Home About us Contact
|
Home About us Contact | ||
|
|
||
Molecular Epidemiology (molecular + epidemiology)
Selected AbstractsSearching PubMed for molecular epidemiology studies: The case of chromosome aberrationsENVIRONMENTAL AND MOLECULAR MUTAGENESIS, Issue 4 2006Donatella Ugolini Abstract The available tools for searching literature in the field of Molecular Epidemiology are largely unsatisfactory. To identify major problems in retrieving information on this discipline, we comment here on the results of a literature search on cytogenetic biomarkers in children exposed to environmental pollutants. The search, done on the PubMed/MedLine database, was based on a strategy combining descriptors listed in the PubMed Medical Subject Headings (MeSH) Thesaurus and other available tools (free text or phrase search tools). 178 articles were retrieved by searching the period from January 1, 1980 to November 30, 2004. Only 2 of the 178 articles were indexed by the MeSH term "Epidemiology, molecular" (introduced in 1994) and 30 of 178 by the MeSH term "Biological markers" (introduced in 1989). The case of chromosome aberration (CA) was emblematic of the problem: 44 of 78 articles (56.4%) were not pertinent to the search. The reasons for this poor performance are reported and discussed. Authors and indexers may be able to improve the efficiency of article retrieval in the field of molecular epidemiology by using relevant terms in the title and abstract. This may suggest appropriate MeSH terms to the indexers for the indexing process. As regards the difficulty in identifiyng population studies using CA, the introduction of a specific MeSH term for chromosome aberrations when used as a biomarker would improve the search process. Environ. Mol. Mutagen., 2006. © 2006 Wiley-Liss, Inc. [source] Molecular Epidemiology and Outcome of Helicobacter pylori Infection in Thailand: a Cultural Cross RoadsHELICOBACTER, Issue 5 2004Ratha-Korn Vilaichone ABSTRACT Background., Thailand is at the cultural cross roads between East and South Asia. It has been suggested that this is also the region where the predominant Helicobacter pylori (H. pylori) genotype changes from East Asian to South Asian. Methods., We compared the molecular epidemiology and outcome of H. pylori infections among different ethnic groups in Thailand (Thai, Thai-Chinese and Chinese). H. pylori isolates were genotyped by polymerase chain reaction based on cagA, cag right end junction and vacA genotypes. Results., Ninety-eight isolates from 38 ethnic Thai, 20 ethnic Chinese and 40 Thai-Chinese were categorized into East Asian (45%), South/Central Asian (26%), Western (1%) or mixed type (29%). The East Asian genotype was the most common among Chinese (85%) and Thai-Chinese (55%) (p < .01 compared to ethnic Thai). The ethnicity of the mother among mixed Thai-Chinese marriages predicted the genotype of the child's H. pylori (e.g. when the mother was Chinese, 84% had East Asian type vs. 29% when the mother was Thai) (p < .001). Gastric cancer was common among ethnic Chinese with East Asian genotype (e.g. all Chinese with gastric cancer or peptic ulcer disease had East Asian genotype, whereas only 40% of Chinese with gastritis had this genotype). Conclusions., Immigration, intermarriage and the variety of H. pylori genotypes in Thailand suggest that Thailand is an ideal site for epidemiological studies attempting to relate H. pylori genotypes and host factors to outcome. Our data also support the hypothesis that the primary caretaker of the children is most likely the source of the infection. [source] Book review: Molecular Epidemiology of Chronic DiseasesAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 2 2009Richard H. BartonArticle first published online: 6 JAN 200 No abstract is available for this article. [source] Molecular epidemiology of Yersinia enterocolitica infectionsFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 3 2006Maria Fredriksson-Ahomaa Abstract Yersinia enterocolitica is an important food-borne pathogen that can cause yersiniosis in humans and animals. The epidemiology of Y. enterocolitica infections is complex and remains poorly understood. Most cases of yersiniosis occur sporadically without an apparent source. The main sources of human infection are assumed to be pork and pork products, as pigs are a major reservoir of pathogenic Y. enterocolitica. However, no clear evidence shows that such a transmission route exists. Using PCR, the detection rate of pathogenic Y. enterocolitica in raw pork products is high, which reinforces the assumption that these products are a transmission link between pigs and humans. Several different DNA-based methods have been used to characterize Y. enterocolitica strains. However, the high genetic similarity between strains and the predominating genotypes within the bio- and serotype have limited the benefit of these methods in epidemiological studies. Similar DNA patterns have been obtained among human and pig strains of pathogenic Y. enterocolitica, corroborating the view that pigs are an important source of human yersiniosis. Indistinguishable genotypes have also been found between human strains and dog, cat, sheep and wild rodent strains, indicating that these animals are other possible infection sources for humans. [source] Molecular epidemiology of clinical and environmental isolates of the Cryptococcus neoformans species complex reveals a high genetic diversity and the presence of the molecular type VGII mating type a in ColombiaFEMS YEAST RESEARCH, Issue 4 2006Patricia Escandón Abstract The aim of this study was to investigate the epidemiological relationships of clinical and environmental isolates of the Cryptococcus neoformans species complex in Colombia. The current study reflects data from 1987 to 2004. In Colombia serotypes A and B are most frequently recovered from patients and the environment. Of the 178 clinical isolates studied, 91.1% were of serotype A, 8.4% serotype B and 0.5% serotype C. Of the 247 environmental isolates, 44.2% were of serotype A, 42.6% serotype B and 13.2% serotype C. No serotype D isolates were isolated. Serotype AD has not been recovered in Colombia. PCR fingerprinting with the primers M13, (GACA)4 and (GTG)5 and URA5 gene restriction fragment length polymorphism analysis grouped the majority of clinical serotype A and environmental serotype B isolates into the molecular types VNI (98.1%) and VGII (100%), respectively. Mating type , was determined in 99.3% of serotype A isolates, but 96.6% of serotype B isolates were of mating type a. Similar profiles between clinical and environmental isolates suggest that the patients may have acquired the infection from the environment. The data presented form part of the Colombian contribution to the ongoing global survey of the C. neoformans species complex. [source] Molecular epidemiology of hepatitis A virus in Korea,JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, Issue 5 2001Kwan Soo Byun Abstract Background: The prevalence of antibodies for hepatitis A virus (anti-HAV) in adolescents and young adults has decreased remarkably following the economic growth in Korea. As a result, this age group has a high risk for HAV infection paradoxically, and over 1500 cases of clinically overt hepatitis A occurred in 1998. Human isolates of hepatitis A virus (HAV) are categorized within four genotypes (I, II, III, and VII). In some geographic regions, closely related isolates cluster, suggesting endemic spread of the virus, while in other regions multiple genotypes circulate. Virtually no data are available with regard to the genetic relatedness of Korean strains of HAV. Methods and Results: A 168 base pair segment encompassing the putative VP1/2A junction of the HAV genome was amplified by RT-PCR and sequenced in sera of 18 Korean patients with a sporadic form of acute hepatitis A. Pairwise comparisons of the nucleic acid and amino acid sequences of 18 Korean isolates with one another revealed that the Korean isolates showed > 94.6% and > 96.4% identity, respectively. All of the 18 Korean isolates clustered within genotype IA, irrespective of the geographic locations and the time that hepatitis occurred. Unique amino acid sequence changes that had never been reported in genotype IA were found in nine of the 18 isolates. These changes were Gln,Ser and Lys,Arg in 2A-19 and 2A-10 amino acid positions. Conclusion: The presence of single genotype and unique mutations may be related with the circulation of endemic HAV over a long period of time in Korea. [source] Molecular epidemiology of primary human cytomegalovirus infection in pregnant women and their familiesJOURNAL OF MEDICAL VIROLOGY, Issue 8 2008Maria Grazia Revello Abstract The source of human cytomegalovirus (HCMV) infection was investigated in 29 pregnant women with primary HCMV infection by comparing DNA sequences of UL146, UL144 and a portion of UL55 gene of HCMV strains circulating within each family. Thirteen families were identified in which the pregnant woman, the husband and/or a child were shedding HCMV. In three of these families, both the woman and the husband suffered from a concomitant primary HCMV infection. Phylogenetic analysis of UL146, UL144, and UL55 genes indicated that strains circulating within each family were identical, whereas strains from different families appeared to be distinct. However, identical UL146, UL144, and UL55 DNA sequences were observed sporadically among unrelated strains. A child rather than the husband was the virus source for the great majority of pregnant women. No association was observed between UL144 polymorphisms and intrauterine transmission. J. Med. Virol. 80:1415,1425, 2008. © 2008 Wiley-Liss, Inc. [source] Molecular epidemiology of HIV-1 in Santa Catarina State confirms increases of subtype C in Southern BrazilJOURNAL OF MEDICAL VIROLOGY, Issue 10 2007Dayse Locateli Abstract Recent studies have demonstrated an increased prevalence of human immunodeficiency virus type 1 (HIV-1) subtype C in southern Brazil. Although Santa Catarina State (SC) is located in this area and presents one of the country's highest incidences of HIV/AIDS, knowledge on the molecular epidemiology of HIV-1 in such State is lacking. The aim of this study was to investigate the HIV-1 molecular diversity and epidemiological profile of HIV-1-infected patients from SC. DNA samples were PCR amplified and HIV-1 subtypes were determined using both env and gag genes by direct sequencing. Phylogenetic analyses revealed that 48% were subtype C and 23% were subtype B. Possible recombinant forms were observed for both B/C (23%) and B/F (6%) subtypes. Our results, for the first time, identifies HIV-1 subtype C as a major clade circulating in SC and contributes to the understanding of HIV epidemics in the country by confirming the epidemic spread of the HIV-1 subtype C in southern Brazil. J. Med. Virol. 79:1455,1463, 2007. © Wiley-Liss, Inc. [source] Molecular epidemiology of hepatitis A in St. Petersburg, Russia, 1997,2003JOURNAL OF MEDICAL VIROLOGY, Issue 6 2007Irja Davidkin Abstract The molecular epidemiology of hepatitis A virus (HAV) strains circulating in the St. Petersburg and Karelia regions was studied during 1997,2003. Hepatitis A virus RNA was isolated from both clinical samples (stools or sera) and environmental samples (sewage water). RT-PCR was carried out using different primer pairs from the VP1/2A and VP1 genomic regions, the variable parts of the HAV genome. PCR products were sequenced and 306 nucleotides from the VP1/2A and 332 nucleotides from the VP1 region were used for phylogenetic analysis. The results show that the IA subtype was the most common during the follow-up period: >90% of the isolated HAV strains belonged to that subtype. The HAV strains found in intravenous drug users belonged to subtypes IA and IIIA. Only one out of a total of 88 sequenced strains was of the IB subtype. The subtypes IB and IIIA were found only in 2001,2003, which suggests that new strains were introduced into the endemic situation. The results indicate the usefulness of molecular epidemiological methods in studying changes in the circulating HAV strains and in tracing transmission routes. J. Med. Virol. 79: 657,662, 2007. © 2007 Wiley-Liss, Inc. [source] Molecular epidemiology of hepatitis A virus in a group of Portuguese citizens living in Lisbon areaJOURNAL OF MEDICAL VIROLOGY, Issue 5 2007L. Rodrigues Abstract Hepatitis A virus (HAV) is the most important cause of acute infectious hepatitis worldwide. In Portugal, due to improvements in sanitation epidemic outbreaks of HAV infection have become less frequent. This report is the first, to our knowledge that characterized HAV in Portugal. For the detection and molecular characterization of HAV cases in a group of Portuguese individuals in the Lisbon area, 31 serum samples were tested: 8 from symptomatic children from an acute hepatitis A outbreak in a Roma (Gipsies) community (2004,2005), and 22 from patients with acute HAV from sporadic cases (2005,2006). A sample of CSF involved in a case of meningitis was also included. IgM anti-HAV detection and nested reverse transcription (RT-PCR), with primers located at the VP1-P2a region, was undertaken to detect HAV genome. In positive samples, molecular characterization was followed by phylogenetic analysis. All samples (n,=,31) were positive for IgM anti-HAV. HAV RNA was found in 96.7% of cases. All isolates were classified as genotype I: 22 belonged to sub-genotype IA (73.3%), and 8 to sub-genotype IB (26.7%). All strains obtained from an acute HAV outbreak had sub-genotype IA, in which seven isolates (87.5%) had identical sequences. In HAV sporadic cases sub-genotypes IA and IB were identified, and this may reflect the co-circulation of these two sub-genotypes in Portugal. Molecular epidemiology of HAV infection in this group of Portuguese appears to be similar to other European countries. HAV phylogenetic studies can provide important information for the design of appropriate public health measures. J. Med. Virol. 79:483,487, 2007. © 2007 Wiley-Liss, Inc. [source] Molecular epidemiology of hepatitis B virus in Dakar, SénégalJOURNAL OF MEDICAL VIROLOGY, Issue 3 2006Muriel Vray Abstract Using DNA chip technology and real-time quantitative PCR, molecular profile of HBV strains infecting blood donors and patients in Dakar, Sénégal was studied. All HBsAg-positive blood donors (n,=,175) and all patients who presented with chronic hepatitis B (n,=,29) between 1st June 2003 and 31st July 2003 were studied. One patient, a blood donor, was coinfected by HCV, and nine patients had anti-HDV antibodies. Few persons in either group were HBeAg-positive. Viral load values were relatively low but correlated with biochemical abnormalities. Patients were infected mainly by genotype E (72%). Patients infected by genotype A (28%) tended to be younger than other patients. There was no significant difference between the blood donors and the patients with hepatitis B as regards virological markers, including viral load, when the HBV genotype was taken into account. The BCP A1762T and G1764A mutations were found in four patients and one patient, respectively; the two mutations were never found in the same patient. The W28* mutation at position 1896 of the core was detected in 19 of the 32 genotyped patients, 18 (83%) of whom had genotype E infection. ALT levels were not influenced by HBV mutations. This study shows a low frequency of clinical signs in HBsAg-positive blood donors, a relatively low level of viral replication, and a high frequency of pre-core mutants in this West African population. These results underline the importance of molecular characterization of HBV infection as specific treatments become available in this region. J. Med. Virol. 78:329,334, 2006. © 2006 Wiley-Liss, Inc. [source] Molecular epidemiology of HIV in Ghana: Dominance of CRF02_AGJOURNAL OF MEDICAL VIROLOGY, Issue 2 2004Lucia Fischetti Abstract Recent studies showed the importance of CRF02_AG in West Africa, although the clinical relevance of these recombinant forms of HIV remains unknown. The present study aimed at determining the molecular diversity of HIV in Ghana and investigating the possible epidemiologic advantage of recombinant HIV-1. Plasma samples collected in 1999,2002 from two populations of HIV infected individuals (144 asymptomatic candidate blood donors and 169 AIDS patients) were studied and 249 of them were molecularly characterised in gag, pol, and env regions. Five molecular groups were identified: strains clustering with CRF02_AG in all regions (147/249 or 59%), recombinant strains clustering with CRF02_AG in one or two regions (50/249 or 20%), other subtypes, pure or recombinant, but not involving CRF02_AG (37/249 or 15%), HIV-2 (11/249 or 4.5%), and double infections (4/249 or 1.5%). There was no significant difference in the distribution of HIV-1 recombinant strains according to clinical presentation. No evidence of a significant increase in CRF02_AG prevalence between 1999 and 2002 was found. Irrespective of clinical condition, CRF02_AG is the predominant molecular form of HIV-1 in Kumasi, Ghana. J. Med. Virol. 73:158,166, 2004. © 2004 Wiley-Liss, Inc. [source] Molecular epidemiology of molluscum contagiosum virus and analysis of the host-serum antibody response in Spanish HIV-negative patientsJOURNAL OF MEDICAL VIROLOGY, Issue 2 2002Monica Agromayor Abstract Molluscum contagiosum virus (MCV) lesions from Spanish human immunodeficiency virus (HIV)-negative patients were clinically examined and analyzed for virus detection and typing. In a study of 147 patients, 97 (66%) were children under 10 years, of whom 49% had atopic dermatitis. MCV lesions were morphologically indistinguishable among the different age groups, but atopic patients presented larger lesions compared with patients without the disorder. In adults, lesions were observed mainly on the genitals. MCVI was the predominant subtype. The deduced MCVI/MCVII ratio (146:1) was much higher than that found in other geographical areas. Protein preparations of the virus-induced lesions were immunoblotted with sera from 25 MCVI patients. The host-serum antibody response was weak and variable, although no significant differences were found between atopic and nonatopic patients. Three immunoreactive proteins of 74/80, 60, and 35 kDa were detected in almost all the analyzed sera. The 35 and 74/80-kDa proteins were virus specific, whereas the 60-kDa protein band was composed of a mix of human keratins. Immunoblotting of MCV lesions and vaccinia virus-infected cell extracts with either MCV patient serum or a rabbit antiserum against vaccinia virus showed no cross-reactivity of these two human poxviruses at the antigenic level. J. Med. Virol. 66:151,158, 2002. © 2002 Wiley-Liss, Inc. [source] Molecular epidemiology of hepatitis B virus in Amsterdam 1992,1997,JOURNAL OF MEDICAL VIROLOGY, Issue 2 2002J.E. van Steenbergen Abstract To gain insight into the spread of hepatitis B among various risk groups in Amsterdam a 6-year (1992,1997) retrospective DNA sequencing study was carried out on isolates from stored sera from reported primary cases of acute hepatitis B infection. Cases were classified according to risk behavior, as determined in interviews. Of the available serum, a selected region of hepatitis B-virus-DNA was amplified and sequenced. The nucleotide alignments were subjected to phylogenetic tree analysis. When nucleotide alignments were subjected to phylogenetic analysis, the strains of 54 isolates, 26% of the 204 reported primary cases, clustered in five genotypes: A, C, D, E, and F. In genotype A, a cluster related to men having sex with men was identified. In genotype D, two subclusters could be identified: one was related to injecting drug use and another was related to the Moroccan population in Amsterdam. The remaining strains showed a high genetic variability within three different genotypes: F, E, and C. Of the 14 identical isolates in the "homosexual men cluster," one was isolated from a female heterosexual. Of the 14 identical strains in the "drug users strain," six were from non-drug using heterosexual active individuals. In the cluster of twelve isolates related to hepatitis B-endemic areas, probable modes of transmission were varied. Sequence analysis provides important insight into the spread of hepatitis B among various high-risk groups. The analysis indicates that the prevention strategy in The Netherlands fails to stop transmission of hepatitis B from persistently infected individuals originating from hepatitis Bendemic countries. J. Med. Virol. 66:159,165, 2002. © 2002 Wiley-Liss, Inc. [source] Molecular epidemiology of norovirus gastroenteritis in Soma, Japan, 2001,2003PEDIATRICS INTERNATIONAL, Issue 1 2008Noriko Onishi Abstract Background: The aim of the present paper was to investigate the molecular epidemiology of norovirus gastroenteritis in Japan using polymerase chain reaction (PCR) and subsequent phylogenetic analysis. Methods: From September 2001 to August 2003, 515 stool samples or rectal swabs were collected from almost all children visiting the Department of Pediatrics, Public Soma General Hospital with gastroenteritis. Samples were examined on reverse transcription (RT)-PCR to detect norovirus genome. The nucleotide sequences of the PCR products were determined and phylogenetic analysis performed. Results: The norovirus genome was detected in 66 samples. The peak season of norovirus gastroenteritis was from November 2001 to February 2002 and from September 2002 to December 2002. Norovirus gastroenteritis occurred most frequently in 1-year-old children. Norovirus strains produced four distinct clusters on phylogenetic analysis. Some strains detected in Soma were closely related to the strains detected in other regions in the world. The Mexico type and Lordsdale type were predominant in the 2001/2002 and 2002/2003 seasons, respectively, and the outbreaks continued for several months. Conclusions: Genetically different noroviruses might cause repeated gastroenteritis outbreaks every year in the Soma area. The long duration of the outbreak by a predominant strain in an epidemic season and the prevalence of infection mainly in the young age group suggested that norovirus epidemics were caused by person-to-person transmission rather than foodborne transmission. Based on molecular epidemiology, it is suggested that the annual prevalence of norovirus gastroenteritis in the Soma area might be caused by person-to-person transmission of genetically different norovirus strains, which might be transmitted from other region in the world. [source] Molecular epidemiology of rubella virus in Asia: Utility for reduction in the burden of diseases due to congenital rubella syndromePEDIATRICS INTERNATIONAL, Issue 2 2004Shigetaka Katow AbstractBackground:,Rubella is a mild disease mainly of infants, involving a rash and a fever. However, when women who have no immunity to rubella are infected during the early stage of pregnancy, their babies are often born with congenital rubella syndrome (CRS), which is characterized by a few disorders including deafness, cataracts and heart malformations. To prevent CRS, several strains of live attenuated rubella vaccine have been developed and introduced into immunization programs in many countries. In most Asian countries except Japan, Singapore and Taiwan, rubella remains uncontrolled, and the burden of diseases from CRS is high. In order to develop a control program to reduce the number of CRS cases in Asian countries, it is necessary to conduct a survey of rubella and CRS cases, and to then determine the genotype of the circulating rubella virus in each country. Methods:,Cases of rubella and CRS, based on national reporting systems or active surveillance in the Asian countries, are summarized. Sequences of the E1 gene of the virus isolates from the Asian countries were compared by phylogenic analysis. Results:,Recent studies of the molecular epidemiology of rubella virus worldwide revealed that there are two genotypes, and that genotype I is circulating almost worldwide, while genotype II is an Asian prototype restricted to the Asian continent. Genotype I viruses fall into a number of groups, some of which are geographically localized. Antigenically these two genotypes are cross-reactive and immunization with either virus results in immunity to all rubella viruses. Discussion:,The hypotheses that rubella virus has evolved on the Asian continent is proposed. The World Health Organization (WHO) has recognized that a rubella immunization program can be combined with the measles immuization program. Inclusion of rubella in the expanded program of immunization (EPI) of measles would be ideal in Asian countries, as it would be efficient and cost effective to administer one injection containing a three-combined vaccine (MMR). It would also be desirable given that WHO require laboratory tests to confirm the presence of measles or rubella as part of it's measles control project, because rubella is often misdiagnosed as measles. [source] Molecular epidemiology of measles virus in JapanPEDIATRICS INTERNATIONAL, Issue 2 2004Tetsuo Nakayama AbstractBackground:,Measles virus has been classified into 22 genotypes. The present report examines the molecular epidemiology of measles virus in Japan from 1984 to 2002, and the epidemiological link between imported cases in several foreign countries and Japanese strains was elucidated from the literature. Methods:,B95a or Vero cells was used to isolate the measles virus. The measles virus genome was amplified in the N and H genes by reverse transcriptase-polymerase chain reaction and were partially sequenced. Phylogenetic analysis of a partial sequence of the N gene, from position 1230 to 1685, of the recent measles strains was performed in comparison with the World Health Organization reference strains. Results:,There were large outbreaks of measles in Japan in 1984, 1987,1988, 1991,1993, and 2001,2002 and each outbreak was caused by a different genotype. Genotype C1 was an indigenous strain for a long period before 1985, while D3 was isolated in 1987,1988 and D5 in 1991,1993 outbreaks. In addition, the Chicago-type D3 caused sporadic regional outbreaks from 1998 to 1999. After 2000, H1 became the dominant circulating strain. It should be noted that the Japanese strains were detected as imported cases by epidemiological linkage in several countries. Conclusion:,Among the recent circulating strain of measles virus in Japan the genotype H1 was dominant after 2000 and the Japanese strains D3, D5, and H1 were exported to several countries. It is recommended that Japan should adopt a more extensive and active vaccination strategy for measles elimination in line with other countries in the world. [source] Molecular epidemiology of Neisseria gonorrhoeae, identification of the first presumed Swedish transmission chain of an azithromycin-resistant strain,APMIS, Issue 1 2006DAVID LUNDBÄCK In the present study, 10 azithromycin-resistant Neisseria gonorrhoeae isolates from 6 Swedish male patients in 2004, 3 sporadic Swedish azithromycin-resistant N. gonorrhoeae isolates from recent years and one Swedish N. gonorrhoeae isolate from 2003 that was susceptible to azithromycin but assigned the same serological variant (serovar), i.e. IB-37, as the isolates from 2004 were included. The isolates were characterized phenotypically using antibiograms and serovar determination and genetically with pulsed-field gel electrophoresis (PFGE), entire porB gene sequencing and N. gonorrhoeae multiantigen sequence typing (NG-MAST). The epidemiological information and the results of the thorough phenotypic characterisation and genetic characterisation identified the first presumed domestic transmission of one azithromycin-resistant N. gonorrhoeae strain in Sweden in 2004. This stresses the need for continuous surveillance of the antibiotic susceptibility of N. gonorrhoeae in order to identify emergence of new resistance, monitor the changing patterns of the susceptibility, and be able to update treatment recommendations on a regular basis. [source] Molecular epidemiology of viral infections.APMIS, Issue 2 2000How sequence information helps us understand the evolution, dissemination of viruses Viruses evolve much faster than cellular organisms. Together with recent advances in nucleic acid sequencing and biocomputing, this allows us to distinguish between related strains of viruses, and to deduce the relationships between viruses from different outbreaks or individual patients. Databases of nucleotide sequences contain a large number of viral sequences with which novel sequences from local outbreaks can be compared. In this way the dissemination of viruses can be followed both locally and globally. We here review the biological and technological background to the use of virus nucleic acid sequences in epidemiological studies, and provide examples of how this information can be used to monitor human viruses. Molecular studies are particularly valuable for understanding the dissemination and evolution of viruses. The knowledge obtained is useful in epidemiological reconstructions, in real-time surveillance, and may even enable us to make predictions about the future developments of viral diseases. [source] Molecular epidemiology of hypospadias: Review of genetic and environmental risk factorsBIRTH DEFECTS RESEARCH, Issue 10 2003Jeanne M. Manson Hypospadias is one of the most common congenital anomalies in the United States, occurring in approximately 1 in 125 live male births. It is characterized by altered development of the urethra, foreskin, and ventral surface of the penis. In this review, the embryology, epidemiology, risk factors, genetic predisposition, and likely candidate genes for hypospadias are described. Recent reports have identified increases in the birth prevalence of mild and severe forms of hypospadias in the United States from the 1960s to the present. Studies in consanguineous families and small case series have identified allelic variants in genes controlling androgen action and metabolism that cause hypospadias, but the relevance of these findings to the general population is unknown. Concern has also focused on whether exposure to endocrine disrupting chemicals (EDC) with antiandrogenic activity is the cause of this increase. Hypospadias is believed to have a multifactorial etiology in which allelic variants in genes controlling androgen action and metabolism predispose individuals to develop this condition. When genetic susceptibility is combined with exposure to antiandrogenic agents, a threshold is surpassed, resulting in the manifestation of this birth defect. A clear role for exposure to antiandrogenic environmental chemicals has yet to be established in the etiology of hypospadias, although results from laboratory animal models indicate that a number of environmental chemicals could be implicated. Molecular epidemiology studies that simultaneously examine the roles of allelic variants in genes controlling androgen action and metabolism, and environmental exposures are needed to elucidate the risk factors for these anomalies and the causes of the increased rate of hypospadias. Birth Defects Research (Part A), 2003. © 2003 Wiley-Liss, Inc. [source] Molecular epidemiology of clinically significant antibiotic resistance genesBRITISH JOURNAL OF PHARMACOLOGY, Issue S1 2008P M Hawkey Antimicrobials were first introduced into medical practice a little over 60 years ago and since that time resistant strains of bacteria have arisen in response to the selective pressure of their use. This review uses the paradigm of the evolution and spread of beta-lactamases and in particular beta-lactamases active against antimicrobials used to treat Gram-negative infections. The emergence and evolution particularly of CTX-M extended-spectrum beta-lactamases (ESBLs) is described together with the molecular mechanisms responsible for both primary mutation and horizontal gene transfer. Reference is also made to other significant antibiotic resistance genes, resistance mechanisms in Gram-negative bacteria, such as carbepenamases, and plasmid-mediated fluoroquinolone resistance. The pathogen Staphylococcus aureus is reviewed in detail as an example of a highly successful Gram-positive bacterial pathogen that has acquired and developed resistance to a wide range of antimicrobials. The role of selective pressures in the environment as well as the medical use of antimicrobials together with the interplay of various genetic mechanisms for horizontal gene transfer are considered in the concluding part of this review. British Journal of Pharmacology (2008) 153, S406,S413; doi:10.1038/sj.bjp.0707632 [source] Molecular epidemiology of the nasal colonization by methicillin-susceptible Staphylococcus aureus in Swiss childrenCLINICAL MICROBIOLOGY AND INFECTION, Issue 9 2010C. Mégevand Clin Microbiol Infect 2010; 16: 1414,1420 Abstract Nasal carriage of Staphylococcus aureus contributes to an increased risk of developing an infection with the same bacterial strain. Genetic regulatory elements and toxin-expressing genes are virulence factors associated with the pathogenic potential of S. aureus. We undertook an extensive molecular characterization of methicillin-susceptible S. aureus (MSSA) carried by children. MSSA were recovered from the nostrils of children. The presence of Panton-Valentine leukocidin (PVL), exfoliatins A and B (exfoA and exfoB), and the toxic-shock staphylococcal toxin (TSST-1) and agr group typing were determined by quantitative PCR. A multiple-locus variable-number of tandem repeat analysis (MLVA) assay was also performed for genotyping. Five hundred and seventy-two strains of MSSA were analysed. Overall, 30% were positive for toxin-expressing genes: 29% contained one toxin and 1.6% two toxins. The most commonly detected toxin gene was tst, which was present in 145 (25%) strains. The TSST-1 gene was significantly associated with the agr group 3 (OR 56.8, 95% CI 32.0,100.8). MLVA analysis revealed a large diversity of genetic content and no clonal relationship was demonstrated among the analysed MSSA strains. Multilocus sequence typing confirmed this observation of diversity and identified ST45 as a frequent colonizer. This broad diversity in MSSA carriage strains suggests a limited selection pressure in our geographical area. [source] Molecular epidemiology of tuberculosis in the Tula area, Central Russia, before the introduction of the Directly Observed Therapy StrategyCLINICAL MICROBIOLOGY AND INFECTION, Issue 9 2010S. Dubiley Clin Microbiol Infect 2010; 16: 1421,1426 Abstract Tuberculosis remains a major public health concern in Russia and worldwide. Given the great geographical, ethnic, and socio-economic heterogeneities between Russian regions, epidemiological data cannot be generalized from a regional to a country-wide level. We present data on the epidemiology of tuberculosis in Central Russia. We report a high level of resistance to major antitubercular drugs in both new and previously treated patients in the region. The level of drug resistance in new cases was almost twice as high as the estimated average national level. The Mycobacterium tuberculosis strains that circulated in the region were predominantly represented by LAM-RUS and Beijing genotypes. These two lineages were strongly associated with drug resistance and clustering. Using molecular epidemiology techniques, we showed a high interpenetration by M. tuberculosis strains between the prison and civilian populations. A limited number of identical strains were responsible for the majority of drug-resistant tuberculosis cases in both settings. [source] Hepatitis C virus infection among drug injectors in St Petersburg, Russia: social and molecular epidemiology of an endemic infectionADDICTION, Issue 11 2009Elijah Paintsil ABSTRACT Aims To understand the epidemiology and transmission patterns of hepatitis C virus (HCV), the predominant blood borne-pathogen infecting injection drug users (IDUs), in a part of the former Soviet Union. Design Cross-sectional respondent-driven sample of IDUs. Setting St Petersburg, Russia. Participants A total of 387 IDUs were recruited in late 2005 and throughout 2006. Measurements Participants were surveyed to collect demographic, medical and both general and dyad-specific drug injection and sexual behaviors. A blood sample was collected to detect antibodies to hepatitis C and to amplify viral RNA for molecular analysis. The molecular data, including genotypes, were analyzed spatially and linkage patterns were compared to the social linkages obtained by respondent-driven sampling (RDS) for chains of respondents and among the injection dyads. Findings HCV infection was all but ubiquitous: 94.6% of IDUs were HCV-seropositive. Among the 209 viral sequences amplified, genotype 3a predominated (n = 119, 56.9%), followed by 1b (n = 61, 29.2%) and 1a (n = 25, 11.9%). There was no significant clustering of genotypes spatially. Neither genotypes nor closely related sequences were clustered within RDS chains. Analysis of HCV sequences from dyads failed to find associations of genotype or sequence homology within pairs. Conclusions Genotyping reveals that there have been at least five unique introductions of HCV genotypes into the IDU community in St Petersburg. Analysis of prevalent infections does not appear to correlate with the social networks of IDUs, suggesting that simple approaches to link these networks to prevalent infections, rather than incident transmission, will not prove meaningful. On a more positive note, the majority of IDUs are infected with 3a genotype that is associated with sustained virological response to antiviral therapy. [source] Searching PubMed for molecular epidemiology studies: The case of chromosome aberrationsENVIRONMENTAL AND MOLECULAR MUTAGENESIS, Issue 4 2006Donatella Ugolini Abstract The available tools for searching literature in the field of Molecular Epidemiology are largely unsatisfactory. To identify major problems in retrieving information on this discipline, we comment here on the results of a literature search on cytogenetic biomarkers in children exposed to environmental pollutants. The search, done on the PubMed/MedLine database, was based on a strategy combining descriptors listed in the PubMed Medical Subject Headings (MeSH) Thesaurus and other available tools (free text or phrase search tools). 178 articles were retrieved by searching the period from January 1, 1980 to November 30, 2004. Only 2 of the 178 articles were indexed by the MeSH term "Epidemiology, molecular" (introduced in 1994) and 30 of 178 by the MeSH term "Biological markers" (introduced in 1989). The case of chromosome aberration (CA) was emblematic of the problem: 44 of 78 articles (56.4%) were not pertinent to the search. The reasons for this poor performance are reported and discussed. Authors and indexers may be able to improve the efficiency of article retrieval in the field of molecular epidemiology by using relevant terms in the title and abstract. This may suggest appropriate MeSH terms to the indexers for the indexing process. As regards the difficulty in identifiyng population studies using CA, the introduction of a specific MeSH term for chromosome aberrations when used as a biomarker would improve the search process. Environ. Mol. Mutagen., 2006. © 2006 Wiley-Liss, Inc. [source] Genotypic variability and persistence of Legionella pneumophila PFGE patterns in 34 cooling towers from two different areasENVIRONMENTAL MICROBIOLOGY, Issue 2 2008Inma Sanchez Summary Genotypic variability and clonal persistence are important concepts in molecular epidemiology as they facilitate the search for the source of sporadic cases or outbreaks of legionellosis. We studied the genotypic variability and persistence of Legionella pulsed-field gel electrophoresis (PFGE) patterns over time (period > 6 months) in 34 positive cooling towers from two different areas. In area A, radius of 70 km, 52 indistinguishable PFGE patterns were differentiated among the 27 cooling towers. In 13 cooling towers we observed , 2 PFGE patterns. Each cooling tower had its own indistinguishable Legionella PFGE pattern which was not shared with any other cooling tower. In area B, radius of 1 km, 10 indistinguishable PFGE patterns were obtained from the seven cooling towers. In four, we observed , 2 PFGE patterns. Three of these 10 indistinguishable PFGE patterns were shared by more than one cooling tower. In 27 of 34 cooling towers the same PFGE pattern was recovered after 6 months to up to 5 years of follow-up. The large genotypic diversity of Legionella observed in the cooling towers aids in the investigation of community outbreaks of Legionnaires' disease. However, shared patterns in small areas may confound the epidemiological investigation. The persistence of some PFGE patterns in cooling towers makes the recovery of the Legionella isolate causing the outbreak possible over time. [source] Molecular Epidemiology and Outcome of Helicobacter pylori Infection in Thailand: a Cultural Cross RoadsHELICOBACTER, Issue 5 2004Ratha-Korn Vilaichone ABSTRACT Background., Thailand is at the cultural cross roads between East and South Asia. It has been suggested that this is also the region where the predominant Helicobacter pylori (H. pylori) genotype changes from East Asian to South Asian. Methods., We compared the molecular epidemiology and outcome of H. pylori infections among different ethnic groups in Thailand (Thai, Thai-Chinese and Chinese). H. pylori isolates were genotyped by polymerase chain reaction based on cagA, cag right end junction and vacA genotypes. Results., Ninety-eight isolates from 38 ethnic Thai, 20 ethnic Chinese and 40 Thai-Chinese were categorized into East Asian (45%), South/Central Asian (26%), Western (1%) or mixed type (29%). The East Asian genotype was the most common among Chinese (85%) and Thai-Chinese (55%) (p < .01 compared to ethnic Thai). The ethnicity of the mother among mixed Thai-Chinese marriages predicted the genotype of the child's H. pylori (e.g. when the mother was Chinese, 84% had East Asian type vs. 29% when the mother was Thai) (p < .001). Gastric cancer was common among ethnic Chinese with East Asian genotype (e.g. all Chinese with gastric cancer or peptic ulcer disease had East Asian genotype, whereas only 40% of Chinese with gastritis had this genotype). Conclusions., Immigration, intermarriage and the variety of H. pylori genotypes in Thailand suggest that Thailand is an ideal site for epidemiological studies attempting to relate H. pylori genotypes and host factors to outcome. Our data also support the hypothesis that the primary caretaker of the children is most likely the source of the infection. [source] Cocirculation of and coinfections with hepatitis A virus subgenotypes IIIA and IB in patients from Pune, western IndiaHEPATOLOGY RESEARCH, Issue 2 2007Shobha Chitambar Aim:, During the 1990s, a changing pattern of epidemiology of hepatitis A was reported in different populations of India. The present study was undertaken to investigate the molecular epidemiology of hepatitis A virus (HAV) strains over a period of 10 years. Methods:, Stool/serum samples were collected from hepatitis A patients clinically presenting acute viral hepatitis and hepatic encephalopathy. Reverse transcriptase polymerase chain reaction (RT-PCR) was performed to detect HAV-RNA. HAV genomes were examined by sequencing PCR products of VP1/2A junction (168 bp) and RNA polymerase (116 bp) regions. Results:, Subgenotype IIIA and IB were detected in 74.2% and 9.7% of specimens, respectively, while 16.1% of patients had mixed infections. Sewage samples also showed presence of both IIIA (9/10) and IB (1/10) subgenotypes. RNA polymerase region showed two clusters constituting 51.6% and 19.4% strains closer to Nor21 and HM175 strains, respectively, in clinical specimens. Three isolates appeared as discordant subgenotypes in VP1/2A and RNA polymerase regions. Conclusion:, The data revealed cocirculation of and coinfection with subgenotypes IIIA and IB, with predominance of IIIA and genetic heterogeneity of HAV strains in western India. [source] Phylogenetic analyses and molecular epidemiology of European salmonid alphaviruses (SAV) based on partial E2 and nsP3 gene nucleotide sequencesJOURNAL OF FISH DISEASES, Issue 11 2008E Fringuelli Abstract Sequence data were generated for portions of the E2 and nsP3 genes of 48 salmonid alphaviruses from farmed Atlantic salmon (AS), Salmo salar L., and rainbow trout (RT), Oncorhynchus mykiss (Walbaum), in marine and freshwater environments, respectively, from the Republic of Ireland, Northern Ireland, England, Scotland, Norway, France, Italy and Spain between 1991 and 2007. Based on these sequences, and those of six previously published reference strains, phylogenetic trees were constructed using the parsimony method. Trees generated with both gene segments were similar. Clades corresponding to the three previously recognized subtypes were generated and in addition, two further new clades of viruses were identified. A single further strain (F96-1045) was found to be distinct from all of the other strains in the study. The percentage of nucleotide divergence within clades was generally low (0,4.8% for E2, 0,6.6% for nsP3). Interclade divergence tended to be higher (3.4,19.7% for E2, 6.5,28.1% for nsP3). Based on these results and using current SAV terminology, the two new clades and F96-1045 were termed SAV subtypes 4, 5 and 6, respectively. SAV4 contained AS strains from Ireland and Scotland, while SAV5 contained only Scottish AS strains. Recently identified SAV strains from RT in Italy and Spain were shown to belong to SAV2. In addition, marine AS strains belonging to SAV2 were identified for the first time. Analysis of the origin of several clusters of strains with identical E2 and nsP3 sequences strongly support horizontal transmission of virus between farms and aquaculture companies. Evidence in support of vertical transmission was not found. [source] Serologic and genotypic analysis of a series of herpes simplex virus type 1 isolates from two patients with genital herpesJOURNAL OF MEDICAL VIROLOGY, Issue 9 2009Kenichi Umene Abstract Herpes simplex virus type 1 (HSV-1) has been reported increasingly as a cause of genital herpes, although HSV-1 is usually associated with oro-labial herpes. In the present study, serum specimens and materials for viral isolation were obtained serially from two patients with recrudescent HSV-1 genital infections to study serology and molecular epidemiology. Recurrent episodes, during which HSV-1 was isolated, were followed by an increase in the level of anti-HSV-1 antibody, suggesting a booster effect from re-exposure to viral antigens and the possible usefulness of the variation in the level of anti-HSV-1 antibody to diagnose recurrence. While genotypes of HSV-1 isolates obtained from one patient were different from those from the other patient, genotypes of sequential HSV-1 isolates obtained from the same patient were the same, implying that the recrudescent genital lesions of the two patients could be attributed to endogenous recurrence of a latent virus. Sera from one patient neutralized HSV-1 isolates obtained from the other patient as well as HSV-1 isolates obtained from the same patient. An HSV-1 isolate obtained during a later episode in one patient was neutralized by sera taken before/during the later episode of the same patient, as effectively as an HSV-1 isolate obtained during an earlier episode in the same patient; thus, in these two cases, HSV-1 was assumed to have multiplied during recurrence despite the presence of an anti-HSV-1 antibody that could neutralize experimentally HSV-1. J. Med. Virol. 81:1605,1612, 2009. © 2009 Wiley-Liss, Inc. [source] | |||||||||||||