agents at the molecular level. Molecular tools can increase our understanding of the factors that shape the spatial and temporal distribution of pathogens and disease. Both spatial and molecular aspects have always been important to the field of infectious disease epidemiology, but recently news tools have been developed which increase our ability to consider both elements within a common framework. This enables the epidemiologist to make inferences about disease patterns in space and time. This paper introduces some basic concepts of molecular epidemiology in a veterinary context and illustrates the application of molecular tools at a range of spatio-temporal scales. Case studies - a multi-state outbreak of Serratia mastitis, a national control program for campylobacteriosis, and evolution of foot-and-mouth-disease viruses - are used to demonstrate the importance of considering molecular aspects in modern epidemiological studies. The discipline of molecular epidemiology is in its infancy and our contribution aims to promote awareness, understanding and uptake of molecular epidemiology in veterinary science. Copyright © 2011 Elsevier Ltd. All rights reserved.

  15. 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.

  16. Molecular Epidemiological Study of Mumps Epidemics of 2015 in Okinawa, Japan.

    PubMed

    Kuba, Yumani; Kyan, Hisako; Arakaki, Eri; Takara, Taketoshi; Kato, Takashi; Okano, Sho; Oshiro, Yuko; Kudaka, Jun; Kidokoro, Minoru

    2017-05-24

    Although major mumps epidemics occurred every 4-5 years in Okinawa Prefecture in Japan, no laboratory diagnoses were conducted. A mumps epidemic started in Okinawa in October 2014, and we collected clinical samples from 31 patients in 4 areas (Hokubu, Nanbu, Miyako, and Yaeyama) from July to December 2015, for virus isolation and RT-PCR, whose positive ratios were 52% and 87%, respectively. Phylogenetic analyses showed that all isolates were classified into genotype G, and with one exception, consisted of 2 subgenotypes, Ge (55.6%) and Gw (40.7%), which have been prominent in Japan recently. One isolate was classified in another lineage, which was detected in Japan for the first time, and was similar to a Hong Kong isolate from 2014. Remarkably, the geographic distributions of the 2 major lineages were separated. The Ge viruses were isolated from the main island of Okinawa and the Yaeyama Islands, whereas the Gw isolates were mainly detected from the Miyako Islands. These results suggest that the Ge and Gw mumps viruses mainly caused the mumps epidemics of 2015 in Okinawa, and that they spread independently in separate regions. This is the first report describing the molecular epidemiology of mumps epidemics in Okinawa Prefecture.

  17. Molecular evolution and epidemiological links study of Newcastle disease virus isolates from 1995 to 2016 in Iran.

    PubMed

    Mayahi, Vafa; Esmaelizad, Majid

    2017-09-01

    In the case of Newcastle disease virus, multiple factors such as host adaptation, immune response evasion, and selective pressures have been suggested to result in evolution of viruses and the emergence of genetic variants. Multiple studies on virus classification and global epidemiological links have yielded consistent data. Here, we have performed a molecular analysis study of circulating Newcastle disease viruses in Iran (1995-2016). According to evolutionary divergences, subgenotype VIg, VIj, VIIj, VIId, XIIIa and XIIId isolates have been circulating in the country during a 21-year period. Based on data analysis, VIg isolates shared highest sequence identity with Russian and Polish isolates of the VIg subgenotype, while VIj subgenotype isolates (2012) were most similar to a virus isolated in 2015 in India. Analysis of the evolutionary divergence of subgenotype VIIj suggests that Chinese and Ukrainian viruses may have played a crucial role in the emergence of VIIj isolates. Evolutionary difference studies also indicated that XIIIa isolates circulating in Iran may have caused the emergence of adapted variants of subgenotype XIIId. Therefore, we propose that the evolutionary and epidemiological study of virulent Newcastle disease viruses could help to provide accurate molecular data about variants circulating in the region, thus aiding in the design of more efficient recombinant vaccines.

  18. Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study.

    PubMed

    van Ingen, Jakko; Kohl, Thomas A; Kranzer, Katharina; Hasse, Barbara; Keller, Peter M; Katarzyna Szafrańska, Anna; Hillemann, Doris; Chand, Meera; Schreiber, Peter Werner; Sommerstein, Rami; Berger, Christoph; Genoni, Michele; Rüegg, Christian; Troillet, Nicolas; Widmer, Andreas F; Becker, Sören L; Herrmann, Mathias; Eckmanns, Tim; Haller, Sebastian; Höller, Christiane; Debast, Sylvia B; Wolfhagen, Maurice J; Hopman, Joost; Kluytmans, Jan; Langelaar, Merel; Notermans, Daan W; Ten Oever, Jaap; van den Barselaar, Peter; Vonk, Alexander B A; Vos, Margreet C; Ahmed, Nada; Brown, Timothy; Crook, Derrick; Lamagni, Theresa; Phin, Nick; Smith, E Grace; Zambon, Maria; Serr, Annerose; Götting, Tim; Ebner, Winfried; Thürmer, Alexander; Utpatel, Christian; Spröer, Cathrin; Bunk, Boyke; Nübel, Ulrich; Bloemberg, Guido V; Böttger, Erik C; Niemann, Stefan; Wagner, Dirk; Sax, Hugo

    2017-10-01

    Since 2013, over 100 cases of Mycobacterium chimaera prosthetic valve endocarditis and disseminated disease were notified in Europe and the USA, linked to contaminated heater-cooler units (HCUs) used during cardiac surgery. We did a molecular epidemiological investigation to establish the source of these patients' disease. We included 24 M chimaera isolates from 21 cardiac surgery-related patients in Switzerland, Germany, the Netherlands, and the UK, 218 M chimaera isolates from various types of HCUs in hospitals, from LivaNova (formerly Sorin; London, UK) and Maquet (Rastatt, Germany) brand HCU production sites, and unrelated environmental sources and patients, as well as eight Mycobacterium intracellulare isolates. Isolates were analysed by next-generation whole-genome sequencing using Illumina and Pacific Biosciences technologies, and compared with published M chimaera genomes. Phylogenetic analysis based on whole-genome sequencing of 250 isolates revealed two major M chimaera groups. Cardiac surgery-related patient isolates were all classified into group 1, in which all, except one, formed a distinct subgroup. This subgroup also comprised isolates from 11 cardiac surgery-related patients reported from the USA, most isolates from LivaNova HCUs, and one from their production site. Isolates from other HCUs and unrelated patients were more widely distributed in the phylogenetic tree. HCU contamination with M chimaera at the LivaNova factory seems a likely source for cardiothoracic surgery-related severe M chimaera infections diagnosed in Switzerland, Germany, the Netherlands, the UK, the USA, and Australia. Protective measures and heightened clinician awareness are essential to guarantee patient safety. Partly funded by the EU Horizon 2020 programme, its FP7 programme, the German Center for Infection Research (DZIF), the Swiss National Science Foundation, the Swiss Federal Office of Public Health, and National Institute of Health Research Oxford Health Protection

  19. Molecular epidemiology of cryptosporidiosis: an update.

    PubMed

    Xiao, Lihua

    2010-01-01

    Molecular tools have been developed to detect and differentiate Cryptosporidium at the species/genotype and subtype levels. These tools have been increasingly used in characterizing the transmission of Cryptosporidium spp. in humans and animals. Results of these molecular epidemiologic studies have led to better appreciation of the public health importance of Cryptosporidium species/genotypes in various animals and improved understanding of infection sources in humans. Geographic, seasonal and socioeconomic differences in the distribution of Cryptosporidium spp. in humans have been identified, and have been attributed to differences in infection sources and transmission routes. The transmission of C. parvum in humans is mostly anthroponotic in developing countries, with zoonotic infections play an important role in developed countries. Species of Cryptosporidium and subtype families of C. hominis have been shown to induce different clinical manifestations and have different potential to cause outbreaks. The wide use of a new generation of genotyping and subtyping tools in well designed epidemiologic studies should lead to a more in-depth understanding of the epidemiology of cryptosporidiosis in humans and animals. Published by Elsevier Inc.

  20. [Epidemiologic and molecular study of Entamoeba histolytica and Entamoeba dispar strains in pacients with diarrhea in Cumana, Sucre state, Venezuela].

    PubMed

    Mora, Leonor; García, Ana; De Donato, Marcos; Urdaneta, Haideé

    2008-06-01

    An epidemiological and molecular study on E. histolytica and E. dispar was carried out in 428 patients with gastrointestinal symptomatology of diarrhea from different health centers in Cumana, Sucre state. The samples were processed through: direct examination with 0.85% physiological saline solution, temporal lugol staining, trichromic staining and the Ritchie method of concentration; a sucrose gradient was used for cyst isolation. The small subunit of the 16S RNA was amplified by nested, multiplex PCR for the molecular detection. The E. histolytica/E. dispar prevalences according to the direct, Ritchie and trichromic staining methods were 20.09, 13.79 and 12.15%, respectively; while prevalences according to PCR for E. histolytica and E. dispar were 6.31% and 4.44%, respectively, also detecting four cases of mixed infection. Sequencing of the amplified fragments of E. histolytica showed 100% homology with the sequences with strains from Merida (Venezuela), USA, Brazil, Mexico and GenBank. The infections by E. histolytica and E. dispar were statistically associated with age but not with sex. The presence of mucus, blood and abdominal pain were only associated to E. histolytica infection. The moderate prevalence of E. histolytica shows the endemic status of this population and warns about the potential problem as a morbidity and mortality in Sucre state. The frequency of E. dispar in this population suggests the existence of an overestimation problem in the diagnosis of amoebiasis with its clinical and epidemiological implications, and shows the poor knowledge about the true prevalences of this protozoan. The PCR allowed for the differential identification of E. histolytica and E. dispar, as well as the presence of mixed infections, making a great tool for epidemiological amoebiasis studies.

  1. Molecular Epidemiology for Vector Research on Leishmaniasis

    PubMed Central

    Kato, Hirotomo; Gomez, Eduardo A; Cáceres, Abraham G; Uezato, Hiroshi; Mimori, Tatsuyuki; Hashiguchi, Yoshihisa

    2010-01-01

    Leishmaniasis is a protozoan disease caused by the genus Leishmania transmitted by female phlebotomine sand flies. Surveillance of the prevalence of Leishmania and responsive vector species in endemic and surrounding areas is important for predicting the risk and expansion of the disease. Molecular biological methods are now widely applied to epidemiological studies of infectious diseases including leishmaniasis. These techniques are used to detect natural infections of sand fly vectors with Leishmania protozoa and are becoming powerful tools due to their sensitivity and specificity. Recently, genetic analyses have been performed on sand fly species and genotyping using PCR-RFLP has been applied to the sand fly taxonomy. In addition, a molecular mass screening method has been established that enables both sand fly species and natural leishmanial infections to be identified simultaneously in hundreds of sand flies with limited effort. This paper reviews recent advances in the study of sand flies, vectors of leishmaniasis, using molecular biological approaches. PMID:20617005

  2. Molecular and epidemiological characterization of canine Pseudomonas otitis using a prospective case-control study design.

    PubMed

    Morris, Daniel O; Davis, Meghan F; Palmeiro, Brian S; O'Shea, Kathleen; Rankin, Shelley C

    2017-02-01

    Pseudomonas aeruginosa is an opportunistic pathogen of the canine ear canal and occupies aquatic habitats in the environment. Nosocomial and zoonotic transmission of P. aeruginosa have been documented, including clonal outbreaks. The primary objective of this study was to assess various environmental exposures as potential risk factors for canine Pseudomonas otitis. It was hypothesized that isolates derived from infected ears would be clonal to isolates derived from household water sources and the mouths of human and animal companions of the study subjects. Seventy seven privately owned dogs with otitis were enrolled, along with their human and animal household companions, in a case-control design. Data on potential risk factors for Pseudomonas otitis were collected. Oral cavities of all study subjects, their human and animal companions, and household water sources were sampled. Pulsed field gel electrophoresis was used to estimate clonal relatedness of P. aeruginosa isolates. In a multivariate model, visiting a dog park was associated with 77% increased odds of case status (P = 0.048). Strains clonal to the infection isolates were obtained from subjects' mouths (n = 18), companion pets' mouths (n = 5), pet owners' mouths (n = 2), water bowls (n = 7) and water taps (n = 2). Clonally related P. aeruginosa isolates were obtained from dogs that had no clear epidemiological link. Genetic homology between otic and environmental isolates is consistent with a waterborne source for some dogs, and cross-contamination with other human and animal members within some households. © 2016 ESVD and ACVD.

  3. Molecular epidemiological study of cutaneous leishmaniasis in Beni Mellal and Fquih Ben Saleh provinces in Morocco.

    PubMed

    Faiza, Sebti; Asmae, Hmamouch; Fatima, Amarir; Afafe, Fahmi; Bouchra, Delouane; Ibrahim, Abbasi; Abderrahim, Sadak; Khalid, Habbari; Mohamed, Rhajaoui; Hajiba, Fellah

    2015-09-01

    Leishmaniases are parasitic diseases frequent in the Mediterranean Basin. Cutaneous leishmaniasis (CL) has been recently emerged in several new foci, causing a public health problem in Morocco. This study was performed to evaluate the epidemiological status of cutaneous leishmaniasis (CL) in Beni Mellal and Fquih Ben Saleh Provinces and to identify the causative agent. A total of 584 (56% female, 44% male) confirmed cases of CL were enrolled during the study period 2000-2012. Majority of cases (56%) were recorded in three sectors: Zaouiat Cheikh, Beni Mellal and Oulad Ayad. Fisher statistical test showed that there is a significant effect of the total cases of CL affected in the 185 localities. The age distribution of CL cases was relatively stable, with the majority of patients (62.34%) aged less than 9 years old with significant differences (p-value<2.2e-16). CL lesions were mostly located on the face (89%). The average number of lesions per patient was 1.38. Leishmania tropica was identified as the causative agent based on species-specific ITS1-PCR-RFLP assay. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Molecular Epidemiology and Antifungal Susceptibility of Candida glabrata in China (August 2009 to July 2014): A Multi-Center Study

    PubMed Central

    Hou, Xin; Xiao, Meng; Chen, Sharon C.-A.; Kong, Fanrong; Wang, He; Chu, Yun-Zhuo; Kang, Mei; Sun, Zi-Yong; Hu, Zhi-Dong; Li, Ruo-Yu; Lu, Juan; Liao, Kang; Hu, Tie-Shi; Ni, Yu-Xing; Zou, Gui-Ling; Zhang, Ge; Fan, Xin; Zhao, Yu-Pei; Xu, Ying-Chun

    2017-01-01

    Candida glabrata is an increasingly important cause of invasive candidiasis. In China, relatively little is known of the molecular epidemiology of C. glabrata and of its antifungal susceptibility patterns. Here we studied 411 non-duplicate C. glabrata isolates from 411 patients at 11 hospitals participating in the National China Hospital Invasive Fungal Surveillance Net program (CHIF-NET; 2010-2014). Genotyping was performed using multilocus sequence typing (MLST) employing six genetic loci and by microsatellite analysis. Antifungal susceptibility testing was performed using Sensititre YeastOne™ YO10 methodology. Of 411 isolates, 35 sequence types (ST) were identified by MLST and 79 different genotypes by microsatellite typing; the latter had higher discriminatory power than MLST in the molecular typing of C. glabrata. Using MLST, ST7 and ST3 were the most common STs (66.4 and 9.5% of all isolates, respectively) with 24 novel STs identified; the most common microsatellite types were T25 (30.4% of all isolates) and T31 (12.4%). Resistance to fluconazole (MIC > 32 μg/mL) was seen in 16.5% (68/411) of isolates whilst MICs of >0.5 μg/mL for voriconazole, >2 μg/mL for itraconazole and >2 μg/mL for posaconazole were seen for 28.7, 6.8, and 7.3% of isolates, respectively; 14.8% of all isolates cross-resistant/non-wide-type to fluconazole and voriconazole. Fluconazole resistant rates increased 3-fold over the 5-year period whilst that of isolates with non-WT MICs to voriconazole, 7-fold. All echinocandins exhibited >99% susceptibility rates against all isolates but notably one isolate exhibited multi-drug resistance to the azoles and echinocandins. The study has provided a global picture of the molecular epidemiology and drug resistance rates of C. glabrata in China during the period of the study. PMID:28588560

  5. Molecular Epidemiology and Antifungal Susceptibility of Candida glabrata in China (August 2009 to July 2014): A Multi-Center Study.

    PubMed

    Hou, Xin; Xiao, Meng; Chen, Sharon C-A; Kong, Fanrong; Wang, He; Chu, Yun-Zhuo; Kang, Mei; Sun, Zi-Yong; Hu, Zhi-Dong; Li, Ruo-Yu; Lu, Juan; Liao, Kang; Hu, Tie-Shi; Ni, Yu-Xing; Zou, Gui-Ling; Zhang, Ge; Fan, Xin; Zhao, Yu-Pei; Xu, Ying-Chun

    2017-01-01

    Candida glabrata is an increasingly important cause of invasive candidiasis. In China, relatively little is known of the molecular epidemiology of C. glabrata and of its antifungal susceptibility patterns. Here we studied 411 non-duplicate C. glabrata isolates from 411 patients at 11 hospitals participating in the National China Hospital Invasive Fungal Surveillance Net program (CHIF-NET; 2010-2014). Genotyping was performed using multilocus sequence typing (MLST) employing six genetic loci and by microsatellite analysis. Antifungal susceptibility testing was performed using Sensititre YeastOne™ YO10 methodology. Of 411 isolates, 35 sequence types (ST) were identified by MLST and 79 different genotypes by microsatellite typing; the latter had higher discriminatory power than MLST in the molecular typing of C. glabrata. Using MLST, ST7 and ST3 were the most common STs (66.4 and 9.5% of all isolates, respectively) with 24 novel STs identified; the most common microsatellite types were T25 (30.4% of all isolates) and T31 (12.4%). Resistance to fluconazole (MIC > 32 μg/mL) was seen in 16.5% (68/411) of isolates whilst MICs of >0.5 μg/mL for voriconazole, >2 μg/mL for itraconazole and >2 μg/mL for posaconazole were seen for 28.7, 6.8, and 7.3% of isolates, respectively; 14.8% of all isolates cross-resistant/non-wide-type to fluconazole and voriconazole. Fluconazole resistant rates increased 3-fold over the 5-year period whilst that of isolates with non-WT MICs to voriconazole, 7-fold. All echinocandins exhibited >99% susceptibility rates against all isolates but notably one isolate exhibited multi-drug resistance to the azoles and echinocandins. The study has provided a global picture of the molecular epidemiology and drug resistance rates of C. glabrata in China during the period of the study.

  6. 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

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

    PubMed

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

    2006-01-13

    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. 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. 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.

  8. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Large scale human metabolic phenotyping and molecular epidemiological studies via 1H NMR spectroscopy of urine: Investigation of borate preservation

    PubMed Central

    Smith, Leon M.; Maher, Anthony D.; Want, Elizabeth J.; Elliott, Paul; Stamler, Jeremiah; Hawkes, Geoffrey E.; Holmes, Elaine; Lindon, John C.; Nicholson, Jeremy K.

    2009-01-01

    Borate is an antibacterial preservative widely used in clinical and large scale epidemiological studies involving urine sample analysis. Since it readily forms covalent adducts and reversible complexes with hydroxyl and carboxylate groups, the effects of borate preservation in 1H NMR spectroscopy-based metabolic profiling of human urine samples have been assessed. Effects of various concentrations of borate (range 0–30 mM) on 1H NMR spectra of urine were observed at sequential time points over a 12 month period. Consistent with known borate chemistry, the principal alterations in the 1H resonance metabolite patterns were observed for compounds such as mannitol, citrate and α-hydroxyisobutyrate and confirmed by ESI-MS analysis. These included line-broadening, T1 and T2 relaxation and chemical shift changes consistent with complex formation and chemical exchange processes. To further investigate complexation behavior in the urinary metabolite profiles, a new tool for visualization of multi-component relaxation variations in which the spectra were color-coded according to the T1 and T2 proton relaxation times respectively (T1 or T2 Ordered Projection SpectroscopY, TOPSY) was also developed and applied. Addition of borate caused a general decrease in 1H T1 values consistent with non-specific effects such as solution viscosity changes. Minor changes in proton T2 relaxation rates were observed for the most strongly complexing metabolites. From a molecular phenotyping and epidemiologic viewpoint, typical interpersonal biological variation was shown to be vastly greater than any variation introduced by the borate complexation which had a negligible effect on the metabolic mapping and classification of samples. Whilst caution is indicated in the assignment of biomarker signals where metabolites have diol groupings or where there are adjacent hydroxyl and carboxylate functions, it is concluded that borate preservation is “fit-forpurpose” for 1H NMR

  10. A molecular epidemiological study of human respiratory syncytial virus in Croatia, 2011-2014.

    PubMed

    Slovic, Anamarija; Ivancic-Jelecki, Jelena; Ljubin-Sternak, Sunčanica; Galinović, Gordana Mlinarić; Forcic, Dubravko

    2016-10-01

    Human respiratory syncytial virus (HRSV) causes common respiratory tract infections in infants, young children and the elderly. The diversity of HRSV strains circulating in Croatia was investigated throughout a period of four consecutive years from March 2011-March 2014. The analysis was based on sequences from the second hypervariable region of the G gene. A predominance of HRSV group A was observed in the first three years of the study, while group B became slightly predominant during the first few months of 2014. Overall, 76% of viruses belonged to group A including the genotypes NA1, ON1 and GA5. NA1 was by far the most common genotype within group A in 2011-2013; however, only ON1 and a few GA5 viruses were detected in the first three months of 2014. The majority of group B strains were of genotype BA9 (97%), and a few BA10 genotypes were detected. BA9 had the highest substitution rate of all the detected genotypes, followed by ON1. Multiple analyses showed that HRSV group A strains were more diverse than group B strains. Gly at residue 232 (previously described to be specific for ON1) was also detected in three NA1 strains, which were phylogenetically placed on separate branches within the NA1 genotype. For all genotypes, the diversity was higher at the amino acid level than at the nucleotide level, although positive selection of mutations was shown for only a few sites using four different methods of codon-based analysis of selective pressure. More codons were predicted to be negatively selected. The complexity of the HRSV pools present during each epidemic peak was determined and compared to previous epidemiological data. In addition to presenting genetic versatility of HRSV in this geographic region, the collected sequences provide data for further geographical and temporal comparative analyses of HRSV and its evolutionary pathways.

  11. Defining high-risk individuals in a population-based molecular-epidemiological study of lung cancer.

    PubMed

    Cassidy, Adrian; Myles, Jonathan P; Liloglou, Triantafillos; Duffy, Stephen W; Field, John K

    2006-05-01

    Within the framework of the Liverpool Lung Project (LLP), population-based case-control and prospective cohort studies are in progress to identify molecular and epidemiological risk factors and define populations and individuals most at risk of developing lung cancer. This report describes a strategy for selection of a high-risk population and further provides support for the inclusion of occupational and genetic risk factors in future models. Data from the case-control study (256 incident cases and 314 population controls) were analysed to define a high-risk population. Detailed lifestyle and occupational information were collected during structured interviews. Models were constructed using conditional logistic regression and included terms for age, tobacco consumption and previous respiratory disease. Smoking duration was chosen as the most important predictor of lung cancer risk [>50 years (OR 15.65, 95% CI 6.10-40.15)]. However, such a model would preclude younger individuals. Several combinations of previous respiratory disease were also considered, of which a history of bronchitis, emphysema or pneumonia (BEP) was the most significant (OR 1.86, 95% CI 1.28-2.69). A high-risk subset (based on combinations of smoking duration and BEP) was identified, which have a 4.5-fold greater risk of developing lung cancer (OR 4.5, 95% CI 2.33-8.68). Future refinement of the risk model to include individuals occupationally exposed to asbestos and with the p21 genotypes is discussed. There is real potential for environmental and genetic factors to improve on risk prediction and targeting of susceptible individuals beyond the traditional models based only on smoking and age. The development of a molecular-epidemiological model will inform the development of effective surveillance, early detection and chemoprevention strategies.

  12. 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.

  13. A Molecular Epidemiological Study of var Gene Diversity to Characterize the Reservoir of Plasmodium falciparum in Humans in Africa

    PubMed Central

    Leliwa-Sytek, Aleksandra; Smith, Terry-Ann; Peterson, Ingrid; Brown, Stuart M.; Migot-Nabias, Florence; Deloron, Philippe; Kortok, Moses M.; Marsh, Kevin; Daily, Johanna P.; Ndiaye, Daouda; Sarr, Ousmane; Mboup, Souleymane; Day, Karen P.

    2011-01-01

    Background The reservoir of Plasmodium infection in humans has traditionally been defined by blood slide positivity. This study was designed to characterize the local reservoir of infection in relation to the diverse var genes that encode the major surface antigen of Plasmodium falciparum blood stages and underlie the parasite's ability to establish chronic infection and transmit from human to mosquito. Methodology/Principal Findings We investigated the molecular epidemiology of the var multigene family at local sites in Gabon, Senegal and Kenya which differ in parasite prevalence and transmission intensity. 1839 distinct var gene types were defined by sequencing DBLα domains in the three sites. Only 76 (4.1%) var types were found in more than one population indicating spatial heterogeneity in var types across the African continent. The majority of var types appeared only once in the population sample. Non-parametric statistical estimators predict in each population at minimum five to seven thousand distinct var types. Similar diversity of var types was seen in sites with different parasite prevalences. Conclusions/Significance Var population genomics provides new insights into the epidemiology of P. falciparum in Africa where malaria has never been conquered. In particular, we have described the extensive reservoir of infection in local African sites and discovered a unique var population structure that can facilitate superinfection through minimal overlap in var repertoires among parasite genomes. Our findings show that var typing as a molecular surveillance system defines the extent of genetic complexity in the reservoir of infection to complement measures of malaria prevalence. The observed small scale spatial diversity of var genes suggests that var genetics could greatly inform current malaria mapping approaches and predict complex malaria population dynamics due to the import of var types to areas where no widespread pre-existing immunity in the population

  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. Copyright © 2016 European Society of Clinical Microbiology

  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.

  16. [Molecular epidemiologic study on Mycobacterium tuberculosis from drug resistance monitoring sites of Guangdong Province, 2015].

    PubMed

    Huang, X C; Guo, H X; Wu, Z H; Guo, C X; Wei, W J; Li, H C; Sun, Q; Zhang, C C; Li, Z Y; Chen, T; Zhong, Q; Zhou, L

    2017-05-12

    Objective: To understand the characteristics of Mycobacterium tuberculosis (MTB) in epidemiology and distribution from Guangdong Province, and to explore the risk factors associated with drug resistance. Methods: A total of 225 clinical strains of MTB collected from 5 drug resistance monitoring sites of Guangdong Province in 2015 were tested by Regions of Difference 105 (RD105) deletion test and 15 loci mycobacterial interspersed repetitive units (MIRU) were used for genotyping. Gene clustering was analyzed using BioNumerics7.6. Drug susceptibility test was tested by proportion method. The statistical analysis used chi-square test and multivariate logistic regression. Results: There were 158 (70.2%) Beijing family strains from the 225 cases. Hunter-gaston index of MIRU loci varied from each other. The MTBs from Guangdong Province were categorized into 2 gene clusters by clustering analysis in which the rate of cluster of complexⅠwas significantly higher than complexⅡ(χ(2) values were 9.331, P values were 0.020). It was found by multivariate logistic regression that Qub11b was associated with resistance to rifampicin and isoniazid (P values were 0.013, 0.012 respectively.), ETR F with resistance to isoniazid, streptomycin, ethambutol and ofloxacin (P values were 0.039, 0.040, 0.023 and 0.003 respectively), Mtub21 with resistance to capreomycin (P values were 0.040), and QUB26 with resistance to ethionamide (P values were 0.047). Conclusions: The genes of MTB from Guangdong Province were of polymorphisms and the distribution of strains were stable. QUB11b, ETR F, Mtub21 and QUB26 could be related to biomarkers for predicting drug resistance.

  17. Sixty years of follow-up of Hiroshima and Nagasaki survivors: current progress in molecular epidemiology studies.

    PubMed

    Nakachi, Kei; Hayashi, Tomonori; Hamatani, Kiyohiro; Eguchi, Hidetaka; Kusunoki, Yoichiro

    2008-01-01

    This article provides an overview of the on-going molecular epidemiology studies among atomic-bomb survivors conducted at the Radiation Effects Research Foundation in Japan. The focus is on: (a) inter-individual variations in sensitivity to radiation-induced somatic mutations (glycophorin A (GPA) mutations) and their potential relevance to differences in susceptibility to radiation-related cancers and (b) the role of specific mutations/rearrangements in radiation-induced thyroid and colorectal cancers. The glycophorin A mutant fractions showed large differences between the survivors at each of the estimated bone marrow doses. Of note is the finding at doses>or=1 Gy; that the slope of the mutant fraction was significantly higher in the 'cancer group' than in the 'non-cancer group'. This study provided the basis for validating the use of gammaH2AX and reticulocyte micronucleus assays for evaluating radiosensitivity differences and genetic instability, respectively, in our studies in the coming years. Preliminary results from our molecular oncology studies on adult-onset papillary thyroid cancer provide evidence for the induction of RET/PTC rearrangements and BRAF point mutation (both known to be early stage events in adult-onset papillary thyroid cancer) but with a difference: cases associated with the rearrangements were more frequent at high doses, and developed sooner than those with BRAF mutation. In the case of colorectal cancer, the results suggest that radiation exposure might influence microsatellite instability (MSI) status through MSI-related epigenetic and genetic alterations-processes that might occur in the early stage of colorectal carcinogenesis.

  18. Molecular Epidemiology of Cryptosporidiosis in China

    PubMed Central

    Feng, Yaoyu; Xiao, Lihua

    2017-01-01

    Molecular epidemiology of cryptosporidiosis is an active research area in China. The use of genotyping and subtyping tools in prevalence studies has led to the identification of unique characteristics of Cryptosporidium infections in humans and animals. Human cryptosporidiosis in China is exemplified by the high diversity of Cryptosporidium spp. at species and subtype levels, with dominant C. hominis and C. parvum subtypes being rarely detected in other countries. Similarly, preweaned dairy calves, lambs, and goat kids are mostly infected with non-pathogenic Cryptosporidium species (C. bovis in calves and C. xiaoi in lambs and goat kids), with C. parvum starting to appear in dairy calves as a consequence of concentrated animal feeding operations. The latter Cryptosporidium species is dominated by IId subtypes, with IIa subtypes largely absent from the country. Unlike elsewhere, rodents in China appear to be commonly infected with C. parvum IId subtypes, with identical subtypes being found in these animals, calves, other livestock, and humans. In addition to cattle, pigs and chickens appear to be significant contributors to Cryptosporidium contamination in drinking water sources, as reflected by the frequent detection of C. suis, C. baileyi, and C. meleagridis in water samples. Chinese scientists have also made significant contributions to the development of new molecular epidemiological tools for Cryptosporidium spp. and improvements in our understanding of the mechanism involved in the emergence of hyper-transmissible and virulent C. hominis and C. parvum subtypes. Despite this progress, coordinated research efforts should be made to address changes in Cryptosporidium transmission because of rapid economic development in China and to prevent the introduction and spread of virulent and zoonotic Cryptosporidium species and subtypes in farm animals. PMID:28932217

  19. Molecular Epidemiology of Cryptosporidiosis in China.

    PubMed

    Feng, Yaoyu; Xiao, Lihua

    2017-01-01

    Molecular epidemiology of cryptosporidiosis is an active research area in China. The use of genotyping and subtyping tools in prevalence studies has led to the identification of unique characteristics of Cryptosporidium infections in humans and animals. Human cryptosporidiosis in China is exemplified by the high diversity of Cryptosporidium spp. at species and subtype levels, with dominant C. hominis and C. parvum subtypes being rarely detected in other countries. Similarly, preweaned dairy calves, lambs, and goat kids are mostly infected with non-pathogenic Cryptosporidium species (C. bovis in calves and C. xiaoi in lambs and goat kids), with C. parvum starting to appear in dairy calves as a consequence of concentrated animal feeding operations. The latter Cryptosporidium species is dominated by IId subtypes, with IIa subtypes largely absent from the country. Unlike elsewhere, rodents in China appear to be commonly infected with C. parvum IId subtypes, with identical subtypes being found in these animals, calves, other livestock, and humans. In addition to cattle, pigs and chickens appear to be significant contributors to Cryptosporidium contamination in drinking water sources, as reflected by the frequent detection of C. suis, C. baileyi, and C. meleagridis in water samples. Chinese scientists have also made significant contributions to the development of new molecular epidemiological tools for Cryptosporidium spp. and improvements in our understanding of the mechanism involved in the emergence of hyper-transmissible and virulent C. hominis and C. parvum subtypes. Despite this progress, coordinated research efforts should be made to address changes in Cryptosporidium transmission because of rapid economic development in China and to prevent the introduction and spread of virulent and zoonotic Cryptosporidium species and subtypes in farm animals.

  20. 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.

  1. Minimum Cost Estimation of a Baseline Survey for a Molecular Epidemiology Cohort Study: Collecting Participants in a Model Region in Japan

    PubMed Central

    Sawada, Norie; Iwasaki, Motoki; Ohashi, Kayo; Tsugane, Shoichiro

    2016-01-01

    Background Some recent molecular epidemiology studies of the effects of genetic and environmental factors on human health have required the enrollment of more than 100 000 participants and the involvement of regional study offices across the country. Although regional study office investigators play a critical role in these studies, including the acquisition of funds, this role is rarely discussed. Methods We first differentiated the functions of the regional and central study offices. We then investigated the minimum number of items required and approximate cost of a molecular epidemiology study enrolling 7400 participants from a model region with a population of 100 000 for a 4-year baseline survey using a standard protocol developed based on the protocol of Japan Public Health Center-based Prospective Study for the Next Generation. Results The functions of the regional study office were identified, and individual expenses were itemized. The total cost of the 4-year baseline survey was 153 million yen, excluding consumption tax. Accounting difficulties in conducting the survey were clarified. Conclusions We investigated a standardized example of the tasks and total actual costs of a regional study office. Our approach is easy to utilize and will help improve the management of regional study offices in future molecular epidemiology studies. PMID:27001116

  2. Minimum Cost Estimation of a Baseline Survey for a Molecular Epidemiology Cohort Study: Collecting Participants in a Model Region in Japan.

    PubMed

    Mishiro, Izumi; Sawada, Norie; Iwasaki, Motoki; Ohashi, Kayo; Tsugane, Shoichiro

    2016-10-05

    Some recent molecular epidemiology studies of the effects of genetic and environmental factors on human health have required the enrollment of more than 100 000 participants and the involvement of regional study offices across the country. Although regional study office investigators play a critical role in these studies, including the acquisition of funds, this role is rarely discussed. We first differentiated the functions of the regional and central study offices. We then investigated the minimum number of items required and approximate cost of a molecular epidemiology study enrolling 7400 participants from a model region with a population of 100 000 for a 4-year baseline survey using a standard protocol developed based on the protocol of Japan Public Health Center-based Prospective Study for the Next Generation. The functions of the regional study office were identified, and individual expenses were itemized. The total cost of the 4-year baseline survey was 153 million yen, excluding consumption tax. Accounting difficulties in conducting the survey were clarified. We investigated a standardized example of the tasks and total actual costs of a regional study office. Our approach is easy to utilize and will help improve the management of regional study offices in future molecular epidemiology studies.

  3. The application of HIV molecular epidemiology to public health.

    PubMed

    Paraskevis, D; Nikolopoulos, G K; Magiorkinis, G; Hodges-Mameletzis, I; Hatzakis, A

    2016-12-01

    HIV is responsible for one of the largest viral pandemics in human history. Despite a concerted global response for prevention and treatment, the virus persists. Thus, urgent public health action, utilizing novel interventions, is needed to prevent future transmission events, critical to eliminating HIV. For public health planning to prove effective and successful, we need to understand the dynamics of regional epidemics and to intervene appropriately. HIV molecular epidemiology tools as implemented in phylogenetic, phylodynamic and phylogeographic analyses have proven to be powerful tools in public health planning across many studies. Numerous applications with HIV suggest that molecular methods alone or in combination with mathematical modelling can provide inferences about the transmission dynamics, critical epidemiological parameters (prevalence, incidence, effective number of infections, Re, generation times, time between infection and diagnosis), or the spatiotemporal characteristics of epidemics. Molecular tools have been used to assess the impact of an intervention and outbreak investigation which are of great public health relevance. In some settings, molecular sequence data may be more readily available than HIV surveillance data, and can therefore allow for molecular analyses to be conducted more easily. Nonetheless, classic methods have an integral role in monitoring and evaluation of public health programmes, and should supplement emerging techniques from the field of molecular epidemiology. Importantly, molecular epidemiology remains a promising approach in responding to viral diseases. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Longitudinal Study of the Molecular Epidemiology of Campylobacter jejuni in Cattle on Dairy Farms▿

    PubMed Central

    Kwan, Patrick S. L.; Birtles, Andrew; Bolton, Frederick J.; French, Nigel P.; Robinson, Susan E.; Newbold, Lynne S.; Upton, Mathew; Fox, Andrew J.

    2008-01-01

    Multilocus sequence typing (MLST), an accurate and phylogenetically robust characterization method for population studies of Campylobacter, was applied to Campylobacter jejuni isolates (n = 297) from the fecal samples of cattle from five dairy farms in Cheshire, United Kingdom, collected throughout 2003. The population dynamics of the C. jejuni strains, as identified by the occurrence of sequence types and clonal complexes, demonstrated variations within and between cattle populations over time. Three clonal lineages have emerged to predominate among the cattle isolates, namely, the ST-61 complex (24.2%), ST-21 complex (23.6%), and ST-42 complex (20.5%). This provided further evidence that the ST-61 clonal complex may present a cattle-adapted C. jejuni genotype. In addition, the ST-42 clonal complex may also represent an important cattle-associated genotype. Strong geographical associations for these genotypes were also found among the farms. This is the first longitudinal study and the largest study to date for C. jejuni involving cattle populations using MLST for accurate strain characterization. This study shows the important associations between cattle and C. jejuni clonal complexes ST-61, ST-21, and ST-42, and it suggests that cattle and/or dairy products are likely to be a source of the human Campylobacter gastroenteritis caused by such genotypes. The reported findings have significant implications for the design of effective intervention strategies for disease control and prevention. PMID:18424539

  5. The evolution of pigeon paramyxovirus type 1 (PPMV-1) in Great Britain: a molecular epidemiological study.

    PubMed

    Aldous, E W; Fuller, C M; Ridgeon, J H; Irvine, R M; Alexander, D J; Brown, I H

    2014-04-01

    Newcastle disease (ND), caused by virulent strains of avian paramyxovirus type 1 (APMV-1), is considered throughout the world as one of the most important animal diseases. For over three decades now, there has been a continuing panzootic caused by a variant virulent APMV-1 strain, so-called pigeon paramyxovirus type 1 (PPMV-1), primarily in racing pigeons, which has also spread to wild birds and poultry. PPMV-1 isolations have been made in Great Britain every year since 1983. In this study, we have completed a comparative phylogenetic analysis based on a 374 nucleotide section of the fusion protein gene of 63 isolates of PPMV-1 that were isolated over a 26-year period; 43 of these were sequenced for this study. Phylogenetic analysis of these sequences revealed that all were closely related and placed in the genetic sublineage 4b (VIb), subdivision 4biif.

  6. The molecular epidemiological study of bovine leukemia virus infection in Myanmar cattle.

    PubMed

    Polat, Meripet; Moe, Hla Hla; Shimogiri, Takeshi; Moe, Kyaw Kyaw; Takeshima, Shin-Nosuke; Aida, Yoko

    2017-02-01

    Bovine leukemia virus (BLV) is the etiological agent of enzootic bovine leukosis, which is the most common neoplastic disease of cattle. BLV infects cattle worldwide and affects both health status and productivity. However, no studies have examined the distribution of BLV in Myanmar, and the genetic characteristics of Myanmar BLV strains are unknown. Therefore, the aim of this study was to detect BLV infection in Myanmar and examine genetic variability. Blood samples were obtained from 66 cattle from different farms in four townships of the Nay Pyi Taw Union Territory of central Myanmar. BLV provirus was detected by nested PCR and real-time PCR targeting BLV long terminal repeats. Results were confirmed by nested PCR targeting the BLV env-gp51 gene and real-time PCR targeting the BLV tax gene. Out of 66 samples, six (9.1 %) were positive for BLV provirus. A phylogenetic tree, constructed using five distinct partial and complete env-gp51 sequences from BLV strains isolated from three different townships, indicated that Myanmar strains were genotype-10. A phylogenetic tree constructed from whole genome sequences obtained by sequencing cloned, overlapping PCR products from two Myanmar strains confirmed the existence of genotype-10 in Myanmar. Comparative analysis of complete genome sequences identified genotype-10-specific amino acid substitutions in both structural and non-structural genes, thereby distinguishing genotype-10 strains from other known genotypes. This study provides information regarding BLV infection levels in Myanmar and confirms that genotype-10 is circulating in Myanmar.

  7. HIV transmission patterns among The Netherlands, Suriname, and The Netherlands Antilles: a molecular epidemiological study.

    PubMed

    Kramer, Merlijn A; Cornelissen, Marion; Paraskevis, Dimitrios; Prins, Maria; Coutinho, Roel A; van Sighem, Ard I; Sabajo, Lesley; Duits, Ashley J; Winkel, Cai N; Prins, Jan M; van der Ende, Marchina E; Kauffmann, Robert H; Op de Coul, Eline L

    2011-02-01

    We aimed to study patterns of HIV transmission among Suriname, The Netherlands Antilles, and The Netherlands. Fragments of env, gag, and pol genes of 55 HIV-infected Surinamese, Antillean, and Dutch heterosexuals living in The Netherlands and 72 HIV-infected heterosexuals living in Suriname and the Antilles were amplified and sequenced. We included 145 pol sequences of HIV-infected Surinamese, Antillean, and Dutch heterosexuals living in The Netherlands from an observational cohort. All sequences were phylogenetically analyzed by neighbor-joining. Additionally, HIV-1 mobility among ethnic groups was estimated. A phylogenetic tree of all pol sequences showed two Surinamese and three Antillean clusters of related strains, but no clustering between ethnic groups. Clusters included sequences of individuals living in Suriname and the Antilles as well as those who have migrated to The Netherlands. Similar clustering patterns were observed in env and gag. Analysis of HIV mobility among ethnic groups showed significantly lower migration between groups than expected under the hypothesis of panmixis, apart from higher HIV migration between Antilleans in The Netherlands and all other groups. Our study shows that HIV transmission mainly occurs within the ethnic group. This suggests that cultural factors could have a larger impact on HIV mobility than geographic distance.

  8. An outbreak of Burkholderia cepacia bacteremia in hemodialysis patients: an epidemiologic and molecular study.

    PubMed

    Kaitwatcharachai, C; Silpapojakul, K; Jitsurong, S; Kalnauwakul, S

    2000-07-01

    The risk of blood stream infections increases in patients undergoing chronic hemodialysis. Outbreaks of infection are usually caused by contamination of the water supply, water treatment, distribution system, or dialyzer reprocessing. We report an outbreak of subclavian catheter-related Burkholderia cepacia bacteremia in nine patients undergoing hemodialysis. Using randomly amplified polymorphic DNA (RAPD) analysis, the bacterial isolates were clonally identical to Burkholderia cepacia isolated from residue of the diluted chlorhexidine-cetrimide solution used to disinfect the transfer forceps. These forceps were used to pick up cotton balls and gauze for dressing the subclavian catheter. Antibiotic therapy failed to cure the infections, and all patients required catheter removal. Pathology showed numerous bacilli embedded in the biofilm on the inner surface of the removed catheters. In conclusion, our study showed that contaminated chlorhexidine-cetrimide solution was the source of a bacteremic outbreak in nine patients who developed catheter-related Burkholderia cepacia infection.

  9. Molecular epidemiological studies of Mycobacterium bovis infections in humans and animals in Sweden.

    PubMed Central

    Szewzyk, R; Svenson, S B; Hoffner, S E; Bölske, G; Wahlström, H; Englund, L; Engvall, A; Källenius, G

    1995-01-01

    Forty-nine isolates of Mycobacterium bovis from humans and animals in Sweden were analyzed by restriction fragment length polymorphism (RFLP) patterns probed by the insertion element IS6110. Most isolates had patterns indicating the presence of only one or two genomic copies of the IS6110 insertion element. This simple type of pattern was found in all human isolates. In contrast, isolates from M. bovis infections in five herds of farmed deer in Sweden showed a specific RFLP pattern with seven bands, indicating seven copies of the IS6110 sequence. In 1958, Sweden was declared free from M. bovis in cattle. However, in 1987, M. bovis was reintroduced with imported farmed deer, and since 1991, 11 outbreaks in deer herds, but not in other livestock or wildlife, have been diagnosed. Continued RFLP studies of the new Swedish M. bovis isolates can reveal possible transmission of this deer strain to other animals or humans. PMID:8586698

  10. Molecular Characterization and Epidemiologic Study of NDM-1-Producing Extensively Drug-Resistant Escherichia coli.

    PubMed

    Du, Jia; Li, Bin; Cao, Jianming; Wu, Qing; Chen, Huale; Hou, Yuanbo; Zhang, En; Zhou, Tieli

    2016-07-06

    The emergence and dissemination of NDM-1 (New Delhi metallo-β-lactamase-1)-producing Enterobacteriaceae have resulted in a worldwide public health risk. This study described a high incidence and endemic spread of NDM-1-producing extensively drug-resistant Escherichia coli in a teaching hospital in Zhejiang province, China. We recovered six nonduplicated NDM-1-producing E. coli isolates from May 2014 to August 2014 with positive modified Hodge test and EDTA synergistic test. These isolates were highly resistant to β-lactam antimicrobials, aminoglycosides, and quinolones. PCR and DNA sequences analysis showed that all isolates carried the blaNDM-1, blaSHV-11, aac(6')-ib-cr, and qnrB. Several isolates also harbored blaCTX-M-1, blaCTX-M-9, rmtB, and qnrA. Southern blot confirmed that blaNDM-1 was located on the same ∼55 kb plasmid and conjugation experiments further proved the contransferable characteristic of blaNDM-1. The ompC sequences showed various mutations, which was related to multidrug resistance in E. coli. Pulsed-field gel electrophoresis identified four of six isolates that belonged to the same genotype. Multilocus sequence typing assigned them to ST2, except one strain that belonged to ST594. Our study demonstrated that the resistance-associated genes and the loss of the outer membrane proteins could account for high resistance of NDM-1-producing E. coli to multiple antimicrobial drugs. Both horizontal transfer of IncN and transmission of ST2 were responsible for the spread of drug resistance. These findings highlighted an urgent need to limit the further dissemination of NDM-1-producing E. coli in this region.

  11. The use of S-phenylmercapturic acid as a biomarker in molecular epidemiology studies of benzene.

    PubMed

    Farmer, Peter B; Kaur, Balvinder; Roach, Jonathan; Levy, Len; Consonni, Dario; Bertazzi, Pietro A; Pesatori, Angela; Fustinoni, Silvia; Buratti, Marina; Bonzini, Matteo; Colombi, Antonio; Popov, Todor; Cavallo, Domenico; Desideri, Arianna; Valerio, Federico; Pala, Mauro; Bolognesi, Claudia; Merlo, Franco

    2005-05-30

    S-Phenylmercapturic acid (S-PMA), is a urinary metabolite of benzene, thought to be derived from the condensation product of benzene oxide with glutathione. S-PMA may be determined by GC, HPLC (UV or fluorescence detection), GC-MS, LC-MS/MS or immunoassays. The limit of sensitivities of most of these techniques is 1 microg/l urine or below. It has been suggested that S-PMA may have value as a biomarker for low level human exposure to benzene, in view of the facts that urinary excretion of S-PMA has been found to be related to airborne benzene in occupationally exposed workers, and that only low background levels of S-PMA have been found in control subjects. We have evaluated the use of S-PMA as a biomarker, using a commercially available analytical service, in a multicentre European study of populations exposed to varying levels of benzene, in Italy (Milan, Genoa) and in Bulgaria (Sofia). These were filling station attendants, urban policemen, bus drivers, petrochemical workers and referents (a total of 623 subjects). S-PMA was measured at the end of the work shift by an immunoassay procedure. Urinary benzene (in Milan only) and the benzene metabolite trans,trans-muconic acid (t,t-MA) were measured before and after the work shift. Air-borne benzene was measured as a monitor of exposure. Urinary benzene was the most discriminatory biomarker and showed a relationship with airborne benzene at all levels of exposure studied (including groups exposed to <0.1 ppm benzene), whereas t,t-MA and S-PMA, as determined by immunoassay, were suitable only in the highest exposed workers (petrochemical industry, geometric mean 1765 microg/m3 (0.55 ppm) benzene). All three biomarkers were positively correlated with smoking as measured by urinary cotinine).

  12. The molecular epidemiology of bovine rotaviruses circulating in Iran: a two-year study.

    PubMed

    Pourasgari, Farzaneh; Kaplon, Jérôme; Karimi-Naghlani, Shahla; Fremy, Céline; Otarod, Vahid; Ambert-Balay, Katia; Mirjalili, Ali; Pothier, Pierre

    2016-12-01

    Bovine group A rotavirus (bovine RVA) is recognized as a major cause of severe gastroenteritis in newborn calves. The purpose of this study was to estimate the prevalence and identify the genotypes of circulating bovine RVA in newborn diarrheic calves. Two hundred fifty-three stool samples of diarrheic calves up to 1 month old were collected from 42 industrial dairy farms in two Iranian provinces during March 2010 to February 2012. All collected samples were screened for the presence of bovine RVA by RT-PCR, and the G and P genotypes were determined by semi-nested multiplex RT-PCR assay. The results of RT-PCR indicated that 49.4 % (125 out of 253) of the samples were positive for bovine RVA. The G and P genotyping of a subset of positive samples (n = 85) by semi-nested multiplex RT-PCR revealed that G6 (55.3 %) and G10 (43.5 %) and P[5] (51.8 %) and P[11] (27 %) were the most prevalent G and P genotypes, respectively. G6P[5] was the dominant genotype (35.3 %), followed by G10P[5], G10P[11] and G6P[11], with prevalence rates of 16.5 %, 15.3 % and 10.6 %, respectively. Sequence analysis of 20 VP7 and four VP4 genes showed highest nucleotide sequence identity with the corresponding genes of strains RVA/Cow-tc/GBR/UK/1973/G6P7[5] and RVA/Cow-tc/USA/B223/XXXX/G10P[11]. The results of this study reveal the diversity of G and P genotypes in bovine RVA samples from diarrheic Iranian calves and expands our knowledge of bovine RVA infections in the Middle East. These results also highlight the importance of producing of an effective rotavirus vaccine and its inclusion in the national cattle immunization program.

  13. Physical activity and lung cancer among non-smokers: a pilot molecular epidemiological study within EPIC.

    PubMed

    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, Josèr; Agudo, Antonio; Berglund, Goran; Jarvholm, Bengt; Bingham, Sheila; Key, Timothy J; Gormally, Emmanuelle; Saracci, Rodolfo; Kaaks, Rudolf; Riboli, Elio; Vineis, Paolo

    2010-02-01

    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 (32)P-post-labelling and glutathione (GSH) in red blood cells were available from a subset of cases and controls. Compared with the first quartile, the fourth quartile of recreational physical activity was associated with a lower lung cancer risk (odds ratio (OR) 0.56, 95% confidence interval (CI) 0.35-0.90), higher GSH levels (+1.87 micromol GSH g(-1) haemoglobin, p = 0.04) but not with the presence of high levels of adducts (OR 1.05, 95% CI 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 (OR 0.95, 95% CI 0.84-1.07 per unit increase in GSH levels). Household and occupational activity was not associated with lung cancer risk or biomarker levels.

  14. Clinical and molecular epidemiological study of xeroderma pigmentosum in China: A case series of 19 patients.

    PubMed

    Zhou, Eray Yihui; Wang, Huijun; Lin, Zhimiao; Xu, Guiwen; Ma, Zhihong; Zhao, Jiahui; Feng, Cheng; Duo, Lina; Yin, Jinghua; Yang, Yong

    2017-01-01

    Xeroderma pigmentosum (XP) is a rare genetic disorder which is divided into eight complementation groups: XP-A to XP-G and XP-V. Some XP patients demonstrate severe cutaneous and neurological manifestations, management of which requires timely diagnosis and intervention. We performed clinical evaluation and genetic analysis on 19 patients, the largest cohort of XP to date in China. Twenty-three mutations from six groups were identified, 16 of which were novel. All patients developed marked freckle-like pigmentation on sun-exposed sites while patients with XP-A, XP-D, XP-F and XP-G showed acute sunburn reactions. Only XP-A patients displayed progressive neurological degeneration. A relatively larger proportion of XP-A and XP-C were found in Chinese XP patients. One XP case and two carriers were prenatally determined. This study extended the mutation spectrum of XP in China and may aid in the diagnosis and treatment of Chinese XP patients.

  15. 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

  16. Human enterovirus 71 disease in Sarawak, Malaysia: a prospective clinical, virological, and molecular epidemiological study.

    PubMed

    Ooi, Mong How; Wong, See Chang; Podin, Yuwana; Akin, Winnie; del Sel, Syvia; Mohan, Anand; Chieng, Chae Hee; Perera, David; Clear, Daniela; Wong, Darin; Blake, Emma; Cardosa, Jane; Solomon, Tom

    2007-03-01

    Human enterovirus (HEV)-71 causes large outbreaks of hand-foot-and-mouth disease with central nervous system (CNS) complications, but the role of HEV-71 genogroups or dual infection with other viruses in causing severe disease is unclear. We prospectively studied children with suspected HEV-71 (i.e., hand-foot-and-mouth disease, CNS disease, or both) over 3.5 years, using detailed virological investigation and genogroup analysis of all isolates. Seven hundred seventy-three children were recruited, 277 of whom were infected with HEV-71, including 28 who were coinfected with other viruses. Risk factors for CNS disease in HEV-71 included young age, fever, vomiting, mouth ulcers, breathlessness, cold limbs, and poor urine output. Genogroup analysis for the HEV-71-infected patients revealed that 168 were infected with genogroup B4, 68 with C1, and 41 with a newly emerged genogroup, B5. Children with HEV-71 genogroup B4 were less likely to have CNS complications than those with other genogroups (26 [15%] of 168 vs. 30 [28%] of 109; odds ratio [OR], 0.48; 95% confidence interval [CI], 0.26-0.91; P=.0223) and less likely to be part of a family cluster (12 [7%] of 168 vs. 29 [27%] of 109; OR, 0.21; 95% CI, 0.10-0.46; P<.0001); children with HEV-71 genogroup B5 were more likely to be part of a family cluster (OR, 6.26; 95% CI, 2.77-14.18; P<.0001). Children with HEV-71 and coinfected with another enterovirus or adenovirus were no more likely to have CNS disease. Genogroups of HEV-71 may differ with regard to the risk of causing CNS disease and the association with family clusters. Dual infections are common, and all possible causes should be excluded before accepting that the first virus identified is the causal agent.

  17. Study on molecular epidemiology of the alpha-thalassemias in Liuzhou City, Guangxi Autonomous Region, China.

    PubMed

    Cai, Ren; Liu, Jingzhong; Wang, Lirong; Liang, Xin; Xiao, Bai; Su, Liu; Zhou, Yan; Pan, Lizhen

    2004-01-01

    Guangxi is one of the provinces of Southern China with the highest incidence of alpha-thalassemia (thal). Liuzhou is the second biggest city in Guangxi. To find out the incidence of the various alpha-thal genotypes, and their distribution in the Liuzhou area, an F820 Blood Cell Analysis System was used to measure the parameters of red blood cells. A SPIFE Rapid Auto-Electrophoresis System was used to analyze the normal and abnormal hemoglobins (Hbs). Multiplex polymerase chain reaction (mPCR) was used to detect the alpha-globin genotypes. Thirty-two (2.05%) out of 7805 young couples undergoing pre-marriage counseling, were diagnosed as having an Hb H (beta4) disease. The study of 1228 cord blood samples revealed 138 newborn children carrying an alpha-thal determinant with nine different genotypes, thus making the total incidence of alpha-thal 11.24%. Among 185 cases of Hb H, 119 (64.1%) were confirmed as being deletional, and 66 cases (35.7%) nondeletional types. The severity of the Hb H diseases could be classified in the following order: alphaCSalpha/--SEA (alphaConstant (Spring)alpha/--Southeast Asia); alpha(-4.2)/--SEA; alpha(-3.7)/--SEA. Ten cases of alpha-thal determinants were found in combination with beta-thal. The mPCR technique can detect all kinds of combinations of the three common large deletions (--SEA, alpha(-4.2) and alpha(-3.7)) accurately and conveniently.

  18. Molecular epidemiological and virological study of dengue virus infections in Guangzhou, China, during 2001–2010

    PubMed Central

    2013-01-01

    Background Dengue virus (DENV) infection is the most prevalent arthropod-borne viral infection in tropical and subtropical regions worldwide. Guangzhou has the ideal environment for DENV transmission and DENV epidemics have been reported in this region for more than 30 years. Methods Information for DENV infection cases in Guangzhou from 2001 to 2010 were collected and analyzed. The DENV strains were cultured and isolated from patients’ sera. Viral RNA was extracted from cell culture supernatants. cDNA was synthesized by reverse transcription PCR. Phylogenetic trees of four DENV serotypes were constructed respectively. Results In total, 2478 DENV infection cases were reported; 2143 of these (86.43%) occurred during 3 months of the year: August, September and October. Of these, 2398 were local cases (96.77%) and 80 were imported cases (3.23%). Among the imported cases, 69 (86.25%) were from Southeast Asian countries. From the 90 isolated strains, 66.67%, 3.33%, 14.44%, and 15.56% belonged to DENV serotypes 1, 2, 3, and 4, respectively. DENV-1 was predominant in most of the years, including during 2 outbreaks in 2002 and 2006; however, none of the strains or genotypes identified in this study were found to be predominant. Interestingly, DENV strains from different years had different origins. Moreover, the strains from each year belonged to different serotypes and/or genotypes. Conclusions Southeast Asia countries were found to be the possible source of DENV in Guangzhou. These findings suggest that there is increasing diversity in DENV strains in Guangzhou, which could increase the risk of DENV outbreaks in the near future. PMID:23282129

  19. Molecular epidemiological and virological study of dengue virus infections in Guangzhou, China, during 2001-2010.

    PubMed

    Jiang, Liyun; Wu, Xinwei; Wu, Yejian; Bai, Zhijun; Jing, Qinglong; Luo, Lei; Dong, Zhiqiang; Yang, Zhicong; Xu, Yang; Cao, Yimin; Di, Biao; Wang, Yulin; Wang, Ming

    2013-01-02

    Dengue virus (DENV) infection is the most prevalent arthropod-borne viral infection in tropical and subtropical regions worldwide. Guangzhou has the ideal environment for DENV transmission and DENV epidemics have been reported in this region for more than 30 years. Information for DENV infection cases in Guangzhou from 2001 to 2010 were collected and analyzed. The DENV strains were cultured and isolated from patients' sera. Viral RNA was extracted from cell culture supernatants. cDNA was synthesized by reverse transcription PCR. Phylogenetic trees of four DENV serotypes were constructed respectively. In total, 2478 DENV infection cases were reported; 2143 of these (86.43%) occurred during 3 months of the year: August, September and October. Of these, 2398 were local cases (96.77%) and 80 were imported cases (3.23%). Among the imported cases, 69 (86.25%) were from Southeast Asian countries. From the 90 isolated strains, 66.67%, 3.33%, 14.44%, and 15.56% belonged to DENV serotypes 1, 2, 3, and 4, respectively. DENV-1 was predominant in most of the years, including during 2 outbreaks in 2002 and 2006; however, none of the strains or genotypes identified in this study were found to be predominant. Interestingly, DENV strains from different years had different origins. Moreover, the strains from each year belonged to different serotypes and/or genotypes. Southeast Asia countries were found to be the possible source of DENV in Guangzhou. These findings suggest that there is increasing diversity in DENV strains in Guangzhou, which could increase the risk of DENV outbreaks in the near future.

  20. Diet, Helicobacter pylori, and p53 mutations in gastric cancer: a molecular epidemiology study in Italy.

    PubMed

    Palli, D; Caporaso, N E; Shiao, Y H; Saieva, C; Amorosi, A; Masala, G; Rice, J M; Fraumeni, J F

    1997-12-01

    A series of 105 gastric cancer (GC) cases with paraffin-embedded specimens interviewed in a previous population-based case-control study conducted in a high-risk area around Florence, Italy, was examined for the presence of p53 mutations. Overall, 33 of 105 cases had a mutation (p53+) identified by single-strand conformational polymorphism and confirmed by sequencing (Y-H. Shiao et al., submitted for publication). p53+ cases had a more traditional dietary pattern (i.e., corn meal mush, meat soup, and other homemade dishes) and reported less frequent consumption of raw vegetables (particularly lettuce and raw carrots). A positive association with a high nitrite intake and a negative association with raw vegetables and diffuse type histology persisted in a multivariate analysis. In addition, p53+ cases tended to be located in the upper portion of the stomach and to be associated with advanced age and blood group A. No relation was found between the presence of p53 mutations and histologically defined Helicobacter pylori infection, smoking history, family history of gastric cancer, education, and social class. Of the 33 p53+ cases, 19 had G:C-->A:T transitions at CpG sites. These tumors tended to occur in females and in association with H. pylori infection but not other risk factors. The remaining 14 cases with a p53 mutation had mainly transversions but also two deletions and two transitions at non-CpG sites. These tumors showed a strong positive association with a traditional dietary pattern and with the estimated intake of selected nutrients (nitrite, protein, and fat, particularly from animal sources). The findings of this case-case analysis suggest that p53 mutations at non-CpG sites are related to exposure to alkylating compounds from diet, whereas p53 mutations at CpG sites might be related to H. pylori infection.

  1. 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

  2. Molecular epidemiology of Usher syndrome in Italy

    PubMed Central

    Vozzi, Diego; Aaspõllu, Anu; Athanasakis, Emmanouil; Berto, Anna; Fabretto, Antonella; Licastro, Danilo; Külm, Maigi; Testa, Francesco; Trevisi, Patrizia; Vahter, Marju; Ziviello, Carmela; Martini, Alessandro; Simonelli, Francesca; Banfi, Sandro

    2011-01-01

    Purpose Usher syndrome is an autosomal recessive disorder characterized by hearing and vision loss. Usher syndrome is divided into three clinical subclasses (type 1, type 2, and type 3), which differ in terms of the severity and progression of hearing loss and the presence or absence of vestibular symptoms. Usher syndrome is defined by significant genetic heterogeneity, with at least 12 distinct loci described and 9 genes identified. This study aims to provide a molecular epidemiology report of Usher syndrome in Italy. Methods Molecular data have been obtained on 75 unrelated Italian patients using the most up-to date technology available for the screening of Usher syndrome gene mutations, i.e., the genotyping microarray developed by Asper Biotech (Tartu, Estonia), which simultaneously investigates 612 different marker positions using the well established arrayed primer extension methodology (APEX). Results Using this method, we found that 12% of cases (9 out of 75) harbored homozygous or compound heterozygous mutations in the gene positions analyzed, whereas 20% (15 out of 75) of the patients were characterized by the presence of only one mutated allele based on the positions analyzed. One patient was found to be compound heterozygous for mutations in two different genes and this represents an example of possible digenic inheritance in Usher syndrome. A total of 66.6% of cases (50 out of 75) were found to be completely negative for the presence of Usher syndrome gene mutations in the detected positions. Mutations detected by the array were confirmed by direct sequencing. Conclusions These findings highlight the efficacy of the APEX-based genotyping approach in the molecular assessment of Usher patients, suggesting the presence of alleles not yet identified and/or the involvement of additional putative genes that may account for the pathogenesis of Usher syndrome. PMID:21738395

  3. The molecular epidemiology of parasite infections: tools and applications.

    PubMed

    Lymbery, A J; Thompson, R C A

    2012-02-01

    Molecular epidemiology, broadly defined, is the application of molecular genetic techniques to the dynamics of disease in a population. In this review, we briefly describe molecular and analytical tools available for molecular epidemiological studies and then provide an overview of how they can be applied to better understand parasitic disease. A range of new molecular tools have been developed in recent years, allowing for the direct examination of parasites from clinical or environmental samples, and providing access to relatively cheap, rapid, high throughput molecular assays. At the same time, new analytical approaches, in particular those derived from coalescent theory, have been developed to provide more robust estimates of evolutionary processes and demographic parameters from multilocus, genotypic data. To date, the primary application of molecular epidemiology has been to provide specific and sensitive identification of parasites and to resolve taxonomic issues, particularly at the species level and below. Population genetic studies have also been used to determine the extent of genetic diversity among populations of parasites and the degree to which this diversity is associated with different host cycles or epidemiologically important phenotypes. Many of these studies have also shed new light on transmission cycles of parasites, particularly the extent to which zoonotic transmission occurs, and on the prevalence and importance of mixed infections with different parasite species or intraspecific variants (polyparasitism). A major challenge, and one which is now being addressed by an increasing number of studies, is to find and utilize genetic markers for complex traits of epidemiological significance, such as drug resistance, zoonotic potential and virulence. Copyright © 2011 Elsevier B.V. All rights reserved.

  4. Molecular epidemiology of norovirus in South Korea

    PubMed Central

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

    2015-01-01

    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. [BMB Reports 2015; 48(2): 61-67] PMID:25441425

  5. Yersinia enterocolitica: Epidemiological Studies and Outbreaks

    PubMed Central

    Rahman, Atiqur; Bonny, Tania S.; Stonsaovapak, Siriporn; Ananchaipattana, Chiraporn

    2011-01-01

    Yersinia enterocolitica is the most common bacteriological cause of gastrointestinal disease in many developed and developing countries. Although contaminated food is the main source of human infection due to Y. enterocolitica, animal reservoir and contaminated environment are also considered as other possible infection sources for human in epidemiological studies. Molecular based epidemiological studies are found to be more efficient in investigating the occurrence of human pathogenic Y. enterocolitica in natural samples, in addition to conventional culture based studies. PMID:22567324

  6. 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...

  7. 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...

  8. 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

  9. The spread of artemisinin-resistant Plasmodium falciparum in the Greater Mekong subregion: a molecular epidemiology observational study.

    PubMed

    Imwong, Mallika; Suwannasin, Kanokon; Kunasol, Chanon; Sutawong, Kreepol; Mayxay, Mayfong; Rekol, Huy; Smithuis, Frank M; Hlaing, Tin Maung; Tun, Kyaw M; van der Pluijm, Rob W; Tripura, Rupam; Miotto, Olivo; Menard, Didier; Dhorda, Mehul; Day, Nicholas P J; White, Nicholas J; Dondorp, Arjen M

    2017-05-01

    Evidence suggests that the PfKelch13 mutations that confer artemisinin resistance in falciparum malaria have multiple independent origins across the Greater Mekong subregion, which has motivated a regional malaria elimination agenda. We aimed to use molecular genotyping to assess antimalarial drug resistance selection and spread in the Greater Mekong subregion. In this observational study, we tested Plasmodium falciparum isolates from Myanmar, northeastern Thailand, southern Laos, and western Cambodia for PfKelch13 mutations and for Pfplasmepsin2 gene amplification (indicating piperaquine resistance). We collected blood spots from patients with microscopy or rapid test confirmed uncomplicated falciparum malaria. We used microsatellite genotyping to assess genetic relatedness. As part of studies on the epidemiology of artemisinin-resistant malaria between Jan 1, 2008, and Dec 31, 2015, we collected 434 isolates. In 2014-15, a single long PfKelch13 C580Y haplotype (-50 to +31·5 kb) lineage, which emerged in western Cambodia in 2008, was detected in 65 of 88 isolates from northeastern Thailand, 86 of 111 isolates from southern Laos, and 14 of 14 isolates from western Cambodia, signifying a hard transnational selective sweep. Pfplasmepsin2 amplification occurred only within this lineage, and by 2015 these closely related parasites were found in ten of the 14 isolates from Cambodia and 15 of 15 isolates from northeastern Thailand. C580Y mutated parasites from Myanmar had a different genetic origin. Our results suggest that the dominant artemisinin-resistant P falciparum C580Y lineage probably arose in western Cambodia and then spread to Thailand and Laos, outcompeting other parasites and acquiring piperaquine resistance. The emergence and spread of fit artemisinin-resistant P falciparum parasite lineages, which then acquire partner drug resistance across the Greater Mekong subregion, threatens regional malaria control and elimination goals. Elimination of falciparum

  10. An epidemiological study on Mycobacterium leprae infection and prevalence of leprosy in endemic villages by molecular biological technique.

    PubMed

    Izumi, S; Budiawan, T; Saeki, K; Matsuoka, M; Kawatsu, K

    1999-01-01

    One of the most important unsolved questions in epidemiology of leprosy is the highly uneven geographic distribution of the disease. There are many hyperendemic "pockets" in endemic countries. Little is known about the reasons why leprosy is hyperendemic in these areas. We conducted, therefore, a series of epidemiological studies on Mycobacterium leprae infection and prevalence of leprosy in North Maluku district, Maluku Province, Indonesia where leprosy is highly endemic. It was found that considerable number of general inhabitants are seropositive to various mycobacterial antigens and 27% of the villagers were carrying leprosy bacilli on their surface of nasal cavity. These results suggested the importance of M. leprae in the residential environment in infection of the leprosy bacillus and the resulting transmission of the disease. Based on these observations, we conclude that new preventive measures are essential for global elimination of leprosy in addition to early diagnosis and multidrug therapy (MDT).

  11. 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

  12. The Role of Molecular Pathological Epidemiology in the Study of Neoplastic and Non-Neoplastic Diseases in the Era of Precision Medicine

    PubMed Central

    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.

    2016-01-01

    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 (MPE) Meeting Series, and the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE)-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

  13. Fish rhabdoviruses: molecular epidemiology and evolution.

    PubMed

    Hoffmann, B; Beer, M; Schütze, H; Mettenleiter, T C

    2005-01-01

    Rhabdoviruses may cause serious diseases in wild and farmed fish. Within the Rhabdoviridae six genera have been established: Ephemerovirus, Cytorhabdovirus, Nucleorhabdovirus, Lyssavirus, Vesiculovirus, and Novirhabdovirus. Viruses that infect fish are official or tentative members of the genera Vesiculovirus and Novirhabdovirus, or are listed as unassigned rhabdoviruses. In this report, we summarize and discuss published and our own unpublished data on the molecular epidemiology and phylogeography of fish rhabdoviruses including intrapopulational differences and subgrouping of fish rhabdoviruses, in particular the species spring viremia of carp virus (SVCV), infectious hematopoietic necrosis virus (IHNV) and viral hemorrhagic septicemia virus (VHSV).

  14. Molecular Epidemiology of Human Immunodeficiency Virus

    PubMed Central

    2017-01-01

    During the evolution of human immunodeficiency virus (HIV), transmissions between humans and primates resulted in multiple HIV lineages in humans. This evolution has been rapid, giving rise to a complex classification and allowing for worldwide spread and intermixing of subtypes, which has consequently led to dozens of circulating recombinant forms. In the Republic of Korea, 12,522 cases of HIV infection have been reported between 1985, when AIDS was first identified, and 2015. This review focuses on the evolution of HIV infection worldwide and the molecular epidemiologic characteristics of HIV in Korea. PMID:28332348

  15. Genotyping of Mycobacterium tuberculosis: application in epidemiologic studies

    PubMed Central

    Kato-Maeda, Midori; Metcalfe, John Z.; Flores, Laura

    2014-01-01

    Genotyping is used to track specific isolates of Mycobacterium tuberculosis in a community. It has been successfully used in epidemiologic research (termed ‘molecular epidemiology’) to study the transmission dynamics of TB. In this article, we review the genetic markers used in molecular epidemiologic studies including the use of whole-genome sequencing technology. We also review the public health application of molecular epidemiologic tools. PMID:21366420

  16. Molecular biology, epidemiology, and the elusive nature of pancreatitis.

    PubMed

    Tenner, Scott

    2015-03-05

    The myriad of presentations of pancreatitis can cause confusion and controversy among clinicians affecting the diagnosis, treatment, and research of patients with these disorders. Although the disease is best thought of as a spectrum with classic presentations, the underlying pathophysiologic reasons for the differences in manifestations remains unknown. In this issue of the Journal, LaRusch and colleagues provide an elegant study combining epidemiology and molecular biology to explain why some patients with pancreatitis develop fibrosis chronic pancreatitis. The implications of the findings add to the growing request to support large multidisciplinary, combined genetic, and epidemiologic studies in pancreatic disease.

  17. Stress and breast cancer: from epidemiology to molecular biology

    PubMed Central

    2011-01-01

    Stress exposure has been proposed to contribute to the etiology of breast cancer. However, the validity of this assertion and the possible mechanisms involved are not well established. Epidemiologic studies differ in their assessment of the relative contribution of stress to breast cancer risk, while physiological studies propose a clear connection but lack the knowledge of intracellular pathways involved. The present review aims to consolidate the findings from different fields of research (including epidemiology, physiology, and molecular biology) in order to present a comprehensive picture of what we know to date about the role of stress in breast cancer development. PMID:21575279

  18. Molecular markers in the epidemiology and diagnosis of coccidioidomycosis.

    PubMed

    Duarte-Escalante, Esperanza; Frías-De-León, María Guadalupe; Zúñiga, Gerardo; Martínez-Herrera, Erick; Acosta-Altamirano, Gustavo; Reyes-Montes, María Del Rocío

    2014-01-01

    The prevalence of coccidioidomycosis in endemic areas has been observed to increase daily. To understand the causes of the spread of the disease and design strategies for fungal detection in clinical and environmental samples, scientists have resorted to molecular tools that allow fungal detection in a natural environment, reliable identification in clinical cases and the study of biological characteristics, such as reproductive and genetic structure, demographic history and diversification. We conducted a review of the most important molecular markers in the epidemiology of Coccidioides spp. and the diagnosis of coccidioidomycosis. A literature search was performed for scientific publications concerning the application of molecular tools for the epidemiology and diagnosis of coccidioidomycosis. The use of molecular markers in the epidemiological study and diagnosis of coccidioidomycosis has allowed for the typing of Coccidioides spp. isolates, improved understanding of their mode of reproduction, genetic variation and speciation and resulted in the development specific, rapid and sensitive strategies for detecting the fungus in environmental and clinical samples. Molecular markers have revealed genetic variability in Coccidioides spp. This finding influences changes in the epidemiology of coccidioidomycosis, such as the emergence of more virulent or antifungal resistant genotypes. Furthermore, the molecular markers currently used to identify Coccidioides immitis and Coccidioides posadasii are specific and sensitive. However, they must be validated to determine their application in diagnosis. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  19. 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.

  20. Absence of Putative Artemisinin Resistance Mutations Among Plasmodium falciparum in Sub-Saharan Africa: A Molecular Epidemiologic Study

    PubMed Central

    Taylor, Steve M.; Parobek, Christian M.; DeConti, Derrick K.; Kayentao, Kassoum; Coulibaly, Sheick Oumar; Greenwood, Brian M.; Tagbor, Harry; Williams, John; Bojang, Kalifa; Njie, Fanta; Desai, Meghna; Kariuki, Simon; Gutman, Julie; Mathanga, Don P.; Mårtensson, Andreas; Ngasala, Billy; Conrad, Melissa D.; Rosenthal, Philip J.; Tshefu, Antoinette K.; Moormann, Ann M.; Vulule, John M.; Doumbo, Ogobara K.; ter Kuile, Feiko O.; Meshnick, Steven R.; Bailey, Jeffrey A.; Juliano, Jonathan J.

    2015-01-01

    Plasmodium falciparum parasites that are resistant to artemisinins have been detected in Southeast Asia. Resistance is associated with several polymorphisms in the parasite's K13-propeller gene. The molecular epidemiology of these artemisinin resistance genotypes in African parasite populations is unknown. We developed an assay to quantify rare polymorphisms in parasite populations that uses a pooled deep-sequencing approach to score allele frequencies, validated it by evaluating mixtures of laboratory parasite strains, and then used it to screen P. falciparum parasites from >1100 African infections collected since 2002 from 14 sites across sub-Saharan Africa. We found no mutations in African parasite populations that are associated with artemisinin resistance in Southeast Asian parasites. However, we observed 15 coding mutations, including 12 novel mutations, and limited allele sharing between parasite populations, consistent with a large reservoir of naturally occurring K13-propeller variation. Although polymorphisms associated with artemisinin resistance in P. falciparum in Southeast Asia are not prevalent in sub-Saharan Africa, numerous K13-propeller coding polymorphisms circulate in Africa. Although their distributions do not support a widespread selective sweep for an artemisinin-resistant phenotype, the impact of these mutations on artemisinin susceptibility is unknown and will require further characterization. Rapid, scalable molecular surveillance offers a useful adjunct in tracking and containing artemisinin resistance. PMID:25180240

  1. 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. © 2015 Blackwell Verlag GmbH.

  2. Zoonotic potential and molecular epidemiology of Giardia species and giardiasis.

    PubMed

    Feng, Yaoyu; Xiao, Lihua

    2011-01-01

    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.

  3. 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

  4. 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

  5. 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

  6. Evolution, phylogeny, and molecular epidemiology of Chlamydia.

    PubMed

    Nunes, Alexandra; Gomes, João P

    2014-04-01

    The Chlamydiaceae are a family of obligate intracellular bacteria characterized by a unique biphasic developmental cycle. It encompasses the single genus Chlamydia, which involves nine species that affect a wide range of vertebral hosts, causing infections with serious impact on human health (mainly due to Chlamydia trachomatis infections) and on farming and veterinary industries. It is believed that Chlamydiales originated ∼700mya, whereas C. trachomatis likely split from the other Chlamydiaceae during the last 6mya. This corresponds to the emergence of modern human lineages, with the first descriptions of chlamydial infections as ancient as four millennia. Chlamydiaceae have undergone a massive genome reduction, on behalf of the deletional bias "use it or lose it", stabilizing at 1-1.2Mb and keeping a striking genome synteny. Their phylogeny reveals species segregation according to biological properties, with huge differences in terms of host range, tissue tropism, and disease outcomes. Genome differences rely on the occurrence of mutations in the >700 orthologous genes, as well as on events of recombination, gene loss, inversion, and paralogous expansion, affecting both a hypervariable region named the plasticity zone, and genes essentially encoding polymorphic and transmembrane head membrane proteins, type III secretion effectors and some metabolic pathways. Procedures for molecular typing are still not consensual but have allowed the knowledge of molecular epidemiology patterns for some species as well as the identification of outbreaks and emergence of successful clones for C. trachomatis. This manuscript intends to provide a comprehensive review on the evolution, phylogeny, and molecular epidemiology of Chlamydia. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Update on molecular epidemiology of Shigella infection.

    PubMed

    Lima, Ila F N; Havt, Alexandre; Lima, Aldo A M

    2015-01-01

    Shigella spp. are important etiologic agents of diarrhea worldwide. This review summarizes the recent findings on the epidemiology, diagnosis, virulence genes, and pathobiology of Shigella infection. Shigella flexneri and Shigella sonnei have been identified as the main serogroups circulating in developing and developed countries, respectively. However, a shift in the dominant species from S. flexneri to S. sonnei has been observed in countries that have experienced recent improvements in socioeconomic conditions. Despite the increasing usage of molecular methods in the diagnosis and virulence characterization of Shigella strains, researchers have been unsuccessful in finding a specific target gene for this bacillus. New research has demonstrated the role of proteins whose expressions are temperature-regulated, as well as genes involved in the processes of adhesion, invasion, dissemination, and inflammation, aiding in the clarification of the complex pathobiology of shigellosis. Knowledge about the epidemiologic profile of circulating serogroups of Shigella and an understanding of its pathobiology as well as of the virulence genes is important for the development of preventive measures and interventions to reduce the worldwide spread of shigellosis.

  8. Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study

    PubMed Central

    Rückert, Christian; Nübel, Ulrich; Blom, Jochen; Wirth, Thierry; Jaenicke, Sebastian; Schuback, Sieglinde; Rüsch-Gerdes, Sabine; Supply, Philip; Kalinowski, Jörn; Niemann, Stefan

    2013-01-01

    Background Understanding Mycobacterium tuberculosis (Mtb) transmission is essential to guide efficient tuberculosis control strategies. Traditional strain typing lacks sufficient discriminatory power to resolve large outbreaks. Here, we tested the potential of using next generation genome sequencing for identification of outbreak-related transmission chains. Methods and Findings During long-term (1997 to 2010) prospective population-based molecular epidemiological surveillance comprising a total of 2,301 patients, we identified a large outbreak caused by an Mtb strain of the Haarlem lineage. The main performance outcome measure of whole genome sequencing (WGS) analyses was the degree of correlation of the WGS analyses with contact tracing data and the spatio-temporal distribution of the outbreak cases. WGS analyses of the 86 isolates revealed 85 single nucleotide polymorphisms (SNPs), subdividing the outbreak into seven genome clusters (two to 24 isolates each), plus 36 unique SNP profiles. WGS results showed that the first outbreak isolates detected in 1997 were falsely clustered by classical genotyping. In 1998, one clone (termed “Hamburg clone”) started expanding, apparently independently from differences in the social environment of early cases. Genome-based clustering patterns were in better accordance with contact tracing data and the geographical distribution of the cases than clustering patterns based on classical genotyping. A maximum of three SNPs were identified in eight confirmed human-to-human transmission chains, involving 31 patients. We estimated the Mtb genome evolutionary rate at 0.4 mutations per genome per year. This rate suggests that Mtb grows in its natural host with a doubling time of approximately 22 h (400 generations per year). Based on the genome variation discovered, emergence of the Hamburg clone was dated back to a period between 1993 and 1997, hence shortly before the discovery of the outbreak through epidemiological surveillance

  9. Molecular Epidemiology of Oropouche Virus, Brazil

    PubMed Central

    Vasconcelos, Helena Baldez; Nunes, Márcio R.T.; Casseb, Lívia M.N.; Carvalho, Valéria L.; Pinto da Silva, Eliana V.; Silva, Mayra; Casseb, Samir M.M.

    2011-01-01

    Oropouche virus (OROV) is the causative agent of Oropouche fever, an urban febrile arboviral disease widespread in South America, with >30 epidemics reported in Brazil and other Latin American countries during 1960–2009. To describe the molecular epidemiology of OROV, we analyzed the entire N gene sequences (small RNA) of 66 strains and 35 partial Gn (medium RNA) and large RNA gene sequences. Distinct patterns of OROV strain clustered according to N, Gn, and large gene sequences, which suggests that each RNA segment had a different evolutionary history and that the classification in genotypes must consider the genetic information for all genetic segments. Finally, time-scale analysis based on the N gene showed that OROV emerged in Brazil ≈223 years ago and that genotype I (based on N gene data) was responsible for the emergence of all other genotypes and for virus dispersal. PMID:21529387

  10. Molecular epidemiology of Oropouche virus, Brazil.

    PubMed

    Vasconcelos, Helena Baldez; Nunes, Márcio R T; Casseb, Lívia M N; Carvalho, Valéria L; Pinto da Silva, Eliana V; Silva, Mayra; Casseb, Samir M M; Vasconcelos, Pedro F C

    2011-05-01

    Oropouche virus (OROV) is the causative agent of Oropouche fever, an urban febrile arboviral disease widespread in South America, with >30 epidemics reported in Brazil and other Latin American countries during 1960-2009. To describe the molecular epidemiology of OROV, we analyzed the entire N gene sequences (small RNA) of 66 strains and 35 partial Gn (medium RNA) and large RNA gene sequences. Distinct patterns of OROV strain clustered according to N, Gn, and large gene sequences, which suggests that each RNA segment had a different evolutionary history and that the classification in genotypes must consider the genetic information for all genetic segments. Finally, time-scale analysis based on the N gene showed that OROV emerged in Brazil ≈223 years ago and that genotype I (based on N gene data) was responsible for the emergence of all other genotypes and for virus dispersal.

  11. 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

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

    PubMed

    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; Pacheco, M Andreina; Vallejo, Andres F; Herrera, Socrates; Felger, Ingrid

    2015-09-01

    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. © The American Society of Tropical Medicine and Hygiene.

  13. Molecular epidemiology of mycobacteriosis in wildlife and pet animals.

    PubMed

    Schrenzel, Mark D

    2012-01-01

    The ecology of mycobacteria is shifting in accordance with environmental change and new patterns of interaction between wildlife, humans, and nondomestic animals. Infection of vertebrate hosts throughout the world is greater now than ever and includes a growing prevalence in free ranging and captive wild animals. Molecular epidemiologic studies using standardized methods with high discriminatory power are useful for tracking individual cases and outbreaks, identifying reservoirs, and describing patterns of transmission and are used with increasing frequency to characterize disease wildlife. This review describes current features of mycobacteriosis in wildlife species based on traditional descriptive studies and recent molecular applications.

  14. Molecular epidemiology of tuberculosis transmission: Contextualizing the evidence through social network theory.

    PubMed

    Hollm-Delgado, Maria-Graciela

    2009-09-01

    Despite a long-standing recognition that factors such as age, gender, and socioeconomic status play a fundamental role in tuberculosis transmission and susceptibility, few molecular epidemiological studies have fully elucidated the etiological mechanisms by which each of these social factors may influence transmission of the disease. In this paper, we propose that in order to achieve this goal, molecular epidemiology must move towards a more holistic approach for disease transmission, thus enabling social theory to be integrated into molecular epidemiological studies on tuberculosis. We then present a social network model to illustrate how molecular and social epidemiology can be combined to study disease transmission patterns, and provide preliminary molecular epidemiological evidence to support the role of social networks in tuberculosis transmission.

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

    PubMed Central

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

    2014-01-01

    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 in studying cancer cases), but they must utilize non-diseased 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 timepoint (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 regarding disease etiology. However, measures of association calculated in tumor-based case-control studies are prone to over- or under-estimating the relationship between infections and subsequent cancer risk. PMID:25063520

  16. A Prospective Cohort Multicenter Study of Molecular Epidemiology and Phylogenomics of Staphylococcus aureus Bacteremia in Nine Latin American Countries.

    PubMed

    Arias, Cesar A; Reyes, Jinnethe; Carvajal, Lina Paola; Rincon, Sandra; Diaz, Lorena; Panesso, Diana; Ibarra, Gabriel; Rios, Rafael; Munita, Jose M; Salles, Mauro J; Alvarez-Moreno, Carlos; Labarca, Jaime; Garcia, Coralith; Luna, Carlos M; Mejia-Villatoro, Carlos; Zurita, Jeannete; Guzman-Blanco, Manuel; Rodriguez-Noriega, Eduardo; Narechania, Apurva; Rojas, Laura J; Planet, Paul J; Weinstock, George M; Gotuzzo, Eduardo; Seas, Carlos

    2017-10-01

    Staphylococcus aureus is an important pathogen causing a spectrum of diseases ranging from mild skin and soft tissue infections to life-threatening conditions. Bloodstream infections are particularly important, and the treatment approach is complicated by the presence of methicillin-resistant S. aureus (MRSA) isolates. The emergence of new genetic lineages of MRSA has occurred in Latin America (LA) with the rise and dissemination of the community-associated USA300 Latin American variant (USA300-LV). Here, we prospectively characterized bloodstream MRSA recovered from selected hospitals in 9 Latin American countries. All isolates were typed by pulsed-field gel electrophoresis (PFGE) and subjected to antibiotic susceptibility testing. Whole-genome sequencing was performed on 96 MRSA representatives. MRSA represented 45% of all (1,185 S. aureus) isolates. The majority of MRSA isolates belonged to clonal cluster (CC) 5. In Colombia and Ecuador, most isolates (≥72%) belonged to the USA300-LV lineage (CC8). Phylogenetic reconstructions indicated that MRSA isolates from participating hospitals belonged to three major clades. Clade A grouped isolates with sequence type 5 (ST5), ST105, and ST1011 (mostly staphylococcal chromosomal cassette mec [SCCmec] I and II). Clade B included ST8, ST88, ST97, and ST72 strains (SCCmec IV, subtypes a, b, and c/E), and clade C grouped mostly Argentinian MRSA belonging to ST30. In summary, CC5 MRSA was prevalent in bloodstream infections in LA with the exception of Colombia and Ecuador, where USA300-LV is now the dominant lineage. Clonal replacement appears to be a common phenomenon, and continuous surveillance is crucial to identify changes in the molecular epidemiology of MRSA. Copyright © 2017 American Society for Microbiology.

  17. 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.

  18. The role of epidemiology in the era of molecular epidemiology and genomics: Summary of the 2013 AJE-sponsored Society of Epidemiologic Research Symposium.

    PubMed

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

    2013-11-01

    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.

  19. Epidemiological bases and molecular mechanisms linking obesity, diabetes, and cancer.

    PubMed

    Gutiérrez-Salmerón, María; Chocarro-Calvo, Ana; García-Martínez, José Manuel; de la Vieja, Antonio; García-Jiménez, Custodia

    2017-02-01

    The association between diabetes and cancer was hypothesized almost one century ago. Today, a vast number of epidemiological studies support that obese and diabetic populations are more likely to experience tissue-specific cancers, but the underlying molecular mechanisms remain unknown. Obesity, diabetes, and cancer share many hormonal, immune, and metabolic changes that may account for the relationship between diabetes and cancer. In addition, antidiabetic treatments may have an impact on the occurrence and course of some cancers. Moreover, some anticancer treatments may induce diabetes. These observations aroused a great controversy because of the ethical implications and the associated commercial interests. We report an epidemiological update from a mechanistic perspective that suggests the existence of many common and differential individual mechanisms linking obesity and type 1 and 2 diabetes mellitus to certain cancers. The challenge today is to identify the molecular links responsible for this association. Classification of cancers by their molecular signatures may facilitate future mechanistic and epidemiological studies. Copyright © 2016 SEEN. Publicado por Elsevier España, S.L.U. All rights reserved.

  20. 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

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

    PubMed

    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.

  2. Α molecular epidemiological analysis of adenoviruses from excess conjunctivitis cases.

    PubMed

    Balasopoulou, A; Κokkinos, P; Pagoulatos, D; Plotas, P; Makri, O E; Georgakopoulos, C D; Vantarakis, A

    2017-04-24

    Τo perform a molecular epidemiological analysis of viral conjunctivitis among excess conjunctivitis cases recorded at the University Hospital of Patras, Greece, for the period March to June 2012. A structured questionnaire containing demographic and clinical data was developed in order to collect retrospective data on the cases. Eye swab specimens were collected and molecular detection of adenoviruses was performed by nested PCR. Positive results were confirmed by sequencing. To determine the relatedness between the isolated sequences, a phylogenetic analysis was conducted. The epidemiological analysis (including retrospective data) included 231 conjunctivitis cases (47.1% male, and 52.8% female). Based on clinical features 205 of the cases were diagnosed of viral origin (46.3% male and 53.7% female), 4 of bacterial origin (50% male and 50% female) while 22 were undefined conjunctivitis. The outbreak excess cases (included 156 cases) affected all age groups regardless gender predilection. For the positive samples indicated that 29 samples (72.5%) were AdV17, and 5 (12.5%) as AdV54. Molecular analysis could define the cause of viral conjunctivitis, while epidemiological data contributed to the assessment of the risk factors and underlined possible preventive measures. This study is one of the very few on viral conjunctivitis in Greece. This outbreak underscores the need for a national surveillance system for acute infectious conjunctivitis outbreaks. The epidemiological as well as molecular investigation on HAdV ocular infections is rather absent in Greece, which has no surveillance system for viral conjunctivitis.

  3. Nationwide study of the prevalence, characteristics, and molecular epidemiology of extended-spectrum-beta-lactamase-producing Enterobacteriaceae in France.

    PubMed

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

    2008-02-01

    Among 10,872 isolates of Enterobacteriaceae from a nationwide study of 88 French hospitals in 2005, 169 (1.7%) expressed an extended-spectrum beta-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.

  4. [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.

  5. 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.

  6. Evaluation of Whole Genome Mapping as a Fast and Automated Molecular Epidemiological Tool for the Study of Cronobacter spp. in Powdered Infant Formula Processing Facilities.

    PubMed

    Tang, Yanjie; Rasschaert, Geertrui; Yu, Liping; Chilton, Claire; Baert, Leen

    2017-09-01

    Cronobacter has been identified as the causative agent of outbreaks or sporadic cases of meningitis, necrotizing enterocolitis, and septicemia associated with powdered infant formula. Food processing environments may provide a possible contamination route. The purpose of this study was to evaluate whole genome mapping (WGM) as a fast and automated molecular epidemiological method for characterizing Cronobacter spp. in the processing environment. This is the first study indicating the applicability of WGM to Cronobacter. WGM was compared with ribotyping, which is often used as an automated typing tool, and with pulsed-field gel electrophoresis, which is a well-known and highly discriminating tool that is also based on restriction site analysis. The comparison of the three tools was carried out on a subset of Cronobacter isolates collected from 2011 to 2014 through a monitoring program. The performance characteristics of WGM have not yet been described; therefore, in the current study its performance was evaluated based on five criteria: typeability, reproducibility, stability, epidemiological concordance, and the discrimination power. WGM was shown to produce typeable, reproducible, and stable results. With a similar cut-off of 98%, WGM was shown to have a discriminatory power equivalent to pulsed-field gel electrophoresis and higher than ribotyping. Future studies are needed to confirm the indicated cut-off level of 98%.

  7. Epidemiology and molecular biology of Barrett esophagus.

    PubMed

    Casson, Alan G; Williams, Lara; Guernsey, Duane L

    2005-01-01

    Over the past three decades, there has been a marked change in the epidemiology of esophageal malignancy, with an increasing incidence of esophageal adenocarcinoma. The reasons for this are largely unknown and remain controversial, but several lifestyle risk factors have been proposed, including gastroesophageal reflux disease (GERD). It is hypothesized that chronic GERD results in acute mucosal injury, promotes cellular proliferation, and induces specialized columnar metaplasia (Barrett esophagus). Progression of Barrett esophagus to invasive adenocarcinoma is reflected histologically by the metaplasia-dysplasia-carcinoma sequence. Dysplasia is widely regarded as the precursor of invasive cancer, and high-grade dysplasia in Barrett epithelium is frequently associated with esophageal adenocarcinoma. Although several molecular alterations have been described in Barrett esophagus, it is anticipated that relatively few will prove to be clinically useful. To date, biomarkers which currently appear to predict the progression of Barrett esophagus to invasive malignancy include aneuploidy, loss of heterozygosity of 17p (implicating the p53 tumor suppressor gene), and cyclin D1 protein overexpression, and with further validation, will most likely be incorporated into routine clinical practice. It is anticipated that models incorporating objective scores of sociodemographic and lifestyle risk factors (ie, age, gender, body mass index), severity of reflux symptoms, endoscopic and histologic findings, and an assessment of a panel of biomarkers will be developed to further define subsets of patients with Barrett esophagus at increased risk for malignant progression, thereby permitting the development of more rational endoscopic surveillance and screening programs.

  8. [TP53 mutations and molecular epidemiology].

    PubMed

    Otsuka, Kazunori; Ishioka, Chikashi

    2007-05-01

    Tumor suppressor p53 protein is activated by a variety of cellular stresses through several pathways and transactivates its downstream genes, including regulators of cell cycle, apoptosis and DNA repair. The loss of p53 function by TP53 gene mutations therefore fails to activate these genes and is thought to be a critical cause of carcinogenesis and/or tumor progression. TP53 is one of the most frequently mutated genes in human cancer. TP53 mutations are found in about 50% of human cancers, although the frequency of TP53 mutations differs among tumor types. However, the degree of functional disorder of mutant p53 varies according to the type of TP53 mutation. And the effects of p53 on cancer formation and/or progression are influenced by the degree of p53 dysfunction. So it is important to analyze the effects of TP53 mutations carefully according to the oncogenicity of each mutation from the molecular epidemiological point of view. Here, together with some cautions needed for analyzing and interpreting the significance of TP53 gene mutations, we present some examples of the identified specific mutation spectrum and the correlation between the prognosis and TP53 mutation in some cancers.

  9. [Workshop on Molecular Epidemiology of Viral Diseases].

    PubMed

    Gómez, B; Cabrera, L; Arias, C F

    1997-01-01

    A workshop on viral epidemiology was held on September 29, 1995 at the Medical School of the Universidad Nacional Autónoma de Mexico. The aim of this workshop was to promote interaction among scientists working in viral epidemiology. Eighteen scientists from ten institutions presented their experiences and work. General aspects of the epidemiology of meaningful viral diseases in the country were discussed, and lectures presented on the rota, polio, respiratory syncytial, dengue, papiloma, rabies, VIH and hepatitis viruses.

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

    PubMed

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

    2008-05-01

    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.

  11. Molecular epidemiological study of Bacillus anthracis isolated in Mongolia by multiple-locus variable-number tandem-repeat analysis for 8 loci (MLVA-8).

    PubMed

    Okutani, Akiko; Tungalag, Hurelsukh; Boldbaatar, Bazartseren; Yamada, Akio; Tserennorov, Damdindorj; Otgonchimeg, Ishtsog; Erdenebat, Adiya; Otgonbaatar, Dashdavaa; Inoue, Satoshi

    2011-01-01

    The incidence of anthrax, which is caused by Bacillus anthracis, in the human and animal population of Mongolia has increased recently, and control of this infection is a nationwide concern. In this study, 29 isolates obtained from animals and various regions in Mongolia from 2001 to 2007 were analyzed by performing multiple-locus variable-number tandem-repeat analysis for 8 loci (MLVA-8) to understand the genetic relationship between the Mongolian B. anthracis isolates. We found that all the Mongolian isolates can be classified into A3 cluster along with the Japanese and the Chinese B. anthracis isolates. Our data revealed that MLVA-8 is useful for studying the molecular epidemiology of the Mongolian B. anthracis isolates and would help characterize B. anthracis infections in Mongolia.

  12. Molecular pathological epidemiology in diabetes mellitus and risk of hepatocellular carcinoma

    PubMed Central

    Gao, Chun

    2016-01-01

    Molecular pathological epidemiology (MPE) is a multidisciplinary and transdisciplinary study field, which has emerged as an integrated approach of molecular pathology and epidemiology, and investigates the relationship between exogenous and endogenous exposure factors, tumor molecular signatures, and tumor initiation, progression, and response to treatment. Molecular epidemiology broadly encompasses MPE and conventional-type molecular epidemiology. Hepatocellular carcinoma (HCC) is the third most common cause of cancer-associated death worldwide and remains as a major public health challenge. Over the past few decades, a number of epidemiological studies have demonstrated that diabetes mellitus (DM) is an established independent risk factor for HCC. However, how DM affects the occurrence and development of HCC remains as yet unclearly understood. MPE may be a promising approach to investigate the molecular mechanisms of carcinogenesis of DM in HCC, and provide some useful insights for this pathological process, although a few challenges must be overcome. This review highlights the recent advances in this field, including: (1) introduction of MPE; (2) HCC, risk factors, and DM as an established independent risk factor for HCC; (3) molecular pathology, molecular epidemiology, and MPE in DM and HCC; and (4) MPE studies in DM and risk of HCC. More MPE studies are expected to be performed in future and I believe that this field can provide some very important insights on the molecular mechanisms, diagnosis, personalized prevention and treatment for DM and risk of HCC. PMID:27721917

  13. Molecular pathological epidemiology gives clues to paradoxical findings.

    PubMed

    Nishihara, Reiko; VanderWeele, Tyler J; Shibuya, Kenji; Mittleman, Murray A; Wang, Molin; Field, Alison E; Giovannucci, Edward; Lochhead, Paul; Ogino, Shuji

    2015-10-01

    A number of epidemiologic studies have described what appear to be paradoxical associations, where an incongruous relationship is observed between a certain well-established risk factor for disease incidence and favorable clinical outcome among patients with that disease. For example, the "obesity paradox" represents the association between obesity and better survival among patients with a certain disease such as coronary heart disease. Paradoxical observations cause vexing clinical and public health problems as they raise questions on causal relationships and hinder the development of effective interventions. Compelling evidence indicates that pathogenic processes encompass molecular alterations within cells and the microenvironment, influenced by various exogenous and endogenous exposures, and that interpersonal heterogeneity in molecular pathology and pathophysiology exists among patients with any given disease. In this article, we introduce methods of the emerging integrative interdisciplinary field of molecular pathological epidemiology (MPE), which is founded on the unique disease principle and disease continuum theory. We analyze and decipher apparent paradoxical findings, utilizing the MPE approach and available literature data on tumor somatic genetic and epigenetic characteristics. Through our analyses in colorectal cancer, renal cell carcinoma, and glioblastoma (malignant brain tumor), we can readily explain paradoxical associations between disease risk factors and better prognosis among disease patients. The MPE paradigm and approach can be applied to not only neoplasms but also various non-neoplastic diseases where there exists indisputable ubiquitous heterogeneity of pathogenesis and molecular pathology. The MPE paradigm including consideration of disease heterogeneity plays an essential role in advancements of precision medicine and public health.

  14. 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

  15. 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. Copyright © 2009 International Union of Biochemistry and Molecular Biology, Inc.

  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. Molecular epidemiology, phylogeny and evolution of dermatophytes.

    PubMed

    Cafarchia, Claudia; Iatta, Roberta; Latrofa, Maria Stefania; Gräser, Yvonne; Otranto, Domenico

    2013-12-01

    Dermatophytes are fungi that invade and propagate in the keratinized skin of mammals, including humans, often causing contagious infections. The species of medical concern belong to the genera Microsporum, Trichophyton, Epidermophyton (in their anamorphic state) and Arthroderma (in their telomorphic state), which were traditionally identified based on their morphology and biochemical characters. Nonetheless, limitations linked to the differentiation of closely related agents at species and strains level have been recently overcome by molecular studies. Indeed, an accurate identification of dermatophytes is pivotal for the establishment of effective control and prevention programs as well as for determining the most appropriate and effective antifungal therapies to be applied. This article reviews the DNA techniques and the molecular markers used to identify and to characterize dermatophyte species, as well as aspects of their phylogeny and evolution. The applications of typing molecular strain to both basic and applied research (e.g., taxonomy, ecology, typing of infection, antifungal susceptibility) have also been discussed.

  18. 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…

  19. 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…

  20. Molecular fingerprinting of Salmonella typhimurium by IS200-typing as a tool for epidemiological and evolutionary studies.

    PubMed

    Soria, G; Barbé, J; Gibert, I

    1994-01-01

    The aim of this work was to develop and evaluate a molecular typing strategy for Salmonella based on hybridization of chromosomal DNA with two different probes derived from insertion sequence IS200. Probe IS200-TT was specifically constructed for this study as a trimer of a 112 pb TaqI-TaqI fragment of IS200. Among several restriction enzymes evaluated, two were selected: EcoRI, which cuts the insertion sequence in two pieces, each one complementary to one of the probes used, and PstI, a restriction enzyme with no recognition site into IS200. With several combinations of these restrictions enzymes and probes, 43 Salmonella typhimurium strains were analyzed for copy number and location of IS200, as well as reproducibility and stability of the patterns. IS200 types have been shown to be stable, both in strains isolated from different patients implicated in the same salmonellosis outbreak and in strains isolated from the same patient at different times or from different specimens. The discriminatory power of the method has been 0.91 to 0.94. As a comparison, S. typhimurium strains were also ribotyped. Discriminatory power of the ribotypes oscillated between 0.44 and 0.55, depending on the enzyme used, and achieved a 0.78 value when the information obtained with two restriction enzymes was combined. Moreover, IS200 typing was able to differentiate among a group of S. typhimurium strains which were identical by ribotype and enzymatic electrophoretic mobility. These results enable us to conclude that, for the stability, reproducibility and discriminatory power of the patterns generated, IS200 probes can be a very useful tool in the molecular typing of S. typhimurium.

  1. Standardised PCR-based molecular epidemiology of tuberculosis.

    PubMed

    Allix-Béguec, C; Supply, P; Wanlin, M; Bifani, P; Fauville-Dufaux, M

    2008-05-01

    A population-based molecular epidemiology investigation has been undertaken to evaluate tuberculosis transmission and control in the Brussels-Capital Region (Belgium). All tuberculosis cases reported from January 2003 to December 2004 were investigated. In total, 536 Mycobacterium tuberculosis isolates (89% of culture-positive samples) were genotyped by the newly standardised 24 loci-based mycobacterial interspersed repetitive unit-variable number tandem-repeat typing, spoligotyping and IS6110 fingerprinting. Of all the patients, 30% were grouped based on strain clusters, suggesting a transmission index of 20%. An unsuspected outbreak entailing > or = 23 patients was evidenced by molecular typing analysis and confirmed by contact tracing. Foreign-born status accounted for 79% of the studied patients, including 37.9% illegal immigrants and asylum seekers. Among foreign-born patients, asylum seekers and illegal immigrants were significantly less abundant in strain clusters than settled residents. Tuberculosis in the Brussels-Capital Region is a bi-faceted problem, comprising both persisting recent transmission and "imported diseases". Molecular epidemiology based on real-time genotyping techniques has proven invaluable in better understanding tuberculosis transmission. However, it will most efficiently contribute to tuberculosis control when implemented in an integrated public health system.

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

    PubMed

    Snow, Michael

    2011-04-05

    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

  3. The molecular epidemiology of variant CJD

    PubMed Central

    Mackay, Graham A; Knight, Richard SG; Ironside, James W

    2011-01-01

    The emergence of the novel prion diseases bovine spongiform encephalopathy (BSE) and, subsequently, variant Creutzfeldt-Jakob disease (vCJD) in epidemic forms has attracted much scientific attention. The oral transmission of these disorders, the causative relationship of vCJD to BSE and the resistance of the transmissible agents in both disorders to conventional forms of decontamination has caused great public health concern. The size of the still emerging vCJD epidemic is thankfully much lower than some early published estimates. This paper reviews current knowledge of the factors that influence the development of vCJD: the properties of the infectious agent; the route of inoculation and individual susceptibility factors. The current epidemiological data are reviewed, along with relevant animal transmission studies. In terms of genetic susceptibility, the best characterised is the common single nucleotide polymorphism at codon 129 of prion protein gene. Current biomarkers and future areas of research will be discussed. These issues are important in informing precautionary measures and the ongoing monitoring of vCJD. PMID:21915360

  4. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. 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.

  6. 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.

  7. 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

  8. Molecular epidemiology of antimicrobial resistance in veterinary medicine: where do we go?

    PubMed

    Boerlin, Patrick

    2004-06-01

    Molecular epidemiology allows us to trace specific microorganisms and mobile genetic elements and to assess their epidemiological and evolutionary relationships. Examples of molecular epidemiology investigations in veterinary hospitals are discussed. They demonstrate the great similarities with the situation in human medicine and the potential usefulness of molecular epidemiology in our fight against antimicrobial resistance and nosocomial infections in veterinary hospitals. A broad knowledge of the diversity of antimicrobial resistance determinants in some major groups of pathogens and commensals from animals such as Enterobacteriaceae, Pasteurellaceae, enterococci and staphylococci is emerging. However, there are important gaps in this knowledge, which are discussed here. Many more molecular epidemiology studies will be necessary to understand and follow the evolution of the problem in veterinary medicine and agriculture on a global scale. To be able to build useful surveillance programs and reliable epidemiological models, and to identify critical intervention points, we need to improve our understanding of antimicrobial resistance at the animal and farm levels. Studies assessing the dynamics of bacterial populations and of resistance determinants at these levels are desperately needed. Understanding the relationships between antimicrobial resistance, colonization factors, and virulence also represents a major issue for which molecular epidemiology investigations will be needed.

  9. 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

  10. Vitamin D and Colorectal Cancer: Molecular, Epidemiological, and Clinical Evidence

    PubMed Central

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

    2016-01-01

    In many cells throughout the body, vitamin D is converted into its active form calcitriol, and binds to vitamin D receptor (VDR), which functions as a transcription factor to regulate various biological processes including cellular differentiation and immune response. Vitamin D metabolizing enzymes (including CYP24A1 and CYP27B1) and VDR play major roles in exerting and regulating effects of vitamin D. Preclinical and epidemiological studies provide evidence for anticancer effects of vitamin D (in particular, against colorectal cancer), though clinical trials have yet to prove its benefit. Additionally, 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. Here 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

  11. Molecular epidemiology of Mycobacterium bovis: usefulness in international trade.

    PubMed

    Milian-Suazo, Feliciano; Harris, Beth; Arriaga Díaz, Camila; Romero Torres, Cecilia; Stuber, Tod; Alvarez Ojeda, Genoveva; Morales Loredo, Alberto; Perez Soria, Martina; Payeur, Janet B

    2008-11-17

    Tuberculosis (TB) represents a barrier for free trade of livestock between Mexico and the United States of America (US). In spite of efforts from Mexico to export TB-free animals, some of those found with TB lesions in slaughterhouses in the US are traced back to that country. Therefore, the purpose of this study was to determine, through molecular epidemiology, the most probable source of infection for cattle found with TB lesions in the US. Ninety M. bovis isolates, 50 from Mexico obtained from cattle in 8 different states, and 40 from the US from cattle, deer, elk and feral pigs from 7 different states were included in the study. All samples were analyzed in both laboratories, Mexico and the US, following the same protocol for molecular analysis by spoligotyping. Twenty-seven clusters, ranging from 1 to 18 genetically similar strains were found. Some clustering by country was observed, strains from cattle and deer in Michigan in the US fell into the same cluster, suggesting transmission between species. These results, combined with epidemiological information suggest that despite of the possibility that some animals with lesions in the US come from Mexico as false negatives, the US has its own source of infection, must probably in dairy cattle and wildlife. Genetic diversity of isolates from Mexico was larger than that in the US, which could be a consequence of the endemic status of the disease and the indiscriminate movement of animals between regions.

  12. Molecular Epidemiology of Gastric Cancer: Current Status and Future Prospects

    PubMed Central

    Hu, Zhibin; Ajani, Jaffer A.; Wei, Qingyi

    2007-01-01

    Gene-environment interaction appears to contribute to the etiology of gastric cancer, as suggested by the varying geographic patterns of gastric cancer incidence. Even in areas with a high rate Helicobacter pylori (H. pylori) infection, only a small proportion of infected individuals develop gastric cancer. It is likely that genetic factors, particularly relatively common genetic variants, such as single nucleotide polymorphisms (SNPs), may modulate the effects of environmental risk factors by regulating multiple biologic pathways involved in gastric carcinogenesis. Thus, common genetic variants can pose a substantial influence on the population attributable risk, even though the absolute risk associated with each of these variants may be low. Remarkable progress has been made in the field of molecular epidemiology, but it appears that an initial view on the magnitude of the effects of inherited variants was overestimated. Nevertheless, evidence suggests that genetic variants may contribute to the etiology of gastric cancer, particularly those SNPs in genes that are involved in inflammatory response, metabolism of chemical carcinogens, DNA repair, and tumor suppression. Although previous molecular epidemiologic studies of potentially functional polymorphisms in candidate genes and gastric cancer susceptibility lack consistency, they have advanced our knowledge of the role of genetic susceptibility in the etiology of gastric cancer. Future, welldesigned large population-based studies will validate current findings and provide the rationale for identifying at-risk subpopulations for primary prevention of gastric cancer. PMID:19262698

  13. Epidemiologic studies of microwave effects

    SciTech Connect

    Silverman, C.

    1980-01-01

    Presented is a selective review of human epidemiological studies and related information concerning biological and health effects of microwave (MW) radiation. Two unpublished studies of MW effects are discussed: a study of U.S. Navy personnel occupationally exposed to radar, and a study of U.S. Embassy personnel in Moscow. MW effects in the following categories are discussed: ocular effects, nervous and behavioral effects, congenital anomalies, and cancer. Areas for future research are outlined.

  14. Molecular Epidemiology of Female Lung Cancer

    PubMed Central

    Yim, Seon-Hee; Chung, Yeun-Jun

    2011-01-01

    Lung cancer is still a leading cause of cancer mortality in the world. The incidence of lung cancer in developed countries started to decrease mainly due to global anti-smoking campaigns. However, the incidence of lung cancer in women has been increasing in recent decades for various reasons. Furthermore, since the screening of lung cancer is not as yet very effective, clinically applicable molecular markers for early diagnosis are much required. Lung cancer in women appears to have differences compared with that in men, in terms of histologic types and susceptibility to environmental risk factors. This suggests that female lung cancer can be derived by carcinogenic mechanisms different from those involved in male lung cancer. Among female lung cancer patients, many are non-smokers, which could be studied to identify alternative carcinogenic mechanisms independent from smoking-related ones. In this paper, we reviewed molecular susceptibility markers and genetic changes in lung cancer tissues observed in female lung cancer patients, which have been validated by various studies and will be helpful to understand the tumorigenesis of lung cancer. PMID:24212786

  15. Molecular Pathological Epidemiology Gives Clues to Paradoxical Findings

    PubMed Central

    Nishihara, Reiko; VanderWeele, Tyler J.; Shibuya, Kenji; Mittleman, Murray A.; Wang, Molin; Field, Alison E.; Giovannucci, Edward; Lochhead, Paul; Ogino, Shuji

    2015-01-01

    A number of epidemiologic studies have described what appear to be paradoxical associations, where an incongruous relationship is observed between a certain well-established risk factor for disease incidence and favorable clinical outcome among patients with that disease. For example, the “obesity paradox” represents the association between obesity and better survival among patients with a certain disease such as coronary heart disease. Paradoxical observations cause vexing clinical and public health problems as they raise questions on causal relationships and hinder the development of effective interventions. Compelling evidence indicates that pathogenic processes encompass molecular alterations within cells and the microenvironment, influenced by various exogenous and endogenous exposures, and that interpersonal heterogeneity in molecular pathology and pathophysiology exists among patients with any given disease. In this article, we introduce methods of the emerging integrative interdisciplinary field of molecular pathological epidemiology (MPE), which is founded on the unique disease principle and disease continuum theory. We analyze and decipher apparent paradoxical findings, utilizing the MPE approach and available literature data on tumor somatic genetic and epigenetic characteristics. Through our analyses in colorectal cancer, renal cell carcinoma, and glioblastoma (malignant brain tumor), we can readily explain paradoxical associations between disease risk factors and better prognosis among disease patients. The MPE paradigm and approach can be applied to not only neoplasms but also various non-neoplastic diseases where there exists indisputable ubiquitous heterogeneity of pathogenesis and molecular pathology. The MPE paradigm including consideration of disease heterogeneity plays an essential role in advancements of precision medicine and public health. PMID:26445996

  16. Antimicrobial susceptibility and molecular epidemiology of Neisseria gonorrhoeae in Germany.

    PubMed

    Horn, Nicole Nari; Kresken, Michael; Körber-Irrgang, Barbara; Göttig, Stephan; Wichelhaus, Cornelia; Wichelhaus, Thomas A

    2014-07-01

    Antimicrobial drug resistance in Neisseria gonorrhoeae has become an increasing public health problem. Hence, surveillance of resistance development is of crucial importance to implement adequate treatment guidelines. Data on the spread of antibiotic resistance among gonococcal isolates in Germany, however, is scarce. In a resistance surveillance study conducted by the Paul Ehrlich Society for Chemotherapy between October 2010 and December 2011, 23 laboratories all over Germany were requested to send N. gonorrhoeae isolates to the study laboratory in Frankfurt am Main. Species verification was performed biochemically using ApiNH and with Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). Antimicrobial susceptibility testing was performed using the Etest method. For molecular epidemiological analysis, N. gonorrhoeae strains were genotyped by means of N. gonorrhoeae multi-antigen sequence typing. A total of 213 consecutive gonococcal isolates were analyzed in this nationwide study. Applying EUCAST breakpoints, high resistance rates were found for ciprofloxacin (74%) and tetracycline (41%). Penicillin non-susceptibility was detected in 80% of isolates. The rate of azithromycin resistance was 6%, while all strains were susceptible to spectinomycin, cefixime, and ceftriaxone. Molecular typing of gonococcal isolates revealed a great heterogeneity of 99 different sequence types (ST), but ST1407 predominated (n=39). This is the first comprehensive German multi-centre surveillance study on antibiotic susceptibility and molecular epidemiology of N. gonorrhoeae with implications for antibiotic choice for treatment of gonorrhoea. The World Health Organization supports the concept that an efficacious treatment of gonorrhoea results in at least 95% of infections being cured. Accordingly, as spectinomycin is not available on the German market, only the third generation cephalosporins cefixime and ceftriaxone are regarded as valuable drugs

  17. Molecular epidemiological study of feline coronavirus strains in Japan using RT-PCR targeting nsp14 gene.

    PubMed

    Tanaka, Yoshikazu; Sasaki, Takashi; Matsuda, Ryo; Uematsu, Yosuke; Yamaguchi, Tomohiro

    2015-03-11

    Feline infectious peritonitis is a fatal disease of cats caused by infection with feline coronavirus (FCoV). For detecting or genotyping of FCoV, some RT-PCR plus nested PCR techniques have been reported previously. However, referring to the whole genome sequences (WGSs) registered at NCBI, there are no detection methods that can tolerate the genetic diversity among FCoV population. In addition, the quasispecies nature of FCoV, which consists of heterogeneous variants, has been also demonstrated; thus, a universal method for heteropopulations of FCoV variants in clinical specimens is desirable. To develop an RT-PCR method for detection and genotyping of FCoV, we performed comparative genome analysis using WGSs of 32 FCoV, 7 CCoV and 5 TGEV strains obtained from NCBI. As the PCR target, we focused on the nsp14 coding region, which is highly conserved and phylogenetically informative, and developed a PCR method targeting nsp14 partial sequences. Among 103 ascites, 45 pleural effusion and 214 blood specimens from clinically ill cats, we could detect FCoV in 55 (53.4%), 14 (31.1%) and 19 (8.9%) specimens using the present method. Direct sequencing of PCR products and phylogenetic analysis allowed discrimination between type I- and II-FCoV serotypes. Our nsp14 amino acid sequence typing (nsp14 aa ST) showed that the FCoV clone with sequence type (ST) 42, which was the most predominant genotype of WGS strains, was prevalent in domestic cats in Japan. Our nsp14 PCR scheme will contribute to virus detection, epidemiology and ecology of FCoV strains.

  18. Factors Associated with Differences between Conventional Contact Tracing and Molecular Epidemiology in Study of Tuberculosis Transmission and Analysis in the City of Barcelona, Spain ▿

    PubMed Central

    Borrell, Sònia; Español, Montserrat; Orcau, Àngels; Tudó, Griselda; March, Francesca; Caylà, Joan A.; Jansà, Josep Maria; Alcaide, Fernando; Martín-Casabona, Núria; Salvadó, Margarita; Martínez, José Antonio; Vidal, Rafael; Sánchez, Francesca; Altet, Neus; Coll, Pere; González-Martín, Juliàn

    2009-01-01

    The aim of this study was to analyze the factors associated with conventional contact tracing (CCT) and molecular epidemiology (ME) methods in assessing tuberculosis (TB) transmission, comparing the populations studied and the epidemiological links established by both methods. Data were obtained from TB case and CCT registries, and ME was performed using IS6110-based restriction fragment length polymorphism (RFLP) analysis and mycobacterial interspersed repetitive unit 12 (MIRU12) typing as a secondary typing method. During two years (2003 and 2004), 892 cases of TB were reported, of which 687 (77%) were confirmed by culture. RFLP analysis was performed with 463 (67.4%) of the 687 isolated strains, and MIRU12 types in 75 strains were evaluated; 280 strains (60.5%) had a unique RFLP pattern, and 183 (39.5%) shared patterns, grouping into 65 clusters. CCT of 613 (68.7%) of 892 cases detected 44 clusters involving 101 patients. The results of both CCT and ME methods yielded 96 clusters involving 255 patients. The household link was the one most frequently identified by CCT (corresponding to 80.7% of the cases clustered by this method), whereas nonhousehold and unknown links were associated with 94.1% of the strains clustered by ME. When both methods were used in 351 cases (39.3%), they showed the same results in 214 cases (61%). Of the remainder, 106 (30.2%) were clustered only by ME, 19 (5.5%) were clustered only by CCT, and 12 (3.4%) were clustered by both methods but into different clusters. Patients with factors potentially associated with social problems were less frequently studied by CCT (P = 0.002), whereas patients of <15 years of age, most with negative cultures, were less frequently studied by ME (P = 0.005). Significant differences in the populations studied by ME versus CCT were observed, possibly explaining the scarce correlation found between the results of these methods. Moreover, ME allowed the detection of nonhousehold contact relationships, whereas

  19. [Molecular epidemiology of cattle and human tuberculosis in Mexico].

    PubMed

    Pérez-Guerrero, Laura; Milián-Suazo, Feliciano; Arriaga-Díaz, Camila; Romero-Torres, Cecilia; Escartín-Chávez, Minerva

    2008-01-01

    The purpose of the study was to determine the role of bovine TB in cases of human TB. Two-hundred and fifty-five samples from symptomatic patients were included in the study. All samples were cultured in Stonebrink and Lowënstein-Jensen media and analyzed using a nested PCRMPB70. The molecular analysis was performed by spoligotyping. From 255 samples, 74 were PCR-positive and 20 were culture-positive. From 94 samples positive to PCR or to isolation, 66 (70%) showed a spoligotype compatible with M. tuberculosis, and 13 (13.8%) with M. bovis. Four fingerprints of M. bovis from humans were identical to the fingerprints of M. bovis from cattle in the same region. Our study shows that M. bovis plays an important role in the epidemiology of TB in humans and that TB in cattle represents a risk to public health.

  20. Sampling designs for HIV molecular epidemiology with application to Honduras.

    PubMed

    Shepherd, Bryan E; Rossini, Anthony J; Soto, Ramon Jeremias; De Rivera, Ivette Lorenzana; Mullins, James I

    2005-11-01

    Proper sampling is essential to characterize the molecular epidemiology of human immunodeficiency virus (HIV). HIV sampling frames are difficult to identify, so most studies use convenience samples. We discuss statistically valid and feasible sampling techniques that overcome some of the potential for bias due to convenience sampling and ensure better representation of the study population. We employ a sampling design called stratified cluster sampling. This first divides the population into geographical and/or social strata. Within each stratum, a population of clusters is chosen from groups, locations, or facilities where HIV-positive individuals might be found. Some clusters are randomly selected within strata and individuals are randomly selected within clusters. Variation and cost help determine the number of clusters and the number of individuals within clusters that are to be sampled. We illustrate the approach through a study designed to survey the heterogeneity of subtype B strains in Honduras.

  1. Molecular epidemiological study of Arctic rabies virus isolates from Greenland and comparison with isolates from throughout the Arctic and Baltic regions.

    PubMed

    Mansfield, K L; Racloz, V; McElhinney, L M; Marston, D A; Johnson, N; Rønsholt, L; Christensen, L S; Neuvonen, E; Botvinkin, A D; Rupprecht, C E; Fooks, A R

    2006-03-01

    We report a molecular epidemiological study of rabies in Arctic countries by comparing a panel of novel Greenland isolates to a larger cohort of viral sequences from both Arctic and Baltic regions. Rabies virus isolates originating from wildlife (Arctic/red foxes, raccoon-dogs and reindeer), from domestic animals (dogs/cats) and from two human cases were investigated. The resulting 400 bp N-gene sequences were compared with isolates representing neighbouring Arctic or Baltic countries from North America, the former Soviet Union and Europe. Phylogenetic analysis demonstrated similarities between sequences from the Arctic and Arctic-like viruses, which were distinct from rabies isolates originating in the Baltic region of Europe, the Steppes in Russia and from North America. The Arctic-like group consist of isolates from India, Pakistan, southeast Siberia and Japan. The Arctic group was differentiated into two lineages, Arctic 1 and Arctic 2, with good bootstrap support. Arctic 1 is mainly comprised of Canadian isolates with a single fox isolate from Maine in the USA. Arctic 2 was further divided into sub-lineages: 2a/2b. Arctic 2a comprises isolates from the Arctic regions of Yakutia in northeast Siberia and Alaska. Arctic 2b isolates represent a biotype, which is dispersed throughout the Arctic region. The broad distribution of rabies in the Arctic regions including Greenland, Canada and Alaska provides evidence for the movement of rabies across borders.

  2. A molecular epidemiologic study of thalassemia using newborns' cord blood in a multiracial Asian population in Singapore: results and recommendations for a population screening program.

    PubMed

    Kham, S K; Yin, Shirley Kham Kow; Quah, Thuan Chong; Loong, Ai Mei; Tan, Poh Lin; Fraser, Angus; Chong, S S; Chuan, Samuel Chong Siong; Yeoh, A E; Eng-Juh, Allen Yeoh

    2004-12-01

    DNA technology provides a new avenue to perform neonatal screening tests for single-gene diseases in populations of high frequency. Thalassemia is one of the high-frequency single-gene disorders affecting Singapore and many countries in the malaria belt. The authors explored the feasibility of using PCR-based diagnostic screening on 1,116 unselected sequential cord blood samples for neonatal screening. The cord blood samples were screened for the most common reported alpha- and beta-thalassemia mutations in each ethnic group (Chinese, Malays, and Indians) in a multiracial population. The carrier frequency for alpha-thalassemia mutations was about 6.4% in the Chinese (alpha deletions = 3.9%, alpha deletions = 2.5%), 4.8% in Malays, and 5.2% in Indians. Only alpha deletions were observed in the Chinese. The carrier frequency for beta-thalassemia mutations was 2.7% in the Chinese, 6.3% in Malays, and 0.7% in Indians. Extrapolating to the population distribution of Singapore, the authors found a higher overall expected carrier frequency for alpha- and beta-thalassemia mutations of 9% compared with a previous population study of 6% by phenotype. The highly accurate results make this molecular epidemiologic screening an ideal method to screen for and prevent severe thalassemia in high-risk populations.

  3. Molecular epidemiology of rotaviruses in India.

    PubMed

    Broor, Shobha; Ghosh, Dhrubaa; Mathur, Purva

    2003-08-01

    Rotaviruses cause an estimated 140 million cases of gastroenteritis and 800,000 deaths in children between the ages of 6 months to 2 yr in developing countries. In India, one of every 250 children or about 100-150,000 children die of rotavirus diarrhoea each year. The prevalence of rotavirus diarrhoea in India has been found to vary from 5-71 per cent in hospitalized children <5 yr of age with acute gastroenteritis. The seasonal variation of rotavirus diarrhoea in India varies in different geographical regions with high incidence in winter months at low relative humidity in north India. The distinctive features of rotavirus infection in India include the occurrence of severe disease at an early age and common neonatal rotavirus infections which are often asymptomatic. Rotavirus shows genetic and antigenic diversity in terms of subgroup, electropherotypes and G and P serotypes/genotypes. There are a few studies in terms of prevalence of different antigenic and genetic variants from various regions of India. In most studies on subgroup distribution from India a higher prevalence of subgroup II was reported compared to subgroup I. Electropherotyping has also demonstrated that a number of multiple electropherotypes co-circulate at one time in a particular community leading to extensive genomic variation and the appearance of new strains which may become the predominant electropherotype during the peak season. The most common G types reported from India are G1 and G2 and P types are P[4] and P[8]. A significant number of children also have mixed rotavirus infections. G9 strains are also quite commonly seen in Indian children. In addition P6 strains of probable bovine origin have been reported from India. A novel neonatal strain P type 11 human rotavirus (116 E) was isolated from neonates in Delhi, the VP4 of which was closely related to the bovine serotype G10P[11] strain B223 and VP7 was closely related to the human serotype G9 strain. Another neonatal strain G10P[11

  4. Multicenter, International Study of MIC/MEC Distributions for Definition of Epidemiological Cutoff Values for Sporothrix Species Identified by Molecular Methods.

    PubMed

    Espinel-Ingroff, A; Abreu, D P B; Almeida-Paes, R; Brilhante, R S N; Chakrabarti, A; Chowdhary, A; Hagen, F; Córdoba, S; Gonzalez, G M; Govender, N P; Guarro, J; Johnson, E M; Kidd, S E; Pereira, S A; Rodrigues, A M; Rozental, S; Szeszs, M W; Ballesté Alaniz, R; Bonifaz, A; Bonfietti, L X; Borba-Santos, L P; Capilla, J; Colombo, A L; Dolande, M; Isla, M G; Melhem, M S C; Mesa-Arango, A C; Oliveira, M M E; Panizo, M M; Pires de Camargo, Z; Zancope-Oliveira, R M; Meis, J F; Turnidge, J

    2017-10-01

    Clinical and Laboratory Standards Institute (CLSI) conditions for testing the susceptibilities of pathogenic Sporothrix species to antifungal agents are based on a collaborative study that evaluated five clinically relevant isolates of Sporothrixschenckii sensu lato and some antifungal agents. With the advent of molecular identification, there are two basic needs: to confirm the suitability of these testing conditions for all agents and Sporothrix species and to establish species-specific epidemiologic cutoff values (ECVs) or breakpoints (BPs) for the species. We collected available CLSI MICs/minimal effective concentrations (MECs) of amphotericin B, five triazoles, terbinafine, flucytosine, and caspofungin for 301 Sporothrix schenckii sensu stricto, 486 S. brasiliensis, 75 S. globosa, and 13 S. mexicana molecularly identified isolates. Data were obtained in 17 independent laboratories (Australia, Europe, India, South Africa, and South and North America) using conidial inoculum suspensions and 48 to 72 h of incubation at 35°C. Sufficient and suitable data (modal MICs within 2-fold concentrations) allowed the proposal of the following ECVs for S. schenckii and S. brasiliensis, respectively: amphotericin B, 4 and 4 μg/ml; itraconazole, 2 and 2 μg/ml; posaconazole, 2 and 2 μg/ml; and voriconazole, 64 and 32 μg/ml. Ketoconazole and terbinafine ECVs for S. brasiliensis were 2 and 0.12 μg/ml, respectively. Insufficient or unsuitable data precluded the calculation of ketoconazole and terbinafine (or any other antifungal agent) ECVs for S. schenckii, as well as ECVs for S. globosa and S. mexicana These ECVs could aid the clinician in identifying potentially resistant isolates (non-wild type) less likely to respond to therapy. Copyright © 2017 American Society for Microbiology.

  5. Proceedings of the third international molecular pathological epidemiology (MPE) meeting.

    PubMed

    Campbell, Peter T; Rebbeck, Timothy R; Nishihara, Reiko; Beck, Andrew H; Begg, Colin B; Bogdanov, Alexei A; Cao, Yin; Coleman, Helen G; Freeman, Gordon J; Heng, Yujing J; Huttenhower, Curtis; Irizarry, Rafael A; Kip, N Sertac; Michor, Franziska; Nevo, Daniel; Peters, Ulrike; Phipps, Amanda I; Poole, Elizabeth M; Qian, Zhi Rong; Quackenbush, John; Robins, Harlan; Rogan, Peter K; Slattery, Martha L; Smith-Warner, Stephanie A; Song, Mingyang; VanderWeele, Tyler J; Xia, Daniel; Zabor, Emily C; Zhang, Xuehong; Wang, Molin; Ogino, Shuji

    2017-02-01

    Molecular pathological epidemiology (MPE) is a transdisciplinary and relatively new scientific discipline that integrates theory, methods, and resources from epidemiology, pathology, biostatistics, bioinformatics, and computational biology. The underlying objective of MPE research is to better understand the etiology and progression of complex and heterogeneous human diseases with the goal of informing prevention and treatment efforts in population health and clinical medicine. Although MPE research has been commonly applied to investigating breast, lung, and colorectal cancers, its methodology can be used to study most diseases. Recent successes in MPE studies include: (1) the development of new statistical methods to address etiologic heterogeneity; (2) the enhancement of causal inference; (3) the identification of previously unknown exposure-subtype disease associations; and (4) better understanding of the role of lifestyle/behavioral factors on modifying prognosis according to disease subtype. Central challenges to MPE include the relative lack of transdisciplinary experts, educational programs, and forums to discuss issues related to the advancement of the field. To address these challenges, highlight recent successes in the field, and identify new opportunities, a series of MPE meetings have been held at the Dana-Farber Cancer Institute in Boston, MA. Herein, we share the proceedings of the Third International MPE Meeting, held in May 2016 and attended by 150 scientists from 17 countries. Special topics included integration of MPE with immunology and health disparity research. This meeting series will continue to provide an impetus to foster further transdisciplinary integration of divergent scientific fields.

  6. A bibliometric analysis of scientific production in cancer molecular epidemiology.

    PubMed

    Ugolini, Donatella; Puntoni, Riccardo; Perera, Frederica P; Schulte, Paul A; Bonassi, Stefano

    2007-08-01

    The main purpose of this research was to compare the scientific production in the field of cancer molecular epidemiology among countries and to evaluate the publication trend between 1995 and 2004. A bibliometric study was carried out searching the PubMed database with a combined search strategy based on the keywords listed in the medical subject headings and a free text search. Only articles from a representative subset of 92 journals--accounting for 80% of papers identified--were selected for the analysis, and the resulting 13,240 abstracts were manually checked according to a list of basic inclusion criteria. The study evaluated the number of publications and the impact factor (mean and sum), absolute and normalized by country population and gross domestic product. A total of 3,842 citations were finally selected for the analysis. Thirty-seven percent came from the European Union (UK, Germany, Italy, France and Sweden ranking at the top), 31.6% from USA and 9.7% from Japan. The highest mean impact factor was reported for Canada (6.3), USA (5.9), Finland (5.8) and UK (5.2). Finland, Sweden and Israel had the best ratio between scientific production and available resources. 'Genetic polymorphism, glutathione transferase, breast neoplasm, risk factors, case-control studies and polymerase chain reaction' were the most used keywords in each of the subgroups evaluated, although inclusion criteria may have privileged studies dealing with exogenous carcinogens. Cancer molecular epidemiology is an expanding area attracting an increasing interest. The identification of an operative definition is a necessary condition to give to this discipline a unique scientific identity.

  7. 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

  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

    2016-09-09

    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.

  9. Molecular epidemiology of Legionella pneumophila serogroup 1.

    PubMed Central

    van Ketel, R J; ter Schegget, J; Zanen, H C

    1984-01-01

    The DNA of patient and environmental isolates of Legionella pneumophila serogroup 1 was analyzed by restriction endonuclease cleavage. The electrophoretic patterns of the DNA digests of isolates from a group of patients with Legionnaires disease acquired in a hospital were indistinguishable from one another and were identical to the DNA pattern of a strain isolated from the hot water supply of the hospital. On the other hand, they were easily differentiated from strains isolated from patients and hot water supplies in other hospitals in the same city. The homogeneity of populations of L. pneumophila serogroup 1 colonizing plumbing systems was also investigated by DNA restriction endonuclease analysis in three hospitals. We distinguished two subtypes in one hospital; the two other hospitals had homogeneous populations. Restriction endonuclease digest analysis of L. pneumophila serogroup 1 DNA enables subtyping and appears to be a useful method for examining the epidemiology of outbreaks of Legionnaires disease. Images PMID:6092423

  10. Molecular epidemiology of HIV transmission in a dental practice.

    PubMed

    Ou, C Y; Ciesielski, C A; Myers, G; Bandea, C I; Luo, C C; Korber, B T; Mullins, J I; Schochetman, G; Berkelman, R L; Economou, A N

    1992-05-22

    Human immunodeficiency virus type 1 (HIV-1) transmission from infected patients to health-care workers has been well documented, but transmission from an infected health-care worker to a patient has not been reported. After identification of an acquired immunodeficiency syndrome (AIDS) patient who had no known risk factors for HIV infection but who had undergone an invasive procedure performed by a dentist with AIDS, six other patients of this dentist were found to be HIV-infected. Molecular biologic studies were conducted to complement the epidemiologic investigation. Portions of the HIV proviral envelope gene from each of the seven patients, the dentist, and 35 HIV-infected persons from the local geographic area were amplified by polymerase chain reaction and sequenced. Three separate comparative genetic analyses--genetic distance measurements, phylogenetic tree analysis, and amino acid signature pattern analysis--showed that the viruses from the dentist and five dental patients were closely related. These data, together with the epidemiologic investigation, indicated that these patients became infected with HIV while receiving care from a dentist with AIDS.

  11. Seroepidemiology and Molecular Epidemiology of Enterovirus 71 in Russia

    PubMed Central

    Akhmadishina, Ludmila V.; Eremeeva, Tatiana P.; Trotsenko, Olga E.; Ivanova, Olga E.; Mikhailov, Mikhail I.; Lukashev, Alexander N.

    2014-01-01

    Enterovirus 71 (EV71) is an emerging human pathogen causing massive epidemics of hand, foot and mouth disease with severe neurological complications in Asia. EV71 also circulates in Europe, however it does not cause large outbreaks. The reason for distinct epidemiological patterns of EV71 infection in Europe and Asia and the risk of EV71 epidemic in Europe and Russia remain unknown. Seroepidemiology of EV71 and molecular epidemiology of occasional EV71 isolates were studied to explore circulation of EV71 in Russia. In six regions of Russian Federation, seroprevalence of EV71 in sera collected in 2008 ranged from 5% to 20% in children aged 1–2 years and from 19% to 83% in children aged 3–5 years. The seroprevalence among elder children was significantly higher (41–83% vs. 19–27%) in Asian regions of Russia. EV71 strains identified in Russia in 2001–2011 belonged to subtypes C1 and C2, while genotype C4 that was causing epidemics in Asia since 1998 emerged in 2009 and became dominant in 2013. PMID:24819617

  12. Seroepidemiology and molecular epidemiology of enterovirus 71 in Russia.

    PubMed

    Akhmadishina, Ludmila V; Eremeeva, Tatiana P; Trotsenko, Olga E; Ivanova, Olga E; Mikhailov, Mikhail I; Lukashev, Alexander N

    2014-01-01

    Enterovirus 71 (EV71) is an emerging human pathogen causing massive epidemics of hand, foot and mouth disease with severe neurological complications in Asia. EV71 also circulates in Europe, however it does not cause large outbreaks. The reason for distinct epidemiological patterns of EV71 infection in Europe and Asia and the risk of EV71 epidemic in Europe and Russia remain unknown. Seroepidemiology of EV71 and molecular epidemiology of occasional EV71 isolates were studied to explore circulation of EV71 in Russia. In six regions of Russian Federation, seroprevalence of EV71 in sera collected in 2008 ranged from 5% to 20% in children aged 1-2 years and from 19% to 83% in children aged 3-5 years. The seroprevalence among elder children was significantly higher (41-83% vs. 19-27%) in Asian regions of Russia. EV71 strains identified in Russia in 2001-2011 belonged to subtypes C1 and C2, while genotype C4 that was causing epidemics in Asia since 1998 emerged in 2009 and became dominant in 2013.

  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. Dengue in Latin America: Systematic Review of Molecular Epidemiological Trends

    PubMed Central

    Ramos-Castañeda, José; Barreto dos Santos, Flavia; Martínez-Vega, Ruth; Galvão de Araujo, Josélio Maria; Joint, Graham; Sarti, Elsa

    2017-01-01

    Dengue, the predominant arthropod-borne viral disease affecting humans, is caused by one of four distinct serotypes (DENV-1, -2, -3 or -4). A literature analysis and review was undertaken to describe the molecular epidemiological trends in dengue disease and the knowledge generated in specific molecular topics in Latin America, including the Caribbean islands, from 2000 to 2013 in the context of regional trends in order to identify gaps in molecular epidemiological knowledge and future research needs. Searches of literature published between 1 January 2000 and 30 November 2013 were conducted using specific search strategies for each electronic database that was reviewed. A total of 396 relevant citations were identified, 57 of which fulfilled the inclusion criteria. All four dengue virus serotypes were present and co-circulated in many countries over the review period (with the predominance of individual serotypes varying by country and year). The number of countries in which more than one serotype circulated steadily increased during the period under review. Molecular epidemiology data were found for Argentina, Bolivia, Brazil, the Caribbean region, Colombia, Ecuador, Mexico and Central America, Paraguay, Peru and Venezuela. Distinct lineages with different dynamics were found in each country, with co-existence, extinction and replacement of lineages occurring over the review period. Despite some gaps in the literature limiting the possibility for comparison, our review has described the molecular epidemiological trends of dengue infection. However, several gaps in molecular epidemiological information across Latin America and the Caribbean were identified that provide avenues for future research; in particular, sequence determination of the dengue virus genome is important for more precise phylogenetic classification and correlation with clinical outcome and disease severity. PMID:28068335

  15. Dengue in Latin America: Systematic Review of Molecular Epidemiological Trends.

    PubMed

    Ramos-Castañeda, José; Barreto Dos Santos, Flavia; Martínez-Vega, Ruth; Galvão de Araujo, Josélio Maria; Joint, Graham; Sarti, Elsa

    2017-01-01

    Dengue, the predominant arthropod-borne viral disease affecting humans, is caused by one of four distinct serotypes (DENV-1, -2, -3 or -4). A literature analysis and review was undertaken to describe the molecular epidemiological trends in dengue disease and the knowledge generated in specific molecular topics in Latin America, including the Caribbean islands, from 2000 to 2013 in the context of regional trends in order to identify gaps in molecular epidemiological knowledge and future research needs. Searches of literature published between 1 January 2000 and 30 November 2013 were conducted using specific search strategies for each electronic database that was reviewed. A total of 396 relevant citations were identified, 57 of which fulfilled the inclusion criteria. All four dengue virus serotypes were present and co-circulated in many countries over the review period (with the predominance of individual serotypes varying by country and year). The number of countries in which more than one serotype circulated steadily increased during the period under review. Molecular epidemiology data were found for Argentina, Bolivia, Brazil, the Caribbean region, Colombia, Ecuador, Mexico and Central America, Paraguay, Peru and Venezuela. Distinct lineages with different dynamics were found in each country, with co-existence, extinction and replacement of lineages occurring over the review period. Despite some gaps in the literature limiting the possibility for comparison, our review has described the molecular epidemiological trends of dengue infection. However, several gaps in molecular epidemiological information across Latin America and the Caribbean were identified that provide avenues for future research; in particular, sequence determination of the dengue virus genome is important for more precise phylogenetic classification and correlation with clinical outcome and disease severity.

  16. [Progress of the micronucleus test in the field of molecular cancer epidemiology].

    PubMed

    Xu, Huadong; Jia, Guang

    2015-01-01

    The micronucleus test (MNT) can be used to detect multiple genetic end points simultaneously, including chromosome aberration, mis-repaired DNA damage, apoptosis, parts of mutation and so on, which MNT has been an important part of the study of cancer epidemiology.Here, we reviewed the progress of MNT in the field of molecular cancer epidemiology in recent years, including early detection and diagnosis of cancer, evaluation of carcinogenic substances, genetic susceptibility biomarkers, micronutrient and cohort studies.

  17. Retinal sensitivity in subjects with type 2 diabetes mellitus: Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetics Study (SN-DREAMS II, Report No. 4).

    PubMed

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

    2016-06-01

    To evaluate retinal sensitivity (RS) in subjects with diabetes in a population-based study and to elucidate associated risk factors for abnormal RS. A subset of 357 subjects from Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetics Study-II was included in this study. All subjects underwent detailed ophthalmic evaluation including microperimetry and spectral domain optical coherence tomography. The prevalence of abnormal mean retinal sensitivity (MRS) was 89.1%. MRS was significantly reduced in subjects with diabetes but no retinopathy when compared with non-diabetic subjects. MRS was reduced in moderate non-proliferative diabetic retinopathy (DR) and macular oedema (ME) at 8° (p=0.04, p=0.01, respectively) and in ME at 10° (p=0.009) and 12° (p=0.036) compared with no DR. Significant negative correlation was found between MRS and best corrected visual acuity, duration of diabetes, glycosylated haemoglobin and central foveal thickness. Increased retinal thickness remained a significant risk factor (OR, 1.02; p=0.044) for abnormal MRS. Altered inner retinal layers and foveal contour were associated with reduced MRS among subjects with DR and presence of epiretinal membrane, altered foveal contour and altered retinal pigment epithelium were associated with reduced MRS. Reduced RS in those subjects with diabetes but no retinopathy suggests the early neuronal damage in type 2 diabetes mellitus. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  18. Molecular Epidemiology of EGFR Mutations in Asian Patients with Advanced Non-Small-Cell Lung Cancer of Adenocarcinoma Histology - Mainland China Subset Analysis of the PIONEER study.

    PubMed

    Shi, Yuankai; Li, Junling; Zhang, Shucai; Wang, Mengzhao; Yang, Shujun; Li, Ning; Wu, Gang; Liu, Wei; Liao, Guoqing; Cai, Kaican; Chen, Liang'an; Zheng, Meizhen; Yu, Ping; Wang, Xiuwen; Liu, Yunpeng; Guo, Qisen; Nie, Ligong; Liu, Jiwei; Han, Xiaohong

    2015-01-01

    Epidermal growth factor receptor (EGFR) mutations are the strongest response predictors to EGFR tyrosine kinase inhibitors (TKI) therapy, but knowledge of the EGFR mutation frequency on lung adenocarcinoma is still limited to retrospective studies. The PIONEER study (NCT01185314) is a prospective molecular epidemiology study in Asian patients with newly diagnosed advanced lung adenocarcinoma, aiming to prospectively analyze EGFR mutation status in IIIB/IV treatment-naïve lung adenocarcinomas in Asia. We report the mainland China subset results. Eligible patients (≥20 yrs old, IIIB/IV adenocarcinoma and treatment-naïve) were registered in 17 hospitals in mainland China. EGFR was tested for mutations by amplification refractory mutation system using biopsy samples. Demographic and clinical characteristics were collected for subgroup analyses. A total of 747 patients were registered. Successful EGFR mutation analysis was performed in 741, with an overall mutation rate of 50.2%. The EGFR active mutation rate is 48.0% (with 1.3% of combined active and resistance mutations). Tobacco use (>30 pack-year vs. 0-10 pack-year, OR 0.27, 95%CI: 0.17-0.42) and regional lymph nodes involvement (N3 vs. N0, OR 0.47, 95%CI: 0.29-0.76) were independent predictors of EGFR mutation in multivariate analysis. However, even in regular smokers, the EGFR mutation frequency was 35.3%. The EGFR mutation frequency was similar between diverse biopsy sites and techniques. The overall EGFR mutation frequency of the mainland China subset was 50.2%, independently associated with the intensity of tobacco use and regional lymph nodes involvement. The relatively high frequency of EGFR mutations in the mainland China subset suggest that any effort to obtain tissue sample for EGFR mutation testing should be encouraged.

  19. 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

  20. Molecular and epidemiologic study of Clostridium difficile reveals unusual heterogeneity in clinical strains circulating in different regions in Portugal.

    PubMed

    Santos, A; Isidro, J; Silva, C; Boaventura, L; Diogo, J; Faustino, A; Toscano, C; Oleastro, M

    2016-08-01

    Clostridium difficile infection (CDI) represents a great healthcare burden in developed countries. The emergence of the epidemic PCR ribotype (RT) 027 and its acquired fluoroquinolones resistance have accentuated the need for an active surveillance of CDI. Here we report the first countrywide study of CDI in Portugal with the characterization of 498 C. difficile clinical isolates from 20 hospitals in four regions in Portugal regarding RT, virulence factors and antimicrobial susceptibility. We identified 96 RTs with marked variations between and within regions, as only six RTs appeared in all four regions. RT027 was the most frequent RT overall (18.5%) and among healthcare facility-associated isolates (19.6%), while RT014 was the most common among community-associated isolates (12%). The north showed a high RT diversity among isolates and a low moxifloxacin (MXF) resistance rate (11.9%), being the only region in which RT027 was not predominant. In contrast, the isolates from the centre presented the highest RT027 frequency, and 53.4% were resistant to MXF. Overall, MXF resistance (33.2%) was associated (p <0.001) with the presence of binary toxin genes and mutations in tcdC regardless of the RT. Both traits appeared in almost 30% of the strains. RT027 showed a reduced susceptibility to metronidazole (p <0.01), and RT126 had higher minimum inhibitory concentrations to vancomycin (p = 0.03) compared to other RTs. The present study highlights an unusual heterogeneity of RTs in Portugal, with a high frequency of hypervirulent RTs and the emergence of virulence factors in non-027 RTs, emphasizing the need for a surveillance system for CDI in Portugal.

  1. Cystic echinococcosis: Future perspectives of molecular epidemiology

    USDA-ARS?s Scientific Manuscript database

    Human cystic echinococcosis (CE) has been conceived to be caused predominantly by Echinococcus granulosus sensu stricto (the dog-sheep strain). Recent molecular approaches on CE, however, have revealed that human cases are also commonly caused by another species, Echinococcus canadensis. All indices...

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

    PubMed

    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.

  3. 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

  4. A molecular epidemiologic study of human adenovirus type 8 isolates causing epidemic keratoconjunctivitis in Kawasaki City, Japan in 2011.

    PubMed

    Fujimoto, Tsuguto; Matsushima, Yuki; Shimizu, Hideaki; Ishimaru, Yoko; Kano, Atsuko; Nakajima, Etsuko; Adhikary, Arun Kumar; Hanaoka, Nozomu; Okabe, Nobuhiko

    2012-01-01

    A local outbreak of epidemic keratoconjunctivitis (EKC) caused by human adenovirus type 8 (HAdV-D8) occurred in Kawasaki city, Japan in July-August 2011. Since the cases were sporadic in nature, the source of the infection could not be identified. The results of PCR analysis and the appearance of cytopathic effects in the samples indicated that 22 patients were positive for HAdV. The mean age of the patients (10 men and 12 women) was 64.3 ± 17.3 years (median, 68 years; range, 11-86 years). The sequences of hexon, which included hypervariable loop 1; the penton, which included RGD loops; and the fiber, which included the knob-coding regions, were identical in all the HAdV-positive cases. Phylogenetic analysis of the major capsid protein-encoding regions of HAdV confirmed that the isolates were HAdV-D8. Although the incidence of HAdV-D8 outbreaks has decreased in Japan since 1997, the results of our study imply that HAdV-D8 is still a causative agent for EKC outbreaks in Japan.

  5. A molecular epidemiological study of the hepatitis B virus in Thailand after 22 years of universal immunization.

    PubMed

    Yimnoi, Parichat; Posuwan, Nawarat; Wanlapakorn, Nasamon; Tangkijvanich, Pisit; Theamboonlers, Apiradee; Vongpunsawad, Sompong; Poovorawan, Yong

    2016-04-01

    Hepatitis B virus (HBV) infection affects an estimated two billion people worldwide. Since 1992, Thailand implemented universal HBV vaccination as part of the expanded program on immunization (EPI) for newborns. This study aims to compare genotypes and characterize HBV by assessing pre-S/S and basic core promoter (BCP)/precore (PC) mutations in populations born before and after EPI implementation. A nationwide serosurvey conducted in 2014 assessed the impact of universal HBV vaccination in Thailand. Two cohort groups were established based on whether they were born before or after 1992. HBV DNA was amplified from HBsAg positive samples by PCR and sequenced. HBV genotypes, pre-S/S regions, and BCP/PC mutations were characterized. From a total of 5,964 subjects, there were 2,805 (47.0%) and 3,159 (53.0%) individuals who were born before and after EPI implementation, respectively. The overall prevalence of HBsAg was 2.2%. The prevalence of HBsAg was significantly higher in the before EPI group (4.3%) than in the after EPI group (0.3%) (P < 0.001). HBV DNA was detected in 119 samples; 111 HBV-positive samples (93%) were genotype C (subgenotype C1). The "a" determinant mutation was only detected in the "before EPI" group. Twenty-two years after implementation of the EPI program, the HBV carrier rate is significantly reduced. The most prevalent genotype for the remaining HBV was C1. The "vaccine escape" mutant, especially the "a" determinant, was not detected after the launch of the EPI program, and the current HBV vaccine remains highly effective.

  6. Molecular epidemiology of rabies virus in Vietnam (2006-2009).

    PubMed

    Nguyen, Anh K T; Nguyen, Dong V; Ngo, Giang C; Nguyen, Thu T; Inoue, Satoshi; Yamada, Akio; Dinh, Xuyen K; Nguyen, Dung V; Phan, Thao X; Pham, Bao Q; Nguyen, Hien T; Nguyen, Hanh T H

    2011-01-01

    This study was aimed at determining the molecular epidemiology of rabies virus (RABV) circulating in Vietnam. Intra vitam samples (saliva and cerebrospinal fluid) were collected from 31 patients who were believed to have rabies and were admitted to hospitals in northern provinces of Vietnam. Brain samples were collected from 176 sick or furious rabid dogs from all over the country. The human and canine samples were subjected to reverse transcription-polymerase chain reaction analysis. The findings showed that 23 patients tested positive for RABV. Interestingly, 5 rabies patients did not have any history of dog or cat bites, but they had an experience of butchering dogs or cats, or consuming their meat. RABV was also detected in 2 of the 100 sick dogs from slaughterhouses. Molecular epidemiological analysis of 27 RABV strains showed that these viruses could be classified into two groups. The RABVs classified into Group 1 were distributed throughout Vietnam and had sequence similarity with the strains from China, Thailand, Malaysia, and the Philippines. However, the RABVs classified into Group 2 were only found in the northern provinces of Vietnam and showed high sequence similarity with the strain from southern China. This finding suggested the recent influx of Group 2 RABVs between Vietnam and China across the border. Although the incidence of rabies due to circulating RABVs in slaughterhouses is less common than that due to dog bite, the national program for rabies control and prevention in Vietnam should include monitoring of the health of dogs meant for human consumption and vaccination for workers at dog slaughterhouses. Further, monitoring of and research on the circulating RABVs in dog markets may help to determine the cause of rabies and control the spread of rabies in slaughterhouses in Vietnam.

  7. Prospective Multicenter Study of the Epidemiology, Molecular Identification, and Antifungal Susceptibility of Candida parapsilosis, Candida orthopsilosis, and Candida metapsilosis Isolated from Patients with Candidemia ▿

    PubMed Central

    Cantón, Emilia; Pemán, Javier; Quindós, Guillermo; Eraso, Elena; Miranda-Zapico, Ilargi; Álvarez, María; Merino, Paloma; Campos-Herrero, Isolina; Marco, Francesc; de la Pedrosa, Elia Gomez G.; Yagüe, Genoveva; Guna, Remedios; Rubio, Carmen; Miranda, Consuelo; Pazos, Carmen; Velasco, David

    2011-01-01

    A 13-month prospective multicenter study including 44 hospitals was carried out to evaluate the epidemiology of Candida parapsilosis complex candidemia in Spain. Susceptibility to amphotericin B, flucytosine, fluconazole, itraconazole, voriconazole, posaconazole, anidulafungin, caspofungin, and micafungin was tested by the microdilution colorimetric method. A total of 364 C. parapsilosis complex isolates were identified by molecular methods: C. parapsilosis (90.7%), Candida orthopsilosis (8.2%), and Candida metapsilosis (1.1%). Most candidemias (C. parapsilosis, 76.4%; C. orthopsilosis, 70.0%; C. metapsilosis, 100%) were observed in adults. No C. orthopsilosis or C. metapsilosis candidemias occurred in neonates. C. parapsilosis was most frequent in adult intensive care unit (28.8%), surgery (20.9%), and internal medicine (19.7%) departments; and C. orthopsilosis was most frequent in hematology (28.6%), pediatrics (12.0%), and neonatology (11.5%) departments. The geographic distribution of C. orthopsilosis and C. metapsilosis was not uniform. According to CLSI clinical breakpoints, all C. orthopsilosis and C. metapsilosis isolates were susceptible to the nine agents tested. Resistance (MICs > 1 mg/liter) was observed only in C. parapsilosis: amphotericin B, posaconazole, itraconazole, and caspofungin (0.3% each), anidulafungin (1.9%), and micafungin (2.5%). Applying the new species-specific fluconazole and echinocandin breakpoints, the rates of resistance to fluconazole for C. parapsilosis and C. orthopsilosis increased to 4.8% and 0.3%, respectively; conversely, for C. parapsilosis they shifted from 1.9 to 0.6% (anidulafungin) and from 2.5 to 0.6% (micafungin). Our study confirms the different prevalence of C. parapsilosis complex candidemia among age groups: neither C. orthopsilosis nor C. metapsilosis was isolated from neonates; interestingly, C. metapsilosis was isolated only from adults and the elderly. The disparity in antifungal susceptibility among species

  8. 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

  9. Bias in occupational epidemiology studies

    PubMed Central

    Pearce, Neil; Checkoway, Harvey; Kriebel, David

    2007-01-01

    The design of occupational epidemiology studies should be based on the need to minimise random and systematic error. The latter is the focus of this paper, and includes selection bias, information bias and confounding. Selection bias can be minimised by obtaining a high response rate (and by appropriate selection of the control group in a case‐control study). In general, it is important to ensure that information bias is minimised and is also non‐differential (for example, that the misclassification of exposure is not related to disease status) by collecting data in a standardised manner. A major concern in occupational epidemiology studies usually relates to confounding, because exposure has not been randomly allocated, and the groups under study may therefore have different baseline disease risks. For each of these types of bias, the goal should be to avoid the bias by appropriate study design and/or appropriate control in the analysis. However, it is also important to attempt to assess the likely direction and strength of biases that cannot be avoided or controlled. PMID:17053019

  10. 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.

  11. Molecular epidemiology of malaria in Cameroon. XXVI. Twelve-year in vitro and molecular surveillance of pyrimethamine resistance and experimental studies to modulate pyrimethamine resistance.

    PubMed

    Tahar, Rachida; Basco, Leonardo K

    2007-08-01

    In vitro pyrimethamine response of Plasmodium falciparum isolates and dihydrofolate reductase (dhfr) gene sequences were analyzed in 2004-2005 and compared with our previous data. Most isolates (n = 103, all dhfr mutants) had 50% inhibitory concentrations (IC(50)s) > or = 119 nM, and six isolates had low IC(50)s (five wild-type or mixed dhfr, 0.04-1.37 nM; one triple mutant, 6.4 nM). Of 194 isolates, only 7 had the wild-type dhfr and 187 were mutants. The results of the two methods were highly concordant and indicated a significant increase (P < 0.05) in the prevalence of mutant, pyrimethamine-resistant P. falciparum between 1994 and 2005. The addition of probenecid or sulfinpyrazone to pyrimethamine resulted in a slight-to-moderate decrease in the level of in vitro pyrimethamine resistance without rendering the parasites susceptible to pyrimethamine. Analysis of molecular markers may be useful for the long-term surveillance of antifolate-resistant malaria.

  12. Molecular epidemiology of Streptococcus agalactiae recovered from significant bacteriuria.

    PubMed

    Schuab, Rôde B B; Arêas, Glauber P; Souza, Viviane C; Barros, Rosana R

    2015-09-01

    Streptococcus agalactiae has been implicated in urinary tract infections, but the molecular epidemiology of such infections is poorly characterized. In this study, 194 isolates recovered from significant bacteriuria of non-pregnant individuals were submitted to antimicrobial susceptibility testing, molecular characterization of macrolide resistance, PCR-based capsular typing and analysis of genetic diversity by pulsed-field gel electrophoresis (PFGE). By disk diffusion, all isolates were susceptible to ceftriaxone, levofloxacin, penicillin G and vancomycin; 87.6% and 9.3% of isolates were non-susceptible to tetracycline and clindamycin, respectively. The minimum inhibitory concentration (MIC) confirmed that 11.3% of isolates were resistant to erythromycin. Macrolide resistance determinants were iMLSB (n = 9), cMLSB (n = 9) and M (n = 4), associated with ermA, ermB and mefA/E. Predominant capsular types were V, Ia, II and III. No significant association was observed between any capsular type and the occurrence of pyuria. However, type III was associated with erythromycin resistance, while type II was associated with erythromycin-susceptible isolates. Distinct PFGE profiles were observed among different types, but identical profiles were found among erythromycin-susceptible and -resistant isolates of the same type. A variety of capsular and PFGE types are involved in significant bacteriuria. Although capsular types found here are prevalent in different infections, the frequency of each type seems to be unique. Erythromycin resistance is due to polyclonal origin instead of the expansion of few clones of S. agalactiae.

  13. Global Molecular Epidemiology of IMP-Producing Enterobacteriaceae.

    PubMed

    Matsumura, Yasufumi; Peirano, Gisele; Motyl, Mary R; Adams, Mark D; Chen, Liang; Kreiswirth, Barry; DeVinney, Rebekah; Pitout, Johann D D

    2017-04-01

    International data on the molecular epidemiology of Enterobacteriaceae with IMP carbapenemases are lacking. We performed short-read (Illumina) whole-genome sequencing on a global collection of 38 IMP-producing clinical Enterobacteriaceae (2008 to 2014). IMP-producing Enterobacteriaceae (7 varieties within 11 class 1 integrons) were mainly present in the South Pacific and Asia. Specific blaIMP-containing integrons (In809 with blaIMP-4, In722 with blaIMP-6, and In687 with blaIMP-14) were circulating among different bacteria in countries such as Australia, Japan, and Thailand. In1312 with blaIMP-1 was present in Klebsiella pneumoniae from Japan and Citrobacter freundii from Brazil. Klebsiella pneumoniae (n = 22) was the most common species; clonal complex 14 (CC14) from Philippines and Japan was the most common clone and contained In1310 with blaIMP-26 and In1321 with blaIMP-6 The Enterobacter cloacae complex (n = 9) consisted of Enterobacter hormaechei and E. cloacae cluster III. CC78 (from Taiwan) containing In73 with blaIMP-8 was the most common clone among the E. cloacae complex. This study highlights the importance of surveillance programs using the latest molecular techniques for providing insight into the characteristics and global distribution of Enterobacteriaceae with blaIMP genes.

  14. Molecular epidemiology of Corynebacterium pseudotuberculosis isolated from horses in California.

    PubMed

    Haas, Dionei J; Dorneles, Elaine M S; Spier, Sharon J; Carroll, Scott P; Edman, Judy; Azevedo, Vasco A; Heinemann, Marcos B; Lage, Andrey P

    2017-04-01

    Corynebacterium pseudotuberculosis biovar Equi is an important pathogen of horses. It is increasing in frequency in the United States, and is responsible for various clinical forms of infection, including external abscesses, internal abscesses of the abdominal or thoracic cavities, and ulcerative lymphangitis. The host/pathogen factors dictating the form or severity of infection are currently unknown. Our recent investigations have shown that genotyping C. pseudotuberculosis isolates using enterobacterial repetitive intergenic consensus (ERIC)-PCR is useful for understanding the evolutionary genetics of the species as well for molecular epidemiology studies. The aims of the present study were to assess (i) the genetic diversity of C. pseudotuberculosis strains isolated from horses in California, United States and (ii) the epidemiologic relationships among isolates. One hundred and seven C. pseudotuberculosis biovar Equi isolates from ninety-five horses, and two C. pseudotuberculosis biovar Ovis strains, C. pseudotuberculosis ATCC 19410(T) type strain and C. pseudotuberculosis 1002 vaccine strain, were fingerprinted using the ERIC 1+2-PCR. C. pseudotuberculosis isolated from horses showed a high genetic diversity, clustering in twenty-seven genotypes with a diversity index of 0.91. Minimal spanning tree showed four major clonal complexes with a pattern of temporal clustering. Strains isolated from the same horse showed identical ERIC 1+2-PCR genotype, with the exception of two strains isolated from the same animal that showed distinct genotypes, suggesting a co-infection. We found no strong genetic signals related to clinical form (including internal versus external infections). However, temporal clustering of genotypes was observed.

  15. Carbapenemases in Enterobacteriaceae: types and molecular epidemiology.

    PubMed

    Martínez-Martínez, Luis; González-López, Juan José

    2014-12-01

    The most important mechanism of carbapenem resistance in Enterobacteriaceae is the production of carbapenemases, although resistance can also result from the synergistic activity between AmpC-type or (to a lesser extent) extended-spectrum beta-lactamases combined with decreased outer membrane permeability. Three major molecular classes of carbapenemases are recognized: A, B and D. Classes A and D are serine-beta-lactamases, whereas class B are metallo-beta-lactamases (their hydrolytic activity depends on the presence of zinc). In addition to carbapenems, carbapenemases also hydrolyze other beta-lactams, but the concrete substrate profile depends on the enzyme type. In general terms, class A enzymes are to some extent inhibited by clavulanic acid, and class B enzymes do not affect monobactams and are inhibited by zinc chelators. Given Enterobacteriaceae producing carbapenemases usually also contain gene coding for other mechanisms of resistance to beta-lactams, it is not unusual for the organisms to present complex beta-lactam resistance phenotypes. Additionally, these organisms frequently contain other genes that confer resistance to quinolones, aminoglycosides, tetracyclines, sulphonamides and other families of antimicrobial agents, which cause multiresistance or even panresistance. Currently, the most important type of class A carbapenemases are KPC enzymes, whereas VIM, IMP and (particularly) NDM in class B and OXA-48 (and related) in class D are the more relevant enzymes. Whereas some enzymes are encoded by chromosomal genes, most carbapenemases are plasmid-mediated (with genes frequently located in integrons), which favors the dissemination of the enzymes. Detailed information of the genetic platforms and the context of the genes coding for the most relevant enzymes will be presented in this review.

  16. 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

  17. Association of obesity with diabetic retinopathy: Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetics Study (SN-DREAMS Report no. 8).

    PubMed

    Raman, Rajiv; Rani, Padmaja Kumari; Gnanamoorthy, Perumal; Sudhir, R R; Kumaramanikavel, Govindasamy; Sharma, Tarun

    2010-09-01

    The aim of the study was to report the prevalence of obesity indices in individuals with diabetes and find out their association with diabetic retinopathy in the urban Indian population. Subjects (n = 1,414) were recruited from Sankara Nethralaya Diabetic Retinopathy Epidemiology And Molecular Genetics Study (SN-DREAMS-I), a cross-sectional study between 2003 and 2006. Anthropometric measurements were carried out, and all patients' fundi were photographed using 45 degrees four-field stereoscopic digital photography. The diagnosis of diabetic retinopathy was based on the modified Klein classification. Generalized obesity and abdominal obesity were defined using WHO Asia Pacific guidelines with the BMI (body mass index) cutoff as > or =23 kg/m(2), WC (waist circumference) cutoffs as > or =90 cm in men and > or =80 cm in women and WHO guidelines using WHR (waist-to-hip ratio) cutoffs as > or =0.90 for men and > or =0.85 for women. Prevalence of obesity defined by BMI and WC was more in women compared to men, and that defined by WHR was more in men compared to women (P < 0.001). The prevalence of isolated generalized obesity, isolated abdominal obesity and combined obesity were 5.4, 10.1 and 58% in men and 4.5, 10.8 and 74.4% in women, respectively. The prevalence of any diabetic retinopathy and sight-threatening diabetic retinopathy was more in the isolated abdominal obesity group (26.35 and 6.08%, respectively) than in other subgroups. On logistic regression analysis, isolated abdominal obesity (OR 2.02, 95% CI: 1.06-3.86) and increased WHR in women (OR 1.48 95% CI: 1.10-2.38) were associated with diabetic retinopathy; BMI > or = 23 (OR 0.66, 95% CI: 0.48-0.90) and combined obesity (OR 0.72, 95% CI: 0.53-0.99) had a protective role for any diabetic retinopathy in the overall group. In the urban south Indian population, isolated abdominal obesity and higher WHR in women were associated with diabetic retinopathy, but not with the severity of diabetic retinopathy.

  18. Molecular epidemiology, phylogeny and evolution of Candida albicans.

    PubMed

    McManus, Brenda A; Coleman, David C

    2014-01-01

    A small number of Candida species form part of the normal microbial flora of mucosal surfaces in humans and may give rise to opportunistic infections when host defences are impaired. Candida albicans is by far the most prevalent commensal and pathogenic Candida species. Several different molecular typing approaches including multilocus sequence typing, multilocus microsatellite typing and DNA fingerprinting using C. albicans-specific repetitive sequence-containing DNA probes have yielded a wealth of information regarding the epidemiology and population structure of this species. Such studies revealed that the C. albicans population structure consists of multiple major and minor clades, some of which exhibit geographical or phenotypic enrichment and that C. albicans reproduction is predominantly clonal. Despite this, losses of heterozygosity by recombination, the existence of a parasexual cycle, toleration of a wide range of aneuploidies and the recent description of viable haploid strains have all demonstrated the extensive plasticity of the C. albicans genome. Recombination and gross chromosomal rearrangements are more common under stressful environmental conditions, and have played a significant role in the evolution of this opportunistic pathogen. Surprisingly, Candida dubliniensis, the closest relative of C. albicans exhibits more karyotype variability than C. albicans, but is significantly less adaptable to unfavourable environments. This disparity most likely reflects the evolutionary processes that occurred during or soon after the divergence of both species from their common ancestor. Whilst C. dubliniensis underwent significant gene loss and pseudogenisation, C. albicans expanded gene families considered to be important in virulence. It is likely that technological developments in whole genome sequencing and data analysis in coming years will facilitate its routine use for population structure, epidemiological investigations, and phylogenetic analyses of

  19. Gallbladder cancer epidemiology, pathogenesis and molecular genetics: Recent update.

    PubMed

    Sharma, Aarti; Sharma, Kiran Lata; Gupta, Annapurna; Yadav, Alka; Kumar, Ashok

    2017-06-14

    Gallbladder cancer is a malignancy of biliary tract which is infrequent in developed countries but common in some specific geographical regions of developing countries. Late diagnosis and deprived prognosis are major problems for treatment of gallbladder carcinoma. The dramatic associations of this orphan cancer with various genetic and environmental factors are responsible for its poorly defined pathogenesis. An understanding to the relationship between epidemiology, molecular genetics and pathogenesis of gallbladder cancer can add new insights to its undetermined pathophysiology. Present review article provides a recent update regarding epidemiology, pathogenesis, and molecular genetics of gallbladder cancer. We systematically reviewed published literature on gallbladder cancer from online search engine PubMed (http://www.ncbi.nlm.nih.gov/pubmed). Various keywords used for retrieval of articles were Gallbladder, cancer Epidemiology, molecular genetics and bullion operators like AND, OR, NOT. Cross references were manually searched from various online search engines (http://www.ncbi.nlm.nih.gov/pubmed,https://scholar.google.co.in/, http://www.medline.com/home.jsp). Most of the articles published from 1982 to 2015 in peer reviewed journals have been included in this review.

  20. Gallbladder cancer epidemiology, pathogenesis and molecular genetics: Recent update

    PubMed Central

    Sharma, Aarti; Sharma, Kiran Lata; Gupta, Annapurna; Yadav, Alka; Kumar, Ashok

    2017-01-01

    Gallbladder cancer is a malignancy of biliary tract which is infrequent in developed countries but common in some specific geographical regions of developing countries. Late diagnosis and deprived prognosis are major problems for treatment of gallbladder carcinoma. The dramatic associations of this orphan cancer with various genetic and environmental factors are responsible for its poorly defined pathogenesis. An understanding to the relationship between epidemiology, molecular genetics and pathogenesis of gallbladder cancer can add new insights to its undetermined pathophysiology. Present review article provides a recent update regarding epidemiology, pathogenesis, and molecular genetics of gallbladder cancer. We systematically reviewed published literature on gallbladder cancer from online search engine PubMed (http://www.ncbi.nlm.nih.gov/pubmed). Various keywords used for retrieval of articles were Gallbladder, cancer Epidemiology, molecular genetics and bullion operators like AND, OR, NOT. Cross references were manually searched from various online search engines (http://www.ncbi.nlm.nih.gov/pubmed,https://scholar.google.co.in/, http://www.medline.com/home.jsp). Most of the articles published from 1982 to 2015 in peer reviewed journals have been included in this review. PMID:28652652

  1. 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.

  2. Molecular Epidemiology and Genomics of Group A Streptococcus

    PubMed Central

    Bessen, Debra E.; McShan, W. Michael; Nguyen, Scott V.; Shetty, Amol; Agrawal, Sonia; Tettelin, Hervé

    2014-01-01

    Streptococcus pyogenes (group A streptococcus; GAS) is a strict human pathogen with a very high prevalence worldwide. This review highlights the genetic organization of the species and the important ecological considerations that impact its evolution. Recent advances are presented on the topics of molecular epidemiology, population biology, molecular basis for genetic change, genome structure and genetic flux, phylogenomics and closely related streptococcal species, and the long- and short-term evolution of GAS. The application of whole genome sequence data to addressing key biological questions is discussed. PMID:25460818

  3. 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.

  4. Molecular epidemiology of cutaneous leishmaniasis in Venezuela.

    PubMed

    Rodriguez, Noris; De Lima, Hector; Aguilar, Cruz M; Rodriguez, Armando; Barker, Douglas C; Convit, Jacinto

    2002-04-01

    This paper discusses the utility of a set of primers (3J1, 3J2) designed from a repetitive nuclear deoxyribonucleic acid sequence for the diagnosis of Leishmania braziliensis infection in samples obtained from humans, insect vectors and mammalian reservoir hosts from different endemic areas in Venezuela. A high incidence of Leishmania (Viannia) braziliensis infection was found in the endemic areas studied. The sensitivity and specificity of the primers used were adequate for the identification of the natural vectors and reservoir hosts of L. (V.) braziliensis. The polymerase chain reaction was more sensitive than culture and stained smear examination in the diagnosis of cutaneous leishmaniasis, detecting 80% of cases compared to 42% and 72%, respectively.

  5. Molecular epidemiology of human metapneumovirus in Ireland.

    PubMed

    Carr, Michael J; Waters, Allison; Fenwick, Fiona; Toms, Geoffrey L; Hall, William W; O'Kelly, Edwin

    2008-03-01

    Human metapneumovirus (hMPV) is a cause of respiratory illness ranging from wheezing to bronchiolitis and pneumonia in children. A quantitative real-time reverse-transcriptase polymerase chain reaction (RT-PCR) assay was developed for the detection of all four main genetic lineages of hMPV and employed to validate an indirect immunofluorescence (IF) assay to detect hMPV positive specimens. The IF assay detected 24 positives from a screen of 625 randomly selected pediatric respiratory specimens collected (3.8% prevalence). From this cohort of 625 specimens, 229 were also tested by real-time RT-PCR assay. This included the 24 IF positive specimens and 205 randomly selected specimens from both study periods. In addition to confirming all the IF positives, the real-time assay detected an additional six hMPV positive specimens giving rise to a combined prevalence of 4.8%. Phylogenetic analysis showed that hMPV subtypes A2b and B2 to be the most prevalent genotypes circulating in our population and surprisingly no hMPV subgroups A1 or B1 were detected during this study period. Based on this phylogenetic analysis, we propose the existence of sub-clusters of hMPV genotype B2 present in our population which we term subtypes B2a and B2b. The mean log 10 copies/ml of quantitative RT-PCR determinations from these 30 hMPV positive respiratory specimens was 6.35 (range = 4.44-8.15). Statistical analysis of quantitative RT-PCR determinations of viral load from these 30 respiratory specimens suggests that hMPV genotype B specimens have a higher viral load than hMPV genotype A isolates (P < 0.03).

  6. Report of the Integrative Molecular Cancer Epidemiology International Symposium, Lyon, France.

    PubMed

    Raimondi, S

    2008-01-01

    An International Symposium on Integrative Molecular Cancer Epidemiology took place in Lyon, France, on 3-5 July 2008. The Symposium focused on aetiological and mechanistic aspects of molecular and genetic cancer epidemiology research and was divided into the following three sections: Molecular epidemiology-application of novel molecular markers to cancer epidemiology.Genomic epidemiology in the era of whole genome scan.INTEGRATIVE MOLECULAR EPIDEMIOLOGY: visions for the future.Participants included epidemiologists, geneticists, biochemical and molecular biologists, pharmacologists, pathologists and all researchers interested in this field. The Symposium provided a complete and clear overview of the present and future programmes in molecular cancer epidemiology. It also served to encourage international scientific collaboration between investigators working in this specific research field, and to stimulate transdisciplinary research with experts of other research areas. Highlights of each of the scientific presentations are summarized below.

  7. Molecular epidemiology of Mycobacterium tuberculosis complex in Brussels, 2010-2013.

    PubMed

    Vluggen, Christelle; Soetaert, Karine; Groenen, Guido; Wanlin, Maryse; Spitaels, Martine; Arrazola de Oñate, Wouter; Fauville-Dufaux, Maryse; Saegerman, Claude; Mathys, Vanessa

    2017-01-01

    The tuberculosis (TB) incidence rate in Brussels-Capital Region is 3-fold higher than in Belgium as a whole. Eight years after the realization of initial prospective population-based molecular epidemiology investigations in this Region, a similar study over the period 2010-2013 was conducted. TB strains isolated from 945 patients were submitted to genotyping by standardized 24-locus-MIRU-VNTR typing and spoligotyping. The phylogenetic analysis showed that the LAM (16.7%) and Haarlem (15.7%) branches are the two most prevalent TB lineages circulating in Brussels. Analysis of the MDR subgroup showed an association with Beijing strains (39.9%) and patients native of Eastern Europe (40.7%). Genotyping detected 113 clusters involving 321 patients, giving a recent transmission index of 22.9%. Molecular-guided epidemiological investigations and routine surveillance activities revealed family transmission or social contact for patients distributed over 34 clusters. Most of the patients were foreign-born (75.7%). However, cluster analysis revealed only limited trans-national transmission. Comparison with the previous study shows a stable epidemiological situation except for the mean age difference between Belgian-born and foreign-born patients which has disappeared. This study confirms that molecular epidemiology has become an important determinant for TB control programs. However, sufficient financial means need to be available to perform all required epidemiological investigations.

  8. Molecular epidemiology of Mycobacterium tuberculosis complex in Brussels, 2010–2013

    PubMed Central

    Vluggen, Christelle; Soetaert, Karine; Groenen, Guido; Wanlin, Maryse; Spitaels, Martine; Arrazola de Oñate, Wouter; Fauville-Dufaux, Maryse; Saegerman, Claude

    2017-01-01

    The tuberculosis (TB) incidence rate in Brussels-Capital Region is 3-fold higher than in Belgium as a whole. Eight years after the realization of initial prospective population-based molecular epidemiology investigations in this Region, a similar study over the period 2010–2013 was conducted. TB strains isolated from 945 patients were submitted to genotyping by standardized 24-locus-MIRU-VNTR typing and spoligotyping. The phylogenetic analysis showed that the LAM (16.7%) and Haarlem (15.7%) branches are the two most prevalent TB lineages circulating in Brussels. Analysis of the MDR subgroup showed an association with Beijing strains (39.9%) and patients native of Eastern Europe (40.7%). Genotyping detected 113 clusters involving 321 patients, giving a recent transmission index of 22.9%. Molecular-guided epidemiological investigations and routine surveillance activities revealed family transmission or social contact for patients distributed over 34 clusters. Most of the patients were foreign-born (75.7%). However, cluster analysis revealed only limited trans-national transmission. Comparison with the previous study shows a stable epidemiological situation except for the mean age difference between Belgian-born and foreign-born patients which has disappeared. This study confirms that molecular epidemiology has become an important determinant for TB control programs. However, sufficient financial means need to be available to perform all required epidemiological investigations. PMID:28222189

  9. Molecular epidemiology of Mycobacterium africanum in Ghana.

    PubMed

    Asante-Poku, Adwoa; Otchere, Isaac Darko; Osei-Wusu, Stephen; Sarpong, Esther; Baddoo, Akosua; Forson, Audrey; Laryea, Clement; Borrell, Sonia; Bonsu, Frank; Hattendorf, Jan; Ahorlu, Collins; Koram, Kwadwo A; Gagneux, Sebastien; Yeboah-Manu, Dorothy

    2016-08-09

    Mycobacterium africanum comprises two phylogenetic lineages within the M. tuberculosis complex (MTBC) and is an important cause of human tuberculosis (TB) in West Africa. The reasons for this geographic restriction of M. africanum remain unclear. Here, we performed a prospective study to explore associations between the characteristics of TB patients and the MTBC lineages circulating in Ghana. We genotyped 1,211 MTBC isolates recovered from pulmonary TB patients recruited between 2012 and 2014 using single nucleotide polymorphism typing and spoligotyping. Associations between patient and pathogen variables were assessed using univariate and multivariate logistic regression. Of the 1,211 MTBC isolates analysed, 71.9 % (871) belonged to Lineage 4; 12.6 % (152) to Lineage 5 (also known as M. africanum West-Africa 1), 9.2 % (112) to Lineage 6 (also known as M. africanum West-Africa 2) and 0.6 % (7) to Mycobacterium bovis. Univariate analysis revealed that Lineage 6 strains were less likely to be isoniazid resistant compared to other strains (odds ratio = 0.25, 95 % confidence interval (CI): 0.05-0.77, P < 0.01). Multivariate analysis showed that Lineage 5 was significantly more common in patients from the Ewe ethnic group (adjusted odds ratio (adjOR): 2.79; 95 % CI: 1.47-5.29, P < 0.001) and Lineage 6 more likely to be found among HIV-co-infected TB patients (adjOR = 2.2; 95 % confidence interval (CI: 1.32-3.7, P < 0.001). Our findings confirm the importance of M. africanum in Ghana and highlight the need to differentiate between Lineage 5 and Lineage 6, as these lineages differ in associated patient variables.

  10. Cytochrome P450s and molecular epidemiology

    NASA Astrophysics Data System (ADS)

    Gonzalez, Frank J.; Gelboin, Harry V.

    1993-03-01

    Cytochrome P450 (P450) represent a superfamily of heme-containing monooxygenases that are found throughout the animal and plant kingdoms and in many microorganisms. A number of these enzymes are involved in biosynthetic pathways of steroid synthesis but in mammals the vast majority of P450s function to metabolize foreign chemicals or xenobiotics. In the classical phase I reactions on the latter, a membrane-bound P450 will hydroxylate a compound, usually hydrophobic in nature, and the hydroxyl group will serve as a substrate for the various transferases or phase II enzymes that attach hydrophilic substituents such as glutathione, sulfate or glucuronic acid. Some chemicals, however, are metabolically-activated by P450s to electrophiles capable of reacting with cellular macromolecules. The cellular concentrations of the chemical and P450, reactivity of the active metabolite with nucleic acid and the repairability of the resultant adducts, in addition to the nature of the cell type, likely determines whether a chemical will be toxic and kill the cell or will transform the cell. Immunocorrelative and cDNA-directed expression have been used to define the substrate specificities of numerous human P450s. Levels of expression of different human P450 forms have been measured by both in vivo and in vitro methodologies leading to the realization that a large degree of interindividual differences occur in P450 expression. Reliable procedures for measuring P450 expression in healthy and diseased subjects will lead to prospective and case- cohort studies to determine whether interindividual differences in levels of P450 are associated with susceptibility or resistance to environmentally-based disease.

  11. Enhanced HIV-1 surveillance using molecular epidemiology to study and monitor HIV-1 outbreaks among intravenous drug users (IDUs) in Athens and Bucharest.

    PubMed

    Paraskevis, Dimitrios; Paraschiv, Simona; Sypsa, Vana; Nikolopoulos, Georgios; Tsiara, Chryssa; Magiorkinis, Gkikas; Psichogiou, Mina; Flampouris, Andreas; Mardarescu, Mariana; Niculescu, Iulia; Batan, Ionelia; Malliori, Meni; Otelea, Dan; Hatzakis, Angelos

    2015-10-01

    A significant increase in HIV-1 diagnoses was reported among Injecting Drug Users (IDUs) in the Athens (17-fold) and Bucharest (9-fold) metropolitan areas starting 2011. Molecular analyses were conducted on HIV-1 sequences from IDUs comprising 51% and 20% of the diagnosed cases among IDUs during 2011-2013 for Greece and Romania, respectively. Phylodynamic analyses were performed using the newly developed birth-death serial skyline model which allows estimating of important epidemiological parameters, as implemented in BEAST programme. Most infections (>90%) occurred within four and three IDU local transmission networks in Athens and Bucharest, respectively. For all Romanian clusters, the viral strains originated from local circulating strains, whereas in Athens, the local strains seeded only two of the four sub-outbreaks. Birth-death skyline plots suggest a more explosive nature for sub-outbreaks in Bucharest than in Athens. In Athens, two sub-outbreaks had been controlled (Re<1.0) by 2013 and two appeared to be endemic (Re∼1). In Bucharest one outbreak continued to expand (Re>1.0) and two had been controlled (Re<1.0). The lead times were shorter for the outbreak in Athens than in Bucharest. Enhanced molecular surveillance proved useful to gain information about the origin, causal pathways, dispersal patterns and transmission dynamics of the outbreaks that can be useful in a public health setting. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Norovirus infection in Belarus: occurrence and molecular epidemiology.

    PubMed

    Paklonskayal, Natallia Uladzimirauna; Amvrosieva, Tamara Vasil'evna; Dziadziulia, Kanstantsin Leanidavich; Baranouskaya, Natallia Mikalaeuna; Kishkurno, Elena Petrovna; Kluiko, Nina Leonidovna

    2015-03-01

    The objective of the study is to analyze molecular epidemiologic surveillance for norovirus infection in Belarus over the past five years (2009-2013). Laboratory diagnostics was carried out by RT-PCR in 684 patients. Two regions of norovirus genome, localized in RNA-polymerase and capsid protein genes, were used for phylogenetic analysis. Noroviruses were predominant causative agents in adults and second only to rotaviruses in children, they also prevailed among aetiological agents of outbreaks (66.7% of outbreaks). In 2009-2013, the major norovirus genotype was GII.4 (58.3% of all genotyped isolates). Genovariant GII.4 2006b circulated in 2009 and 2010, genovariant GII.4 2009 New Orleans - in 2010 and 2012. In addition to GII.4, genotypes GII.6 (16.6%), GII.2 (4.1%), GII.3 (2.2%), and recombinant genotypes GII.g-GII.12 and GII.g-GII.1 (10.4% and 8.3%, respectively) circulated in Belarus. The findings indicate a significant contribution of noroviruses in development of sporadic morbidity and outbreaks of acute gastroenteritis in Belarus. Outbreaks or prominent increases of sporadic morbidity were mostly due to the emergence of a new genotype, or an epidemic genovariant.

  13. 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

  14. Molecular epidemiology of Aspergillus collected from cystic fibrosis patients.

    PubMed

    Sabino, Raquel; Ferreira, Jose A G; Moss, Richard B; Valente, Joana; Veríssimo, Cristina; Carolino, Elisabete; Clemons, Karl V; Everson, Cassie; Banaei, Niaz; Penner, John; Stevens, David A

    2015-07-01

    Aspergillus respiratory infection is a common complication in cystic fibrosis (CF) and is associated with loss of pulmonary function and allergic disease. Fifty-three Aspergillus isolates recovered from CF patients were identified to species by Internal Transcribed Spacer Region (ITS), β-tubulin, and calmodulin sequencing. Three species complexes (Terrei, Nigri, and Fumigati) were found. Identification to species level gave a single Aspergillus terreus sensu stricto, one Aspergillus niger sensu stricto and 51 Aspergillus fumigatus sensu stricto isolates. No cryptic species were found. To our knowledge, this is the first prospective study of Aspergillus species in CF using molecular methods. The paucity of non-A. fumigatus and of cryptic species of A. fumigatus suggests a special association of A. fumigatus sensu stricto with CF airways, indicating it likely displays unique characteristics making it suitable for chronic residence in that milieu. These findings could refine an epidemiologic and therapeutic approach geared to this pathogen. Copyright © 2014 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

  15. Proceedings of the second international molecular pathological epidemiology (MPE) meeting.

    PubMed

    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

    2015-07-01

    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 Big Data to Knowledge, Genetic Associations and Mechanisms in Oncology, and Precision Medicine Initiative of the US National Institute of Health. The MPE meeting series can help advance transdisciplinary population science and optimize training and education systems for twenty-first century medicine and

  16. Nationwide Trends in Molecular Epidemiology of HIV-1 in China.

    PubMed

    Li, Xiaoshan; Li, Wei; Zhong, Ping; Fang, Kun; Zhu, Kexin; Musa, Taha Hussein; Song, Yue; Du, Guoping; Gao, Rong; Guo, Yan; Yan, Wenjuan; Xuan, Yang; Wei, Pingmin

    2016-09-01

    To estimate the nationwide and regional distribution of HIV-1 genotypes in China in the past three decades, province-specific HIV-1 molecular epidemiology data were derived from 260 independent studies of HIV molecular prevalence through searching PubMed, VIP Chinese Journal Database (VIP), China National Knowledge Infrastructure, and Wanfang Data from January 1981 to December 2015. The nationwide and regional distribution of HIV-1 genotypes was estimated by weighting the genotype distribution from each province- and risk-specific subpopulation with the number of reported cases in the corresponding subgroups in the relevant periods. A sharp transition of HIV-1 subtypes and recombinant distribution was observed in various risk groups and regions over time. CRF01_AE has rapidly surged among almost all risk groups and in all areas, and it has become dominant among men who have sex with men and heterosexuals. A wide variety of new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were rapidly appearing in several risk groups and regions. After 2007, CRF01_AE was the most prevalent strain, accounting for 42.5% of all national infections, followed by CRF07_BC (28.9%), subtype B'/B (10.9%), CRF08_BC (10.0%), and subtype C (2.8%). URFs and other CRFs were responsible for 2.6% and fewer than 1% of infections nationwide, respectively. The nationwide and regional distributions of HIV-1 subtypes and recombinants were sharply shifting in China. CRF01_AE and new CRFs played an increasing role in the nationwide or regional HIV pandemic. The nationwide diversity of HIV-1 poses a formidable challenge to HIV vaccine development and disease prevention.

  17. Snowboard traumatology: an epidemiological study.

    PubMed

    Pigozzi, F; Santori, N; Di Salvo, V; Parisi, A; Di-Luigi, L

    1997-06-01

    In the past 10 years, snowboarding has become a popular winter sport among young people, and the number of accidents has increased proportionately. The incidence of traumas from snowboarding is shown to be 4 to 6 for every 1000 medical examinations, which is similar to that of downhill skiing. However, other important statistical differences exist between the two sports. This study of 106 snowboarding-related injury cases analyzes the epidemiology of these injuries in Italy. Results found that 45.1% of injuries are located in the upper limbs and that significant advantages are obtained with the introduction of guards to protect the upper limbs during descent. Serious ligament injuries to the knee are more rare in snowboarding than in downhill skiing. In both sports, injuries are more common with rigid boots, which lead to a higher incidence of injury to the upper limbs. Finally, a high percentage of injury to beginners was found in this study. Training courses for those who are considering taking up the sport of snowboarding could significantly lower their risk of trauma.

  18. Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID): an extension of the STROBE statement.

    PubMed

    Field, Nigel; Cohen, Ted; Struelens, Marc J; Palm, Daniel; Cookson, Barry; Glynn, Judith R; Gallo, Valentina; Ramsay, Mary; Sonnenberg, Pam; Maccannell, Duncan; Charlett, Andre; Egger, Matthias; Green, Jonathan; Vineis, Paolo; Abubakar, Ibrahim

    2014-04-01

    Molecular data are now widely used in epidemiological studies to investigate the transmission, distribution, biology, and diversity of pathogens. Our objective was to establish recommendations to support good scientific reporting of molecular epidemiological studies to encourage authors to consider specific threats to valid inference. The statement Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) builds upon the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) initiative. The STROME-ID statement was developed by a working group of epidemiologists, statisticians, bioinformaticians, virologists, and microbiologists with expertise in control of infection and communicable diseases. The statement focuses on issues relating to the reporting of epidemiological studies of infectious diseases using molecular data that were not addressed by STROBE. STROME-ID addresses terminology, measures of genetic diversity within pathogen populations, laboratory methods, sample collection, use of molecular markers, molecular clocks, timeframe, multiple-strain infections, non-independence of infectious-disease data, missing data, ascertainment bias, consistency between molecular and epidemiological data, and ethical considerations with respect to infectious-disease research. In total, 20 items were added to the 22 item STROBE checklist. When used, the STROME-ID recommendations should advance the quality and transparency of scientific reporting, with clear benefits for evidence reviews and health-policy decision making.

  19. 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

  20. Molecular epidemiology, and possible real-world applications in breast cancer.

    PubMed

    Ito, Hidemi; Matsuo, Keitaro

    2016-01-01

    Gene-environment interaction, a key idea in molecular epidemiology, has enabled the development of personalized medicine. This concept includes personalized prevention. While genome-wide association studies have identified a number of genetic susceptibility loci in breast cancer risk, however, the application of this knowledge to practical prevention is still underway. Here, we briefly review the history of molecular epidemiology and its progress in breast cancer epidemiology. We then introduce our experience with the trial combination of GWAS-identified loci and well-established lifestyle and reproductive risk factors in the risk prediction of breast cancer. Finally, we report our exploration of the cumulative risk of breast cancer based on this risk prediction model as a potential tool for individual risk communication, including genetic risk factors and gene-environment interaction with obesity.

  1. The promise of molecular epidemiology in defining the association between radiation and cancer

    SciTech Connect

    Neta, R.

    2000-07-01

    Molecular epidemiology involves the inclusion in epidemiologic studies of biologic measurements made at a genetic and molecular level and aims to improve the current knowledge of disease etiology and risk. One of the goals of molecular epidemiology studies of cancer is to determine the role of environmental and genetic factors in initiation and progression of malignancies and to use this knowledge to develop preventive strategies. This approach promises extraordinary opportunities for revolutionizing the practice of medicine and reducing risk. However, this will be accompanied by the need to address and resolve many challenges, such as ensuring the appropriate interpretation of molecular testing and resolving associated ethical, legal, and social issues. Traditional epidemiologic approaches determined that exposure to ionizing radiation poses significantly increased risk of leukemia and several other types of cancer. Such studies provided the basis for setting exposure standards to protect the public and the workforce from potentially adverse effects of ionizing radiation. These standards were set by using modeling approaches to extrapolate from the biological effects observed in high-dose radiation studies to predicted, but mostly immeasurable, effects at low radiation doses. It is anticipated that the addition of the molecular parameters to the population-based studies will help identify the genes and pathways characteristic of cancers due to radiation exposure of individuals, as well as identify susceptible or resistant subpopulations. In turn, the information about the molecular mechanisms should aid to improve risk assessment. While studies on radiogenic concerns are currently limited to only a few candidate genes, the exponential growth of scientific knowledge and technology promises expansion of knowledge about identity of participating genes and pathways in the future. This article is meant to provide an introductory overview of recent advances in

  2. Comparison of pulsed-field gel electrophoresis & repetitive sequence-based PCR methods for molecular epidemiological studies of Escherichia coli clinical isolates

    PubMed Central

    Bae, Il Kwon; Kim, Juwon; Sun, Je Young Hannah; Jeong, Seok Hoon; Kim, Yong-Rok; Wang, Kang-Kyun; Lee, Kyungwon

    2014-01-01

    Background & objectives: PFGE, rep-PCR, and MLST are widely used to identify related bacterial isolates and determine epidemiologic associations during outbreaks. This study was performed to compare the ability of repetitive sequence-based PCR (rep-PCR) and pulsed-field gel electrophoresis (PFGE) to determine the genetic relationships among Escherichia coli isolates assigned to various sequence types (STs) by two multilocus sequence typing (MLST) schemes. Methods: A total of 41 extended-spectrum β-lactamase- (ESBL-) and/or AmpC β-lactamase-producing E. coli clinical isolates were included in this study. MLST experiments were performed following the Achtman's MLST scheme and the Whittam's MLST scheme, respectively. Rep-PCR experiments were performed using the DiversiLab system. PFGE experiments were also performed. Results: A comparison of the two MLST methods demonstrated that these two schemes yielded compatible results. PFGE correctly segregated E. coli isolates belonging to different STs as different types, but did not group E. coli isolates belonging to the same ST in the same group. Rep-PCR accurately grouped E. coli isolates belonging to the same ST together, but this method demonstrated limited ability to discriminate between E. coli isolates belonging to different STs. Interpretation & conclusions: These results suggest that PFGE would be more effective when investigating outbreaks in a limited space, such as a specialty hospital or an intensive care unit, whereas rep-PCR should be used for nationwide or worldwide epidemiology studies. PMID:25579152

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

    PubMed Central

    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

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

    PubMed

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

    2014-01-01

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

  5. 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

  6. Sampling Bias in the Molecular Epidemiology of Tuberculosis

    PubMed Central

    2002-01-01

    Among the goals of the molecular epidemiology of infectious disease are to quantify the extent of ongoing transmission of infectious agents and to identify host- and strain-specific risk factors for disease spread. I demonstrate the potential bias in estimates of recent transmission and the impact of risk factors for clustering by using computer simulations to reconstruct populations of tuberculosis patients and sample from them. The bias consistently results in underestimating recent transmission and the impact of risk factors for recent transmission. PMID:11971768

  7. 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

  8. Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology.

    PubMed

    Elliott, Briony; Androga, Grace O; Knight, Daniel R; Riley, Thomas V

    2017-04-01

    Over the recent decades, Clostridium difficile infection (CDI) has emerged as a global public health threat. Despite growing attention, C. difficile remains a poorly understood pathogen, however, the exquisite sensitivity offered by next generation sequencing (NGS) technology has enabled analysis of the genome of C. difficile, giving us access to massive genomic data on factors such as virulence, evolution, and genetic relatedness within C. difficile groups. NGS has also demonstrated excellence in investigations of outbreaks and disease transmission, in both small and large-scale applications. This review summarizes the molecular epidemiology, evolution, and phylogeny of C. difficile, one of the most important pathogens worldwide in the current antibiotic resistance era.

  9. Molecular epidemiology tools in the management of healthcare-associated infections: towards the definition of recommendations.

    PubMed

    Boccia, Stefania; Pasquarella, Cesira; Colotto, Marco; Barchitta, Martina; Quattrocchi, Annalisa; Agodi, Antonella

    2015-01-01

    Healthcare-Associated Infections (HAIs) are an important cause of morbidity and mortality worldwide and have a significant economic impact for health systems. Molecular epidemiology tools have a central role in HAI prevention programs. In order to give an overview of their specific advantages and disadvantages we reported current and new molecular typing methods for HAI outbreak detection and epidemiological surveillance. The current review was drafted as a short version of a longer document written by the Public Health Genomics (GSP) working group, and the Italian Study Group of Hospital Hygiene (GISIO), entitled Molecular epidemiology of Healthcare Associated Infections: recommendations from the Italian Society of Hygiene, Preventive Medicine and Public Health (SItI). This text considers various aspects related to HAIs: the role of genotyping and bioinformatics, the organizational levels of laboratories, as well as ethical and economic aspects. The use of molecular epidemiology represents a key tool in the management of HAIs, to be used as a complement to conventional control measures. The present contribution aims to increase knowledge on the proper use of such methods, given the major challenge HAI represents for National Health systems.

  10. 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.

  11. 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

  12. Molecular epidemiology of hepatitis A virus infection in Northeast India.

    PubMed

    Bose, Moumita; Bose, Sujoy; Saikia, Anjan; Medhi, Subhash; Deka, Manab

    2015-07-01

    The present study was undertaken to screen the molecular epidemiology of Hepatitis A virus (HAV) in Northeast India (NEI) who are ethnically distinct, tribal dominated and of lower socio-economic status with almost no information available from NEI on these aspects. Briefly, 3 ml blood was collected from 324 random liver disease cases with jaundice, receiving care at Central Hospital, N.F. Railway, Guwahati, Assam with informed consent. The patients detected with HAV-IgM positive status were included and were stratified as acute viral hepatitis (AVH) and fulminant hepatitis (FHF) based on clinical profile. Viral RNA was isolated and HAV-RNA was detected by Real-time PCR using primers for the VP3-VP1 region. HAV genotyping was studied by PCR-direct sequencing-phylogenetic analysis approach using the VP1/2A region of HAV isolates. Statistical analysis was performed using SPSS13.0 software. A total of 69 cases were HAV infected with two HBV co-infected cases (n = 69 + 2 = 71), 62 cases and two co-infected cases were AVH and others were FHF cases. HAV infection was predominant in especially in the young and adult age group. HAV-RNA was detected in 28 cases, out of which 19 cases could be genotyped (12 AVH, 7 FHF); which showed the prevalence of genotype IIIA or IA only. Although HAV genotype IIIA was the major genotype in both the AVH (10/12, 83.33%) and FHF (5/7, 71.43%) group, but the difference in distribution of genotypes in AVH and FHF cases was statistically non-significant (P = 0.550). HAV genotype IIIA is associated with the majority of HAV infected cases and severity in NEI. © 2015 Wiley Periodicals, Inc.

  13. Molecular Epidemiology of Laguna Negra Virus, Mato Grosso State, Brazil

    PubMed Central

    Travassos da Rosa, Elizabeth S.; Medeiros, Daniele B.A.; Nunes, Márcio R.T.; Simith, Darlene B.; Pereira, Armando de S.; Elkhoury, Mauro R.; Santos, Elizabeth Davi; Lavocat, Marília; Marques, Aparecido A.; Via, Alba V.G.; Kohl, Vânia A.; Terças, Ana C.P.; D`Andrea, Paulo; Bonvícino, Cibele R.; Sampaio de Lemos, Elba R.

    2012-01-01

    We associated Laguna Negra virus with hantavirus pulmonary syndrome in Mato Grosso State, Brazil, and a previously unidentified potential host, the Calomys callidus rodent. Genetic testing revealed homologous sequencing in specimens from 20 humans and 8 mice. Further epidemiologic studies may lead to control of HPS in Mato Grosso State. PMID:22607717

  14. A Case-Control Study of Molecular Epidemiology in Relation to Azithromycin Resistance in Neisseria gonorrhoeae Isolates Collected in Amsterdam, the Netherlands, between 2008 and 2015.

    PubMed

    Wind, Carolien M; Bruisten, Sylvia M; Schim van der Loeff, Maarten F; Dierdorp, Mirjam; de Vries, Henry J C; van Dam, Alje P

    2017-06-01

    Neisseria gonorrhoeae resistance to ceftriaxone and azithromycin is increasing, which threatens the recommended dual therapy. We used molecular epidemiology to identify N. gonorrhoeae clusters and associations with azithromycin resistance in Amsterdam, the Netherlands. N. gonorrhoeae isolates (n = 143) were selected from patients visiting the Amsterdam STI Outpatient Clinic from January 2008 through September 2015. We included all 69 azithromycin-resistant isolates (MIC ≥ 2.0 mg/liter) and 74 frequency-matched susceptible controls (MIC ≤ 0.25 mg/liter). The methods used were 23S rRNA and mtrR sequencing, N. gonorrhoeae multiantigen sequence typing (NG-MAST), N. gonorrhoeae multilocus variable-number tandem-repeat analysis (NG-MLVA), and a specific PCR to detect mosaic penA genes. A hierarchical cluster analysis of NG-MLVA related to resistance and epidemiological characteristics was performed. Azithromycin-resistant isolates had C2611T mutations in 23S rRNA (n = 62, 89.9%, P < 0.001) and were NG-MAST genogroup G2992 (P < 0.001), G5108 (P < 0.001), or G359 (P = 0.02) significantly more often than susceptible isolates and were more often part of NG-MLVA clusters (P < 0.001). Two resistant isolates (2.9%) had A2059G mutations, and five (7.3%) had wild-type 23S rRNA. No association between mtrR mutations and azithromycin resistance was found. Twenty-four isolates, including 10 azithromycin-resistant isolates, showed reduced susceptibility to extended-spectrum cephalosporins. Of these, five contained a penA mosaic gene. Four of the five NG-MLVA clusters contained resistant and susceptible isolates. Two clusters consisting mainly of resistant isolates included strains from men who have sex with men and from heterosexual males and females. The co-occurrence of resistant and susceptible strains in NG-MLVA clusters and the frequent occurrence of resistant strains outside of clusters suggest that azithromycin resistance develops independently from the background genome

  15. Molecular approaches to epidemiology and clinical aspects of malaria.

    PubMed

    Brown, G V; Beck, H P; Molyneux, M; Marsh, K

    2000-10-01

    Malaria is a problem of global importance, responsible for 1-2 million deaths per year, mainly in African children, as well as considerable morbidity manifested as severe anaemia and encephalopathy in young children. Fundamental to the development of new tools for malaria control in humans is an increased understanding of key features of malaria infection, such as the diversity of outcome in different individuals, the understanding of different manifestations of the disease and of the mechanisms of immunity that allow clinical protection in the face of ongoing low-grade infection (concomitant immunity or premunition). Here, Graham Brown and colleagues review some of the ways in which molecular approaches might be used to increase our understanding of the epidemiology and clinical manifestations of malaria, as discussed at the Molecular Approaches to Malaria conference (MAM2000), Lorne, Australia, 2-5 February 2000.

  16. Molecular epidemiology of hepatitis B virus in Misiones, Argentina.

    PubMed

    Mojsiejczuk, Laura Noelia; Torres, Carolina; Sevic, Ina; Badano, Inés; Malan, Richard; Flichman, Diego Martin; Liotta, Domingo Javier; Campos, Rodolfo Hector

    2016-10-01

    Hepatitis B virus (HBV) infection is a major public health problem worldwide. The aims of this study were to describe the molecular epidemiology of HBV in the Province of Misiones, Argentina and estimate the phylodynamic of the main groups in a Bayesian coalescent framework. To this end, partial or complete genome sequences were obtained from 52 blood donor candidates. The phylogenetic analysis based on partial sequences of S/P region showed a predominance of genotype D (65.4%), followed by genotype F (30.8%) and genotype A as a minority (3.8%). At subgenotype level, the circulation of subgenotypes D3 (42.3%), D2 (13.5%), F1b (11.5%) and F4 (9.6%) was mainly identified. The Bayesian coalescent analysis of 29 complete genome sequences for the main groups revealed that the subgenotypes D2 and D3 had several introductions to the region, with ancestors dating back from 1921 to 1969 and diversification events until the late '70s. The genotype F in Misiones has a more recent history; subgenotype F4 isolates were intermixed with sequences from Argentina and neighboring countries and only one significant cluster dated back in 1994 was observed. Subgenotype F1b isolates exhibited low genetic distance and formed a closely related monophyletic cluster, suggesting a very recent introduction. In conclusion, the phylogenetic and coalescent analyses showed that the European genotype D has a higher circulation, a longer history of diversification and may be responsible for the largest proportion of chronic HBV infections in the Province of Misiones. Genotype F, especially subgenotype F1b, had a more recent introduction and its diversification in the last 20years might be related to its involvement in new transmission events.

  17. Phylogeography and molecular epidemiology of Yersinia pestis in Madagascar.

    PubMed

    Vogler, Amy J; Chan, Fabien; Wagner, David M; Roumagnac, Philippe; Lee, Judy; Nera, Roxanne; Eppinger, Mark; Ravel, Jacques; Rahalison, Lila; Rasoamanana, Bruno W; Beckstrom-Sternberg, Stephen M; Achtman, Mark; Chanteau, Suzanne; Keim, Paul

    2011-09-01

    Plague was introduced to Madagascar in 1898 and continues to be a significant human health problem. It exists mainly in the central highlands, but in the 1990s was reintroduced to the port city of Mahajanga, where it caused extensive human outbreaks. Despite its prevalence, the phylogeography and molecular epidemiology of Y. pestis in Madagascar has been difficult to study due to the great genetic similarity among isolates. We examine island-wide geographic-genetic patterns based upon whole-genome discovery of SNPs, SNP genotyping and hypervariable variable-number tandem repeat (VNTR) loci to gain insight into the maintenance and spread of Y. pestis in Madagascar. We analyzed a set of 262 Malagasy isolates using a set of 56 SNPs and a 43-locus multi-locus VNTR analysis (MLVA) system. We then analyzed the geographic distribution of the subclades and identified patterns related to the maintenance and spread of plague in Madagascar. We find relatively high levels of VNTR diversity in addition to several SNP differences. We identify two major groups, Groups I and II, which are subsequently divided into 11 and 4 subclades, respectively. Y. pestis appears to be maintained in several geographically separate subpopulations. There is also evidence for multiple long distance transfers of Y. pestis, likely human mediated. Such transfers have resulted in the reintroduction and establishment of plague in the port city of Mahajanga, where there is evidence for multiple transfers both from and to the central highlands. The maintenance and spread of Y. pestis in Madagascar is a dynamic and highly active process that relies on the natural cycle between the primary host, the black rat, and its flea vectors as well as human activity.

  18. Molecular Epidemiology of Mycobacterium tuberculosis among South African Gold Miners

    PubMed Central

    Lewis, James J.; Connors, Jeremy; Chihota, Violet N.; Shashkina, Elena; van der Meulen, Minty; Graviss, Edward A.; Ha, Ngan P.; Kreiswirth, Barry N.; Grant, Alison D.; Fielding, Katherine L.; Dorman, Susan E.; Churchyard, Gavin J.

    2015-01-01

    Rationale: HIV-associated tuberculosis remains a major health problem among the gold-mining workforce in South Africa. We postulate that high levels of recent transmission, indicated by strain clustering, are fueling the tuberculosis epidemic among gold miners. Objectives: To combine molecular and epidemiologic data to describe Mycobacterium tuberculosis genetic diversity, estimate levels of transmission, and examine risk factors for clustering. Methods: We conducted a cross-sectional study of culture-positive M. tuberculosis isolates in 15 gold mine shafts across three provinces in South Africa. All isolates were subject IS6110-based restriction fragment length polymorphisms, and we performed spoligotyping analysis and combined it with basic demographic and clinical information. Measurements and Main Results: Of the 1,602 M. tuberculosis patient isolates, 1,240 (78%) had genotyping data available for analysis. A highly diverse bacillary population was identified, comprising a total of 730 discrete genotypes. Four genotypic families (Latin American Mediterranean spoligotype family; W-Beijing; AH or X; and T1–T4) accounted for over 50% of all strains. Overall, 45% (560/1,240) of strains were genotypically clustered. The minimum estimate for recent transmission (n − 1 method) was 32% (range, 27–34%). There were no individual-level risk factors for clustering, apart from borderline evidence for being non–South African and having self-reported HIV infection. Conclusions: The high M. tuberculosis genetic diversity and lack of risk factors for clustering are indicative of a universal risk for disease among gold miners and likely mixing with nonmining populations. Our results underscore the urgent need to intensify interventions to interrupt transmission across the entire gold-mining workforce in South Africa. PMID:25419914

  19. 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

  20. Evaluation and validity of a polymerase chain reaction-based open reading frame typing method to dissect the molecular epidemiology for Acinetobacter baumannii in an epidemiologic study of a hospital outbreak.

    PubMed

    Fujikura, Yuji; Yuki, Atsushi; Hamamoto, Takaaki; Ichimura, Sadahiro; Kawana, Akihiko; Ohkusu, Kiyofumi; Matsumoto, Tetsuya

    2016-11-01

    Acinetobacter baumannii is regarded as one of the most important pathogens in hospital outbreaks. To obtain an efficient and simple epidemiologic method of surveillance during outbreaks, we assessed the applicability of the polymerase chain reaction-based open reading frames typing (POT) method and compared it with pulsed-field gel electrophoresis. The POT method was found to have sufficient discriminatory power to identify the strains and would be widely applicable to epidemiologic surveillance during hospital outbreaks.

  1. 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

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

    PubMed

    Castro-Nallar, Eduardo; 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.

  3. 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.

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

    PubMed Central

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

    2016-01-01

    SUMMARY 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

  5. 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

  6. Molecular epidemiology of rotavirus in cats in the United Kingdom.

    PubMed

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

    2015-02-01

    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. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  7. 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

  8. Commonly used molecular epidemiology markers of Streptococcus agalactiae do not appear to predict virulence.

    PubMed

    Lin, Frank; Sintchenko, Vitali; Kong, Fanrong; Gilbert, Gwendolyn L; Coiera, Enrico

    2009-01-01

    Several virulent clones of group B streptococcus (GBS) are known to be associated with certain serotypes and molecular epidemiological markers. It is unclear, however, whether the clinical significance of GBS can be predicted based solely on such molecular markers. The aim of this study was to test the hypothesis that GBS virulence can be predicted by using the molecular epidemiology markers. We examined 912 human GBS isolates in which 18 distinct molecular markers (including virulence-associated mobile genetic elements, polysaccharide capsule determinants, variants of a surface antigen and invasin, and antibiotic resistance-related genes) were characterised using multiplex PCR based reverse line blot assay. All strains were classified in clinically relevant invasive and colonising categories. Relationships between molecular markers and clinical phenotypes were tested using statistical and machine learning analyses. Classifier performance was evaluated by the area under receiver operator characteristic curve (AUC). The distribution of serotypes was comparable with those in previous reports (Ia, 22.1%; III, 34.7%; V, 17.7%). From single marker analyses, only alp3 (which encodes a surface protein antigen, commonly associated with serotype V) showed an increased association with invasive diseases (OR = 2.93, p = 0.0003). Molecular serotype (MS) II (OR = 10.0, p = 0.0007) had a significant association with early-onset neonatal disease when compared with late-onset diseases. Predictive analysis with logistic regression and machine learning classifiers, however, only yielded weak predictive power (AUC 0.56-0.71, stratified 10-fold cross-validation) across all the subgroups. While some molecular epidemiological markers are important in defining GBS clusters, a definitive predictive relationship between the molecular markers and clinical outcomes may be lacking.

  9. Molecular Epidemiology of Mycobacterium avium subsp. paratuberculosis on Dairy Farms.

    PubMed

    Li, Lingling; Katani, Robab; Schilling, Megan; Kapur, Vivek

    2016-01-01

    Mycobacterium avium subspecies paratuberculosis (MAP) is the etiological agent of severe chronic intestinal inflammatory disease in ruminants, termed Johne's disease, and can infect many other animal species, including humans. MAP has a long incubation period prior to manifestation of clinical signs including diarrhea, weight loss, and loss of production. MAP has a high prevalence in dairy herds and results in considerable adverse impacts on animal health and productivity throughout the world. Recent investigations have leveraged the characterization of the MAP genome for the development of powerful new molecular techniques for MAP strain differentiation. These approaches are providing key insights into the epidemiology and transmission of MAP on and between dairy herds. We summarize the state of the art for MAP diagnostics and strain differentiation and our current knowledge of mechanisms of within- and between-herd transmission of MAP, along with future needs for the development of rational MAP infection control programs.

  10. Molecular and epidemiologic analysis of dengue virus isolates from Somalia.

    PubMed

    Kanesa-thasan, N; Chang, G J; Smoak, B L; Magill, A; Burrous, M J; Hoke, C H

    1998-01-01

    Nucleotide sequence analysis was performed on 14 dengue virus isolates (13 dengue-2 viruses and 1 dengue-3 virus) recovered from febrile soldiers in Somalia in 1993. The dengue-2 viruses were most closely related to dengue-2 virus recovered in Somalia in 1984. However, differences in nucleotide sequence (0.35% to 1.35%) were evident among the 1993 isolates. These differences were closely associated with the geographic location of the infection as well as with different times of infection at the same location. Genetic difference between strains was not associated with differences in clinical features. Molecular analysis of dengue viruses is a useful adjunct to epidemiologic investigation of their distribution over distance and time.

  11. Biliary Tract Cancer: Epidemiology, Radiotherapy, and Molecular Profiling.

    PubMed

    Bridgewater, John A; Goodman, Karyn A; Kalyan, Aparna; Mulcahy, Mary F

    2016-01-01

    Biliary tract cancer, or cholangiocarcinoma, arises from the biliary epithelium of the small ducts in the periphery of the liver (intrahepatic) and the main ducts of the hilum (extrahepatic), extending into the gallbladder. The incidence and epidemiology of biliary tract cancer are fluid and complex. It is shown that intrahepatic cholangiocarcinoma is on the rise in the Western world, and gallbladder cancer is on the decline. Radiation therapy has emerged as an important component of adjuvant therapy for resected disease and definitive therapy for locally advanced disease. The emerging sophisticated techniques of imaging tumors and conformal dose delivery are expanding the indications for radiotherapy in the management of bile duct tumors. As we understand more about the molecular pathways driving biliary tract cancers, targeted therapies are at the forefront of new therapeutic combinations. Understanding the gene expression profile and mutational burden in biliary tract cancer allows us to better discern the pathogenesis and identify promising new developmental therapeutic targets.

  12. A molecular epidemiological study of human parainfluenza virus type 3 at a tertiary university hospital during 2013-2015 in Catalonia, Spain.

    PubMed

    Godoy, Cristina; Peremiquel-Trillas, Paula; Andrés, Cristina; Gimferrer, Laura; Uriona, Sonia María; Codina, María Gema; Armadans, Lluis; Martín, María Del Carmen; Fuentes, Francisco; Esperalba, Juliana; Campins, Magda; Pumarola, Tomàs; Antón, Andrés

    2016-10-01

    Human parainfluenza virus type 3 (HPIV-3) is one of the most common respiratory viruses particularly among young children and immunocompromised patients. The seasonality, prevalence and genetic diversity of HPIV-3 at a Spanish tertiary-hospital from 2013 to 2015 are reported. HPIV-3 infection was laboratory-confirmed in 102 patients (76%, under 5 years of age). Among <5 years-old patients, 9 (11.5%) were under any degree of immunosuppression, whereas this percentage was significantly higher (19; 79.2%) among patients older than 5 years. HPIV-3 was detected at varying levels, but mainly during spring and summer. All characterized HN/F sequences fell within C1b, C5 and in other two closely C3a-related groups. Furthermore, a new genetic lineage (C1c) was described. Genetic similarity and epidemiological data confirmed some nosocomial infections, highlighting the importance of the HPIV-3 surveillance, particularly in high-risk patients. This study provides valuable information on HPIV-3 diversity due to the scarce information in Europe.

  13. Molecular epidemiology of genital Chlamydia trachomatis infection in Shenzhen, China.

    PubMed

    Zhang, Juan-Juan; Zhao, Guang-Lu; Wang, Feng; Hong, Fu-Chang; Luo, Zhen-Zhou; Lan, Li-Na; Zhang, Chun-Lai; Peng, Yi; Liu, Xiao-Li; Feng, Tie-Jian; Chen, Xiang-Sheng

    2012-06-01

    To investigate molecular epidemiology of Chlamydia trachomatis infection among patients recruited from different clinic settings in Shenzhen, China. A total of 2534 patients from the sexually transmitted disease (STD) clinics, obstetrics and gynaecology (OBGYN) clinics and genitourinary medicine (GUM) clinics in 34 hospitals participated in the study. The C trachomatis infection was determined using COBAS Amplicor system. DNA extracted in C trachomatis-positive samples was amplified using a nested PCR based on ompA gene and then genotyped using a microsphere suspension array. The overall prevalence of genital C trachomatis infection was 17.7%. The prevalence in patients at STD or GUM clinics was significantly higher than that in patients at OBGYN clinics. Being male (adjusted OR (AOR) 2.5, 95% CI 1.8 to 3.4), having no consistent use of a condom with casual partners in the past 3 months (AOR 1.7, 95% CI 1.1 to 2.8) and having any STD symptoms (AOR 3.3, 95% CI 2.0 to 5.4) were independently associated with C trachomatis infection. Eight genotypes were identified. The most prevalent genotypes were F (22.3%), E (22.0%) and D/Da (12.7%). Other genotypes were G/Ga (8.0%), J (7.3%), K (2.7%), H (2.7%) and I/Ia (0.4%). Eighty-two samples (18.3%) were infected with multiple genotypes. Genotype D/Da among patients from GUM clinics was more common than those from STD or OBGYN clinics. Infections with genotypes G and F were statistically associated with abnormal vaginal discharge (p=0.001) and being married (p=0.014), respectively. Infection with multiple genotypes was more common among patients with a higher income (p=0.011). A substantial prevalence of genital C trachomatis infection in Shenzhen suggests the importance of detection and treatment of the infection in high-risk groups.

  14. Cutaneous Pythiosis in calves: An epidemiologic, pathologic, serologic and molecular characterization.

    PubMed

    Konradt, Guilherme; Bassuino, Daniele Mariath; Bianchi, Matheus Viezzer; Castro, Lismara; Caprioli, Rafaela Albuquerque; Pavarini, Saulo Petinatti; Santurio, Janio M; Azevedo, Maria Isabel; Jesus, Francielli P; Driemeier, David

    2016-12-01

    This study reports the epidemiological, pathological and mycological findings of cutaneous pythiosis in cattle in southern Brazil. 23 calves, that were kept next to a river with extensive marshy regions, presented ulcerated cutaneous lesions in thoracic and pelvic limbs, sometimes extending to the ventral thoracic region. Histopathological examination revealed multifocal pyogranulomas in the superficial and deep dermis. The Grocott-Methenamine silver, immunohistochemistry anti-Pythium insidiosum, ELISA serology and molecular characterization demonstrated the agent P. insidiosum in these cases.

  15. 77 FR 2072 - Proposed Collection; Comment Request; Prevalence, Incidence, Epidemiology and Molecular Variants...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-13

    ..., Epidemiology and Molecular Variants of HIV in Blood Donors in Brazil SUMMARY: In compliance with the..., Epidemiology and Molecular Variants of HIV in Blood Donors in Brazil. Type of Information Collection Request... prevalence and incidence rates, and identifying behavioral risk behaviors for HIV infection among donors...

  16. Mongoose rabies in southern Africa: a re-evaluation based on molecular epidemiology.

    PubMed

    Nel, L H; Sabeta, C T; von Teichman, B; Jaftha, J B; Rupprecht, C E; Bingham, J

    2005-05-01

    Relative to the developed world, rabies has been poorly studied in the vast African continent. The southern African countries of Zimbabwe and South Africa, however, are known to sustain a great diversity of lyssaviruses, with large biological variations amongst genotype 1 (rabies viruses) at present more apparent here than elsewhere on the continent. One recognized biotype of rabies virus in the subcontinent appears to be specifically adapted to a variety of mongooses, belonging to the Viverrinae subfamily (family Herpestidae) and are commonly referred to as viverrid viruses, although the term mongoose rabies would be more correct, considering the taxonomic status of the host species involved. It was our objective to study the genetic relationships of 77 rabies virus isolates of this mongoose biotype, isolated in South Africa and Zimbabwe, towards elucidation of the molecular epidemiology of this interesting group of African viruses. In our study of a 592 nucleotide sequence encompassing the cytoplasmic domain of the glycoprotein and the G-L intergenic region of the viral genomes, we provide the first comprehensive data on the molecular epidemiology of these viruses and indicate a history of extended evolutionary adaptation in this geographical domain. The molecular epidemiological observations reported here are highly unlikely to be limited to the small geographical areas of South Africa and Zimbabwe and illustrate the need for lyssavirus surveillance in the rest of sub-Saharan Africa and throughout the entire continent.

  17. A prospective, molecular epidemiology study of EGFR mutations in Asian patients with advanced non-small-cell lung cancer of adenocarcinoma histology (PIONEER).

    PubMed

    Shi, Yuankai; Au, Joseph Siu-Kie; Thongprasert, Sumitra; Srinivasan, Sankar; Tsai, Chun-Ming; Khoa, Mai Trong; Heeroma, Karin; Itoh, Yohji; Cornelio, Gerardo; Yang, Pan-Chyr

    2014-02-01

    PIONEER (NCT01185314) was a prospective, multinational, epidemiological study of epidermal growth factor receptor (EGFR) mutations in patients from Asia with newly diagnosed advanced lung adenocarcinoma. Eligible patients (aged ≥20 years) had untreated stage IIIB/IV adenocarcinoma. The EGFR mutation status (primary end point: positive, negative, or undetermined) of tumor samples (biopsy, surgical specimen, or cytology) was determined (Scorpion amplification refractory mutation system). EGFR mutation frequency was calculated and compared between demographic and clinical subgroups. Of 1482 patients from seven Asian regions, 43.4% of patients were female, median age was 60 years (range, 17-94), and 52.6% of patients were never-smokers. EGFR mutation status was evaluable in tumors from 1450 patients (97.8%) (746 [51.4%] positive; 704 [48.6%] negative). Country, sex, ethnicity, smoking status, pack-years (all p < 0.001), disease stage (p = 0.009), and histology type (p = 0.016) correlated significantly with EGFR mutation frequency. Mutation frequency was 61.1% in females, 44.0% in males; lower in patients from India (22.2%) compared with other areas (47.2%-64.2%); highest among never-smokers (60.7%); and decreased as pack-year number increased (>0-10 pack-years, 57.9%; >50 pack-years, 31.4%) (similar trend by sex). Ethnic group (p < 0.001) and pack-years (p < 0.001) had statistically significant associations with mutation frequency (multivariate analysis); sex was not significant when adjusted for smoking status. PIONEER is the first prospective study to confirm high EGFR mutation frequency (51.4% overall) in tumors from Asian patients with adenocarcinoma. The observed high mutation frequency in demographic/clinical subgroups compared with white populations suggests that mutation testing should be considered for all patients with stage IIIB/IV adenocarcinoma, even males and regular smokers, among Asian populations.

  18. Development of search filters for retrieval of literature on the molecular epidemiology of cancer.

    PubMed

    Ugolini, Donatella; Neri, Monica; Casilli, Cristina; Bonassi, Stefano

    2010-08-30

    The available tools for searching literature in the area of molecular epidemiology of cancer, a relatively novel discipline, are largely unsatisfactory. The aim of this project was to develop two search filters in MEDLINE that would facilitate the retrieval of studies on cancer molecular epidemiology and to compare their performance. Citations of all articles published in 2007 in three top journals in this area were hand-screened to establish a gold standard reference set of relevant papers. Two filters were created with this set: the first was based on the frequency of descriptors listed in the National Library of Medicine (NLM) Medical Subject Headings Thesaurus (MeSH terms) only, the second was based on the frequency of words in titles and abstracts (text-words), besides MeSH terms. The sensitivity, specificity, precision and accuracy rates of the two filters were calculated as performance measures. Out of all 1602 published articles, 344 were found to be pertinent to cancer molecular epidemiology; these formed the gold standard set. The first filter was the most specific (99%) and showed a good precision (93.2%), the second showed a higher sensitivity (78.2%) and accuracy (91.6%). The two filters proposed here represent a balance between sensitivity and specificity. Redefinition and elaboration of more appropriate NLM MeSH terms could greatly facilitate the retrieval of studies on the molecular epidemiology of cancer. Authors themselves could facilitate this by inserting adequate words in title or abstract of their articles. 2010 Elsevier B.V. All rights reserved.

  19. Molecular epidemiology and phylogeography of Schistosoma mansoni around Lake Victoria.

    PubMed

    Standley, C J; Kabatereine, N B; Lange, C N; Lwambo, N J S; Stothard, J R

    2010-11-01

    Intestinal schistosomiasis continues to be a major public health problem in sub-Saharan Africa, and is endemic in communities around Lake Victoria. Interest is growing in the molecular evolution and population genetic structure of Schistosoma mansoni and we describe a detailed analysis of the molecular epidemiology and phylogeography of S. mansoni from Lake Victoria. In total, 388 cytochrome oxidase 1 (COI) sequences were obtained from 25 sites along the Ugandan, Tanzanian and Kenyan shorelines of Lake Victoria, and 122 unique barcodes were identified; 9 corresponded to previously discovered barcodes from Lakes Victoria and Albert. A subset of the data, composed of COI sequences from miracidia from 10 individual children, was used for population genetics analyses; these results were corroborated by microsatellite analysis of 4 isolates of lab-passaged adult worms. Overall, 12 barcodes were found to be shared across all 3 countries, whereas the majority occurred singly and were locally restricted. The population genetics analyses were in agreement in revealing high diversity at the level of the human host and negligible population structuring by location. The lack of correlation between genetic distance and geographical distance in these data may be attributed to the confounding influence of high intra-individual diversity as well as human migration between communities.

  20. 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.

  1. Molecular Pathologic Epidemiology of Colorectal Neoplasia: An Emerging Transdisciplinary and Interdisciplinary Field

    PubMed Central

    Ogino, Shuji; Chan, Andrew T.; Fuchs, Charles S.; Giovannucci, Edward

    2011-01-01

    Colorectal cancer is a complex disease resulting from somatic genetic and epigenetic alterations, including locus-specific CpG island methylation and global DNA or LINE-1 hypomethylation. Global molecular characteristics such as microsatellite instability (MSI), CpG island methylator phenotype (CIMP), global DNA hypomethylation, and chromosomal instability cause alterations of gene function in a genome-wide scale. Activation of oncogenes including KRAS, BRAF and PIK3CA affects intracellular signaling pathways and has been associated with CIMP and MSI. Traditional epidemiology research has investigated various factors in relation to an overall risk of colon and/or rectal cancer. However, colorectal cancers comprise a heterogeneous group of diseases with different sets of genetic and epigenetic alterations. To better understand how a particular exposure influences the carcinogenic process, somatic molecular changes and tumor biomarkers have been studied in relation to the exposure of interest. Moreover, an investigation of interactive effects of tumor molecular changes and the exposures of interest on tumor behavior (prognosis or clinical outcome) can lead to a better understanding of tumor molecular changes, which may be prognostic or predictive tissue biomarkers. These new research efforts represent “Molecular Pathologic Epidemiology”, which is a multidisciplinary field of investigations of the interrelationship between exogenous and endogenous (e.g., genetic) factors, tumoral molecular signatures and tumor progression. Furthermore, integrating genome-wide association studies (GWAS) with molecular pathologic investigation is a promising area. Examining the relationship between susceptibility alleles identified by GWAS and specific molecular alterations can help elucidate the function of these alleles and provide insights into whether susceptibility alleles are truly causal. Although there are challenges, molecular pathologic epidemiology has unique strengths

  2. Epidemiological studies of esophageal cancer in the era of genome-wide association studies

    PubMed Central

    Wang, An-Hui; Liu, Yuan; Wang, Bo; He, Yi-Xuan; Fang, Ye-Xian; Yan, Yong-Ping

    2014-01-01

    Esophageal cancer (EC) caused about 395000 deaths in 2010. China has the most cases of EC and EC is the fourth leading cause of cancer death in China. Esophageal squamous cell carcinoma (ESCC) is the predominant histologic type (90%-95%), while the incidence of esophageal adenocarcinoma (EAC) remains extremely low in China. Traditional epidemiological studies have revealed that environmental carcinogens are risk factors for EC. Molecular epidemiological studies revealed that susceptibility to EC is influenced by both environmental and genetic risk factors. Of all the risk factors for EC, some are associated with the risk of ESCC and others with the risk of EAC. However, the details and mechanisms of risk factors involved in the process for EC are unclear. The advanced methods and techniques used in human genome studies bring a great opportunity for researchers to explore and identify the details of those risk factors or susceptibility genes involved in the process of EC. Human genome epidemiology is a new branch of epidemiology, which leads the epidemiology study from the molecular epidemiology era to the era of genome wide association studies (GWAS). Here we review the epidemiological studies of EC (especially ESCC) in the era of GWAS, and provide an overview of the general risk factors and those genomic variants (genes, SNPs, miRNAs, proteins) involved in the process of ESCC. PMID:25133033

  3. The virulence phenotypes and molecular epidemiological characteristics of Vibrio fluvialis in China

    PubMed Central

    2013-01-01

    Background Vibrio fluvialis is considered to be an emerging foodborne pathogen and has been becoming a high human public health hazard all over the world, especially in coastal areas of developing countries and regions with poor sanitation. The distribution of virulence factors, microbiological and molecular epidemiological features of V. fluvialis isolates in China remains to be examined. Methods and results PCR targeted at the virulence determinants and phenotype tests including metabolism, virulence and antibiotic susceptibility were performed. Pulsed-field gel electrophoresis (PFGE) analysis was used to access the relatedness of isolates. A strain with deletion of the arginine dihydrolase system was first reported and proved in molecular level by PCR. Virulence genes vfh, hupO and vfpA were detected in all strains, the ability to produce hemolysin, cytotxin, protease and biofilm formation varied with strains. High resistance rate to β-lactams, azithromycin and sulfamethoxazole were observed. Twenty-seven percent of test strains showed resistant to two and three antibiotics. PFGE analysis demonstrated great genetic heterogeneity of test V. fluvialis strains. Conclusion This study evaluated firstly the biological characteristics and molecular epidemiological features of V. fluvialis in China. Some uncommon biochemical characteristics were found. Virulence genes were widely distributed in the isolates from patient and seafood sources, and the occurrence of virulence phenotypes varied with strains. Continued and enhanced laboratory based-surveillance is needed in the future together with systematically collection of the epidemiological information of the cases or the outbreaks. PMID:23522652

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

    PubMed

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

    2015-12-08

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

  5. 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. Copyright © 2016 Hainan Medical College. Production and hosting by Elsevier B.V. All rights reserved.

  6. Molecular Epidemiology of Staphylococcus aureus in the General Population in Northeast Germany: Results of the Study of Health in Pomerania (SHIP-TREND-0)

    PubMed Central

    Holtfreter, Silva; Grumann, Dorothee; Balau, Veronika; Barwich, Annette; Kolata, Julia; Goehler, André; Weiss, Stefan; Holtfreter, Birte; Bauerfeind, Stephanie S.; Döring, Paula; Friebe, Erika; Haasler, Nicole; Henselin, Kristin; Kühn, Katrin; Nowotny, Sophie; Radke, Dörte; Schulz, Katrin; Schulz, Sebastian R.; Trübe, Patricia; Vu, Chi Hai; Walther, Birgit; Westphal, Susanne; Cuny, Christiane; Witte, Wolfgang; Völzke, Henry; Grabe, Hans Jörgen; Kocher, Thomas; Steinmetz, Ivo

    2016-01-01

    Population-based studies on Staphylococcus aureus nasal colonization are scarce. We examined the prevalence, resistance, and molecular diversity of S. aureus in the general population in Northeast Germany. Nasal swabs were obtained from 3,891 adults in the large-scale population-based Study of Health in Pomerania (SHIP-TREND). Isolates were characterized using spa genotyping, as well as antibiotic resistance and virulence gene profiling. We observed an S. aureus prevalence of 27.2%. Nasal S. aureus carriage was associated with male sex and inversely correlated with age. Methicillin-resistant S. aureus (MRSA) accounted for 0.95% of the colonizing S. aureus strains. MRSA carriage was associated with frequent visits to hospitals, nursing homes, or retirement homes within the previous 24 months. All MRSA strains were resistant to multiple antibiotics. Most MRSA isolates belonged to the pandemic European hospital-acquired MRSA sequence type 22 (HA-MRSA-ST22) lineage. We also detected one livestock-associated MRSA ST398 (LA-MRSA-ST398) isolate, as well as six livestock-associated methicillin-susceptible S. aureus (LA-MSSA) isolates (clonal complex 1 [CC1], CC97, and CC398). spa typing revealed a diverse but also highly clonal S. aureus population structure. We identified a total of 357 spa types, which were grouped into 30 CCs or sequence types. The major seven CCs (CC30, CC45, CC15, CC8, CC7, CC22, and CC25) included 75% of all isolates. Virulence gene patterns were strongly linked to the clonal background. In conclusion, MSSA and MRSA prevalences and the molecular diversity of S. aureus in Northeast Germany are consistent with those of other European countries. The detection of HA-MRSA and LA-MRSA within the general population indicates possible transmission from hospitals and livestock, respectively, and should be closely monitored. PMID:27605711

  7. Scotomas in molecular virology and epidemiology of hepatitis C virus.

    PubMed

    Wang, Yue

    2013-11-28

    In the 1970s, scientists learned of a new pathogen causing non-A, non-B hepatitis. Classical approaches were used to isolate and characterize this new pathogen, but it could be transmitted experimentally only to chimpanzees and progress was slow until the pathogen was identified as hepatitis C virus (HCV) in 1989. Since then, research and treatment of HCV have expanded with the development of modern biological medicine: HCV genome organization and polyprotein processing were delineated in 1993; the first three-dimensional structure of HCV nonstructural protein (NS3 serine protease) was revealed in 1996; an infectious clone of HCV complementary DNA was first constructed in 1997; interferon and ribavirin combination therapy was established in 1998 and the therapeutic strategy gradually optimized; the HCV replicon system was produced in 1999; functional HCV pseudotyped viral particles were described in 2003; and recombinant infectious HCV in tissue culture was produced successfully in 2005. Recently, tremendous advances in HCV receptor discovery, understanding the HCV lifecycle, decryption of the HCV genome and proteins, as well as new anti-HCV compounds have been reported. Because HCV is difficult to isolate and culture, researchers have had to avail themselves to the best of modern biomedical technology; some of the major achievements in HCV research have not only advanced the understanding of HCV but also promoted knowledge of virology and cellular physiology. In this review, we summarize the advancements and remaining scotomas in the molecular virology and epidemiology of HCV.

  8. Molecular epidemiology, cancer-related symptoms, and cytokines pathway

    PubMed Central

    Reyes-Gibby, Cielito C; Wu, Xifeng; Spitz, Margaret; Kurzrock, Razelle; Fisch, Michael; Bruera, Eduardo; Shete, Sanjay

    2012-01-01

    The Human Genome Project and HapMap have led to a better appreciation of the importance of common genetic variation in determining cancer risk, created potential for predicting response to therapy, and made possible the development of targeted prevention and therapeutic interventions. Advances in molecular epidemiology can be used to explore the role of genetic variation in modulating the risk for severe and persistent symptoms, such as pain, depression, and fatigue, in patients with cancer. The same genes that are implicated in cancer risk might also be involved in the modulation of therapeutic outcomes. For example, polymorphisms in several cytokine genes are potential markers for genetic susceptibility both for cancer risk and for cancer-related symptoms. These genetic polymorphisms are stable markers and easily and reliably assayed to explore the extent to which genetic variation might prove useful in identifying patients with cancer at high-risk of symptom development. Likewise, they could identify subgroups who might benefit most from symptom intervention, and contribute to developing personalised and more effective therapies for persistent symptoms. PMID:18672213

  9. 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

  10. Molecular epidemiology of Staphylococcus epidermidis in neonatal intensive care units.

    PubMed

    Soeorg, Hiie; Huik, Kristi; Parm, Ülle; Ilmoja, Mari-Liis; Metsvaht, Tuuli; Lutsar, Irja

    2017-01-01

    Late-onset sepsis (LOS) in preterm neonates is increasingly reported to be associated with gut-colonizing Staphylococcus epidermidis. We aimed to describe the molecular epidemiology of S. epidermidis colonizing the gut of neonates hospitalized in two neonatal intensive care units. S. epidermidis from rectal swabs were typed by multilocus variable-number tandem-repeat analysis (MLVA), randomly chosen isolates of predominant MLVA types additionally by multilocus sequence typing. Antimicrobial susceptibility, the presence of icaA, IS256, arginine catabolic mobile element (ACME), agr type, and SCCmec type were determined. Of 276 neonates (38.4%), 106 were colonized with S. epidermidis, yielding a total of 139 isolates (62 in one unit and 77 in another unit). Of the 55 MLVA types identified, the five predominant detected in both units corresponded to sequence type (ST) 2, ST5, and ST59 or its single locus variant ST81 and formed three major MLVA clonal complexes accounting for 74.8% of all isolates. Overall, the prevalence of mecA, icaA, IS256, and ACME was 91.4%, 28.1%, 64%, and 77%, respectively. Of the mecA-positive isolates (n = 127), 43.9% carried SCCmec type IV. Of eight episodes of LOS, four were caused by ST2 and two by ST5. Preventing gut colonization with nosocomial epidemic S. epidermidis in hospitalized neonates could contribute to the prevention of LOS.

  11. An exercise in molecular epidemiology: human rhinovirus prevalence and genetics.

    PubMed

    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 for classifying new isolates of HRV were reported. The genetic change of this virus in specific populations over time is of great interest to understand the evolution and epidemiology of viruses. To facilitate the collections of HRV sequences over a number of years, a virology experiment was designed in which students test nasal lavage samples to look for HRV infection. Students will learn a variety of techniques including RNA isolation, cDNA synthesis, qPCR, and agarose gel electrophoresis as well as bioinformatic skills though examination of sequences from the HRV-field isolates. Furthermore, students can look at symptom data from subjects to investigate correlations between symptom severity and factors such as stress and sleep patterns. Such information can be used to examine hypotheses regarding HRV mutation, symptom severity and epidemiology. Copyright © 2011 Wiley Periodicals, Inc.

  12. Coffee and cancer risk, epidemiological evidence, and molecular mechanisms.

    PubMed

    Bøhn, Siv Kjølsrud; Blomhoff, Rune; Paur, Ingvild

    2014-05-01

    Although early studies suggested that coffee consumption might increase risk of some cancers, more comprehensive epidemiological and experimental data now generally indicate either neutral or beneficial effects. In this review, we summarize the current evidence for associations between breast, prostate, colorectal, and liver cancers and the consumption of coffee, and discuss the experimental evidence for potential chemopreventive mechanisms of coffee and coffee constituents. The epidemiological evidence consistently indicates that coffee protects against liver cancer, and also point toward protective effects for risk of colorectal cancers (with relative risks of 0.50 (95% CI: 0.42-0.59) and 0.83 (95% CI: 0.75-0.92), respectively, in the most recent meta-analyses). There seems to be no association between the overall risk of breast and prostate cancer and coffee intake. However, for subgroups such as postmenopausal breast cancers, advanced prostate cancers, and breast and prostate cancer survivors, an inverse association with coffee intake is indicated. Potential mechanisms for chemopreventive effects of coffee phytochemicals includes inhibition of oxidative stress and oxidative damage, regulation of DNA repair, phase II enzymatic activity, apoptosis, inflammation, as well as having antiproliferative, antiangiogenetic effects and antimetastatic effects. The experimental evidence for effects of coffee and coffee constituents on each of these processes is discussed.

  13. Epidemiologic study and molecular detection of Leishmania and sand fly species responsible of cutaneous leishmaniasis in Foum Jamâa (Azilal, Atlas of Morocco).

    PubMed

    Arroub, Hassan; Hamdi, Salsabil; Ajaoud, Malika; Habbari, Khalid; Lemrani, Meryem

    2013-07-01

    The region of Foum Jamâa (province of Azilal) has become endemic for cutaneous leishmaniasis (CL) since 2006. The objective of this study was to investigate molecular identification of the etiological agent of CL in this region; we also carried out an entomological survey of Phlebotomine sand flies (Diptera: Psychodidae) in this focus to study the sand fly fauna, species composition, and the monthly prevalence of sand flies during 1 year. In the period between 2009 and 2010, skin scrapings spotted on glass slides were collected from 119 patients, aged from 9 months to 70 years old, who came from 43 localities distributed in 3 sectors in Foum Jamâa (FJ). The ITS1 PCR-RFLP was used to identify the Leishmania parasite responsible for the recent cases of CL in FJ. Our results revealed that the disease is caused by L. tropica. No significant association was observed between gender and the rate of CL in presenting patients, while the highest rate of positive lesions was found in the age group of 9 years old or under (86.67%). In this study, we found also that L. tropica infection mostly caused single lesions (67.90%) that were located in the face (96.30%). Morphological identification was performed on a total of 1152 sand flies (23% females and 77% males) collected by sticky paper traps. 57% of the total collected flies were identified as Phlebotomus (Paraphlebotomus) sergenti (Parrot). Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Molecular pathological epidemiology of colorectal cancer in Chinese patients with KRAS and BRAF mutations

    PubMed Central

    Li, Wenbin; Qiu, Tian; Ling, Yun; Guo, Lei; Li, Lin; Ying, Jianming

    2015-01-01

    An investigation of interactive effects of exogenous and endogenous factors and tumor molecular changes can lead to a better understanding of tumor molecular signatures in colorectal cancer. We here report a molecular pathological epidemiology study in a large cohort of 945 colorectal cancer patients. Mutations of KRAS (36.6%) and BRAF (3.46%) were nearly mutually exclusive. KRAS-mutated tumors were more common in female patients (odds ratio [OR] = 1.68; P = 0.0001) and never smokers (OR = 1.60; P = 0.001). Whereas BRAF-mutated tumors demonstrated no discrepancy in aspects of gender and smoking status compared with wild-type tumors. In addition, tumors with BRAF or KRAS mutations were in correlation with elevated serum level of carbohydrate antigen (CA19-9) and carcinoma embryonic antigen (CEA) and the combination of serum biomarkers and molecular mutation status may enhance the more precise risk stratification of CRC patients. Further studies are needed to define the mechanism brought about by the aforementioned epidemiologic and clinicopathologic characteristics that may help optimize cancer prevention and precision therapy. PMID:26530529

  15. 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

  16. Molecular subtyping of human T-cell lymphotropic virus type 2 by single-strand conformation polymorphism analysis. Retrovirus Epidemiology Donor Study Group.

    PubMed Central

    Heneine, W; Switzer, W M; Busch, M; Khabbaz, R F; Kaplan, J E

    1995-01-01

    Molecular subtyping of human T-cell lymphotropic virus type 2 (HTLV-2) by the currently used method of restriction fragment length polymorphism analysis may not be sufficiently discriminatory for transmission studies because of the predominance of single restriction types in various HTLV-2-infected populations. The utility of single-strand conformations polymorphism (SSCP) analysis was evaluated as a tool to improve the sensitivity of the subtyping of HTLV-2. The assay was designed to target a highly variable region in the long terminal repeat and was shown to be able to detect single nucleotide changes in cloned HTLV-2 sequences. Analysis of 52 HTLV-2 samples, of which 32 were from 16 sex partner pairs (16 males, 16 females), showed nine different SSCP patterns. Identical SSCP results were obtained for each of the 16 couples, suggesting the presence of similar viral genotypes and, therefore, supporting the likelihood of sexual transmission of HTLV-2 in each of these couples. Furthermore, SSCP analysis of seven HTLV-2 samples of the same restriction type (b5) showed five different SSCP patterns. Nucleotide sequencing of two samples with distinct SSCP patterns confirmed the sequence differences. SSCP provides a facile and discriminatory tool for the differentiation of HTLV-2 strains, including those previously indistinguishable by restriction fragment length polymorphism. PMID:8586713

  17. [Molecular markers: an important tool in the diagnosis, treatment and epidemiology of invasive aspergillosis].

    PubMed

    Frías-de León, María Guadalupe; Acosta-Altamirano, Gustavo; Duarte-Escalante, Esperanza; Martínez-Hernández, José Enrique; Martínez-Rivera, María de Los Ángeles; Reyes-Montes, María Del Rocío

    2014-01-01

    Increase in the incidence of invasive aspergillosis has represented a difficult problem for management of patients with this infection due to its high rate of mortality, limited knowledge concerning its diagnosis, and therapeutic practice. The difficulty in management of patients with aspergillosis initiates with detection of the fungus in the specimens of immunosuppressed patients infected with Aspergillus fumigatus; in addition, difficulty exists in terms of the development of resistance to antifungals as a consequence of their indiscriminate use in prophylactic and therapeutic practice and to ignorance concerning the epidemiological data of aspergillosis. With the aim of resolving these problems, molecular markers is employed at present with specific and accurate results. However, in Mexico, the use of molecular markers has not yet been implemented in the routine of intrahospital laboratories; despite the fact that these molecular markers has been widely referred in the literature, it is necessary for it to validated and standardized to ensure that the results obtained in any laboratory would be reliable and comparable. In the present review, we present an update on the usefulness of molecular markers in accurate identification of A. fumigatus, detection of resistance to antifugal triazoles, and epidemiological studies for establishing the necessary measures for prevention and control of aspergillosis.

  18. Colorectal Cancer Epidemiology in the Nurses' Health Study.

    PubMed

    Lee, Dong Hoon; Keum, NaNa; Giovannucci, Edward L

    2016-09-01

    To review the contribution of the Nurses' Health Study (NHS) to identifying risk and protective factors for colorectal adenomas and colorectal cancer (CRC). We performed a narrative review of the publications using the NHS between 1976 and 2016. 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. 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.

  19. 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

  20. Molecular pathological epidemiology of epigenetics: emerging integrative science to analyze environment, host, and disease.

    PubMed

    Ogino, Shuji; Lochhead, Paul; Chan, Andrew T; Nishihara, Reiko; Cho, Eunyoung; Wolpin, Brian M; Meyerhardt, Jeffrey A; Meissner, Alexander; Schernhammer, Eva S; Fuchs, Charles S; Giovannucci, Edward

    2013-04-01

    Epigenetics acts as an interface between environmental/exogenous factors, cellular responses, and pathological processes. Aberrant epigenetic signatures are a hallmark of complex multifactorial diseases (including neoplasms and malignancies such as leukemias, lymphomas, sarcomas, and breast, lung, prostate, liver, and colorectal cancers). Epigenetic signatures (DNA methylation, mRNA and microRNA expression, etc) may serve as biomarkers for risk stratification, early detection, and disease classification, as well as targets for therapy and chemoprevention. In particular, DNA methylation assays are widely applied to formalin-fixed, paraffin-embedded archival tissue specimens as clinical pathology tests. To better understand the interplay between etiological factors, cellular molecular characteristics, and disease evolution, the field of 'molecular pathological epidemiology (MPE)' has emerged as an interdisciplinary integration of 'molecular pathology' and 'epidemiology'. In contrast to traditional epidemiological research including genome-wide association studies (GWAS), MPE is founded on the unique disease principle, that is, each disease process results from unique profiles of exposomes, epigenomes, transcriptomes, proteomes, metabolomes, microbiomes, and interactomes in relation to the macroenvironment and tissue microenvironment. MPE may represent a logical evolution of GWAS, termed 'GWAS-MPE approach'. Although epigenome-wide association study attracts increasing attention, currently, it has a fundamental problem in that each cell within one individual has a unique, time-varying epigenome. Having a similar conceptual framework to systems biology, the holistic MPE approach enables us to link potential etiological factors to specific molecular pathology, and gain novel pathogenic insights on causality. The widespread application of epigenome (eg, methylome) analyses will enhance our understanding of disease heterogeneity, epigenotypes (CpG island methylator

  1. 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…

  2. 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…

  3. Molecular epidemiology of Crimean-Congo hemorrhagic fever in Bulgaria--An update.

    PubMed

    Papa, Anna; Pappa, Styliani; Panayotova, Elitsa; Papadopoulou, Elpida; Christova, Iva

    2016-05-01

    Crimean-Congo hemorrhagic fever (CCHF) is endemic in Bulgaria. During 2013-2014, 11 confirmed CCHF cases have been reported in the country (seven in 2013 and four in 2014). The present study provides the CCHF molecular epidemiology in Bulgaria based on all currently available S, M, and L RNA segment nucleotide sequences spanning the years 1978-2014. A relatively low genetic difference (0-6%, the maximum seen in the M RNA segment) was seen among the CCHFV sequences suggesting that a slow evolving CCHFV strain belonging to "Europe 1" clade is present in Bulgaria. Although the virus emerged in new foci during the recent years, it is more active in the established endemic foci which seem to offer the most suitable ecosystem and environment. Understanding the CCHF epidemiology and virus evolution is the basis for public health programs and vaccine design.

  4. Epidemiological study of dental caries.

    PubMed

    Venugopal, T; Kulkarni, V S; Nerurker, R A; Damle, S G; Patnekar, P N

    1998-01-01

    A total of 2000 children (1-14 year age group) attending pediatric OPD, school clinic & well body clinic of Dr. R.N. Cooper Municipal Hospital & K.E.M Hospital, Mumbai were examined for caries prevalence and 35.6% had dental caries. Parental income was not shown to have any bearing on caries prevalence. Parental literacy, particularly maternal literacy was shown to influence caries prevalence in children. The prevalence was low in well-nourished children and in those taking vegetarian type of diet. Frequency of sweet consumption was shown to be associated with prevalence of dental caries. In 1-4 year age group it was noted that bottle fed children were more affected by dental caries. Tooth brush with paste was the commonest method used for cleaning their teeth in all age groups in our study. Caries prevalence was low in those children using tooth brush than in those using tooth powder. Those children who were using neem datun were found to be less affected with dental caries. Dental caries was also found to be low in those who rinsed their mouth with water after food.

  5. Molecular epidemiology of Echovirus 30 in Taiwan, 1988-2008.

    PubMed

    Ke, Guan-Ming; Lin, Kuei-Hsiang; Lu, Po-Liang; Tung, Yi-Chin; Wang, Chu-Feng; Ke, Liang-Yin; Lee, Min-Sheng; Lin, Pei-Chin; Su, Hui-Ju; Lin, Yi-Ying; Huang, Tzu-Ping; Wang, Jen-Ren; Wang, Sheng-Yu; Hsu, Li-Ching; Chu, Pei-Yu

    2011-04-01

    To investigate the molecular epidemiology of Taiwanese Echovirus 30 (E-30) strains, we analyzed the 876 bp sequence of the VP1 gene from 32 Taiwanese strains isolated in 1988-2008, 498 reference sequences, and one Echovirus 21 strain as the out-group. Phylogenetic analysis detected six E-30 genotypes (designated GI-GVI) that had circulated globally during the past five decades. The genotypes varied widely in geographic distribution and circulation half-life. The GI, GII, and GV were ancient genotypes in which the first strains emerged in the 1950s. The GIII was a reemerging genotype, in which strains had first appeared in Colombia in 1995 before reemerging in the New Independent States (NIS) in 2003. The GIV, an emerging genotype that recently appeared in Asia in 2003, was closely related to the ancient genotypes. The GVI was the circulating genotype, which included eight clusters (A-H) that had circulated since 1967. No GVI-A, C, D, or E strains have been identified during the past 10 years. The GVI-B first appeared in China in 1984 and later in Russia and Asia in the 2000s. The GVI-F, G, and H strains, which comprised the prevalent clusters, had been dominant in Asia Pacific area, globally, and Europe, respectively. Taiwanese strains were classified into GVI-D (1988-1989), GVI-F (1993-2004), and GVI-G (1993-2008). The quiescence period of E-30 is longer in Taiwan (5-8 years) than in other countries (3-5 years).

  6. 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...

  7. 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...

  8. [Social inequality and epidemiological studies: a reflection].

    PubMed

    Ferreira, Maria Angela Fernandes; Latorre, Maria do Rosário Dias de Oliveira

    2012-09-01

    Social indicators are now indispensable in the list of variables of epidemiological studies, based on the fact that the determination of health complaints is complex and multidimensional. From this perspective, social inequality has gained prominence as an explanatory factor for the health conditions of populations. The scope of this article is to discuss the different concepts that underpin the selection of the indicators used in epidemiological studies and examine the psychosocial effects on human beings caused by social inequality. A literature review of epidemiological studies that used social inequality and social capital indicators was conducted for a better understanding of health problems, as well as an investigation in the fields of sociology and social psychology. The research revealed that there is some controversy surrounding the effect of social inequality on health, possibly because these indicators are predominantly based on income and individual consumption capacity. Likewise, social capital indicators at cognitive and structural levels are too limited to understand the dynamism of social relations. Accordingly, further studies are needed for the construction of social indicators capable of examining the complexity of modern societies.

  9. Epidemiologic study of tumors in dinosaurs.

    PubMed

    Rothschild, B M; Tanke, D H; Helbling, M; Martin, L D

    2003-11-01

    Occasional reports in isolated fragments of dinosaur bones have suggested that tumors might represent a population phenomenon. Previous study of humans has demonstrated that vertebral radiology is a powerful diagnostic tool for population screening. The epidemiology of tumors in dinosaurs was here investigated by fluoroscopically screening dinosaur vertebrae for evidence of tumors. Computerized tomography (CT) and cross-sections were obtained where appropriate. Among more than 10,000 specimens x-rayed, tumors were only found in Cretaceous hadrosaurs (duck-billed dinosaurs). These included hemangiomas and metastatic cancer (previously identified in dinosaurs), desmoplastic fibroma, and osteoblastoma. The epidemiology of tumors in dinosaurs seems to reflect a familial pattern. A genetic propensity or environmental mutagens are suspected.

  10. Real-Time Molecular Epidemiology of Tuberculosis by Direct Genotyping of Smear-Positive Clinical Specimens

    PubMed Central

    Alonso, María; Herranz, Marta; Martínez Lirola, Miguel; González-Rivera, Milagros; Bouza, Emilio

    2012-01-01

    We applied MIRU-VNTR (mycobacterial interspersed repetitive-unit–variable-number tandem-repeat typing) to directly analyze the bacilli present in 61 stain-positive specimens from tuberculosis patients. A complete MIRU type (24 loci) was obtained for all but one (no amplification in one locus) of the specimens (98.4%), and the allelic values fully correlated with those obtained from the corresponding cultures. Our study is the first to demonstrate that real-time genotyping of Mycobacterium tuberculosis can be achieved, fully transforming the way in which molecular epidemiology techniques can be integrated into control programs. PMID:22378907

  11. 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.

  12. 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…

  13. 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…

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    PubMed

    López, Myriam Consuelo; León, Cielo M; Fonseca, Jairo; Reyes, Patricia; Moncada, Ligia; Olivera, Mario J; Ramírez, Juan David

    2015-01-01

    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. 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. 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. moshkovskii may have.

  16. Clinical and molecular epidemiology of veterinary blastomycosis in Wisconsin

    PubMed Central

    2013-01-01

    Background Several studies have shown that Blastomyces dermatitidis, the etiologic agent of blastomycosis, is a genetically diverse pathogen. Blastomycosis is a significant health issue in humans and other mammals. Veterinary and human isolates matched with epidemiological case data from the same geographic area and time period were used to determine: (i) if differences in genetic diversity and structure exist between clinical veterinary and human isolates of B. dermatitidis and (ii) if comparable epidemiologic features differ among veterinary and human blastomycosis cases. Results Genetic typing of 301 clinical B. dermatitidis isolates produced 196 haplotypes (59 unique to veterinary isolates, 134 unique to human isolates, and 3 shared between canine and human isolates). Private allelic richness was higher in veterinary (median 2.27) compared to human isolates (median 1.14) (p = 0.005). Concordant with previous studies, two distinct genetic groups were identified among all isolates. Genetic group assignment was different between human and veterinary isolates (p < 0.001), with more veterinary isolates assigned to Group 2. The mean age of dogs diagnosed with blastomycosis was 6 years. Thirty cases were in male dogs (52%) and 24 were females (41%). The breed of dog was able to be retrieved in 38 of 58 cases with 19 (50%) being sporting breeds. Three of four felines infected with blastomycosis were domestic shorthair males between ages 6–12, and presented with disseminated disease. The other was a lynx with pulmonary disease. The equine isolate was from an 11-year-old male Halflinger with disseminated disease. Disseminated disease was reported more often in veterinary (62%) than human cases (19%) (p < 0.001). Conclusions Isolates from all hosts clustered largely into previously identified genetic groups, with 3 haplotypes being shared between human and canine isolates confirming that B. dermatitidis isolates capable of infecting both species occur in nature. Allelic

  17. Clinical and molecular epidemiology of veterinary blastomycosis in Wisconsin.

    PubMed

    Anderson, Jennifer L; Sloss, Brian L; Meece, Jennifer K

    2013-04-22

    Several studies have shown that Blastomyces dermatitidis, the etiologic agent of blastomycosis, is a genetically diverse pathogen. Blastomycosis is a significant health issue in humans and other mammals. Veterinary and human isolates matched with epidemiological case data from the same geographic area and time period were used to determine: (i) if differences in genetic diversity and structure exist between clinical veterinary and human isolates of B. dermatitidis and (ii) if comparable epidemiologic features differ among veterinary and human blastomycosis cases. Genetic typing of 301 clinical B. dermatitidis isolates produced 196 haplotypes (59 unique to veterinary isolates, 134 unique to human isolates, and 3 shared between canine and human isolates). Private allelic richness was higher in veterinary (median 2.27) compared to human isolates (median 1.14) (p = 0.005). Concordant with previous studies, two distinct genetic groups were identified among all isolates. Genetic group assignment was different between human and veterinary isolates (p < 0.001), with more veterinary isolates assigned to Group 2. The mean age of dogs diagnosed with blastomycosis was 6 years. Thirty cases were in male dogs (52%) and 24 were females (41%). The breed of dog was able to be retrieved in 38 of 58 cases with 19 (50%) being sporting breeds. Three of four felines infected with blastomycosis were domestic shorthair males between ages 6-12, and presented with disseminated disease. The other was a lynx with pulmonary disease. The equine isolate was from an 11-year-old male Halflinger with disseminated disease. Disseminated disease was reported more often in veterinary (62%) than human cases (19%) (p < 0.001). Isolates from all hosts clustered largely into previously identified genetic groups, with 3 haplotypes being shared between human and canine isolates confirming that B. dermatitidis isolates capable of infecting both species occur in nature. Allelic diversity measures trended

  18. 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

  19. Genetic characterization, molecular epidemiology, and phylogenetic relationships of insect-specific viruses in the taxon Negevirus.

    PubMed

    Nunes, Marcio R T; Contreras-Gutierrez, María Angélica; Guzman, Hilda; Martins, Livia C; Barbirato, Mayla Feitoza; Savit, Chelsea; Balta, Victoria; Uribe, Sandra; Vivero, Rafael; Suaza, Juan David; Oliveira, Hamilton; Nunes Neto, Joaquin P; Carvalho, Valeria L; da Silva, Sandro Patroca; Cardoso, Jedson F; de Oliveira, Rodrigo Santo; da Silva Lemos, Poliana; Wood, Thomas G; Widen, Steven G; Vasconcelos, Pedro F C; Fish, Durland; Vasilakis, Nikos; Tesh, Robert B

    2017-04-01

    The recently described taxon Negevirus is comprised of a diverse group of insect-specific viruses isolated from mosquitoes and phlebotomine sandflies. In this study, a comprehensive genetic characterization, molecular, epidemiological and evolutionary analyses were conducted on nearly full-length sequences of 91 new negevirus isolates obtained in Brazil, Colombia, Peru, Panama, USA and Nepal. We demonstrated that these arthropod restricted viruses are clustered in two major phylogenetic groups with origins related to three plant virus genera (Cilevirus, Higrevirus and Blunevirus). Molecular analyses demonstrated that specific host correlations are not present with most negeviruses; instead, high genetic variability, wide host-range, and cross-species transmission were noted. The data presented here also revealed the existence of five novel insect-specific viruses falling into two arthropod-restrictive virus taxa, previously proposed as distinct genera, designated Nelorpivirus and Sandewavirus. Our results provide a better understanding of the molecular epidemiology, evolution, taxonomy and stability of this group of insect-restricted viruses.

  20. 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

    USDA-ARS?s Scientific Manuscript database

    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...

  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.

  2. 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

  3. Clinical, epidemiologic, histopathologic and molecular features of an unexplained dermopathy.

    PubMed

    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

    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. 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. 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. This unexplained dermopathy was rare among this population of Northern California residents, but associated with significantly reduced health-related quality of life. No common underlying medical

  4. 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.

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

    PubMed

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

    2014-05-28

    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.

  7. Molecular epidemiology and genotyping of Mycobacterium tuberculosis isolated in Baghdad.

    PubMed

    Mustafa Ali, Ruqaya; Trovato, Alberto; Couvin, David; Al-Thwani, Amina N; Borroni, Emanuele; Dhaer, Fahim H; Rastogi, Nalin; Cirillo, Daniela M

    2014-01-01

    Tuberculosis (TB) remains a major health problem in Iraq but the strains responsible for the epidemic have been poorly characterized. Our aim was to characterize the TB strains circulating in Bagdad (Iraq). A total of 270 Mycobacterium tuberculosis complex (MTBC) strains isolated between 2010 and 2011 from TB patients attending the Center of Chest and Respiratory diseases in Baghdad were analyzed by Spoligotyping. The analysis indicated that 94.1% of the isolates belong to known genotype clades: CAS 39.6%, ill-defined T clade 29.6%, Manu 7.4%, Haarlem 7%, Ural 4.1%, LAM 3.3%, X 0.7%, LAM7-TUR 0.7%, EAI 0.7%, S 0.7%, and unknown 5.9%. Comparison with the international multimarker database SITVIT2 showed that SIT 309 (CAS1-Delhi) and SIT1144 (T1) were the most common types. In addition, 44 strains were included in SITVIT2 database under 16 new Spoligotype International Types (SITs); of these, 6 SITs (SIT3346, SIT3497, SIT3708, SIT3790, SIT3791, and SIT3800) (n = 32 strains) were created within the present study and 10 were created after a match with an orphan in the database. By using 24-loci MIRU-VNTR-typing on a subset of 110 samples we found a high recent transmission index (RTI) of 33.6%. In conclusion, we present the first unifying framework for both epidemiology and evolutionary analysis of M. tuberculosis in Iraq.

  8. Molecular Epidemiology and Genotyping of Mycobacterium tuberculosis Isolated in Baghdad

    PubMed Central

    Mustafa Ali, Ruqaya; Trovato, Alberto; Al-Thwani, Amina N.; Dhaer, Fahim H.; Cirillo, Daniela M.

    2014-01-01

    Tuberculosis (TB) remains a major health problem in Iraq but the strains responsible for the epidemic have been poorly characterized. Our aim was to characterize the TB strains circulating in Bagdad (Iraq). A total of 270 Mycobacterium tuberculosis complex (MTBC) strains isolated between 2010 and 2011 from TB patients attending the Center of Chest and Respiratory diseases in Baghdad were analyzed by Spoligotyping. The analysis indicated that 94.1% of the isolates belong to known genotype clades: CAS 39.6%, ill-defined T clade 29.6%, Manu 7.4%, Haarlem 7%, Ural 4.1%, LAM 3.3%, X 0.7%, LAM7-TUR 0.7%, EAI 0.7%, S 0.7%, and unknown 5.9%. Comparison with the international multimarker database SITVIT2 showed that SIT 309 (CAS1-Delhi) and SIT1144 (T1) were the most common types. In addition, 44 strains were included in SITVIT2 database under 16 new Spoligotype International Types (SITs); of these, 6 SITs (SIT3346, SIT3497, SIT3708, SIT3790, SIT3791, and SIT3800) (n = 32 strains) were created within the present study and 10 were created after a match with an orphan in the database. By using 24-loci MIRU-VNTR-typing on a subset of 110 samples we found a high recent transmission index (RTI) of 33.6%. In conclusion, we present the first unifying framework for both epidemiology and evolutionary analysis of M. tuberculosis in Iraq. PMID:24719873

  9. Molecular Epidemiology of sil Locus in Clinical Streptococcus pyogenes Strains

    PubMed Central

    Plainvert, Céline; Dinis, Márcia; Ravins, Miriam; Hanski, Emanuel; Touak, Gérald; Dmytruk, Nicolas; Fouet, Agnès

    2014-01-01

    Streptococcus pyogenes (group A Streptococcus [GAS]) causes a wide variety of diseases, ranging from mild noninvasive to severe invasive infections. Mutations in regulatory components have been implicated in the switch from colonization to invasive phenotypes. The inactivation of the sil locus, composed of six genes encoding a quorum-sensing complex, gives rise to a highly invasive strain. However, studies conducted on limited collections of GAS strains suggested that sil prevalence is around 15%; furthermore, whereas a correlation between the presence of sil and the genetic background was suggested, no link between the presence of a functional sil locus and the invasive status was assessed. We established a collection of 637 nonredundant strains covering all emm genotypes present in France and of known clinical history; 68%, 22%, and 10% were from invasive infections, noninvasive infections, and asymptomatic carriage, respectively. Among the 637 strains, 206 were sil positive. The prevalence of the sil locus varied according to the emm genotype, being present in >85% of the emm4, emm18, emm32, emm60, emm87, and emm90 strains and absent from all emm1, emm28, and emm89 strains. A random selection based on 2009 French epidemiological data indicated that 16% of GAS strains are sil positive. Moreover, due to mutations leading to truncated proteins, only 9% of GAS strains harbor a predicted functional sil system. No correlation was observed between the presence or absence of a functional sil locus and the strain invasiveness status. PMID:24671796

  10. Molecular epidemiology of Mycobacterium bovis in Texas and Mexico.

    PubMed Central

    Perumaalla, V S; Adams, L G; Payeur, J B; Jarnagin, J L; Baca, D R; Suárez Güemes, F; Ficht, T A

    1996-01-01

    Seventy-nine Mycobacterium bovis isolates recovered from Mexican and Texas cattle were categorized into 16 and 25 distinct types on the basis of IS6110 and direct-repeat fingerprint patterns, respectively. By using a combination of both fingerprint patterns, 30 distinct restriction fragment length polymorphism types were defined. Fifty-eight of 79 isolates (73%) were distributed among nine clusters. Clustered isolates were identified within herds, as well as in geographically disperse herds in Texas and Mexico. This observation is consistent with active transmission within herds and among herds, presumably as a result of active or historical cattle movements. The majority of bovine isolates (64 of 79) exhibited a single copy of IS6110. Interestingly, in contrast to previous studies, a high percentage of bovine isolates (15 of 79) exhibited multiple IS6110 copies (two to five) distributed among 11 different restriction fragment length polymorphism types. It is speculated that transmission from noncattle sources may be responsible. Continued fingerprinting of isolates originating from nonbovine sources and herd surveys is expected to provide useful information regarding the epidemiology of tuberculosis in this region. PMID:8862559

  11. Prevalence of tuberculosis in prisons: risk factors and molecular epidemiology.

    PubMed

    Valença, M S; Scaini, J L R; Abileira, F S; Gonçalves, C V; von Groll, A; Silva, P E A

    2015-10-01

    Tuberculosis (TB) in prisons is a challenge for the public health system. Active and passive case screening are important tools for TB case detection. To characterise TB in a southern Brazil prison in terms of epidemiological variables, diagnostic approaches and clinical isolate genotypes. Inmates of a southern Brazilian prison were assessed using active and passive TB case screening. Sputum microscopy, culture, drug susceptibility testing and genotyping were performed. Data were analysed using descriptive statistics and multivariable logistic regression. TB prevalence was 4712 per 100 000 inmates, and was associated with low educational level, time incarcerated, productive cough, previous TB history, smoking and human immunodeficiency virus (HIV) infection. Overall, 27.8% of TB cases were detected by culture only; the prevalence of drug-resistant strains was 7.8%; 58.3% of clinical isolates had an identical genotypic profile. The study showed extensive circulation of Mycobacterium tuberculosis strains in a highly endemic prison. It is recommended that priority be given to the evaluation of prison inmates with longer jail times, those who are HIV-positive, those with symptoms and those with a previous history of tuberculosis. We observed that active case finding induced passive case detection.

  12. 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.

  13. Incidence, Progression, and Associated Risk Factors of Posterior Vitreous Detachment in Type 2 Diabetes Mellitus: Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetic Study (SN-DREAMS II, Report No. 7).

    PubMed

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

    2017-01-01

    To report the incidence and progression of posterior vitreous detachment (PVD) and factors influencing the same in a cohort of patients with type 2 diabetes in a South Indian population. A subset of 615 subjects from Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetics Study II were included in this study. All of the subjects underwent detailed ophthalmic evaluation including stereo fundus photography. The status of PVD was assessed using B-scan ultrasonography. A p value of <0.05 was considered statistically significant. The incidence of either incomplete PVD (IPVD) or complete PVD (CPVD) from no PVD at baseline visit was 80.8%. Of them, 32.63% converted to CPVD from IPVD at baseline. High prevalence of emmetropia was observed in subjects with stable No PVD. Risk factors associated with the conversion of CPVD from no PVD and IPVD at baseline were age (OR: 1.04, p = 0.002), myopia (OR: 2.14, p = 0.009), and increase in axial length (OR: 1.35, p = 0.004). Subjects undergoing cataract surgery were at 2.32 times higher risk of converting to CPVD (p = 0.038). Independent risk factors for the progression of PVD were increase in age, myopia, increased axial length, and cataract surgery.

  14. 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.

  15. Human Metapneumovirus: Insights from a Ten-Year Molecular and Epidemiological Analysis in Germany

    PubMed Central

    Reiche, Janine; Jacobsen, Sonja; Neubauer, Katrin; Hafemann, Susi; Nitsche, Andreas; Milde, Jeanette; Wolff, Thorsten; Schweiger, Brunhilde

    2014-01-01

    Human metapneumovirus (HMPV) is a cause of respiratory tract illness at all ages. In this study the epidemiological and molecular diversity among patients of different ages was investigated. Between 2000–2001 and 2009–2010, HMPV was detected in 3% (138/4,549) of samples from outpatients with influenza-like illness with a new, sensitive real-time RT-PCR assay. Several hundred (797) clinical specimens from hospitalized children below the age of 4 years with acute respiratory illness were investigated and HMPV was detected in 11.9% of them. Investigation of outpatients revealed that HMPV infections occurred in individuals of all ages but were most prevalent in children (0–4 years) and the elderly (>60 years). The most present clinical features of HMPV infections were cough, bronchitis, fever/shivers and pneumonia. About two thirds of HMPV-positive samples were detected in February and March throughout the study period. Molecular characterization of HMPV revealed a complex cyclic pattern of group dominance where HMPV subgroup A and B viruses predominated in general for three consecutive seasons. German HMPV represented all genetic lineages including A1, A2, B1, B2, sub-clusters A2a and A2b. For Germany, not only time-dependent circulation of lineages and sub-clusters was observed but also co-circulation of two or three predominant lineages. Two newly emerging amino acid substitutions (positions 223 and 280) of lineage B2 were detected in seven German HMPV sequences. Our study gives new insights into the molecular epidemiology of HMPV in in- and outpatients over a time period of 10 years for the first time. It is one of only few long-term surveillance studies in Europe, and allows comparative molecular analyses of HMPV circulating worldwide. PMID:24505479

  16. Recent transmission of tuberculosis in Madrid: application of capture-recapture analysis to conventional and molecular epidemiology.

    PubMed

    Iñigo, J; Arce, A; Martín-Moreno, J M; Herruzo, R; Palenque, E; Chaves, F

    2003-10-01

    Population-based studies using a combination of molecular techniques and conventional epidemiological methods have been used to study the dynamics of tuberculosis (TB) transmission but the relative utility of each technique has not yet been established. A prospective population-based molecular and epidemiological study of patients diagnosed with TB was conducted in three urban districts of Madrid (Spain) during 1997-1999. Analysis was performed using the capture-recapture method including covariates in which conventional epidemiological data and the information on clustered cases obtained by DNA fingerprinting were regarded as independent and complementary procedures. The estimate obtained by molecular analysis alone, that 31.6% of TB cases were due to recent transmission, was revised to 44.8% (95% CI: 31.4-58.2) using the capture-recapture method. The estimated completeness of the combined databases for identification of recent transmission was 59.2%. Underestimation of the true prevalence of recent transmission was higher with conventional epidemiology than molecular analysis, particularly for patients <35 years old and those with a history of imprisonment. In this study, use of the capture-recapture technique allowed us to combine epidemiological information obtained by conventional and molecular methods to quantify the number of cases of recently transmitted TB in the community and identify specific populations at high risk of disease. This information is clearly important because such groups are a prime target for improved TB control measures. In the long term, this combination of techniques may contribute significantly to control the spread of TB.

  17. 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.

  18. 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

  19. 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.

  20. Molecular Epidemiology of Campylobacter jejuni in a Geographically Isolated Country with a Uniquely Structured Poultry Industry▿

    PubMed Central

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

    2010-01-01

    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

  1. Molecular Identification and Epidemiological Tracing of Pasteurella multocida Meningitis in a Baby

    PubMed Central

    Boerlin, Patrick; Siegrist, Hans H.; Burnens, André P.; Kuhnert, Peter; Mendez, Purita; Prétat, Gérard; Lienhard, Reto; Nicolet, Jacques

    2000-01-01

    We report a case of Pasteurella multocida meningitis in a 1-month-old baby exposed to close contact with two dogs and a cat but without any known history of injury by these animals. 16S rRNA gene sequencing of the isolate from the baby allowed identification at the subspecies level and pointed to the cat as a possible source of infection. Molecular typing of Pasteurella isolates from the animals, from the baby, and from unrelated animals clearly confirmed that the cat harbored the same P. multocida subsp. septica strain on its tonsils as the one isolated from the cerebrospinal fluid of the baby. This case stresses the necessity of informing susceptible hosts at risk of contracting zoonotic agents about some basic hygiene rules when keeping pets. In addition, this study illustrates the usefulness of molecular methods for identification and epidemiological tracing of Pasteurella isolates. PMID:10699029

  2. Molecular epidemiology of HIV type 1 in Mexico: emergence of BG and BF intersubtype recombinants.

    PubMed

    Vázquez-Valls, Eduardo; Escoto-Delgadillo, Martha; López-Márquez, Francisco Carlos; Castillero-Manzano, Marcelo; Echegaray-Guerrero, Ernesto; Bitzer-Quintero, Oscar Kurt; Kobayashi-Gutiérrez, Antonio; Torres-Mendoza, Blanca Miriam

    2010-07-01

    The molecular epidemiology of subtypes and intersubtype recombinants (IRs) of human immunodeficiency virus type 1 (HIV-1) in Mexico has not been characterized fully. Understanding its regional distribution, prevalence, adaptability, viral fitness, pathogenicity, and immunogenicity is decisive for any design of an effective HIV vaccine. The aim of this study was to describe the presence of IRs types BG and BF in a Mexican population. Protease and reverse transcriptase regions of the pol gene were sequenced using an automated sequencing system. A phylogenic tree was constructed and genetic distances were calculated using MEGA 3.1. Recombination analysis was done by bootscan using SimPlot software. Two hundred and twenty-three HIV-1-positive individuals were enrolled in the study. At baseline, the mean plasma viral load was 285,500 HIV-1 RNA copies/ml and the mean CD4 cell count was 213 cells/ml. Subtype B was found in 220 (98.6%) samples, whereas IRs were found in three patients (1.4%): two (0.9%) with BG and one (0.45%) with BF. IRs were observed in 2/124 (1.6%) samples from treated patients and in 1/99 (1.0%) from naive patients. The presence of these HIV forms at low frequency points to the need for research on the diversity, geographic distribution, and evolution of other subtypes including circulating recombinant forms and IRs to understand the molecular epidemiology and tendencies of the HIV infection in Mexico.

  3. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Satellite remote sensing in epidemiological studies.

    PubMed

    Sorek-Hamer, Meytar; Just, Allan C; Kloog, Itai

    2016-04-01

    Particulate matter air pollution is a ubiquitous exposure linked with multiple adverse health outcomes for children and across the life course. The recent development of satellite-based remote-sensing models for air pollution enables the quantification of these risks and addresses many limitations of previous air pollution research strategies. We review the recent literature on the applications of satellite remote sensing in air quality research, with a focus on their use in epidemiological studies. Aerosol optical depth (AOD) is a focus of this review and a significant number of studies show that ground-level particulate matter can be estimated from columnar AOD. Satellite measurements have been found to be an important source of data for particulate matter model-based exposure estimates, and recently have been used in health studies to increase the spatial breadth and temporal resolution of these estimates. It is suggested that satellite-based models improve our understanding of the spatial characteristics of air quality. Although the adoption of satellite-based measures of air quality in health studies is in its infancy, it is rapidly growing. Nevertheless, further investigation is still needed in order to have a better understanding of the AOD contribution to these prediction models in order to use them with higher accuracy in epidemiological studies.

  5. 77 FR 21785 - Submission for OMB Review; Comment Request: Prevalence, Incidence, Epidemiology and Molecular...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-11

    ..., Incidence, Epidemiology and Molecular Variants of HIV in Blood Donors in Brazil Summary: Under the... Molecular Variants of HIV in Blood Donors in Brazil. Type of Information Collection Request: Reinstatement... prevalence and incidence rates, and identifying behavioral risk behaviors for HIV infection among donors...

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

    USDA-ARS?s Scientific Manuscript database

    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 ...

  7. Molecular epidemiology of Cryptosporidium and Giardia in cattle

    USDA-ARS?s Scientific Manuscript database

    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...

  8. 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

  9. Molecular epidemiology of Italian clinical Cryptococcus neoformans var. grubii isolates.

    PubMed

    Cogliati, Massimo; Zamfirova, Ralika R; Tortorano, Anna Maria; Viviani, Maria Anna

    2013-07-01

    Cryptococcus neoformans variety grubii is the major etiological agent of cryptococcal meningitis in both immunocompromised and immunocompetent patients. The current PCR-based molecular methods are not sufficient to discriminate among the different populations of this yeast. Therefore, the aim of the present study was to investigate the genotypes of the Italian clinical C. neoformans var. grubii isolates by multilocus sequence typing (MLST). A total of 53 isolates, each representative of a single case, were studied. Genotyping was performed using the ISHAM Cryptococcus MLST consensus scheme and the results were compared to the publically available global C. neoformans var. grubii MLST dataset. A total of 16 genotypes were identified; 14 were new genotypes, one was identical to sequence type (ST) ST81, which had been previously reported from Thailand, and one to ST23 already identified in Uganda, the USA and Korea. Sequence type ST61 was the most numerous, including 16 isolates. Network phylogenetic analysis showed that the Italian isolates could be divided into at least three clusters with similarities with those recovered in Africa, Asia and Americas. Distribution of the STs among the isolates could not be correlated to the hospital in which they were recovered or to the HIV status of the patients. The majority of the isolates belonged to the molecular type VNI; three belonged to the rare molecular type VNII and one to the VNB group, which until now had not been described in Europe. The results reveal that the Italian C. neoformans var. grubii population presents a distinct variability, displaying a high number of new genotypes, and probably recombines sexually.

  10. [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.

  11. Molecular epidemiology of rabies in bat-eared foxes (Otocyon megalotis) in South Africa.

    PubMed

    Sabeta, C T; Mansfield, K L; McElhinney, L M; Fooks, A R; Nel, L H

    2007-10-01

    A panel of 124 rabies viruses from wildlife host species (principally the bat-eared fox, Otocyon megalotis) and domestic carnivore species were collected between 1980 and 2005 from a region of South Africa associated with endemic bat-eared fox rabies. We have studied the molecular epidemiology of bat-eared fox rabies by virtue of nucleotide sequence analyses of PCR amplicons specific to the variable G-L intergenic region as well as the conserved nucleoprotein gene of each of the rabies viruses in this South African panel. Although it was demonstrated that all of these viruses were very closely related, they could be segregated into two major phylogenetic groups. The data presented in this paper complement antigenic and surveillance data on rabies in this host species in South Africa. Most importantly our data support a hypothesis that the bat-eared fox independently maintains rabies cycles in specific geographical loci. This is the first molecular epidemiological investigation describing rabies transmission dynamics in this wildlife carnivore host species in South Africa.

  12. Nosocomial outbreak of Legionnaires' disease: molecular epidemiology and disease control measures.

    PubMed

    Johnston, J M; Latham, R H; Meier, F A; Green, J A; Boshard, R; Mooney, B R; Edelstein, P H

    1987-02-01

    Molecular laboratory techniques were used to study the epidemiology of an outbreak of nosocomial Legionnaires' disease. All patient isolates were Legionella pneumophila serogroup 1 and showed identical plasmid profiles and reactions with serogroup-specific monoclonal antibodies. L pneumophila was also cultured from four of five cooling tower water samples; however, the isolate from only one tower was serogroup 1 of the same subtype as patient isolates. Since the cases were temporally clustered and epidemiologically associated with exposure to cooling tower aerosols, the single cooling tower implicated by molecular analysis was the most likely source of the outbreak. Chlorination of cooling tower ponds has eradicated the epidemic strain. Since potable water also harbored the infecting organism and was the probable source for cooling tower contamination, decontamination of the hospital water system was also undertaken. Superchlorination of hot water holding tanks to 17 ppm on a weekly basis has effectively eradicated L pneumophila from the potable water system and appears to be a reasonable, simple, and relatively inexpensive alternative to previously described methods of control.

  13. Molecular epidemiology of Staphylococcus saprophyticus isolated from women with uncomplicated community-acquired urinary tract infection.

    PubMed

    Widerström, Micael; Wiström, Johan; Ferry, Sven; Karlsson, Carina; Monsen, Tor

    2007-05-01

    Staphylococcus saprophyticus is a common cause of urinary tract infections (UTIs) in women. Little is known about the molecular epidemiology of S. saprophyticus UTIs. In the current study, we compared 76 isolates of S. saprophyticus prospectively isolated from women with uncomplicated UTI participating in a randomized placebo-controlled treatment trial performed in northern Sweden from 1995 to 1997 with 50 strains obtained in 2006 from five different locations in northern Europe with pulsed-field gel electrophoresis (PFGE). The aim was to elucidate the molecular epidemiology of this uropathogenic species and to investigate whether specific clones are associated with UTI in women. A total of 47 different PFGE profiles were detected among the 126 analyzed isolates. Ten clusters consisting of 5 to 12 isolates each showing PFGE DNA similarity of >85% were identified. Several clusters of genetically highly related isolates were detected in the original trial as well as among isolates obtained during 2006 from different locations. In the original trial, clonal persistence was found among 16 of 21 (76%) patients examined in the placebo group at follow-up 8 to 10 days after inclusion, indicating a low spontaneous short-time bacteriological cure rate. We conclude that multiple clones of S. saprophyticus were causing lower UTIs in women. The result suggests that some human-pathogenic clones of S. saprophyticus are spread over large geographical distances and that such clones may persist over long periods of time.

  14. Foveal slope measurements in diabetic retinopathy: Can it predict development of sight-threatening retinopathy? Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetics Study (SN-DREAMS II, Report no 8)

    PubMed Central

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

    2015-01-01

    Aim: The aim was to assess the foveal slope configuration in subjects with type 2 diabetes in a population-based study. Materials and Methods: A subset of 668 subjects from Sankara Nethralaya Diabetic Retinopathy (DR) Epidemiology and Molecular Genetics Study II, a population-based study, were included in the current study. All the subjects underwent comprehensive ophthalmic evaluation including spectral domain optical coherence tomography. Foveal thickness was assessed in five central early treatment DR study quadrants from the three-dimensional scan and foveal slope was calculated in all the four quadrants. Results: Subjects with sight-threatening DR (STDR) had significantly shallow foveal slope in inferior quadrant (STDR: 7.33 ± 6.26 vs. controls: 10.31 ± 3.44; P = 0.021) when compared to controls and in superior (STDR: 7.62 ± 5.81 vs. no DR: 9.11 ± 2.82; P = 0.033), inferior (STDR: 7.33 ± 6.26 vs. no DR: 8.81 ± 2.81; P = 0.048), and temporal quadrants (STDR: 6.69 ± 5.70 vs. no DR: 7.97 ± 2.33; P = 0.030) when compared to subjects with no DR. Foveal slope was significantly shallow among the older age groups in subjects with no DR (P < 0.001) and non-STDR (P = 0.027). Average foveal slope in the diabetic subjects was independently and significantly correlated with increase in age (r = −0.241; P < 0.001) and central subfield thickness (r = −0.542; P < 0.001). Conclusion: Changes in foveal slope were seen with increasing age; however, in diabetes these segmental slope changes can be seen in late DR (STDR). PMID:26265635

  15. Foveal slope measurements in diabetic retinopathy: Can it predict development of sight-threatening retinopathy? Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetics Study (SN-DREAMS II, Report no 8).

    PubMed

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

    2015-06-01

    The aim was to assess the foveal slope configuration in subjects with type 2 diabetes in a population-based study. A subset of 668 subjects from Sankara Nethralaya Diabetic Retinopathy (DR) Epidemiology and Molecular Genetics Study II, a population-based study, were included in the current study. All the subjects underwent comprehensive ophthalmic evaluation including spectral domain optical coherence tomography. Foveal thickness was assessed in five central early treatment DR study quadrants from the three-dimensional scan and foveal slope was calculated in all the four quadrants. Subjects with sight-threatening DR (STDR) had significantly shallow foveal slope in inferior quadrant (STDR: 7.33 ± 6.26 vs. 10.31 ± 3.44; P = 0.021) when compared to controls and in superior (STDR: 7.62 ± 5.81 vs. no DR: 9.11 ± 2.82; P = 0.033), inferior (STDR: 7.33 ± 6.26 vs. no DR: 8.81 ± 2.81; P = 0.048), and temporal quadrants (STDR: 6.69 ± 5.70 vs. no DR: 7.97 ± 2.33; P = 0.030) when compared to subjects with no DR. Foveal slope was significantly shallow among the older age groups in subjects with no DR (P < 0.001) and non-STDR (P = 0.027). Average foveal slope in the diabetic subjects was independently and significantly correlated with increase in age (r = -0.241; P < 0.001) and central subfield thickness (r = -0.542; P < 0.001). Changes in foveal slope were seen with increasing age; however, in diabetes these segmental slope changes can be seen in late DR (STDR).

  16. Standardization of a molecular method for epidemiologic identification of Leishmania strains.

    PubMed

    Rocha, R F; Menezes, E V; Xavier, A R E O; Royo, V A; Oliveira, D A; Júnior, A F M; Dias, E S; Lima, A C V M R; Michalsky, E M

    2016-10-06

    Molecular studies of the evolutionary relationships among Leishmania species suggest the presence of high genetic variation within this genus, which has a direct effect on public health in many countries. The coexistence of species in a particular region can result in different leishmaniasis clinical forms and treatment responses. We aimed to standardize the kinetoplast DNA (kDNA) enterobacterial repetitive intergenic consensus (ERIC) sequence polymerase chain reaction (PCR) method for molecular epidemiological identification of Leishmania strains, and estimate existing inter-strain genomic differences and kDNA signatures using this technique. ERIC-PCR of genomic DNA revealed genetic polymorphisms between species, although some strains shared many DNA fragments. Leishmania guyanensis, L. amazonensis, and L. braziliensis clustered together in a dendrogram with similarities ranging from 42.0 to 61.0%, whereas L. chagasi grouped with these three species with a similarity of 28.0%. After amplification of kDNA, 780-bp bands were extracted from an agarose gel and purified for analysis of its genetic signature. kDNA ERIC-PCR electrophoretic patterns consisted of 100- to 600- bp fragments. Using these profiles, L. braziliensis and L. guyanensis grouped with a similarity of 26.0%, and L. amazonensis and L. chagasi clustered based on a similarity of 100%. The electrophoretic profiles and dendrograms showed that, for epidemiological identification by ERIC-PCR, genomic DNA had greater discriminatory power than kDNA did. More strains need to be analyzed to validate the kDNA ERIC-PCR method. The genomes of these strains should be sequenced for better epidemiological identification of Leishmania species.

  17. Report of the Second International Symposium on Molecular Epidemiology in Childhood Leukaemia and Embryonal Tumours, Rio de Janeiro, Brazil

    PubMed Central

    Pombo de Oliveira, MS; 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. Urolithiasis in Italy: an epidemiological study.

    PubMed

    Prezioso, Domenico; Illiano, Ester; Piccinocchi, Gaetano; Cricelli, Claudio; Piccinocchi, Roberto; Saita, Alberto; Micheli, Carla; Trinchieri, Alberto

    2014-06-30

    Worldwide the urolithiasis is the third most frequent urological disease affecting both males and females. In literature there are not recent Italian epidemiological data about stone disease. The objective of this study is the evaluation of current epidemiology of urolithiasis in Italy using the Health Search/CSD Longitudinal Patient Database (HS) database. An observational, descriptive, retrospective trial was conducted. Inclusion criteria were: family physician- assisted Italian living population member of HS database within 31 December 2012, both genders, age over 17 years, at least two years of clinical history recorded from the beginning the trial. Data were collected by HS database and elaborated by its software Millewin®. In Italy prevalence of urolithiasis in 2012 was 4.14%, it was higher in males than in females (4.53% versus 3.78%) with a positive relation with increasing age. The highest prevalence rate of urolithiasis was reported in the region Campania (6.08%). The general incidence was 2.23 * 1000, with the highest incidence in the region Sicilia (3.15 * 1000). Incidence was higher in group age 65-74 years (3.18 * 1000). In Italy the incidence and prevalence of urolithiasis is increasing with particular distribution in relation to gender, age and regional position.

  19. 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.

  20. A molecular epidemiological study of methicillin-resistant Staphylococci environmental contamination in railway stations and coach stations in Guangzhou of China.

    PubMed

    Lin, J L; Peng, Y; Ou, Q T; Lin, D X; Li, Y; Ye, X H; Zhou, J L; Yao, Z J

    2017-02-01

    Methicillin-resistant Staphylococcus aureus (MRSA) has caused a series of public health problems since it was first found in 1961. However, there are few research studies on the MRSA environmental contamination in railway stations and coach stations. Therefore, the aim of this study was to determine MRSA environmental contamination in public transport stations. Between December 2013 and January 2014, 380 surface samples from three railway stations (180) and four coach stations (200) in Guangzhou were collected to isolate and determine the prevalence and characteristics of Staphylococci strains. 39·21% of all samples were Staphylococci isolates, 1·58% of Staphylococci isolates were MRSA isolates, and 6·05% were methicillin-susceptible S. aureus. The proportion of multidrug resistant among 149 Staphylococci isolates was 75·84%. None of MRSA isolates was identified with the Panton-Valentine Leukocidin (PVL) genes, and one of them was identified with the qac gene. Four MRSA isolates were Staphylococcal Cassette Chromosome mec IVa, and the other two were nontypeable. Staphylococcus aureus isolates were classified into several sequence types (STs), and STs showed possible cross-transmissions of isolates from various sources. Methicillin-resistant Staphylococci contamination prevalence was high, and the environment of stations may be the vectors transmitting the Staphylococci to passengers.

  1. Molecular epidemiology of vancomycin-resistant Enterococcus faecium in Argentina.

    PubMed

    Corso, Alejandra C; Gagetti, Paula S; Rodríguez, Marisa M; Melano, Roberto G; Ceriana, Paola G; Faccone, Diego F; Galas, Marcelo F

    2007-01-01

    To characterize the mechanism of glycopeptide resistance and to determine the genetic relatedness among strains by pulsed-field gel electrophoresis (PFGE) in vancomycin-resistant Enterococcus faecium from Argentina. A total of 189 vancomycin-resistant single-patient isolates of Enterococcus faecium recovered between January 1997 and December 2000 from 30 hospitals in Argentina were studied. Minimum inhibitory concentrations were determined by the agar dilution method and van genes were detected by PCR. PFGE was used for molecular typing. All isolates except three (vanB) were of genotype vanA. For 189 vancomycin-resistant Enterococcus faecium, SmaI-PFGE indicated 35 clonal types. Most of the isolates (56%) belonged to the same clonal type 1, which was present in 19 hospitals and dominant in 17. The emergence of vancomycin-resistant Enterococcus faecium in Argentina seems to be related to the intra- and inter-hospital dissemination of an epidemic clone carrying the vanA element.

  2. Integrated approach of nutritional and molecular epidemiology, mineralogical and chemical pollutant characterisation: the protocol of a cross-sectional study in women

    PubMed Central

    Barchitta, Martina; Quattrocchi, Annalisa; Maugeri, Andrea; Barone, Germana; Mazzoleni, Paolo; Catalfo, Alfio; De Guidi, Guido; Iemmolo, Maria; Crimi, Nunzio; Agodi, Antonella

    2017-01-01

    Introduction Environmentally-related health and disease are the result of the exposome, the totality of a person's environmental exposures, from all sources and routes, across their lifespan. Epigenetic phenomena, including DNA methylation, can be potentially modified by environmental and lifestyle factors, and result in environmental reprogramming of the genome for exposed individuals and for future generations of offspring. Objective The objective of the project is to evaluate the risk of DNA hypomethylation due to air pollution, Mediterranean diet adherence, folate intake, and demographic and socioeconomic factors, in healthy women living in the metropolitan area of Catania, Italy. Methods and analysis Non-pregnant healthy women will be enrolled in a cross-sectional study. Sociodemographic, lifestyle and dietary intake information will be collected. LINE-1 methylation will be measured by pyrosequencing. The participants' home addresses will be geocoded and each woman will be assigned to the closest monitoring station for particulate matter (PM) exposure assessment. Mineralogical-chemical characterisation of PM and cellular model assays will be performed. An integrated approach will be designed to estimate the combined possible effect of air pollution, Mediterranean diet adherence, folate intake and other lifestyle characteristics on LINE-1 methylation levels. Ethics and dissemination The project has been approved by the ethics committees of the involved institution and funded by the University of Catania (Finanziamento della Ricerca, FIR 2014). All participants will be fully informed of the purpose and procedures of the study, and signed written consents will be obtained. All the data collected will be treated confidentially and analysed in an aggregate and anonymous way. The results will be published in peer-reviewed journals and communicated to local public health agencies, in order to provide essential information for timely and effective public health action

  3. Integrated approach of nutritional and molecular epidemiology, mineralogical and chemical pollutant characterisation: the protocol of a cross-sectional study in women.

    PubMed

    Barchitta, Martina; Quattrocchi, Annalisa; Maugeri, Andrea; Barone, Germana; Mazzoleni, Paolo; Catalfo, Alfio; De Guidi, Guido; Iemmolo, Maria; Crimi, Nunzio; Agodi, Antonella

    2017-04-04

    Environmentally-related health and disease are the result of the exposome, the totality of a person's environmental exposures, from all sources and routes, across their lifespan. Epigenetic phenomena, including DNA methylation, can be potentially modified by environmental and lifestyle factors, and result in environmental reprogramming of the genome for exposed individuals and for future generations of offspring. The objective of the project is to evaluate the risk of DNA hypomethylation due to air pollution, Mediterranean diet adherence, folate intake, and demographic and socioeconomic factors, in healthy women living in the metropolitan area of Catania, Italy. Non-pregnant healthy women will be enrolled in a cross-sectional study. Sociodemographic, lifestyle and dietary intake information will be collected. LINE-1 methylation will be measured by pyrosequencing. The participants' home addresses will be geocoded and each woman will be assigned to the closest monitoring station for particulate matter (PM) exposure assessment. Mineralogical-chemical characterisation of PM and cellular model assays will be performed. An integrated approach will be designed to estimate the combined possible effect of air pollution, Mediterranean diet adherence, folate intake and other lifestyle characteristics on LINE-1 methylation levels. The project has been approved by the ethics committees of the involved institution and funded by the University of Catania (Finanziamento della Ricerca, FIR 2014). All participants will be fully informed of the purpose and procedures of the study, and signed written consents will be obtained. All the data collected will be treated confidentially and analysed in an aggregate and anonymous way. The results will be published in peer-reviewed journals and communicated to local public health agencies, in order to provide essential information for timely and effective public health action. Published by the BMJ Publishing Group Limited. For permission to

  4. Linezolid-resistant clinical isolates of enterococci and Staphylococcus cohnii from a multicentre study in China: molecular epidemiology and resistance mechanisms.

    PubMed

    Chen, Hongbin; Wu, Weiyuan; Ni, Ming; Liu, Yingmei; Zhang, Jixia; Xia, Fei; He, Wenqiang; Wang, Qi; Wang, Zhanwei; Cao, Bin; Wang, Hui

    2013-10-01

    Genetic characterisation of linezolid-resistant Gram-positive cocci in a multicentre study in China has not been reported previously. To study the mechanism underlying the resistance of linezolid-resistant isolates, nine Enterococcus faecalis, one Enterococcus faecium and three Staphylococcus cohnii isolates with various levels of resistance were collected from five hospitals across China in 2009-2012. The nine E. faecalis isolates were classified into seven sequence types, indicating that these linezolid-resistant E. faecalis isolates were polyclonal. Enterococci isolates had reduced susceptibility to linezolid (MICs of 4-8 mg/L) and had mutation of ribosomal protein L3, with three also having mutation of L4, but without the multidrug resistance gene cfr or the 23S rRNA mutation G2576T. The three S. cohnii isolates were highly resistant to linezolid (MICs of 64 mg/L to >256 mg/L), harboured the cfr gene and had the 23S rRNA mutation G2576T. Southern blotting indicated that the cfr gene of these three isolates resided on different plasmids (pHK01, pRM01 and pRA01). In plasmid pHK01, IS21-558 and the cfr gene were integrated into transposon Tn558. In plasmids pRM01 and pRA01, the cfr gene was flanked by two copies of an IS256-like insertion sequence, indicating that the transferable form of linezolid resistance is conferred by the cfr gene. In conclusion, the emergence of linezolid-resistant Gram-positive cocci in different regions of China is of concern. The cfr gene and the 23S rRNA mutation contribute to high-level linezolid resistance in S. cohnii, and the L3 and L4 mutations are associated with low-level linezolid resistance in enterococci.

  5. 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

  6. 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

    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

  7. Molecular typing of Salmonella from Sergipe, Northeastern Brazil, showing the epidemiological relationship between poultry and human infection.

    PubMed

    Góis, P B P; Carneiro, M R P; Jain, S; Santos, M I S; Batista, M V A; Cândido, A L

    2015-09-25

    Randomly amplified polymorphic DNA (RAPD) has been widely used for epidemiological and phylogenetic purposes ow-ing to its rapidity and efficiency. The aim of this study was to perform genome typing of Salmonella samples isolated from different sources by RAPD profiling. Thirty-three Salmonella samples from the bacterial collection of the Laboratório de Virologia Comparada, Departamento de Morfologia, Universidade Federal de Sergipe, Brazil, and two standard samples were used. RAPD profiling was conducted using six primers of the Ready-To-Go RAPD system. The amplified products were electro-phoresed on 5% polyacrylamide gel and silver-stained. RAPD analysis resulted in reproducible and stable banding patterns and showed high genetic diversity among the isolated strains. The Primer P1-generated dendrogram showed an epidemiologic relationship between the human and poultry isolated samples, highlighting the usefulness of RAPD for molecular typing and epidemiological studies.

  8. The role of molecular epidemiology in contact investigations: a US perspective.

    PubMed

    Daley, C L; Kawamura, L M

    2003-12-01

    Preventing tuberculosis (TB) transmission through treatment of active cases and contact investigation is the highest priority of TB control programs in the United States. The role of contact investigation is becoming increasingly important as the number of TB cases declines nationally. However, the effectiveness of contact investigation has been difficult to assess because, prior to the availability of molecular genotyping techniques, levels of transmission were crudely measurable. Epidemiological links within and outside the traditional concentric circle approach are limited by the quality of the contact investigation, the skill and knowledge of the investigator and the information provided by the patient. Molecular epidemiology has added a new dimension by enabling the recognition of unsuspected transmission, likely locations of transmission, and quantification of the extent of transmission that is occurring within a given population. In the future, as real-time genotyping becomes more available, the role of molecular epidemiology is likely to expand.

  9. Incidence and Progression of Diabetic Retinopathy in Urban India: Sankara Nethralaya-Diabetic Retinopathy Epidemiology and Molecular Genetics Study (SN-DREAMS II), Report 1.

    PubMed

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

    2017-10-01

    To evaluate the 4-year incidence and progression of and risk factors for diabetic retinopathy (DR) in an Indian population. From a cross-sectional study of 1425 subjects with diabetes, 911 (63.9%) returned for 4-year follow-up. After excluding 21 with ungradable retinal images, data from 890 subjects were analyzed. Participants underwent examinations based on a standard protocol, which included grading of retinal photographs. The incidences of DR, diabetic macular edema (DME), and sight-threatening diabetic retinopathy (STDR) were 9.2%, 2.6%, and 5.0%, respectively. In subjects with DR at baseline, the incidence of DME and STDR had increased (11.5% and 22.7%, respectively). 1-step and 2-step progressions of DR were seen in 30.2% and 12.6% of participants, respectively, and 1-step and 2-step regressions were seen in 12.0% and 1.8%, respectively. Incident DR, DME, and STDR were associated with higher systolic blood pressure (odds ratio, OR, 1.21, 2.11 and 1.72, respectively, for every 10 mmHg increase). Incident DR and DME were associated with increasing duration of diabetes (OR 2.29 and 4.77, respectively, for every 10-year increase) and presence of anemia (OR 1.96 and 10.14, respectively). Incident DR was also associated with higher hemoglobin A1c (OR 1.16 for every 1% increase). Variables associated with 1-step progression were every 10 mg/dL increase in serum total cholesterol (OR 15.65) as a risk factor, and 10 mg/dL increase in serum triglyceride (OR 0.52) as a protective factor. The incidences of STDR and DME were higher in people with pre-existing DR than in those without DR at baseline.

  10. 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.

  11. Molecular Pathological Epidemiology of Epigenetics: Emerging Integrative Science to Analyze Environment, Host, and Disease

    PubMed Central

    Ogino, Shuji; Lochhead, Paul; Chan, Andrew T.; Nishihara, Reiko; Cho, Eunyoung; Wolpin, Brian M.; Meyerhardt, Jeffrey A.; Meissner, Alexander; Schernhammer, Eva S.; Fuchs, Charles S.; Giovannucci, Edward

    2013-01-01

    Epigenetics acts as an interface between environmental / exogenous factors, cellular responses and pathological processes. Aberrant epigenetic signatures are a hallmark of complex multifactorial diseases, including non-neoplastic disorders (e.g., cardiovascular diseases, hypertension, diabetes mellitus, autoimmune diseases, and some infectious diseases) and neoplasms (e.g., leukemias, lymphomas, sarcomas, and breast, lung, prostate, liver and colorectal cancers). Epigenetic signatures (DNA methylation, mRNA and microRNA expression, etc.) may serve as biomarkers for risk stratification, early detection, and disease classification, as well as targets for therapy and chemoprevention. DNA methylation assays are widely applied to formalin-fixed paraffin-embedded archival tissue specimens as clinical pathology tests. To better understand the interplay between etiologic factors, cellular molecular characteristics, and disease evolution, the field of “Molecular Pathological Epidemiology (MPE)” has emerged as an interdisciplinary integration of “molecular pathology” and “epidemiology”, with a similar conceptual framework to systems biology and network medicine. In contrast to traditional epidemiologic research including genome-wide association studies (GWAS), MPE is founded on the unique disease principle; that is, each disease process results from unique profiles of exposomes, epigenomes, transcriptomes, proteomes, metabolomes, microbiomes, and interactomes in relation to the macro-environment and tissue microenvironment. The widespread application of epigenomics (e.g., methylome) analyses will enhance our understanding of disease heterogeneity, epigenotypes (CpG island methylator phenotype, LINE-1 hypomethylation, etc.), and host-disease interactions. MPE may represent a logical evolution of GWAS, termed “GWAS-MPE approach”. Though epigenome-wide association study attracts increasing attention, currently, it has a fundamental problem in that each cell

  12. 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%). Copyright ©ERS 2015.

  13. Epidemiological study of equine piroplasmosis in Mongolia.

    PubMed

    Boldbaatar, Damdinsuren; Xuan, Xuenan; Battsetseg, Badgar; Igarashi, Ikuo; Battur, Banzragch; Batsukh, Zayat; Bayambaa, Badarch; Fujisaki, Kozo

    2005-01-04

    The purpose of this study was to demonstrate the occurrence of equine piroplasmosis in Mongolia, a country in which the disease occurs epidemically in different climatic conditions. Antibodies to Babesia equi and B. caballi were determined in serum samples of 254 pastured horses in different locations of Mongolia using an enzyme-linked immunosorbent assay with recombinant antigens. One hundred and eighty-five (72.8%) and 102 (40.1%) of all serum samples were positive for B. equi and B. caballi infections, respectively. In addition, 78 (30.7%) samples were positive for both B. equi and B. caballi infections. These results indicate that equine piroplasmosis is widespread in Mongolia. To our knowledge, this is the first report describing an epidemiological study on equine piroplasmosis in different geographic regions in Mongolia.

  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.

  15. Oropouche Virus: Clinical, Epidemiological, and Molecular Aspects of a Neglected Orthobunyavirus

    PubMed Central

    Travassos da Rosa, Jorge Fernando; de Souza, William Marciel; Pinheiro, Francisco de Paula; Figueiredo, Mário Luiz; Cardoso, Jedson Ferreira; Acrani, Gustavo Olszanski; Nunes, Márcio Roberto Teixeira

    2017-01-01

    Oropouche virus (OROV) is an important cause of arboviral illness in Latin American countries, more specifically in the Amazon region of Brazil, Venezuela and Peru, as well as in other countries such as Panama. In the past decades, the clinical, epidemiological, pathological, and molecular aspects of OROV have been published and provide the basis for a better understanding of this important human pathogen. Here, we describe the milestones in a comprehensive review of OROV epidemiology, pathogenesis, and molecular biology, including a description of the first isolation of the virus, the outbreaks during the past six decades, clinical aspects of OROV infection, diagnostic methods, genome and genetic traits, evolution, and viral dispersal. PMID:28167595

  16. Oropouche Virus: Clinical, Epidemiological, and Molecular Aspects of a Neglected Orthobunyavirus.

    PubMed

    Travassos da Rosa, Jorge Fernando; de Souza, William Marciel; Pinheiro, Francisco de Paula; Figueiredo, Mário Luiz; Cardoso, Jedson Ferreira; Acrani, Gustavo Olszanski; Nunes, Márcio Roberto Teixeira

    2017-05-01

    AbstractOropouche virus (OROV) is an important cause of arboviral illness in Latin American countries, more specifically in the Amazon region of Brazil, Venezuela and Peru, as well as in other countries such as Panama. In the past decades, the clinical, epidemiological, pathological, and molecular aspects of OROV have been published and provide the basis for a better understanding of this important human pathogen. Here, we describe the milestones in a comprehensive review of OROV epidemiology, pathogenesis, and molecular biology, including a description of the first isolation of the virus, the outbreaks during the past six decades, clinical aspects of OROV infection, diagnostic methods, genome and genetic traits, evolution, and viral dispersal.

  17. 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.

  18. 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.

  19. A 15-year analysis of molecular epidemiology of avian infectious bronchitis coronavirus in China.

    PubMed

    Han, Zongxi; Sun, Chuyang; Yan, Baolong; Zhang, Xiaonan; Wang, Yu; Li, Chengren; Zhang, Qingxia; Ma, Yazhen; Shao, Yuhao; Liu, Qiaoran; Kong, Xiangang; Liu, Shengwang

    2011-01-01

    A comprehensive study of the epidemiology and pathogenicity of infectious bronchitis virus (IBV) in China was carried out by molecular characterization of the S1 gene from 46 isolates obtained for this study and 174 reference strains isolated over a 15-year period. Nine types were found according to sequence analysis and phylogenetic study of the S1 gene. The co-circulation of multiple IBV types and the ongoing emergence of IBV variants are the epidemiological challenges in China. Factors contributing to the continual emergence include mutations, insertions and deletions in the S1 protein genes; recombination between local IBV strains circulating in chicken flocks in China; and recombination between local strains and vaccine strains. Vaccination-challenge analysis between circulating field strains and Mass-type H120 vaccine indicated the need to develop new vaccines from local IBV strains. These results also emphasize the importance of continued IBV surveillance in China. Copyright © 2010 Elsevier B.V. All rights reserved.

  20. Molecular epidemiology of MRSA in 13 ICUs from eight European countries.

    PubMed

    Hetem, D J; Derde, L P G; Empel, J; Mroczkowska, A; Orczykowska-Kotyna, M; Kozińska, A; Hryniewicz, W; Goossens, H; Bonten, M J M

    2016-01-01

    The European epidemiology of MRSA is changing with the emergence of community-associated MRSA (CA-MRSA) and livestock-associated MRSA (LA-MRSA). In this study, we investigated the molecular epidemiology of MRSA during 2 years in 13 ICUs in France, Greece, Italy, Latvia, Luxemburg, Portugal, Slovenia and Spain. Surveillance cultures for MRSA from nose and wounds were obtained on admission and twice weekly from all patients admitted to an ICU for ≥3 days. The first MRSA isolate per patient was genotyped in a central laboratory by MLST, spa typing, agr typing and SCCmec (sub)typing. Risk factors for patients with an unknown history of MRSA colonization were identified. Overall, 14 390 ICU patients were screened, of whom 8519 stayed in an ICU for ≥3 days. Overall MRSA admission prevalence was 3.9% and ranged from 1.0% to 7.0% for individual ICUs. Overall MRSA acquisition rate was 2.5/1000 patient days at risk and ranged from 0.2 to 8/1000 patient days at risk per ICU. In total, 557 putative MRSA isolates were submitted to the central laboratory for typing, of which 511 (92%) were confirmed as MRSA. Each country had a distinct epidemiology, with ST8-IVc (UK-EMRSA-2/-6, USA500) being most prevalent, especially in France and Spain, and detected in ICUs in five of eight countries. Seventeen (3%) and three (<1%) isolates were categorized as CA-MRSA and LA-MRSA, respectively. Risk factors for MRSA carriage on ICU admission were age >70 years and hospitalization within 1 year prior to ICU admission. The molecular epidemiology of MRSA in 13 European ICUs in eight countries was homogeneous within, but heterogeneous between, countries. CA-MRSA and LA-MRSA genotypes and Panton-Valentine leucocidin-producing isolates were detected sporadically. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  1. Multicenter Epidemiological Studies of Atherosclerosis Imaging

    PubMed Central

    Liu, Songtao; Bluemke, David A.

    2011-01-01

    Cardiovascular disease is the leading course of death and disability. Conventional cardiac risk factors do not fully explain the level of cardiovascular risk, incidence of coronary artery disease, and coronary events. Risk stratification and therapy based solely on these conventional risk factors may overlook a population who would benefit from lifestyle and risk factor modification. Thus, research has recently focused on improving risk assessment with new tools in an effort to better identify subjects at highest risk and in need of aggressive management. Cardiovascular imaging, both in coronary and extracoronary arterial beds, has proven to be very helpful in this regard. In this article, we review the current literature from multicenter epidemiology studies on the utility of noninvasive imaging modalities for risk stratification in the context of conventional risk factor evaluation. PMID:20805734

  2. An epidemiological study of histrionic personality disorder.

    PubMed

    Nestadt, G; Romanoski, A J; Chahal, R; Merchant, A; Folstein, M F; Gruenberg, E M; McHugh, P R

    1990-05-01

    In conjunction with the Epidemiological Catchment Area (ECA) survey conducted in Baltimore, MD, a two-stage probability sample of community subjects was developed with a full psychiatric examination employing DSM-III criteria. This report details the observations on those subjects diagnosed with the DSM-III diagnosis Histrionic Personality Disorder. The results indicate that this condition can be diagnosed reliably and that it is a valid construct. It has a prevalence of 2.1% in a general population. Males and females are equally affected, suggesting that prior reports of an increased prevalence in females was an expression of ascertainment bias found in hospital-based studies. The diagnosis is associated with clear evidence of disturbance in the emotional, behavioural, and social realms. Individuals with this disorder tend to use health care facilities more frequently than others.

  3. Prevalence and molecular epidemiology of Clostridium difficile infection in Indonesia.

    PubMed

    Collins, D A; Gasem, M H; Habibie, T H; Arinton, I G; Hendriyanto, P; Hartana, A P; Riley, T V

    2017-07-01

    Clostridium difficile has not been studied in detail in Asia, particularly Southeast Asia. We thus performed a prevalence study across four hospitals in Central Java province, Indonesia. Stool samples were collected from patients with diarrhoea and tested by enzyme immunoassay for glutamate dehydrogenase (GDH) and toxin A/B (C DIFF QUIK CHEK COMPLETE, TechLab). Specimens were cultured and molecular typing was performed. In total, 340 samples were tested, of which 70 (20.6%) were GDH positive, with toxin detected in 19 (5.6%). Toxigenic C. difficile was isolated from 37 specimens (10.9%), while a further 36 (10.6%) nontoxigenic isolates were identified. The most common strain was ribotype 017 (24.3% of 74 isolates), followed by nontoxigenic types QX 224 (9.5%), and QX 238 and QX 108 (both 8.1%). The high prevalence of C. difficile highlights a need for ongoing surveillance of C. difficile infection in Indonesia.

  4. Molecular testing for clinical diagnosis and epidemiological investigations of intestinal parasitic infections.

    PubMed

    Verweij, Jaco J; Stensvold, C Rune

    2014-04-01

    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.

  5. 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

  6. 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

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

    PubMed

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

    2017-03-01

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

  8. 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

  9. A molecular epidemiological perspective of rhinovirus types circulating in Amsterdam from 2007 to 2012.

    PubMed

    van der Linden, L; Bruning, A H L; Thomas, X V; Minnaar, R P; Rebers, S P H; Schinkel, J; de Jong, M D; Pajkrt, D; Wolthers, K C

    2016-12-01

    Rhinoviruses (RVs) are frequently detected respiratory viruses that cause mild common cold symptoms, but may also lead to more severe respiratory tract infections. The large number of RV types, classified into species A, B and C, hampers clear insights into the epidemiology and clinical significance of each RV type. The aim of this study was to map the circulation of RV types in the Amsterdam area. RV-positive nasopharyngeal and oropharyngeal samples, collected from 2007 to 2012 in the Academic Medical Centre (Amsterdam, the Netherlands), were typed based on the sequence of the region coding for capsid proteins VP4 and VP2. RV-A, RV-B and RV-C were found in proportions of of 52.4% (334/637), 11.3% (72/637), and 36.2% (231/637), respectively. We detected 129 of the 167 currently classified types. RVs circulated throughout the entire year with a peak in the autumn and a decline in the summer. Some RV types were observed throughout the entire sampling period and others had a more seasonal pattern. Nine RV-A and four RV-B novel provisionally assigned types were identified. This study provides an insight into the molecular epidemiology of RVs in the Amsterdam area. The RVs circulating are diverse and include several provisionally new types. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  10. The fate of epidemiologic manuscripts: a study of papers submitted to epidemiology.

    PubMed

    Hall, Susan A; Wilcox, Allen J

    2007-03-01

    Little is known about the success rate of epidemiologic manuscripts, or the number of rejections they may go through before being published. In late 2004 we conducted a retrospective follow-up study of the cohort of manuscripts submitted to Epidemiology in 2002. Using an e-mailed invitation, we conducted an online survey of authors identified from journal records. Authors were asked about submission attempts before and after their submission to Epidemiology. Epidemiology received 371 original articles in 2002, of which it published 101 (27%). Survey response rates were 68% among the authors of accepted manuscripts, and 58% among authors of manuscripts rejected by Epidemiology. These responses provided a total sample of 223 manuscripts for analysis. Of the cohort, 83% (n = 184) were eventually accepted for publication (by Epidemiology or others). The acceptance rate by Epidemiology was the same whether or not the manuscripts had been previously rejected by another journal. Of the 155 manuscripts rejected by Epidemiology, 116 (75%) were eventually published or accepted for publication, 11 (7%) were being prepared for resubmission at the time of follow-up (19-34 months after rejection), 5 (3%) were under review by a journal, and 23 (15%) were inactive. Among the papers we could follow from first submission, 62% of those eventually published had been rejected at least once. In general, papers rejected by one journal were subsequently sent to a journal with lower impact factor. These data suggest most epidemiology manuscripts are eventually published, although some persistence on the part of the authors may be necessary.

  11. Epidemiological and Molecular Characterization of Dengue Virus Circulating in Bhutan, 2013-2014

    PubMed Central

    Zangmo, Sangay; Klungthong, Chonticha; Chinnawirotpisan, Piyawan; Tantimavanich, Srisurang; Kosoltanapiwat, Nathamon; Thaisomboonsuk, Butsaya; Phuntsho, Kelzang; Wangchuk, Sonam; Yoon, In-Kyu; Fernandez, Stefan

    2015-01-01

    Dengue is one of the most significant public health problems in tropical and subtropical countries, and is increasingly being detected in traditionally non-endemic areas. In Bhutan, dengue virus (DENV) has only recently been detected and limited information is available. In this study, we analyzed the epidemiological and molecular characteristics of DENV in two southern districts in Bhutan from 2013–2014. During this period, 379 patients were clinically diagnosed with suspected dengue, of whom 119 (31.4%) were positive for DENV infection by NS1 ELISA and/or nested RT-PCR. DENV serotypes 1, 2 and 3 were detected with DENV-1 being predominant. Phylogenetic analysis of DENV-1 using envelope gene demonstrated genotype V, closely related to strains from northern India. PMID:26295474

  12. A Molecular Epidemiology Survey of Respiratory Adenoviruses Circulating in Children Residing in Southern Palestine

    PubMed Central

    Qurei, Lina; Seto, Donald; Salah, Zaidoun; Azzeh, Maysa

    2012-01-01

    A molecular epidemiology survey was performed in order to establish and document the respiratory adenovirus pathogen profiles among children in Southern Palestine. Three hundred and thirty-eight hospitalized pediatric cases with adenovirus-associated respiratory tract infections were analyzed. Forty four cases out of the 338 were evaluated in more detail for the adenoviruses types present. All of the children resided in Southern Palestine, that is, in city, village and refugee camp environments within the districts of Hebron and Bethlehem. Human adenoviruses circulated throughout 2005–2010, with major outbreaks occurring in the spring months. A larger percent of the children diagnosed with adenoviral infections were male infants. DNA sequence analysis of the hexon genes from 44 samples revealed that several distinct adenovirus types circulated in the region; these were HAdV-C1, HAdV-C2, HAdV-B3 and HAdV-C5. However, not all of these types were detected within each year. This is the first study ever conducted in Palestine of the genetic epidemiology of respiratory adenovirus infections. PMID:22880092

  13. A molecular epidemiology survey of respiratory adenoviruses circulating in children residing in Southern Palestine.

    PubMed

    Qurei, Lina; Seto, Donald; Salah, Zaidoun; Azzeh, Maysa

    2012-01-01

    A molecular epidemiology survey was performed in order to establish and document the respiratory adenovirus pathogen profiles among children in Southern Palestine. Three hundred and thirty-eight hospitalized pediatric cases with adenovirus-associated respiratory tract infections were analyzed. Forty four cases out of the 338 were evaluated in more detail for the adenoviruses types present. All of the children resided in Southern Palestine, that is, in city, village and refugee camp environments within the districts of Hebron and Bethlehem. Human adenoviruses circulated throughout 2005-2010, with major outbreaks occurring in the spring months. A larger percent of the children diagnosed with adenoviral infections were male infants. DNA sequence analysis of the hexon genes from 44 samples revealed that several distinct adenovirus types circulated in the region; these were HAdV-C1, HAdV-C2, HAdV-B3 and HAdV-C5. However, not all of these types were detected within each year. This is the first study ever conducted in Palestine of the genetic epidemiology of respiratory adenovirus infections.

  14. The re-emergence of tuberculosis: what have we learnt from molecular epidemiology?

    PubMed

    Borgdorff, M W; van Soolingen, D

    2013-10-01

    Tuberculosis (TB) has re-emerged over the past two decades: in industrialized countries in association with immigration, and in Africa owing to the human immunodeficiency virus epidemic. Drug-resistant TB is a major threat worldwide. The variable and uncertain impact of TB control necessitates not only better tools (diagnostics, drugs, and vaccines), but also better insights into the natural history and epidemiology of TB. Molecular epidemiological studies over the last two decades have contributed to such insights by answering long-standing questions, such as the proportion of cases attributable to recent transmission, risk factors for recent transmission, the occurrence of multiple Mycobacterium tuberculosis infection, and the proportion of recurrent TB cases attributable to re-infection. M. tuberculosis lineages have been identified and shown to be associated with geographical origin. The Beijing genotype is strongly associated with multidrug resistance, and may have escaped from bacille Calmette-Guérin-induced immunity. DNA fingerprinting has quantified the importance of institutional transmission and laboratory cross-contamination, and has helped to focus contact investigations. Questions to be answered in the near future with whole genome sequencing include identification of chains of transmission within clusters of patients, more precise quantification of mixed infection, and transmission probabilities and rates of progression from infection to disease of various M. tuberculosis lineages, as well as possible variations in vaccine efficacy by lineage. Perhaps most importantly, dynamics in the population structure of M. tuberculosis in response to control measures in high-prevalence areas should be better understood.

  15. Molecular epidemiology of enterovirus 71 strains isolated from children in Yamagata, Japan, between 1990 and 2013.

    PubMed

    Mizuta, Katsumi; Aoki, Yoko; Matoba, Yohei; Yahagi, Kazue; Itagaki, Tsutomu; Katsushima, Fumio; Katsushima, Yuriko; Ito, Sueshi; Hongo, Seiji; Matsuzaki, Yoko

    2014-10-01

    Enterovirus 71 infections have become a major public issue in the Asia-Pacific region due to the large number of fatal cases. To clarify the longitudinal molecular epidemiology of enterovirus 71 (EV71) in a community, we isolated 240 strains from children, mainly with hand-foot-and-mouth diseases, between 1990 and 2013 in Yamagata, Japan. We carried out a sequence analysis of the VP1 region (891 bp) using 223 isolates and identified six subgenogroups (B2, B4, B5, C1, C2 and C4) during the study period. Subgenogroups C1 and B2 were found only between 1990 and 1993 and have not reappeared since. In contrast, strains in subgenogroups C2, C4 and B5 appeared repeatedly with genomic variations. Recent reports from several local communities in Japan have suggested that identical predominant subgenogroup strains, which have also been found in the Asia-Pacific region, have been circulating in a wide area in Japan. However, it is likely that there is a discrepancy between the major subgenogroups circulating in the Asia-Pacific region and those in Europe. It is necessary to continue the analysis of the longitudinal epidemiology of EV71 in local communities, as well as on regional and global levels, to develop strategies against severe EV71 infections.

  16. Classification of rare missense substitutions, using risk surfaces, with genetic- and molecular-epidemiology applications.

    PubMed

    Tavtigian, Sean V; Byrnes, Graham B; Goldgar, David E; Thomas, Alun

    2008-11-01

    Many individually rare missense substitutions are encountered during deep resequencing of candidate susceptibility genes and clinical mutation screening of known susceptibility genes. BRCA1 and BRCA2 are among the most resequenced of all genes, and clinical mutation screening of these genes provides an extensive data set for analysis of rare missense substitutions. Align-GVGD is a mathematically simple missense substitution analysis algorithm, based on the Grantham difference, which has already contributed to classification of missense substitutions in BRCA1, BRCA2, and CHEK2. However, the distribution of genetic risk as a function of Align-GVGD's output variables Grantham variation (GV) and Grantham deviation (GD) has not been well characterized. Here, we used data from the Myriad Genetic Laboratories database of nearly 70,000 full-sequence tests plus two risk estimates, one approximating the odds ratio and the other reflecting strength of selection, to display the distribution of risk in the GV-GD plane as a series of surfaces. We abstracted contours from the surfaces and used the contours to define a sequence of missense substitution grades ordered from greatest risk to least risk. The grades were validated internally using a third, personal and family history-based, measure of risk. The Align-GVGD grades defined here are applicable to both the genetic epidemiology problem of classifying rare missense substitutions observed in known susceptibility genes and the molecular epidemiology problem of analyzing rare missense substitutions observed during case-control mutation screening studies of candidate susceptibility genes.

  17. Tracking the molecular epidemiology of Brazilian Infectious bursal disease virus (IBDV) isolates.

    PubMed

    Silva, Fernanda M F; Vidigal, Pedro M P; Myrrha, Luciana W; Fietto, Juliana L R; Silva, Abelardo; Almeida, Márcia R

    2013-01-01

    Infectious bursal disease is a highly contagious disease of young chickens caused by Infectious bursal disease virus (IBDV). Genome segment A encodes the capsid protein (VP2), while segment B encodes the RNA-dependent RNA polymerase (VP1). In the present study, we trace the molecular epidemiology of IBDV in Brazil by analyzing 29 isolates collected in the major regions of poultry production. To genetically characterize the isolates, phylogenetic and population dynamic analyses were conducted using 68 VP1 (2634 nt) and 102 VP2 (1356 nt) coding sequences from IBDV isolates from different regions of the world. Furthermore, the evolution of IBDV was analyzed by characterizing the selective forces that operated during the diversification of viral isolates. We show that IBDV isolates were introduced into Brazil mainly from the Netherlands and the USA. These introductions were associated with all Brazilian poultry production regions analyzed in this work. In addition, we show that the evolution of IBDV has been shaped by a combination of very low recombination rates and relatively high rates of nucleotide substitution (2.988×10(-4) for VP1 and 3.2937×10(-4) for VP2), which themselves are a function of purifying selection operating on VP1 and VP2. Furthermore, our extended Bayesian skyline plot suggests that the increase in the effective population size of isolates of IBDV is consistent with its epidemiological history, with a large increase during the emergence of acute outbreaks of IBD in the 1980s.

  18. VDTs: Field levels, epidemiology, and laboratory studies

    SciTech Connect

    Kavet, R.; Tell, R.A. )

    1991-07-01

    As the use of video display terminals (VDTs) has expanded, questions have been raised as to whether working at a VDT affects the risk of adverse pregnancy outcome. A particular focus for these questions has been the very low frequency (VLF) magnetic field produced by a VDT's horizontal deflection coil. VDTs also produce VLF electric fields, extremely low frequency (ELF) electric and magnetic fields, and static electric fields, Ten studies of pregnancy outcome in VDT operators have been conducted in six countries, and with one exception, none has concluded that magnetic fields from VDTs may predispose pregnant operators to spontaneous abortion or congenital malformation. The epidemiologic studies conducted thus far do not provide a basis for concluding that VDT work and adverse pregnancy outcome are associated. Studies of fetal resorptions and malformations in rodents exposed to VLF magnetic fields have produced inconsistent findings. Two laboratories in Sweden that studied mice have reported positive results, one laboratory showing field-related malformations (but not resorptions) and the other showing field-related resorptions (but not malformations). Two Canadian laboratories have reported negative results in rats and mice. Studies of avian embryos have also yielded inconsistent results, but lacking a maternal-fetal placental interface, avian embryos are a questionable model for evaluating human reproductive risks. Finally, VLF electric and magnetic fields measured at the operator position are in compliance with field strength standards and guidelines that have been established around the world. 55 refs.

  19. Epidemiological and Clinical Studies of Nutrition

    PubMed Central

    Gibson, Todd M.; Ferrucci, Leah M.; Tangrea, Joseph A.; Schatzkin, Arthur

    2010-01-01

    In this review, we briefly summarize some of the key developments in nutritional epidemiology and cancer over the past two decades with a focus on the strengths and limitations of study designs and dietary assessment methods. We present the evidence on dietary fat, meat, fiber, antioxidant nutrients, and calcium in relation to carcinogenesis from large cohort studies and randomized clinical trials (RCTs) and refer to the conclusions of the 2007 World Cancer Research Fund/American Institute for Cancer Research summary report. One prominent theme that emerged is the lack of concordance of results from RCTs and observational studies. There are multiple potential reasons for these discrepancies, including differences in study population, dose and timing of the exposure, adherence to an intervention, length of follow-up, and the primary endpoint. Therefore, null findings of RCTs do not necessarily indicate a lack of effect for the tested dietary factors on cancer risk, as some of these nutrients may have chemopreventive effects if given at the right time and in the right dose. It is likely that potential benefits from the diet are due to a combination of food constituents rather than single components acting in isolation. Future efforts need to recognize the integrative nature of dietary exposures and attempt to study nutrients in the larger context of the foods and diets in which they are consumed. PMID:20709210

  20. Negative and non-positive epidemiological studies.

    PubMed

    Axelson, Olav

    2004-01-01

    The aim of this study was to identify and discuss validity aspects on so called negative and non-positive studies. Arguments and examples are drawn from experiences in occupational health epidemiology regarding the interpretation of more or less equivocal study results. A negative study may be defined as showing a result that goes against the investigated hypothesis of an increased (or prevented) risk. Traditionally, studies with a risk estimate (relative risk or odds ratio) above, but close to unity are also referred to as negative, given a narrow confidence interval (CI) that includes unity. A risk estimate above unity with the CI including unity is non-positive, however, but an estimate below unity with upper CI bond exceeding unity might be seen as possibly negative or non-negative. A weaker "significance" than usually required should perhaps be accepted when evaluating serious hazards. In contrast to positive studies, the negative and non-positive studies tend to escape criticism in spite of questionable validity that may have obscured existing risks (or preventive effects). Even stronger arguments can be made in criticising negative and non-positive studies than positive studies, for example, regarding selection phenomena, and observational problems regarding exposure and outcome. Negative confounding should be considered although usually weak. In case-control studies, so called over-matching may obscure an existing risk as could the "healthy worker effect" in cohort studies. Small scale non-positive studies should be made available for meta-analyses and when considering studies that do not convincingly show a risk; those who are exposed should be given the "benefit of the doubt".

  1. Tea and cancer prevention: epidemiological studies.

    PubMed

    Yuan, Jian-Min; Sun, Canlan; Butler, Lesley M

    2011-08-01

    Experimental studies have consistently shown the inhibitory activities of tea extracts on tumorigenesis in multiple model systems. Epidemiological 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.

  2. 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

  3. 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...

  4. Molecular-based surveillance of campylobacteriosis in New Zealand--from source attribution to genomic epidemiology.

    PubMed

    Muellner, P; Pleydell, E; Pirie, R; Baker, M G; Campbell, D; Carter, P E; French, N P

    2013-01-17

    Molecular-based surveillance of campylobacteriosis in New Zealand contributed to the implementation of interventions that led to a 50% reduction in notified and hospitalised cases of the country's most important zoonosis. From a pre-intervention high of 384 per 100,000 population in 2006, incidence dropped by 50% in 2008; a reduction that has been sustained since. This article illustrates many aspects of the successful use of molecular-based surveillance, including the distinction between control-focused and strategy-focused surveillance and advances in source attribution. We discuss how microbial genetic data can enhance the understanding of epidemiological explanatory and response variables and thereby enrich the epidemiological analysis. Sequence data can be fitted to evolutionary and epidemiological models to gain new insights into pathogen evolution, the nature of associations between strains of pathogens and host species, and aspects of between-host transmission. With the advent of newer sequencing technologies and the availability of rapid, high-coverage genome sequence data, such techniques may be extended and refined within the emerging discipline of genomic epidemiology. The aim of this article is to summarise the experience gained in New Zealand with molecular-based surveillance of campylobacteriosis and to discuss how this experience could be used to further advance the use of molecular tools in surveillance.

  5. 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

    2013-01-24

    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.

  6. 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.

  7. Molecular Epidemiological Interpretation of the Epidemic of Extensively Drug-Resistant Tuberculosis in South Africa.

    PubMed

    Streicher, E M; Sampson, S L; Dheda, K; Dolby, T; Simpson, J A; Victor, T C; Gey van Pittius, N C; van Helden, P D; Warren, R M

    2015-11-01

    We show that the interpretation of molecular epidemiological data for extensively drug-resistant tuberculosis (XDR-TB) is dependent on the number of different markers used to define transmission. Using spoligotyping, IS6110 DNA fingerprinting, and DNA sequence data, we show that XDR-TB in South Africa (2006 to 2008) was predominantly driven by the acquisition of second-line drug resistance.

  8. [Molecular biological and epidemiological -characteristics of the varicella-zoster virus (VZV)].

    PubMed

    Boštíková, Vanda; Chlíbek, Roman; Salavec, Miloslav; Smetana, Jan; Sleha, Radek; Špliňo, Miroslav; Boštík, Pavel

    2013-12-01

    The genetic diversity and epidemiology of VZV results from an interplay of the geographic area, climate conditions, and population factors. Studies of the genetic diversity of VZV can have direct implications for both the epidemiological and evolutionary analyses and identification of the genetic correlates of VZV pathogenicity or resistance to antiviral drugs.

  9. 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

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

    2009-03-16

    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 the 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 microM 8, 24 h 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 nonmutagenic/carcinogenic, these results, if generalizable to other PAH, do not support the widely held

  10. 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

  11. Clinical and Molecular Epidemiology of Staphylococcus argenteus Infections in Thailand

    PubMed Central

    Amornchai, Premjit; Nickerson, Emma K.; Wongsuvan, Gumphol; Wuthiekanun, Vanaporn; Limmathurotsakul, Direk; Peacock, Sharon J.

    2015-01-01

    Molecular typing of 246 Staphylococcus aureus isolates from unselected patients in Thailand showed that 10 (4.1%) were actually Staphylococcus argenteus. Contrary to the suggestion that S. argenteus is less virulent than S. aureus, we demonstrated comparable rates of morbidity, death, and health care-associated infection in patients infected with either of these two species. PMID:25568440

  12. 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.

  13. Mycobacterium tuberculosis population structure shift in a 5-year molecular epidemiology surveillance follow-up study in a low endemic agro-industrial setting in São Paulo, Brazil.

    PubMed

    Santos, Adolfo Carlos Barreto; Gaspareto, Rosângela Maria; Viana, Brunilde Helena Jung; Mendes, Natália Helena; Pandolfi, José Rodrigo Cláudio; Cardoso, Rosilene Fressatti; Sato, Daisy Nakamura; David, Susana Correia de Matos; Saad, Maria Helena Feres; Rastogi, Nalin; Leite, Clarice Queico Fujimura

    2013-09-01

    Starting with 257 outpatients attending the specialized health service for tuberculosis (TB) between 2002 and 2006 in Araraquara, an agro-industrial area with low tuberculosis (TB) incidence in São Paulo state, Brazil, positive mycobacterial cultures were obtained in 130 cases, of which 121 were confirmed as Mycobacterium tuberculosis complex. This report assesses the genetic diversity observed on 69.42% (n=84) of the clinical isolates, for which both spoligotyping and 12-loci MIRU typing data were fully interpretable. In order to monitor changes in the population dynamics of circulating M. tuberculosis strains over time, spoligotypes were compared from this study (n=84) with an earlier study from 1998 to 2001 (n=70 strains); and these two datasets from low-incidence Araraquara area were also compared with a 2-year cohort in the nearby higher-incidence São Paulo city area from 2006 to 2008 (n=93). The results obtained showed that with 58.3% (49/84) of the strains, the Latin-American-Mediterranean (LAM) was the predominant lineage in the present follow-up study; major patterns being SIT42/LAM9 11.9% (10/84), and SIT20/LAM1 10.7% (9/84). As compared with the 1998-2001 period when 40% (28/70) of the isolates belonged to the ill-defined T family, it was replaced by LAM strains between 2002 and 2006 with a visible shift to a population structure characteristic of the metropolitan São Paulo city. Further typing of the follow-up isolates from 2002 to 2006 using 12 loci MIRUs in conjunction with conventional epidemiology did not link this population structure shift to an increase in ongoing transmission or drug-resistance. Instead, it is most probably linked to movements of the important migrant community of Araraquara to higher TB incidence metropolitan areas such as São Paulo city. This is of particular concern owing to the increment in the global burden of LAM strains and the recent association of certain LAM sublineages with multidrug- and extensively drug

  14. 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

  15. Systemic Amyloidosis in England: an epidemiological study

    PubMed Central

    Pinney, Jennifer H; Smith, Colette J; Taube, Jessi B; Lachmann, Helen J; Venner, Christopher P; Gibbs, Simon D J; Dungu, Jason; Banypersad, Sanjay M; Wechalekar, Ashutosh D; Whelan, Carol J; Hawkins, Philip N; Gillmore, Julian D

    2013-01-01

    Epidemiological studies of systemic amyloidosis are scarce and the burden of disease in England has not previously been estimated. In 1999, the National Health Service commissioned the National Amyloidosis Centre (NAC) to provide a national clinical service for all patients with amyloidosis. Data for all individuals referred to the NAC is held on a comprehensive central database, and these were compared with English death certificate data for amyloidosis from 2000 to 2008, obtained from the Office of National Statistics. Amyloidosis was stated on death certificates of 2543 individuals, representing 0·58/1000 recorded deaths. During the same period, 1143 amyloidosis patients followed at the NAC died, 903 (79%) of whom had amyloidosis recorded on their death certificates. The estimated minimum incidence of systemic amyloidosis in the English population in 2008, based on new referrals to the NAC, was 0·4/100 000 population. The incidence peaked at age 60–79 years. Systemic AL amyloidosis was the most common type with an estimated minimum incidence of 0·3/100 000 population. Although there are various limitations to this study, the available data suggest the incidence of systemic amyloidosis in England exceeds 0·8/100 000 of the population. PMID:23480608

  16. Molecular epidemiology of adrenocortical tumors in southern Brazil.

    PubMed

    Custódio, Gislaine; Komechen, Heloisa; Figueiredo, Francisco R O; Fachin, Natasha D; Pianovski, Mara A D; Figueiredo, Bonald C

    2012-03-31

    The high frequency of TP53 R337H carriers in southern Brazil is responsible for the highest known incidence of childhood adrenocortical tumor (ACT). Our aims were to examine other contributing mutations, age-related risk factors, epidemiological differences in ACT and to shed light on a method for increasing the survival rate of children. The fetal zone of the adrenal cortex is believed to be one of the tissues most susceptible to adenoma or carcinoma formation due to loss of p53 function. The founder germline R337H mutation is found in 95% of ACTs of young children, a much greater proportion than in adults. Despite intense educational campaigns about the high incidence of ACT in Paraná State, advanced cases remain common. Four advanced ACT cases (4/5) were admitted to a single institution in the first 6months of 2011 in Paraná State, none of the families knew about ACT, and 2 reported no familial cancer syndrome. Curative resection is possible when a small ACT is detected early. Copyright © 2011. Published by Elsevier Ireland Ltd.

  17. Leptospira species molecular epidemiology in the genomic era.

    PubMed

    Caimi, K; Repetto, S A; Varni, V; Ruybal, P

    2017-10-01

    Leptospirosis is a zoonotic disease which global burden is increasing often related to climatic change. Hundreds of whole genome sequences from worldwide isolates of Leptospira spp. are available nowadays, together with online tools that permit to assign MLST sequence types (STs) directly from raw sequence data. In this work we have applied R7L-MLST to near 500 genomes and strains collection globally distributed. All 10 pathogenic species as well as intermediate were typed using this MLST scheme. The correlation observed between STs and serogroups in our previous work, is still satisfied with this higher dataset sustaining the implementation of MLST to assist serological classification as a complementary approach. Bayesian phylogenetic analysis of concatenated sequences from R7-MLST loci allowed us to resolve taxonomic inconsistencies but also showed that events such as recombination, gene conversion or lateral gene transfer played an important role in the evolution of Leptospira genus. Whole genome sequencing allows us to contribute with suitable epidemiologic information useful to apply in the design of control strategies and also in diagnostic methods for this illness. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Molecular systematics of filarial parasites, with an emphasis on groups of medical and veterinary importance, and its relevance for epidemiology.

    PubMed

    Morales-Hojas, Ramiro

    2009-09-01

    Filarial parasites are members of the Phylum Nemata that comprise several species of medical and veterinary importance. Among the human diseases caused by members of this group of nematodes are river blindness and lymphatic filariasis, which afflict millions of people in the tropics. These diseases not only have an impact on the health of the people affected but also bear a great socioeconomic burden. Despite their relevance, the systematics of the filarial parasites is not well understood yet, and additional molecular phylogenetic studies are required to comprehend the evolution of these parasites. Identifying the patterns of evolution of these parasites will be of relevance in preventing emerging zoonoses. The present review examines the information about the molecular systematics of filarial parasites available in the literature and evaluates the relevance of the different directions of future research. Furthermore, it is also intended to highlight the relevance of molecular systematic studies in the molecular epidemiology research area.

  19. [Mental disorders and migraine: epidemiologic studies].

    PubMed

    Guillem, E; Pelissolo, A; Lepine, J P

    1999-01-01

    Epidemiologic studies in the general population, taking into account certain bias inherent to the clinical observation have confirmed the clinical impression reporting a higher psychiatric comorbidity with persons suffering from migraine than in persons without migraine. Persons with migraine are at increased risk for affective and anxiety disorders, personality traits disorders (neuroticism), suicide attempts, but not for alcohol or illicit drug abuse. The comorbidity is more important in migraine with aura than in migraine without aura. Concerning affective disorders, the lifetime prevalence of major depression is 34.4% in persons with migraine and 10.4% in persons without migraine. For bipolar I disorder, prevalence is 6.8% in migraine with aura versus 0.9% when no migraine. Compared to no migraine, the lifetime prevalence of anxiety disorders in migraine is significantly increased in: panic disorder (10.9% vs 1.8%); generalized anxiety disorder (10.2% vs 1.9%); obsessive-compulsive disorder (8.6% vs 1.8%); phobic disorder (39.8% vs 20.6%). In addition, no psychopathological, biological or genetic explanation seems to be meaningful for the comprehension of this comorbidity pattern. These results remain primarily descriptive but they justify a clinical investigation of affective and anxiety disorders, and suicide attempts, in all person with migraine, and it also justifies the treatment of pain associated with the treatment of eventual affective or anxiety disorders.

  20. 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

  1. Strengthening the Reporting of Observational Studies in Epidemiology - nutritional epidemiology (STROBE-nut): An extension of the STROBE statement.

    PubMed

    Lachat, C; Hawwash, D; Ocké, M C; Berg, C; Forsum, E; Hörnell, A; Larsson, C L; Sonestedt, E; Wirfält, E; Åkesson, A; Kolsteren, P; Byrnes, G; De Keyzer, W; Van Camp, J; Cade, J E; Slimani, N; Cevallos, M; Egger, M; Huybrechts, I

    2016-09-01

    Concerns have been raised about the quality of reporting in nutritional epidemiology. Research reporting guidelines such as the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement can improve quality of reporting in observational studies. Herein, we propose recommendations for reporting nutritional epidemiology and dietary assessment research by extending the STROBE statement into Strengthening the Reporting of Observational Studies in Epidemiology - Nutritional Epidemiology (STROBE-nut). Recommendations for the reporting of nutritional epidemiology and dietary assessment research were developed following a systematic and consultative process, co-ordinated by a multidisciplinary group of 21 experts. Consensus on reporting guidelines was reached through a three-round Delphi consultation process with 53 external experts. In total, 24 recommendations for nutritional epidemiology were added to the STROBE checklist. When used appropriately, reporting guidelines for nutritional epidemiology can contribute to improve reporting of observational studies with a focus on diet and health.

  2. Strengthening the Reporting of Observational Studies in Epidemiology-Nutritional Epidemiology (STROBE-nut): An Extension of the STROBE Statement.

    PubMed

    Lachat, Carl; Hawwash, Dana; Ocké, Marga C; Berg, Christina; Forsum, Elisabet; Hörnell, Agneta; Larsson, Christel; Sonestedt, Emily; Wirfält, Elisabet; Åkesson, Agneta; Kolsteren, Patrick; Byrnes, Graham; De Keyzer, Willem; Van Camp, John; Cade, Janet E; Slimani, Nadia; Cevallos, Myriam; Egger, Matthias; Huybrechts, Inge

    2016-06-01

    Concerns have been raised about the quality of reporting in nutritional epidemiology. Research reporting guidelines such as the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement can improve quality of reporting in observational studies. Herein, we propose recommendations for reporting nutritional epidemiology and dietary assessment research by extending the STROBE statement into Strengthening the Reporting of Observational Studies in Epidemiology-Nutritional Epidemiology (STROBE-nut). Recommendations for the reporting of nutritional epidemiology and dietary assessment research were developed following a systematic and consultative process, coordinated by a multidisciplinary group of 21 experts. Consensus on reporting guidelines was reached through a three-round Delphi consultation process with 53 external experts. In total, 24 recommendations for nutritional epidemiology were added to the STROBE checklist. When used appropriately, reporting guidelines for nutritional epidemiology can contribute to improve reporting of observational studies with a focus on diet and health.

  3. Review, discussion, and summary of epidemiological studies

    SciTech Connect

    Shy, C.M.

    1989-02-01

    This paper reviews and summarizes the epidemiological studies presented at the Symposium on the Health Effects of Acid Aerosols. Two studies of acute episodes examined different indicators of respiratory morbidity before, during, and after the January 1985 air pollution event in western Europe. In the U.K. no increase in respiratory morbidity, as reported by a group of general practitioners, was observed, but measured concentrations of air pollutants failed to substantiate the existence of an identifiable episode. In the Federal Republic of Germany, the air pollution episode was documented and was associated with a 10 to 25% increase in several indicators of respiratory and cardiovascular morbidity, but could not be attributed to acidic aerosols as such. In two further studies, investigators related day-to-day variations in air pollution with admissions to acute care hospitals in southern Ontario for respiratory disease over a 9-year period, and with daily mortality in London from 1963 to 1972. In the study of hospital admissions, significant correlations were observed with sulfate, ozone, and SO/sub 2/ pollution, but the data were insufficient to isolate the separate or combined effects of these pollutants. In the London mortality analysis, the strongest correlations were observed for sulfuric acid levels of the prior day, but prefiltering of the mortality data may have dampened the true relationship, and age- and cause-specific analyses would have been desirable. Finally two reports on chronic effects of residence in high air pollution areas have thus far made little contribution to the evidence for an adverse effect of specific pollutants.

  4. 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...

  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. 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 humans...

  7. 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...

  8. 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... 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. Molecular and epidemiological updates on cystic echinococcosis infecting water buffaloes from Egypt.

    PubMed

    Abbas, Ibrahim

    2016-12-01

    Cystic echinococcosis (CE) represents a serious parasitic disease at both animal and public health levels. The majority of reports negated the CE infection in buffaloes from Egypt; however, one study illustrated their infection with G6 genotype (camel strain). The present work contributed to update the epidemiological and molecular knowledge about CE infecting this economically important animal for better understanding of its role in maintaining the Echinococcus life cycle. A total of 120 slaughtered water buffaloes at Mansoura abattoir, Dakahlia province, Egypt, were inspected for the existence of hydatid cysts. Cysts location and fertility were examined. Five out of 27 revealed cysts were tested molecularly using both cytochrome C oxidase subunit 1 and nicotinamide adenine dinucleotide hydrogen subunit 1 (nadh1) genes. Low prevalence (4.2%) as well as considerably low fertility rate (14.8%) of buffaloes CE was noted. G1 genotype (common sheep strain) was revealed from the five examined cysts. At the level of nadh1 partial sequences, a globally singleton G1 haplotype was reported. This the first report about the G1 infection in buffaloes from Egypt. This study proposed the minimized role of this animal in echinococcosis transmission. These findings could provide preliminary data for the local control of this disease.

  10. Epidemiological and molecular characterization of dengue viruses imported into Guangzhou during 2009-2013.

    PubMed

    Shi, Yongxia; Li, Shufen; Li, Xiaobo; Zheng, Kui; Yuan, Shuai; Huang, Jicheng

    2016-01-01

    Dengue virus causes one of the most significant infectious diseases in tropical and subtropical regions, notable number of which is imported into China every year. In this study, the molecular epidemiologic and phylogenetic analyses of dengue cases imported into Guangzhou in South China during 2009-2013 were conducted. During that period, 46 imported dengue cases were identified, including four serotypes. Most of the dengue patients were travelling from Southeast Asia, South Asia and Africa. The envelope (E) genes of 20 imported dengue viruses introduced from 13 countries and regions, were sequenced and used for phylogenetic analyses. The results indicated that the DENV-1 genotype I and DENV-2 Asian genotype I were the most predominant DENV strains, which were circulating in Southeast Asia and imported into South China. In addition, the new introduction of DENV-3 genotype III from West Asia was observed. This study provided an overview on the genetic diversity of DENV strains imported into South China, and also gave information about the geographic distribution, dynamic transmission and molecular evolution of epidemic DENV strains.

  11. Molecular and epidemiological updates on cystic echinococcosis infecting water buffaloes from Egypt

    PubMed Central

    Abbas, Ibrahim

    2016-01-01

    Aim: Cystic echinococcosis (CE) represents a serious parasitic disease at both animal and public health levels. The majority of reports negated the CE infection in buffaloes from Egypt; however, one study illustrated their infection with G6 genotype (camel strain). The present work contributed to update the epidemiological and molecular knowledge about CE infecting this economically important animal for better understanding of its role in maintaining the Echinococcus life cycle. Materials and Methods: A total of 120 slaughtered water buffaloes at Mansoura abattoir, Dakahlia province, Egypt, were inspected for the existence of hydatid cysts. Cysts location and fertility were examined. Five out of 27 revealed cysts were tested molecularly using both cytochrome C oxidase subunit 1 and nicotinamide adenine dinucleotide hydrogen subunit 1 (nadh1) genes. Results: Low prevalence (4.2%) as well as considerably low fertility rate (14.8%) of buffaloes CE was noted. G1 genotype (common sheep strain) was revealed from the five examined cysts. At the level of nadh1 partial sequences, a globally singleton G1 haplotype was reported. Conclusion: This the first report about the G1 infection in buffaloes from Egypt. This study proposed the minimized role of this animal in echinococcosis transmission. These findings could provide preliminary data for the local control of this disease. PMID:28096605

  12. Integration of Molecular Pathology, Epidemiology, and Social Science for Global Precision Medicine

    PubMed Central

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

    2015-01-01

    Summary 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

  13. [Clinico-epidemiologic study of microtia].

    PubMed

    Sánchez, O; Méndez, J R; Gómez, E; Guerra, D

    1997-12-01

    Microtia is a congenital malformation characterized by total or partial absence of the whole auricle or any of its components, varying from a small auricle to the total absence (anotia). There may be associated atresia of the external auditory meatus. The frequency varies in different parts of the world between 0.4 and 5.5/10,000 newborns. In this paper we report the clinical and epidemiological characterization of this congenital malformation in a sample of 97.759 neonates born at the Ruíz y Páez Hospital in Ciudad Bolivar, Venezuela, between April 1978 and December 1994. A total of 38 patients with microtia were identified. The global frequency was 3.8 per 10,000/newborns. In 47.4% of the patients microtia was an isolated malformation and in 52.6% was associated to other malformations. Sixty three percent of the affected were males. The unilateral form was present in 81.5% of the cases, more frequently on the right side. The annual frequency of the defect was stable over the studied years. The clinical classification of the cases with associated malformations allowed us to establish that 18.4% of the cases correspond to developmental fields defects, associated to preauricular dimples and/or tags, 7.8% were cases of the facio-auriculo-vertebral spectrum and in 15.7% the microtia was part of a monogenic or chromosomal syndrome. In 10.5% it was not possible to define any etiological or pathogenic mechanism. The frequency obtained in this study for microtia shows intermediate values when compared with others reports from Latin America.

  14. 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.

  15. 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.

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

    PubMed

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

    2016-11-18

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

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

    PubMed

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

    2016-07-01

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

  18. Molecular Epidemiology and Antimicrobial Susceptibility of Clostridium difficile Isolates from a University Teaching Hospital in China

    PubMed Central

    Cheng, Jing-Wei; Xiao, Meng; Kudinha, Timothy; Kong, Fanrong; Xu, Zhi-Peng; Sun, Lin-Ying; Zhang, Li; Fan, Xin; Xie, Xiu-Li; Xu, Ying-Chun

    2016-01-01

    While the developed world has seen a significant increase in the number of scientific articles on Clostridium difficile infection (CDI), the developing world still lags behind on this subject due to limited laboratory capacity, low awareness, and limited surveillance of this problem. As such, CDI is considered a neglected but potentially huge problem in developing countries. The major aim of this study was to systemically evaluate the utility of several molecular typing tools for CDI, including their relevance in epidemiological studies in developing countries such as China. A total of 116 non-repetitive toxigenic C. difficile isolates from Chinese patients, were studied. The isolates comprised 83 (71.6%) A+B+CDT- isolates, 27 (23.3%) A-B+CDT- isolates, and 6 (5.1%) A+B+CDT+ isolates. Typing methods evaluated included multilocus variable-number tandem-repeat analysis, PCR ribotyping, multilocus sequence typing, and sequencing of slpA and tcdC genes, which identified 113, 30, 22, 18, and 8 genotypes each and exhibited discriminatory powers of 0.999, 0.916, 0.907, 0.883, and 0.765, respectively. Compared to A+B+ strains, A-B+ strains exhibited higher prevalence of drug resistance to clindamycin, erythromycin, levofloxacin, rifampicin, rifaximin, and tetracycline. Furthermore, drug resistance rates of strains with different PCR ribotypes differed, supporting the importance of molecular typing in management and control of CDI. Based on our earlier suggestion to improve the diagnostic laboratory capacity of CDI in developing countries, setting up efficient surveillance programs complemented by relevant molecular typing methods is warranted. PMID:27799923

  19. Biomarkers for Uranium Risk Assessment for the Development of the CURE (Concerted Uranium Research in Europe) Molecular Epidemiological Protocol.

    PubMed

    Guéguen, Yann; Roy, Laurence; Hornhardt, Sabine; Badie, Christophe; Hall, Janet; Baatout, Sarah; Pernot, Eileen; Tomasek, Ladislav; Laurent, Olivier; Ebrahimian, Teni; Ibanez, Chrystelle; Grison, Stephane; Kabacik, Sylwia; Laurier, Dominique; Gomolka, Maria

    2017-01-01

    Despite substantial experimental and epidemiological research, there is limited knowledge of the uranium-induce health effects after chronic low-dose exposures in humans. Biological markers can objectively characterize pathological processes or environmental responses to uranium and confounding agents. The integration of such biological markers into a molecular epidemiological study would be a useful approach to improve and refine estimations of uranium-induced health risks. To initiate such a study, Concerted Uranium Research in Europe (CURE) was established, and involves biologists, epidemiologists and dosimetrists. The aims of the biological work package of CURE were: 1. To identify biomarkers and biological specimens relevant to uranium exposure; 2. To define standard operating procedures (SOPs); and 3. To set up a common protocol (logistic, questionnaire, ethical aspects) to perform a large-scale molecular epidemiologic study in uranium-exposed cohorts. An intensive literature review was performed and led to the identification of biomarkers related to: 1. retention organs (lungs, kidneys and bone); 2. other systems/organs with suspected effects (cardiovascular system, central nervous system and lympho-hematopoietic system); 3. target molecules (DNA damage, genomic instability); and 4. high-throughput methods for the identification of new biomarkers. To obtain high-quality biological materials, SOPs were established for the sampling and storage of different biospecimens. A questionnaire was developed to assess potential confounding factors. The proposed strategy can be adapted to other internal exposures and should improve the characterization of the biological and health effects that are relevant for risk assessment.

  20. Molecular Epidemiology and Evolution of Human Enterovirus Serotype 68 in Thailand, 2006–2011

    PubMed Central

    Linsuwanon, Piyada; Puenpa, Jiratchaya; Suwannakarn, Kamol; Auksornkitti, Vittawat; Vichiwattana, Preeyaporn; Korkong, Sumeth; Theamboonlers, Apiradee; Poovorawan, Yong

    2012-01-01

    Background Publications worldwide have reported on the re-occurrence of human enterovirus 68 (EV68), a rarely detected pathogen usually causing respiratory illness. However, epidemiological data regarding this virus in particular on the Asian continent has so far been limited. Methodology/Findings We investigated the epidemiology and genetic variability of EV68 infection among Thai children with respiratory illnesses from 2006–2011 (n = 1810). Semi-nested PCR using primer sets for amplification of the 5′-untranslated region through VP2 was performed for rhino-enterovirus detection. Altogether, 25 cases were confirmed as EV68 infection indicating a prevalence of 1.4% in the entire study population. Interestingly, the majority of samples were children aged >5 years (64%). Also, co-infection with other viruses was found in 28%, while pandemic H1N1 influenza/2009 virus was the most common co-infection. Of EV68-positive patients, 36% required hospitalizations with the common clinical presentations of fever, cough, dyspnea, and wheezing. The present study has shown that EV68 was extremely rare until 2009 (0.9%). An increasing annual prevalence was found in 2010 (1.6%) with the highest detection frequency in 2011 (4.3%). Based on analysis of the VP1 gene, the evolutionary rate of EV68 was estimated at 4.93×10−3 substitutions/site/year. Major bifurcation of the currently circulating EV68 strains occurred 66 years ago (1945.31 with (1925.95–1960.46)95% HPD). Among the current lineages, 3 clusters of EV68 were categorized based on the different molecular signatures in the BC and DE loops of VP1 combined with high posterior probability values. Each cluster has branched off from their common ancestor at least 36 years ago (1975.78 with (1946.13–1984.97)95% HPD). Conclusion Differences in epidemiological characteristic and seasonal profile of EV68 have been found in this study. Results from Bayesian phylogenetic investigations also revealed that EV68 should be