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Zhao S, Zhang J, Li Z, Han Y, Kan B. Enumeration of Viable Non-Culturable Vibrio cholerae Using Droplet Digital PCR Combined With Propidium Monoazide Treatment. Front Cell Infect Microbiol 2021; 11:753078. [PMID: 34796126 PMCID: PMC8592976 DOI: 10.3389/fcimb.2021.753078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/12/2021] [Indexed: 11/24/2022] Open
Abstract
Many bacterial species, including Vibrio cholerae (the pathogen that causes cholera), enter a physiologically viable but non-culturable (VBNC) state at low temperature or in conditions of low nutrition; this is a survival strategy to resist environmental stress. Identification, detection, and differentiation of VBNC cells and nonviable cells are essential for both microbiological study and disease surveillance/control. Enumeration of VBNC cells requires an accurate method. Traditional counting methods do not allow quantification of VBNC cells because they are not culturable. Morphology-based counting cannot distinguish between live and dead cells. A bacterial cell possesses one copy of the chromosome. Hence, counting single-copy genes on the chromosome is a suitable approach to count bacterial cells. In this study, we developed quantitative PCR-based methods, including real-time quantitative PCR (qPCR) and droplet digital PCR (ddPCR), to enumerate VBNC V. cholerae cells by counting the numbers of single-copy genes in samples during VBNC-state development. Propidium monoazide (PMA) treatment was incorporated to distinguish dead cells from viable cells. Both PCR methods could be used to quantify the number of DNA copies/mL and determine the proportion of dead cells (when PMA was used). The methods produced comparable counts using three single-copy genes (VC1376, thyA, and recA). However, ddPCR showed greater accuracy and sensitivity than qPCR. ddPCR also allows direct counting without the need to establish a standard curve. Our study develops a PMA-ddPCR method as a new tool to quantify VBNC cells of V. cholerae. The method can be extended to other bacterial species.
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Affiliation(s)
| | | | | | | | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Kanampalliwar A, Singh DV. Virulence Pattern and Genomic Diversity of Vibrio cholerae O1 and O139 Strains Isolated From Clinical and Environmental Sources in India. Front Microbiol 2020; 11:1838. [PMID: 32982995 PMCID: PMC7479179 DOI: 10.3389/fmicb.2020.01838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/14/2020] [Indexed: 01/22/2023] Open
Abstract
Vibrio cholerae is an autochthonous inhabitant of the aquatic environment. Several molecular methods have been used for typing V. cholerae strains, but there is no proper database for such scheme, including multilocus sequence typing (MLST) for V. cholerae O1 and O139 strains. We used 54 V. cholerae O1 and three O139 strains isolated from clinical and environmental sources and regions of India during the time period of 1975-2015 to determine the presence of virulence genes and production of biofilm. We devised a MLST scheme and developed a database for typing V. cholerae strains. Also, we performed pulsed-field gel electrophoresis to see the genomic diversity among them and compared it with MLST. We used the MEGA 7.0 software for the alignment and comparison of different nucleotide sequences. The advanced cluster analysis was performed to define complexes. All strains of V. cholerae, except five strains, showed variation in phenotypic characteristics but carried virulence-associated genes indicating they belonged to the El Tor/hybrid/O139 variants. MLST analysis showed 455 sequences types among V. cholerae strains, irrespective of sources and places of isolation. With these findings, we set up an MLST database on PubMLST.org using the BIGSdb software for V. cholerae O1 and O139 strains, which is available at https://pubmlst.org/vcholerae/ under the O1/O139 scheme. The pulsed-field gel electrophoresis (PFGE) fingerprint showed six fingerprint patterns namely E, F, G, H, I, and J clusters among 33 strains including strain N16961 carrying El Tor ctxB of which cluster J representing O139 strain was entirely different from other El Tor strains. Twenty strains carrying Haitian ctxB showed a fingerprint pattern classified as cluster A. Of the five strains, four carrying classical ctxB comprising two each of El Tor and O139 strains and one El Tor strain carrying Haitian ctxB clustered together under cluster B along with V. cholerae 569B showing pattern D. This study thus indicates that V. cholerae strains are undergoing continuous genetic changes leading to the emergence of new strains. The MLST scheme was found more appropriate compared to PFGE that can be used to determine the genomic diversity and population structure of V. cholerae.
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Affiliation(s)
- Amol Kanampalliwar
- Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Durg Vijai Singh
- Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India.,Department of Biotechnology, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, India
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Phage Transduction is Involved in the Intergeneric Spread of Antibiotic Resistance-Associated bla CTX-M, mel, and tetM Loci in Natural Populations of Some Human and Animal Bacterial Pathogens. Curr Microbiol 2019; 77:185-193. [PMID: 31754824 DOI: 10.1007/s00284-019-01817-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/15/2019] [Indexed: 12/16/2022]
Abstract
The horizontal genetic transfer (HGT) of antibiotic resistance genes (ARGs) mediated by species-specific bacteriophages contributes to the emergence of antibiotic-resistant strains in natural populations of human and animal bacterial pathogens posing a significant threat to global public health. However, it is unclear and needs to be determined whether polyvalent bacteriophages play any role in the intergeneric transmission of ARGs. In this study, we examined the genome sequences of 2239 bacteriophages from different sources for the presence of ARGs. The identified ARG-carrying bacteriophages were then analyzed by PHACTS, PHAST, and HostPhinder programs to determine their lifestyles, genes coding for bacterial cell lysis, recombinases, and a spectrum of their potential host species, respectively. We employed the SplitsTree, RDP4 and SimPlot software packages in recombination tests to identify HGT events of ARGs between these bacteriophages and bacteria. In our analyses, some ARG-carrying bacteriophages exhibited temperate and/or polyvalent patterns. The bootstrap values (97-100) for the SplitsTree-generated parallelograms, fit values (97-100) for splits networks, Phi P values (< 10-17 to 3.9 × 10-16), RDP4 P values (≤ 7.8 × 10-03), and the SimPlot results, provided strong statistical evidence for the phage transduction events of blaCTX-M, mel, and tetM loci on inter-species level. These events involved several host species such as Escherichia coli, Salmonella enterica, Shigella sonnei, Streptococcus pneumoniae and Bacillus coagulans. HGT of mel loci between Erysipelothrix and Streptococcus phages were also detected. These results firmly suggest that certain bacteriophages possibly with temperate properties induce the intergeneric dissemination of blaCTX-M, mel and tetM in the above species.
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Evaluation of Whole-Genome Sequencing for Identification and Typing of Vibrio cholerae. J Clin Microbiol 2018; 56:JCM.00831-18. [PMID: 30135231 DOI: 10.1128/jcm.00831-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/13/2018] [Indexed: 01/09/2023] Open
Abstract
Epidemiological and microbiological data on Vibrio cholerae strains isolated between April 2004 and March 2018 (n = 836) and held at the Public Health England culture archive were reviewed. The traditional biochemical species identification and serological typing results were compared with the genome-derived species identification and serotype for a subset of isolates (n = 152). Of the 836 isolates, 750 (89.7%) were from a fecal specimen, 206 (24.6%) belonged to serogroup O1, and 7 (0.8%) were serogroup O139; 792 (94.7%) isolates were from patients reporting recent travel abroad, most commonly to India (n = 209) and Pakistan (n = 104). Of the 152 V. cholerae isolates identified by use of kmer, 149 (98.1%) were concordant with those identified using the traditional biochemical approach. Traditional serotyping results were 100% concordant with those of the whole-genome sequencing (WGS) analysis for the identification of serogroups O1 and O139 and classical and El Tor biotypes. ctxA was detected in all isolates of V. cholerae O1 El Tor and O139 belonging to sequence type 69 (ST69) and in V. cholerae O1 classical variants belonging to ST73. A phylogeny of isolates belonging to ST69 from U.K. travelers clustered geographically, with isolates from India and Pakistan located on separate branches. Moving forward, WGS data from U.K. travelers will contribute to global surveillance programs and the monitoring of emerging threats to public health and the global dissemination of pathogenic lineages. At the national level, these WGS data will inform the timely reinforcement of direct public health messaging to travelers and mitigate the impact of imported infections and the associated risks to public health.
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Liao F, Mo Z, Chen M, Pang B, Fu X, Xu W, Jing H, Kan B, Gu W. Comparison and Evaluation of the Molecular Typing Methods for Toxigenic Vibrio cholerae in Southwest China. Front Microbiol 2018; 9:905. [PMID: 29867816 PMCID: PMC5951969 DOI: 10.3389/fmicb.2018.00905] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/18/2018] [Indexed: 11/15/2022] Open
Abstract
Vibrio cholerae O1 strains taken from the repository of Yunnan province, southwest China, were abundant and special. We selected 70 typical toxigenic V. cholerae (69 O1 and one O139 serogroup strains) isolated from Yunnan province, performed the pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and MLST of virulence gene (V-MLST) methods, and evaluated the resolution abilities for typing methods. The ctxB subunit sequence analysis for all strains have shown that cholera between 1986 and 1995 was associated with mixed infections with El Tor and El Tor variants, while infections after 1996 were all caused by El Tor variant strains. Seventy V. cholerae obtained 50 PFGE patterns, with a high resolution. The strains could be divided into three groups with predominance of strains isolated during 1980s, 1990s, and 2000s, respectively, showing a good consistency with the epidemiological investigation. We also evaluated two MLST method for V. cholerae, one was used seven housekeeping genes (adk, gyrB, metE, pntA, mdh, purM, and pyrC), and all the isolates belonged to ST69; another was used nine housekeeping genes (cat, chi, dnaE, gyrB, lap, pgm, recA, rstA, and gmd). A total of seven sequence types (STs) were found by using this method for all the strains; among them, rstA gene had five alleles, recA and gmd have two alleles, and others had only one allele. The virulence gene sequence typing method (ctxAB, tcpA, and toxR) showed that 70 strains were divided into nine STs; among them, tcpA gene had six alleles, toxR had five alleles, while ctxAB was identical for all the strains. The latter two sequences based typing methods also had consistency with epidemiology of the strains. PFGE had a higher resolution ability compared with the sequence based typing method, and MLST used seven housekeeping genes showed the lower resolution power than nine housekeeping genes and virulence genes methods. These two sequence typing methods could distinguish some epidemiological special strains in local area.
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Affiliation(s)
- Feng Liao
- Department of Respiratory Medicine, First People's Hospital of Yunnan Province, Kunming, China
| | - Zhishuo Mo
- The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Meiling Chen
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Bo Pang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Xiaoqing Fu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Wen Xu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Huaiqi Jing
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Biao Kan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Wenpeng Gu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China.,Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
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Timofeev VS, Bakhteeva IV, Dyatlov IA. Genotyping of Bacillus anthracis and Closely Related Microorganisms. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418010118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Bhotra T, Das MM, Pal BB, Singh DV. Genomic profile of antibiotic resistant, classical ctxB positive Vibrio cholerae O1 biotype El Tor isolated in 2003 and 2005 from Puri, India: A retrospective study. Indian J Med Microbiol 2017; 34:462-470. [PMID: 27934824 DOI: 10.4103/0255-0857.195356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
OBJECTIVES To examine eight strains of Vibrio cholerae O1 isolated in 2003 and 2005 from Puri, India, for antibiotic susceptibility, presence of virulence and regulatory genes, cholera toxin (CT) production, CTX arrangement and genomic profiles. MATERIALS AND METHODS Bacterial strains were tested for antibiotic susceptibility using disc diffusion assay. Polymerase chain reaction determined the presence of antibiotic resistance, virulence and regulatory genes. To determine the type of cholera toxin subunit B (ctxB), nucleotide sequencing was performed. Southern hybridisation determined the number and arrangement of CTXΦ. Ribotyping and pulsed-field gel electrophoresis (PFGE) were used to determine the genomic profile of isolates. RESULTS All the eight strains, except one strain, showed resistant to nalidixic acid, sulphamethoxazole, streptomycin and trimethoprim and possessed the sullI, strB, dfrA1 and int SXT genes. All the strains carried the toxin-co-regulated pilus pathogenicity island, the CTX genetic element, the repeat in toxin and produced CT. Restriction fragment length polymorphism (RFLP) analysis showed that V. cholerae O1 possess a single copy of the CTX element flanked by tandemly arranged RS element. Nucleotide sequencing of the ctxB gene showed the presence of classical ctxB. RFLP analysis of conserved rRNA gene showed two ribotype patterns. PFGE analysis also showed at least three PFGE patterns, irrespective of year of isolations, indicating the genomic relatedness among them. CONCLUSION Overall, these data suggest that classical ctxB-positive V. cholerae O1 El Tor strains that appeared in 2003 continue to cause infection in 2005 in Puri, India, and belong to identical ribotype(s) and/or pulsotype(s). There is need to continuous monitor the emergence of variant of El Tor because it will improve our understanding of the evolution of new clones of variant of V. cholerae.
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Affiliation(s)
- T Bhotra
- Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - M M Das
- Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - B B Pal
- Department of Infectious Disease Biology, Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - D V Singh
- Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India
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Pretzer C, Druzhinina IS, Amaro C, Benediktsdóttir E, Hedenström I, Hervio-Heath D, Huhulescu S, Schets FM, Farnleitner AH, Kirschner AKT. High genetic diversity of Vibrio cholerae in the European lake Neusiedler See is associated with intensive recombination in the reed habitat and the long-distance transfer of strains. Environ Microbiol 2017; 19:328-344. [PMID: 27871138 PMCID: PMC5718291 DOI: 10.1111/1462-2920.13612] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 10/27/2016] [Accepted: 11/10/2016] [Indexed: 11/29/2022]
Abstract
Coastal marine Vibrio cholerae populations usually exhibit high genetic diversity. To assess the genetic diversity of abundant V. cholerae non-O1/non-O139 populations in the Central European lake Neusiedler See, we performed a phylogenetic analysis based on recA, toxR, gyrB and pyrH loci sequenced for 472 strains. The strains were isolated from three ecologically different habitats in a lake that is a hot-spot of migrating birds and an important bathing water. We also analyzed 76 environmental and human V. cholerae non-O1/non-O139 isolates from Austria and other European countries and added sequences of seven genome-sequenced strains. Phylogenetic analysis showed that the lake supports a unique endemic diversity of V. cholerae that is particularly rich in the reed stand. Phylogenetic trees revealed that many V. cholerae isolates from European countries were genetically related to the strains present in the lake belonging to statistically supported monophyletic clades. We hypothesize that the observed phenomena can be explained by the high degree of genetic recombination that is particularly intensive in the reed stand, acting along with the long distance transfer of strains most probably via birds and/or humans. Thus, the Neusiedler See may serve as a bioreactor for the appearance of new strains with new (pathogenic) properties.
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Affiliation(s)
- Carina Pretzer
- Medical University Vienna, Institute for Hygiene and Applied Immunology, Vienna, Austria.,Vienna University of Technology, Institute of Chemical Engineering, Vienna, Austria
| | - Irina S Druzhinina
- Vienna University of Technology, Institute of Chemical Engineering, Vienna, Austria
| | - Carmen Amaro
- ERI BioTecMed University of Valencia, Valencia, Spain
| | - Eva Benediktsdóttir
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | | | | | | | - Franciska M Schets
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Andreas H Farnleitner
- Vienna University of Technology, Institute of Chemical Engineering, Vienna, Austria.,Interuniversity Cooperation Centre for Water & Health, (www.waterandhealth.at), Vienna, Austria
| | - Alexander K T Kirschner
- Medical University Vienna, Institute for Hygiene and Applied Immunology, Vienna, Austria.,Interuniversity Cooperation Centre for Water & Health, (www.waterandhealth.at), Vienna, Austria
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Cecchini F, Fajs L, Cosnier S, Marks RS. Vibrio cholerae detection: Traditional assays, novel diagnostic techniques and biosensors. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.01.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Genotypic Diversity and Population Structure of Vibrio vulnificus Strains Isolated in Taiwan and Korea as Determined by Multilocus Sequence Typing. PLoS One 2015; 10:e0142657. [PMID: 26599487 PMCID: PMC4658092 DOI: 10.1371/journal.pone.0142657] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 10/26/2015] [Indexed: 12/18/2022] Open
Abstract
The genetic diversity and population structure of Vibrio vulnificus isolates from Korea and Taiwan were investigated using PCR-based assays targeting putative virulence-related genes and multilocus sequence typing (MLST). BOX-PCR genomic fingerprinting identified 52 unique genotypes in 84 environmental and clinical V. vulnificus isolates. The majority (> 50%) of strains had pathogenic genotypes for all loci tested; moreover, many environmental strains had pathogenic genotypes. Although significant (p < 0.05) inter-relationships among the genotypes were observed, the association between genotype and strain source (environmental or clinical) was not significant, indicating that genotypic characteristics alone are not sufficient to predict the isolation source or the virulence of a given V. vulnificus strain and vice versa. MLST revealed 23–35 allelic types per locus analyzed, resulting in a total of 44 unique sequence types (STs). Two major monophyletic groups (lineages A and B) corresponding to the two known lineages of V. vulnificus were observed; lineage A had six STs that were exclusively environmental, whereas lineage B had STs from both environmental and clinical sources. Pathogenic and nonpathogenic genotypes predominated in MLST lineages B and A, respectively. In addition, V. vulnificus was shown to be in linkage disequilibrium (p < 0.05), although two different recombination tests (PHI and Sawyer’s tests) detected significant evidence of recombination. Tajima’s D test also indicated that V. vulnificus might be comprised of recently sub-divided lineages. These results suggested that the two lineages revealed by MLST correspond to two distinct ecotypes of V. vulnificus.
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Rahaman MH, Islam T, Colwell RR, Alam M. Molecular tools in understanding the evolution of Vibrio cholerae. Front Microbiol 2015; 6:1040. [PMID: 26500613 PMCID: PMC4594017 DOI: 10.3389/fmicb.2015.01040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/13/2015] [Indexed: 12/25/2022] Open
Abstract
Vibrio cholerae, the etiological agent of cholera, has been a scourge for centuries. Cholera remains a serious health threat for developing countries and has been responsible for millions of deaths globally over the past 200 years. Identification of V. cholerae has been accomplished using a variety of methods, ranging from phenotypic strategies to DNA based molecular typing and currently whole genomic approaches. This array of methods has been adopted in epidemiological investigations, either singly or in the aggregate, and more recently for evolutionary analyses of V. cholerae. Because the new technologies have been developed at an ever increasing pace, this review of the range of fingerprinting strategies, their relative advantages and limitations, and cholera case studies was undertaken. The task was challenging, considering the vast amount of the information available. To assist the study, key references representative of several areas of research are provided with the intent to provide readers with a comprehensive view of recent advances in the molecular epidemiology of V. cholerae. Suggestions for ways to obviate many of the current limitations of typing techniques are also provided. In summary, a comparative report has been prepared that includes the range from traditional typing to whole genomic strategies.
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Affiliation(s)
- Md Habibur Rahaman
- Department of Biology and Chemistry, North South University, Dhaka Bangladesh
| | - Tarequl Islam
- Enteric and Food Microbiology Lab, Center for Communicable Diseases, International Center for Diarrheal Disease Research, Dhaka Bangladesh
| | - Rita R Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD USA ; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD USA
| | - Munirul Alam
- Enteric and Food Microbiology Lab, Center for Communicable Diseases, International Center for Diarrheal Disease Research, Dhaka Bangladesh
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Janßen T, Voss M, Kühl M, Semmler T, Philipp HC, Ewers C. A combinational approach of multilocus sequence typing and other molecular typing methods in unravelling the epidemiology of Erysipelothrix rhusiopathiae strains from poultry and mammals. Vet Res 2015. [PMID: 26198736 PMCID: PMC4509749 DOI: 10.1186/s13567-015-0216-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Erysipelothrix rhusiopathiae infections re-emerged as a matter of great concern particularly in the poultry industry. In contrast to porcine isolates, molecular epidemiological traits of avian E. rhusiopathiae isolates are less well known. Thus, we aimed to (i) develop a multilocus sequence typing (MLST) scheme for E. rhusiopathiae, (ii) study the congruence of strain grouping based on pulsed-field gel electrophoresis (PFGE) and MLST, (iii) determine the diversity of the dominant immunogenic protein SpaA, and (iv) examine the distribution of genes putatively linked with virulence among field isolates from poultry (120), swine (24) and other hosts (21), including humans (3). Using seven housekeeping genes for MLST analysis we determined 72 sequence types (STs) among 165 isolates. This indicated an overall high diversity, though 34.5% of all isolates belonged to a single predominant ST-complex, STC9, which grouped strains from birds and mammals, including humans, together. PFGE revealed 58 different clusters and congruence with the sequence-based MLST-method was not common. Based on polymorphisms in the N-terminal hyper-variable region of SpaA the isolates were classified into five groups, which followed the phylogenetic background of the strains. More than 90% of the isolates harboured all 16 putative virulence genes tested and only intI, encoding an internalin-like protein, showed infrequent distribution. MLST data determined E. rhusiopathiae as weakly clonal species with limited host specificity. A common evolutionary origin of isolates as well as shared SpaA variants and virulence genotypes obtained from avian and mammalian hosts indicates common reservoirs, pathogenic pathways and immunogenic properties of the pathogen.
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Affiliation(s)
- Traute Janßen
- Center for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Straße 7-13, 14163, Berlin, Germany. .,RIPAC-LABOR GmbH, Am Mühlenberg 11, 14476, Potsdam, Germany.
| | | | - Michael Kühl
- Center for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Straße 7-13, 14163, Berlin, Germany. .,Institute of Animal Hygiene and Environmental Health, Freie Universität Berlin, Robert-von-Ostertag-Straße 7-13, 14163, Berlin, Germany.
| | | | - Hans-Christian Philipp
- Boehringer Ingelheim Veterinary Research Center GmbH & Co. KG, Bemeroder Straße 31, 30559, Hannover, Germany.
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-Universität Giessen, Frankfurter Str. 85-89, 35392, Giessen, Germany.
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Zhang G, Zhang X, Hu Y, Jiao XA, Huang J. Multilocus Sequence Types of Campylobacter jejuni Isolates from Different Sources in Eastern China. Curr Microbiol 2015; 71:341-6. [PMID: 26100240 DOI: 10.1007/s00284-015-0853-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/27/2015] [Indexed: 10/23/2022]
Abstract
Campylobacter jejuni is a major food-borne pathogen that causes human gastroenteritis in many developed countries. In our study, we applied multilocus sequence typing (MLST) technology to 167 C. jejuni isolates from diverse sources in Eastern China to examine their genetic diversity. MLST defined 94 sequence types (STs) belonging to 18 clonal complexes (CCs). Forty-five STs from 60 isolates (36%) and 22 alleles have not been previously documented in an international database. One hundred and two isolates, accounting for 61.1% of all isolates, belonged to eight clonal complexes. The eight major CCs were also the most common complexes from different sources. The most common ST type of isolates from human and food was ST-353. The dominant ST type in chicken and foods was ST-354. Among 21 STs that contained two or more different sources isolates, 15 STs contained human isolates and isolates from other sources, suggesting that potentially pathogenic strains are not restricted to specific lineages.
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Affiliation(s)
- Gong Zhang
- Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 88 South Daxue Road, Yangzhou, 225009, Jiangsu, China
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Molecular Typing of Campylobacter jejuni and Campylobacter coli Isolated from Various Retail Meats by MLST and PFGE. Foods 2014; 3:82-93. [PMID: 28234305 PMCID: PMC5302303 DOI: 10.3390/foods3010082] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 12/24/2013] [Accepted: 01/02/2014] [Indexed: 11/17/2022] Open
Abstract
Campylobacter species are one of the leading causes of foodborne disease in the United States. Campylobacter jejuni and Campylobacter coli are the two main species of concern to human health and cause approximately 95% of human infections. Molecular typing methods, such as pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) are often used to source track foodborne bacterial pathogens. The aim of the present study was to compare PFGE and MLST in typing strains of C. jejuni and C. coli that were isolated from different Oklahoma retail meat sources. A total of 47 Campylobacter isolates (28 C. jejuni and 19 C. coli) isolated from various retail meat samples (beef, beef livers, pork, chicken, turkey, chicken livers, and chicken gizzards) were subjected to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). PFGE was able to group the 47 Campylobacter isolates into two major clusters (one for C. jejuni and one for C. coli) but failed to differentiate the isolates according to their source. MLST revealed 21 different sequence types (STs) that belonged to eight different clonal complexes. Twelve of the screened Campylobacter isolates (8 C. jejuni and 4 C. coli) did not show any defined STs. All the defined STs of C. coli isolates belonged to ST-828 complex. The majority of C. jejuni isolates belonged to ST-353, ST-607, ST-52, ST-61, and ST-21 complexes. It is worthy to mention that, while the majority of Campylobacter isolates in this study showed STs that are commonly associated with human infections along with other sources, most of the STs from chicken livers were solely reported in human cases. In conclusion, retail meat Campylobacter isolates tested in this study particularly those from chicken livers showed relatedness to STs commonly associated with humans. Molecular typing, particularly MLST, proved to be a helpful tool in suggesting this relatedness to Campylobacter human isolates.
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De R, Ghosh JB, Sen Gupta S, Takeda Y, Nair GB. The role of Vibrio cholerae genotyping in Africa. J Infect Dis 2013; 208 Suppl 1:S32-8. [PMID: 24101642 DOI: 10.1093/infdis/jit199] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Toxigenic Vibrio cholerae, the causative agent of the disease cholera, is prevalent in the African continent from the 1970s when the seventh pandemic spread from Asia to Africa. In the past decade, cholera has caused devastating outbreaks in much of Africa, illustrated by the recent cholera epidemics in Zimbabwe and regions of central Africa. Given the extent of cholera in Africa, a robust and efficient surveillance system should be in place to prevent and control the disease in this continent. Such a surveillance system would be greatly bolstered by use of molecular typing techniques to identify genetic subtypes. In this review, we highlight the role that modern molecular typing techniques can play in tracking and aborting the spread of cholera.
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Affiliation(s)
- Rituparna De
- National Institute of Cholera and Enteric Diseases, Beliaghata
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18
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Development of a single multi-locus sequence typing scheme for Taylorella equigenitalis and Taylorella asinigenitalis. Vet Microbiol 2013; 167:609-18. [DOI: 10.1016/j.vetmic.2013.09.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 09/12/2013] [Accepted: 09/13/2013] [Indexed: 11/20/2022]
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Chen CH, Huang CC. Molecular epidemiological study of clinical Acinetobacter baumannii isolates: phenotype switching of antibiotic resistance. Ann Clin Microbiol Antimicrob 2013; 12:21. [PMID: 23965155 PMCID: PMC3851446 DOI: 10.1186/1476-0711-12-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/11/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The presence of clinical Acinetobacter baumannii (A. baumannii) isolates with differing antibiotic resistance phenotypes in the same patient causes difficulties and confusion in treatment. This phenomenon may be caused by reasons such as cross-infection from neighboring patients that switches to different A. baumannii strain, natural mutation of A. baumannii, inducing of different antibiotic resistance genes expression or acquisition of genes conferring resistance from another source. To elucidate this question, clinical A. baumannii strains, isolated from the same individual patients, showed antibiotic resistance phenotypes switching during the same hospitalization period, were attentively collected for further analysis. Molecular approaches for phylogenetic analysis, including pulsed field gel electrophoresis, multilocus sequence typing, and short tandem repeat analysis, were employed for the chronological studies. FINDINGS Our results showed that antibiotic resistance phenotype switching could have occurred as a result through both cross-infection and natural mutation roots. Our results also suggest that rapid phenotype switching between paired isolates could occur during one single course of antibiotic treatment. CONCLUSIONS Though cross infection caused antibiotic resistance phenotype switching does occur, natural mutation of A. baumannii isolates is particularly cautious for antibiotic treatment.
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Affiliation(s)
- Chang-Hua Chen
- Department of Life Science, College of Life Science, National Chung Hsing University, No, 250 Kuo-Kuang Road, Taichung 402, Taiwan, R,O,C.
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20
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Moustafa AM, Bennett MD, Edwards J, Azim K, Mesaik MA, Choudhary MI, Pathanasophon P, Worarach A, Ali Q, Abubakar M, Anjum R. Molecular typing of haemorrhagic septicaemia-associated Pasteurella multocida isolates from Pakistan and Thailand using multilocus sequence typing and pulsed-field gel electrophoresis. Res Vet Sci 2013; 95:986-90. [PMID: 23916592 DOI: 10.1016/j.rvsc.2013.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 05/17/2013] [Accepted: 07/08/2013] [Indexed: 11/25/2022]
Abstract
A comparative genetic study of 23 field isolates and vaccine strains of Pasteurella multocida associated with haemorrhagic septicaemia cases from Pakistan and Thailand was done using pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The MLST sequence type (ST) for all 20 of the 23 isolates tested was 122. The PFGE results showed one band difference between the Pakistani and the Thai isolates. Sequence type 122 is the dominant associated profile with haemorrhagic septicaemia (HS) cases in South Asia. The study supports the concept of using PFGE for short-term epidemiology and MLST for long-term epidemiology.
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Affiliation(s)
- Ahmed M Moustafa
- School of Veterinary and Life Sciences, Murdoch University, South Street, Murdoch, Western Australia 6150, Australia
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21
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Lam C, Octavia S, Reeves PR, Lan R. Multi-locus variable number tandem repeat analysis of 7th pandemic Vibrio cholerae. BMC Microbiol 2012; 12:82. [PMID: 22624829 PMCID: PMC3438101 DOI: 10.1186/1471-2180-12-82] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 05/09/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Seven pandemics of cholera have been recorded since 1817, with the current and ongoing pandemic affecting almost every continent. Cholera remains endemic in developing countries and is still a significant public health issue. In this study we use multilocus variable number of tandem repeats (VNTRs) analysis (MLVA) to discriminate between isolates of the 7th pandemic clone of Vibrio cholerae. RESULTS MLVA of six VNTRs selected from previously published data distinguished 66 V. cholerae isolates collected between 1961-1999 into 60 unique MLVA profiles. Only 4 MLVA profiles consisted of more than 2 isolates. The discriminatory power was 0.995. Phylogenetic analysis showed that, except for the closely related profiles, the relationships derived from MLVA profiles were in conflict with that inferred from Single Nucleotide Polymorphism (SNP) typing. The six SNP groups share consensus VNTR patterns and two SNP groups contained isolates which differed by only one VNTR locus. CONCLUSIONS MLVA is highly discriminatory in differentiating 7th pandemic V. cholerae isolates and MLVA data was most useful in resolving the genetic relationships among isolates within groups previously defined by SNPs. Thus MLVA is best used in conjunction with SNP typing in order to best determine the evolutionary relationships among the 7th pandemic V. cholerae isolates and for longer term epidemiological typing.
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Affiliation(s)
- Connie Lam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, Australia
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22
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Tankouo-Sandjong B, Kinde H, Wallace I. Development of a sequence typing scheme for differentiation of Salmonella Enteritidis strains. FEMS Microbiol Lett 2012; 331:165-75. [PMID: 22486191 DOI: 10.1111/j.1574-6968.2012.02568.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 04/03/2012] [Accepted: 04/04/2012] [Indexed: 11/30/2022] Open
Abstract
A DNA sequence typing scheme based on the caiC and SEN0629 loci was developed for differentiation of Salmonella Enteritidis strains and validated using a diverse collection of 102 isolates representing 38 phage types from different sources, year of isolation, geographical locations and epidemiological backgrounds. caiC encodes a probable crotonobetaine/carnitine-CoA ligase, and SEN0629 is a pseudogene. Our system allowed for discrimination of 16 sequence types (STs) among the 102 isolates analysed and intraphage type differentiation. Our findings also suggested that the stability of phage typing may be adversely affected by the occurrence of phage type conversion events. During a confirmatory phage typing analysis performed by a reference laboratory, 13 of 31 S. Enteritidis strains representing nine phage types were assigned phage types that differed from the ones originally determined by the same reference laboratory. It is possible that this phenomenon passes largely unrecognized in reference laboratories performing routine phage typing analyses. Our results demonstrate that phage typing is an unstable system displaying limited reproducibility and that the two-loci sequence typing scheme is highly discriminatory, stable, truly portable and has the potential to become the new gold standard for epidemiological typing of S . Enteritidis strains.
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Affiliation(s)
- Bertrand Tankouo-Sandjong
- California Animal Health and Food Safety Laboratory System, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
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Genetic diversity of the human pathogen Vibrio vulnificus: a new phylogroup. Int J Food Microbiol 2011; 153:436-43. [PMID: 22227412 DOI: 10.1016/j.ijfoodmicro.2011.12.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 12/01/2011] [Accepted: 12/07/2011] [Indexed: 11/21/2022]
Abstract
The biotype 3 group of the human pathogen Vibrio vulnificus emerged in Israel probably as a result of genome hybridization of two bacterial populations. We performed a genomic and phylogenetic study of V. vulnificus strains isolated from the environmental niche from which this group emerged - fish aquaculture in Israel. The genetic relationships and evolutionary aspects of 188 environmental and clinical isolates of the bacterium were studied by genomic typing. Genetic relations were determined based on variation at 12 variable number tandem repeat (VNTR, also termed SSR) loci. Analysis revealed a new cluster, in addition to the main groups of biotype 1& 2 and biotype 3. Similar grouping results were obtained with three different statistical approaches. Isolates forming this new cluster presented unclear biochemical profile nevertheless were not identified as biotype 1 or biotype 3. Further examination of representative strains by multilocus sequence typing (MLST) of 10 housekeeping genes and 5 conserved hypothetical genes supported the identification of this as yet undiscovered phylogroup (phenotypically diverse), termed clade A herein. This new clonal subgroup includes environmental as well as clinical isolates. The results highlight the fish aquaculture environment, and possibly man-made ecological niches as a whole, as a source for the emergence of new pathogenic strains.
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Phenotypic and genetic analyses of 111 clinical and environmental O1, O139, and non-O1/O139 Vibrio cholerae strains from different geographical areas. Epidemiol Infect 2011; 140:1389-99. [PMID: 22074599 DOI: 10.1017/s0950268811002147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A total of 111 clinical and environmental O1, O139 and non-O1/O139 Vibrio cholerae strains isolated between 1978 and 2008 from different geographical areas were typed using a combination of methods: antibiotic susceptibility, biochemical test, serogroup, serotype, biotype, sequences containing variable numbers of tandem repeats (VNTRs) and virulence genes ctxA and tcpA amplification. As a result of the performed typing work, the strains were organized into four clusters: cluster A1 included clinical O1 Ogawa and O139 serogroup strains (ctxA(+) and tcpA(+)); cluster A2 included clinical non-O1/O139 strains (ctxA(-) and tcpA(-)), as well as environmental O1 Inaba and non-O1/O139 strains (ctxA(-) and tcpA(-)/tcpA(+)); cluster B1 contained two clinical O1 strains and environmental non-O1/O139 strains (ctxA(-) and tcpA(+)/tcpA(-)); cluster B2 contained clinical O1 Inaba and Ogawa strains (ctxA(+) and tcpA(+)). The results of this work illustrate the advantage of combining several typing methods to discriminate between clinical and environmental V. cholerae strains.
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25
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Ecology and genetic structure of a northern temperate Vibrio cholerae population related to toxigenic isolates. Appl Environ Microbiol 2011; 77:7568-75. [PMID: 21926213 DOI: 10.1128/aem.00378-11] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Although Vibrio cholerae is an important human pathogen, little is known about its populations in regions where the organism is endemic but where cholera disease is rare. A total of 31 independent isolates confirmed as V. cholerae were collected from water, sediment, and oysters in 2008 and 2009 from the Great Bay Estuary (GBE) in New Hampshire, a location where the organism has never been detected. Environmental analyses suggested that abundance correlates most strongly with rainfall events, as determined from data averaged over several days prior to collection. Phenotyping, genotyping, and multilocus sequence analysis (MLSA) revealed a highly diverse endemic population, with clones recurring in both years. Certain isolates were closely related to toxigenic O1 strains, yet no virulence genes were detected. Multiple statistical tests revealed evidence of recombination among strains that contributed to allelic diversity equally as mutation. This relatively isolated population discovered on the northern limit of detection for V. cholerae can serve as a model of natural population dynamics that augments predictive models for disease emergence.
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26
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Dashtbani-Roozbehani A, Bakhshi B, Katouli M, Pourshafie MR. Comparative sequence analysis of recA gene among Vibrio cholerae isolates from Iran with globally reported sequences. Lett Appl Microbiol 2011; 53:313-23. [PMID: 21707677 DOI: 10.1111/j.1472-765x.2011.03108.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To study the genetic relatedness between V. cholerae isolates from Iran and other countries based on housekeeping gene recA sequence analysis. METHODS AND RESULTS A 995-bp region of the recA gene from 24 V. cholerae isolates obtained from human and surface water origins in Iran over a 5-year period was sequenced and compared with the sequence data from the isolates belonging to other places. Cluster analysis of the constructed dendrogram based on recA sequence divergence for our clinical isolates showed one sequence type (ST), whereas environmental isolates revealed eight STs. Interestingly, one of our environmental isolates was intermixed with clinical isolates in the largest cluster containing the epidemic strains. Our 24 isolates plus 198 global isolates available in the GenBank showed 77 sequence types (STs) with at least one nucleotide difference. CONCLUSIONS Our result suggested that recA sequencing is a reliable analysis method for understanding the relatedness of the local isolates with the isolates obtained elsewhere. SIGNIFICANCE AND IMPACT OF THE STUDY Understanding the genetic relatedness between V. cholerae isolates could give insights into the health care system for better control and prevention of the cholera.
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27
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Bhowmick TS, Das M, Sarkar BL. Genotypic characterization of Vibrio cholerae isolates using several DNA fingerprint techniques. Future Microbiol 2011; 6:29-42. [PMID: 21162634 DOI: 10.2217/fmb.10.159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Serious pandemics of cholera have occurred throughout the known history of mankind, especially in India, which is a motherland for cholera disease. For the last 20 years several DNA-based typing methods have been employed to study the clonal relatedness between Vibrio cholerae isolates irrespective of their geographical locations. Traditional typing methods, such as biochemical tests, phage typing, serotyping, biotyping and antimicrobial susceptibility tests, have produced reliable and informative data regarding V. cholerae for a long time. Gradually molecular typing techniques have taken the place of traditional typing methods because they produce the same results upon repeat testing of V. cholerae strain. In this article we focus on the discriminatory power of different DNA fingerprint techniques that are generally used to know the homogeneity and heterogeneity among different V. cholerae isolates.
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Affiliation(s)
- Tushar Suvra Bhowmick
- Vibrio Phage Reference Laboratory, National Institute of Cholera and Enteric Diseases, Kolkata, India
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28
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Silva FM, Carmo MS, Silbert S, Gales AC. SPM-1-ProducingPseudomonas aeruginosa: Analysis of the Ancestor Relationship Using Multilocus Sequence Typing, Pulsed-Field Gel Electrophoresis, and Automated Ribotyping. Microb Drug Resist 2011; 17:215-20. [DOI: 10.1089/mdr.2010.0140] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Fernanda M. Silva
- Laboratório Especial de Microbiologia Clínica, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mirian S. Carmo
- Laboratório Especial de Microbiologia Clínica, Universidade Federal de São Paulo, São Paulo, Brazil
- Centro Universitário FIEO—UNIFIEO, São Paulo, Brazil
| | - Suzane Silbert
- Esoteric Testing Laboratory, Tampa General Hospital, Tampa, Florida
| | - Ana C. Gales
- Laboratório Especial de Microbiologia Clínica, Universidade Federal de São Paulo, São Paulo, Brazil
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29
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Woo PCY, Tsang AKL, Wong AYP, Chen H, Chu J, Lau SKP, Yuen KY. Analysis of multilocus sequence typing schemes for 35 different bacteria revealed that gene loci of 10 bacteria could be replaced to improve cost-effectiveness. Diagn Microbiol Infect Dis 2011; 70:316-23. [PMID: 21558049 DOI: 10.1016/j.diagmicrobio.2011.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 03/09/2011] [Accepted: 03/09/2011] [Indexed: 11/17/2022]
Abstract
Although multilocus sequence typing (MLST) has been widely used for bacterial typing, the contribution of the gene loci to the discriminatory power of each MLST scheme is unknown. We analyzed the discriminatory powers of 36 MLST schemes using all combinations of the 7 loci and contributions of each locus to the schemes. In 10 schemes, sequencing 6 loci can achieve the discriminatory powers of 7 loci. For the other 26 schemes, the median marginal increase in discriminatory power when 7 instead of 6 loci were used is 0.0004. Sequencing the 7 loci of 50 strains each of Pseudomonas aeruginosa and Acinetobacter baumannii revealed that the discriminatory power for P. aeruginosa was 0.9861 when either 6 (without trp) or 7 loci were used and that for A. baumannii was 0.9363 when 5, 6, or 7 loci were used. Genes that have no additional or minimal contribution to the overall discriminatory powers should be replaced.
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Affiliation(s)
- Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.
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Teh CSJ, Chua KH, Thong KL. Genetic variation analysis of Vibrio cholerae using multilocus sequencing typing and multi-virulence locus sequencing typing. INFECTION GENETICS AND EVOLUTION 2011; 11:1121-8. [PMID: 21511055 DOI: 10.1016/j.meegid.2011.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 03/25/2011] [Accepted: 04/05/2011] [Indexed: 10/18/2022]
Abstract
This paper describes the development and application of multilocus sequencing typing (MLST) and multi-virulence locus sequencing typing (MVLST) methods in determining the genetic variation and relatedness of 43 Vibrio cholerae strains of different serogroups isolated from various sources in Malaysia. The MLST assay used six housekeeping genes (dnaE, lap, recA, gyrB, cat and gmd), while the MVLST assay incorporated three virulence genes (ctxAB, tcpA and tcpI) and three virulence-associated genes (hlyA, toxR and rtxA). Our data showed that the dnaE and rtxA genes were the most conserved genes in V. cholerae O1 strains. Among the 12 studied genes, transitional substitutions that led to silent mutations were observed in all, except for gmd and hlyA, while non-synonymous substitutions occurred more frequently in virulence and virulence-associated genes. Five V. cholerae O1 strains were found to be the El Tor variant O1 strains because they harboured the classical ctxB gene. In addition, the classical ctxB gene was also observed in O139 V. cholerae. A total of 29 MLST types were observed, and this assay could differentiate V. cholerae within the non-O1/non-O139 serogroups. A total of 27 MVLST types were obtained. MVLST appeared to be more discriminatory than MLST because it could differentiate V. cholerae strains from two different outbreaks and could separate the toxigenic from the non-toxigenic subtypes. Although the O1 V. cholerae strains were closely related, the combined MLST and MVLST analyses differentiated the strains isolated from different localities. In conclusion, sequence-based analysis in this study provided a better understanding of mutation points and the type of mutations in V. cholerae. The MVLST assay is useful to characterise O1 V. cholerae strains, while combined analysis may improve the discriminatory power and is suitable for the local epidemiological study of V. cholerae.
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Affiliation(s)
- Cindy Shuan Ju Teh
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
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31
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Recombination shapes the structure of an environmental Vibrio cholerae population. Appl Environ Microbiol 2010; 77:537-44. [PMID: 21075874 DOI: 10.1128/aem.02062-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae consists of pathogenic strains that cause sporadic gastrointestinal illness or epidemic cholera disease and nonpathogenic strains that grow and persist in coastal aquatic ecosystems. Previous studies of disease-causing strains have shown V. cholerae to be a primarily clonal bacterial species, but isolates analyzed have been strongly biased toward pathogenic genotypes, while representing only a small sample of the vast diversity in environmental strains. In this study, we characterized homologous recombination and structure among 152 environmental V. cholerae isolates and 13 other putative Vibrio isolates from coastal waters and sediments in central California, as well as four clinical V. cholerae isolates, using multilocus sequence analysis of seven housekeeping genes. Recombinant regions were identified by at least three detection methods in 72% of our V. cholerae isolates. Despite frequent recombination, significant linkage disequilibrium was still detected among the V. cholerae sequence types. Incongruent but nonrandom associations were observed for maximum likelihood topologies from the individual loci. Overall, our estimated recombination rate in V. cholerae of 6.5 times the mutation rate is similar to those of other sexual bacteria and appears frequently enough to restrict selection from purging much of the neutral intraspecies diversity. These data suggest that frequent recombination among V. cholerae may hinder the identification of ecotypes in this bacterioplankton population.
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Relatedness of Vibrio cholerae O1/O139 isolates from patients and their household contacts, determined by multilocus variable-number tandem-repeat analysis. J Bacteriol 2010; 192:4367-76. [PMID: 20585059 DOI: 10.1128/jb.00698-10] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genetic relatedness of Vibrio cholerae O1/O139 isolates obtained from 100 patients and 146 of their household contacts in Dhaka, Bangladesh, between 2002 and 2005 was assessed by multilocus variable-number tandem-repeat analysis. Isolate genotypes were analyzed at five loci containing tandem repeats. Across the population, as well as within households, isolates with identical genotypes were clustered in time. Isolates from individuals within the same household were more likely to have similar or identical genotypes than were isolates from different households, but even within a household, isolates from different individuals often had different genotypes. When household contacts were sampled regularly for 3 weeks after the illness of the household index patient, isolates with genotypes related to the index patient appeared in contacts, on average, approximately 3 days after the index patient, while isolates with unrelated genotypes appeared in contacts approximately 6 days after. Limited data revealed that multiple isolates from the same individual collected within days of each other or even from a single stool sample may have identical, similar, or unrelated genotypes as well. Our results demonstrate that genetically related V. cholerae strains cluster in local outbreaks but also suggest that multiple distinct strains of V. cholerae O1 may circulate simultaneously within a household.
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Evaluation of a highly discriminating multiplex multi-locus variable-number of tandem-repeats (MLVA) analysis for Vibrio cholerae. J Microbiol Methods 2009; 78:271-85. [PMID: 19555725 DOI: 10.1016/j.mimet.2009.06.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 06/10/2009] [Accepted: 06/15/2009] [Indexed: 11/23/2022]
Abstract
Vibrio cholerae is the etiological agent of cholera and may be used in bioterror actions due to the easiness of its dissemination, and the public fear for acquiring the cholera disease. A simple and highly discriminating method for connecting clinical and environmental isolates of V. cholerae is needed in microbial forensics. Twelve different loci containing variable numbers of tandem-repeats (VNTRs) were evaluated in which six loci were polymorphic. Two multiplex reactions containing PCR primers targeting these six VNTRs resulted in successful DNA amplification of 142 various environmental and clinical V. cholerae isolates. The genetic distribution inside the V. cholerae strain collection was used to evaluate the discriminating power (Simpsons Diversity Index=0.99) of this new MLVA analysis, showing that the assay have a potential to differentiate between various strains, but also to identify those isolates which are collected from a common V. cholerae outbreak. This work has established a rapid and highly discriminating MLVA assay useful for track back analyses and/or forensic studies of V. cholerae infections.
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Thakur S, White DG, McDermott PF, Zhao S, Kroft B, Gebreyes W, Abbott J, Cullen P, English L, Carter P, Harbottle H. Genotyping of Campylobacter coli isolated from humans and retail meats using multilocus sequence typing and pulsed-field gel electrophoresis. J Appl Microbiol 2009; 106:1722-33. [PMID: 19226383 DOI: 10.1111/j.1365-2672.2008.04142.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIMS To determine the antimicrobial resistant profiles and clonality of Campylobacter coli isolated from clinically ill humans and retail meats. METHODS AND RESULTS A total of 98 C. coli isolates (20 from humans and 78 from retail meats) were phenotypically characterized. Antimicrobial susceptibility testing was done using agar dilution method for ciprofloxacin, gentamicin, erythromycin and doxycycline. Seventy C. coli isolates including humans (n = 20) and retail meats (n = 50) were genotyped by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Resistance to ciprofloxacin was found in 29% and 15% of isolates from retail meats and humans. We observed 61 PFGE profiles using two enzymes (SmaI, KpnI) with an Index of discrimination of 0.99, whereas MLST generated 37 sequence types. Two clonal complexes were identified with 58 (82%) C. coli isolates clustered in the ST-828 complex. CONCLUSIONS Resistance to ciprofloxacin and erythromycin was identified in C. coli obtained from retail meats and ill humans. PFGE typing of C. coli isolates was more discriminatory than MLST. Grouping of C. coli isolates (82%) by MLST in ST-828 clonal complex indicates a common ancestry. SIGNIFICANCE AND IMPACT OF THE STUDY A high frequency of resistance found to ciprofloxacin and erythromycin is concerning from food safety perspective. PFGE using single or double restriction enzymes was found to be more discriminatory than MLST for genotyping C. coli. Overall, the C. coli populations recovered from humans and retail meats were genotypically diverse.
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Affiliation(s)
- S Thakur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA.
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35
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Mohapatra SS, Ramachandran D, Mantri CK, Colwell RR, Singh DV. Determination of relationships among non-toxigenic Vibrio cholerae O1 biotype El Tor strains from housekeeping gene sequences and ribotype patterns. Res Microbiol 2008; 160:57-62. [PMID: 19028569 DOI: 10.1016/j.resmic.2008.10.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2008] [Revised: 10/20/2008] [Accepted: 10/24/2008] [Indexed: 10/21/2022]
Abstract
Sequencing of three housekeeping genes, mdh, dnaE and recA, and ribotyping for seven non-toxigenic Vibrio cholerae O1 strains isolated from different geographic sources indicate a phylogenetic relationship among the strains. Results of MLST and ribotyping indicate a clear difference between three toxigenic strains (N16961, O395, and 569B) and three non-toxigenic strains from India (GS1, GS2, and GW87) and one Guam strain (X392), the latter of which were similar in both MLST and ribotyping, while two other non-toxigenic strains from the USA and India (2740-80 and OR69) appeared to be more closely related to toxigenic strains than to non-toxigenic strains, although this was not supported by ribotyping. These results provide clues to the emergence of toxigenic strains from a non-toxigenic progenitor by acquisition of virulence gene clusters. Results of split decomposition analysis suggest that widespread recombination occurs among the three housekeeping genes and that recombination plays an important role in the emergence of toxigenic strains of V. cholerae O1.
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Affiliation(s)
- Saswat S Mohapatra
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India
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36
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Singh DV, Mohapatra H. Application of DNA-based methods in typing Vibrio cholerae strains. Future Microbiol 2008; 3:87-96. [DOI: 10.2217/17460913.3.1.87] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Molecular biology-based techniques based on microbial genotype or DNA sequence have emerged as a basic tool in biological research and in the establishment of large databases of characterized organisms. Genotyping methods have the potential to provide information on subtypes of the organism and their source and/or origin of infection, and to recognize particularly virulent strains of the organism and monitor vaccination programs. Pulsed-field gel electrophoresis, ribotyping, CTX typing, amplified fragment length polymorphism, enterobacterial intergenic consensus sequence-PCR, multilocus sequence typing and microarray methods are more often used for the determination of genetic changes of toxigenic and nontoxigenic Vibrio cholerae strains, origin of infection and relationship between clinical and environmental strains, with the simultaneous detection of the number of copies and types of CTX prophages and genes required for persistence in diverse aquatic environments. This review will discuss DNA-based techniques for the molecular analysis of V. cholerae, its application and future directions.
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Affiliation(s)
- Durg V Singh
- Institute of Life Sciences, Nalco Square, Bhubaneswar-751023, India
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37
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Labbate M, Boucher Y, Joss MJ, Michael CA, Gillings MR, Stokes HW. Use of chromosomal integron arrays as a phylogenetic typing system for Vibrio cholerae pandemic strains. MICROBIOLOGY-SGM 2007; 153:1488-1498. [PMID: 17464063 DOI: 10.1099/mic.0.2006/001065-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Approximately 200 serogroups of Vibrio cholerae exist, with only two, O1 and O139, responsible for epidemic and pandemic cholera. Strains from these serogroups have evolved from a common progenitor, with lateral gene transfer largely driving their emergence. These strains are so closely related that separation using single- or multi-locus phylogeny has proven difficult. V. cholerae strains contain a genetic system called the integron that is located in the chromosome and that can integrate and excise DNA elements called mobile gene cassettes (MGCs) by site-specific recombination. Large arrays of MGCs are found in V. cholerae strains. For instance, the O1 El Tor strain N16961 contains 179 MGCs. Since integron arrays are dynamic through recombination and excision of MGCs, it was hypothesized that the MGC composition in a given V. cholerae pandemic strain would be useful as a phylogenetic typing system. To address this, a PCR-based method was used to rapidly characterize the MGC composition of V. cholerae arrays. The results showed that the MGC composition of pandemic V. cholerae cassette arrays is relatively conserved, providing further evidence that these strains have evolved from a common progenitor. Comparison of MGC composition between the V. cholerae pandemic strains was also able to resolve the evolution of O139 from a subgroup of O1 El Tor. This level of differentiation of closely related V. cholerae isolates was more sensitive than conventional single-gene phylogeny or multi-locus sequence analysis. Using this method, novel MGCs from an O1 classical strain and an Argentinian O139 isolate were also identified, and a major deletion in the MGC array in all pandemic O139 strains and a subset of O1 El Tor strains was identified. Analysis of sequenced V. cholerae integron arrays showed that their evolution can proceed by rearrangements and deletions/insertions of large portions of MGCs in addition to the insertion or excision of single MGCs.
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Affiliation(s)
- M Labbate
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Y Boucher
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - M J Joss
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - C A Michael
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - M R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - H W Stokes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
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38
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Olsen JS, Skogan G, Fykse EM, Rawlinson EL, Tomaso H, Granum PE, Blatny JM. Genetic distribution of 295 Bacillus cereus group members based on adk-screening in combination with MLST (Multilocus Sequence Typing) used for validating a primer targeting a chromosomal locus in B. anthracis. J Microbiol Methods 2007; 71:265-74. [PMID: 17997177 DOI: 10.1016/j.mimet.2007.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 09/21/2007] [Accepted: 10/01/2007] [Indexed: 10/22/2022]
Abstract
The genetic distribution of 295 Bacillus cereus group members has been investigated by using a modified Multilocus Sequence Typing method (MLST). By comparing the nucleic acid sequence of the adk gene fragment, isolates of B. cereus group members most related to B. anthracis may be easily identified. The genetic distribution, with focus on the B. anthracis close neighbours, was used to evaluate a new primer set for specific identification of B. anthracis. This primer set, BA5510-1/2, targeted the putative B. anthracis specific gene BA5510. Real-time PCR using BA5510-1/2 amplified the target fragment from all B. anthracis strains tested and only two (of 289) non-B. anthracis strains analysed. This is one of the most thoroughly validated chromosomal B. anthracis markers for real-time PCR identification, in which the screened collection contained several very closely related B. anthracis strains.
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Affiliation(s)
- Jaran S Olsen
- Forsvarets forskningsinstitutt FFI, Norwegian Defence Research Establishment, P. O. Box 25, N-2027 Kjeller, Norway.
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39
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Johnson JK, Arduino SM, Stine OC, Johnson JA, Harris AD. Multilocus sequence typing compared to pulsed-field gel electrophoresis for molecular typing of Pseudomonas aeruginosa. J Clin Microbiol 2007; 45:3707-12. [PMID: 17881548 PMCID: PMC2168506 DOI: 10.1128/jcm.00560-07] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For hospital epidemiologists, determining a system of typing that is discriminatory is essential for measuring the effectiveness of infection control measures. In situations in which the incidence of resistant Pseudomonas aeruginosa is increasing, the ability to discern whether it is due to patient-to-patient transmission versus an increase in patient endogenous strains is often made on the basis of molecular typing. The present study compared the discriminatory abilities of pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) for 90 P. aeruginosa isolates obtained from cultures of perirectal surveillance swabs from patients in an intensive care unit. PFGE identified 85 distinct types and 76 distinct groups when similarity cutoffs of 100% and 87%, respectively, were used. By comparison, MLST identified 60 sequence types that could be clustered into 11 clonal complexes and 32 singletons. By using the Simpson index of diversity (D), PFGE had a greater discriminatory ability than MLST for P. aeruginosa isolates (D values, 0.999 versus 0.975, respectively). Thus, while MLST was better for detecting genetic relatedness, we determined that PFGE was more discriminatory than MLST for determining genetic differences in P. aeruginosa.
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Affiliation(s)
- Jennifer K Johnson
- Department of Pathology, University of Maryland School of Medicine, MSTF, Baltimore, MD 21201, USA.
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40
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González-Escalona N, Whitney B, Jaykus LA, DePaola A. Comparison of direct genome restriction enzyme analysis and pulsed-field gel electrophoresis for typing of Vibrio vulnificus and their correspondence with multilocus sequence typing data. Appl Environ Microbiol 2007; 73:7494-500. [PMID: 17720834 PMCID: PMC2168220 DOI: 10.1128/aem.00738-07] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We compared the potential of direct genome restriction enzyme analysis (DGREA) and pulsed-field gel electrophoresis (PFGE) for discriminating Vibrio vulnificus isolates from clinical (23) and environmental (17) sources. The genotypes generated by both methodologies were compared to previous multilocus sequence typing (MLST) data. DGREA established clearer relationships among V. vulnificus strains and was more consistent with MLST than with PFGE. DGREA is a very promising tool for epidemiological and ecological studies of V. vulnificus.
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41
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Goarant C, Reynaud Y, Ansquer D, de Decker S, Merien F. Sequence polymorphism-based identification and quantification of Vibrio nigripulchritudo at the species and subspecies level targeting an emerging pathogen for cultured shrimp in New Caledonia. J Microbiol Methods 2007; 70:30-8. [PMID: 17467831 DOI: 10.1016/j.mimet.2007.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Revised: 03/16/2007] [Accepted: 03/20/2007] [Indexed: 10/23/2022]
Abstract
In a previous study, we demonstrated the existence of an emerging cluster of Vibrio nigripulchritudo that proved to be associated with shrimp mortality events in New Caledonia. Using sequence polymorphisms evidenced in this previous MultiLocus Sequence Typing study, we developed two new quantitative PCR assays permitting the detection and quantification of V. nigripulchritudo at the genospecies level using SYBR Green I chemistry and at the emerging cluster level using Fluorescence Resonance Energy Transfer technology with hybridization probes. The use of this molecular diagnostic tool evidenced the colonization of the shrimp pond ecosystem by the pathogenic cluster at least at the onset of the disease. This new tool will allow better investigation of the dynamics of this bacterial pathogen in the shrimp farm ecosystem.
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Affiliation(s)
- Cyrille Goarant
- Laboratoire de Recherche en Bactériologie, Institut Pasteur de Nouvelle Calédonie, Noumea, New Caledonia.
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42
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Miller MC, Keymer DP, Avelar A, Boehm AB, Schoolnik GK. Detection and transformation of genome segments that differ within a coastal population of Vibrio cholerae strains. Appl Environ Microbiol 2007; 73:3695-704. [PMID: 17449699 PMCID: PMC1932674 DOI: 10.1128/aem.02735-06] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae is an autochthonous member of diverse aquatic ecosystems around the globe. Collectively, the genomes of environmental V. cholerae strains comprise a large repository of encoded functions which can be acquired by individual V. cholerae lineages through uptake and recombination. To characterize the genomic diversity of environmental V. cholerae, we used comparative genome hybridization to study 41 environmental strains isolated from diverse habitats along the central California coast, a region free of endemic cholera. These data were used to classify genes of the epidemic V. cholerae O1 sequenced strain N16961 as conserved, variably present, or absent from the isolates. For the most part, absent genes were restricted to large mobile elements and have known functions in pathogenesis. Conversely, genes present in some, but not all, California isolates were in smaller contiguous clusters and were less likely to be near genes with functions in DNA mobility. Two such clusters of variable genes encoding different selectable metabolic phenotypes (mannose and diglucosamine utilization) were transformed into the genomes of environmental isolates by chitin-dependent competence, indicating that this mechanism of general genetic exchange is conserved among V. cholerae. The transformed DNA had an average size of 22.7 kbp, demonstrating that natural competence can mediate the movement of large chromosome fragments. Thus, whether variable genes arise through the acquisition of new sequences by horizontal gene transfer or by the loss of preexisting DNA though deletion, natural transformation provides a mechanism by which V. cholerae clones can gain access to the V. cholerae pan-genome.
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Affiliation(s)
- Michael C Miller
- Department of Medicine, Stanford University School of Medicine, CA 94305, USA.
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43
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Danin-Poleg Y, Cohen LA, Gancz H, Broza YY, Goldshmidt H, Malul E, Valinsky L, Lerner L, Broza M, Kashi Y. Vibrio cholerae strain typing and phylogeny study based on simple sequence repeats. J Clin Microbiol 2006; 45:736-46. [PMID: 17182751 PMCID: PMC1829105 DOI: 10.1128/jcm.01895-06] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae is the etiological agent of cholera. Its natural reservoir is the aquatic environment. To date, practical typing of V. cholerae is mainly serological and requires about 200 antisera. Simple sequence repeats (SSR), also termed VNTR (for variable number of tandem repeats), provide a source of high genomic polymorphism used in bacterial typing. Here we describe an SSR-based typing method that combines the variation in highly mutable SSR loci, with that of shorter, relatively more stable mononucleotide repeat (MNR) loci, for accurate and rapid typing of V. cholerae. In silico screening of the V. cholerae genome revealed thousands of perfect SSR tracts with an average frequency of one SSR every 152 bp. A panel of 32 V. cholerae strains, representing both clinical and environmental isolates, was tested for polymorphism in SSR loci. Two strategies were applied to identify SSR variation: polymorphism of SSR tracts longer than 12 bp (L-SSR) assessed by capillary fragment-size analysis and MNR polymorphism assessed by sequencing. The nine L-SSR loci tested were all polymorphic, displaying 2 to 13 alleles per locus. Sequence analysis of eight MNR-containing loci (MNR-multilocus sequence typing [MLST]) provided information on both variations in the MNR tract itself, and single nucleotide polymorphism (SNP) in their flanking sequences. Phylogenetic analysis of the combined SSR data showed a clear discrimination between the clinical strains belonging to O1 and O139 serogroups, and the environmental isolates. Furthermore, discrimination between 27 strains of the 32 strains was achieved. SSR-based typing methods combining L-SSR and MNR-MLST were found to be efficient for V. cholerae typing.
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Affiliation(s)
- Yael Danin-Poleg
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
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44
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Lee JH, Han KH, Choi SY, Lucas MES, Mondlane C, Ansaruzzaman M, Nair GB, Sack DA, von Seidlein L, Clemens JD, Song M, Chun J, Kim DW. Multilocus sequence typing (MLST) analysis of Vibrio cholerae O1 El Tor isolates from Mozambique that harbour the classical CTX prophage. J Med Microbiol 2006; 55:165-170. [PMID: 16434708 DOI: 10.1099/jmm.0.46287-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Vibrio cholerae O1 isolates belonging to the Ogawa serotype, El Tor biotype, harbouring the classical CTX prophage were first isolated in Mozambique in 2004. Multilocus sequence typing (MLST) analysis using nine genetic loci showed that the Mozambique isolates have the same sequence type (ST) as O1 El Tor N16961, a representative of the current seventh cholera pandemic. Analysis of the CTX prophage in the Mozambique isolates indicated that there is one type of rstR in these isolates: the classical CTX prophage. It was also found that the ctxB-rstR-rstA-rstB-phs-cep fragment was PCR-amplified from these isolates, which indicates the presence of a tandem repeat of the classical CTX prophage in the genome of the Mozambique isolates. The possible origin of these isolates and the presence of the tandem repeat of the classical prophage in them implicate the presence of the classical CTX phage.
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Affiliation(s)
- Je Hee Lee
- School of Biological Sciences, Seoul National University, Seoul, 151-742, Republic of Korea
- International Vaccine Institute, San 4-8 Bongcheon 7 dong, Kwanak gu, Seoul, 151-818, Republic of Korea
| | - Kyung Ho Han
- International Vaccine Institute, San 4-8 Bongcheon 7 dong, Kwanak gu, Seoul, 151-818, Republic of Korea
| | - Seon Young Choi
- School of Biological Sciences, Seoul National University, Seoul, 151-742, Republic of Korea
- International Vaccine Institute, San 4-8 Bongcheon 7 dong, Kwanak gu, Seoul, 151-818, Republic of Korea
| | | | - C Mondlane
- Centro De Higiene Ambiental E Exames Medicos, Rua Correia De Brito N° 1815 Sofala - Beira, Mozambique
| | - M Ansaruzzaman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - G Balakrish Nair
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - David A Sack
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Lorenz von Seidlein
- International Vaccine Institute, San 4-8 Bongcheon 7 dong, Kwanak gu, Seoul, 151-818, Republic of Korea
| | - John D Clemens
- International Vaccine Institute, San 4-8 Bongcheon 7 dong, Kwanak gu, Seoul, 151-818, Republic of Korea
| | - Manki Song
- International Vaccine Institute, San 4-8 Bongcheon 7 dong, Kwanak gu, Seoul, 151-818, Republic of Korea
| | - Jongsik Chun
- School of Biological Sciences, Seoul National University, Seoul, 151-742, Republic of Korea
- International Vaccine Institute, San 4-8 Bongcheon 7 dong, Kwanak gu, Seoul, 151-818, Republic of Korea
| | - Dong Wook Kim
- International Vaccine Institute, San 4-8 Bongcheon 7 dong, Kwanak gu, Seoul, 151-818, Republic of Korea
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45
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Deurenberg RH, Vink C, Oudhuis GJ, Mooij JE, Driessen C, Coppens G, Craeghs J, De Brauwer E, Lemmen S, Wagenvoort H, Friedrich AW, Scheres J, Stobberingh EE. Different clonal complexes of methicillin-resistant Staphylococcus aureus are disseminated in the Euregio Meuse-Rhine region. Antimicrob Agents Chemother 2006; 49:4263-71. [PMID: 16189107 PMCID: PMC1251497 DOI: 10.1128/aac.49.10.4263-4271.2005] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Euregio Meuse-Rhine (EMR) is formed by the border regions of Belgium, Germany, and The Netherlands. Cross-border health care requires infection control measures, in particular since the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) differs among the three countries. To investigate the dissemination of MRSA in the EMR, 152 MRSA isolates were characterized by pulsed-field gel electrophoresis (PFGE), SCCmec typing, and multilocus sequence typing. PFGE revealed major clonal groups A, G, L, and Q, suggesting dissemination of MRSA in the EMR. Group A harbored mainly SCCmec type III and sequence types (STs) 239 and 241. The majority of the strains from group G harbored SCCmec type I and ST8 and ST247, whereas most strains from group L carried either SCCmec type IV or type I. Within group L, ST8 and ST228 were found, belonging to clonal complexes 8 and 5, respectively. Most strains from group Q included SCCmec type II and were sequence typed as ST225. Both ST225-MRSA-II and ST241-MRSA-III were novel findings in Germany. In addition, the SCCmec type of two isolates has not been described previously. One strain was classified as SCCmec type III but harbored the pls gene and the dcs region. Another strain was characterized as SCCmec type IV but lacked the dcs region. In addition, one isolate harbored both SCCmec type V and Panton-Valentine leukocidin. Finally, the SCCmec type of the strains was found to be correlated with the antibiotic susceptibility pattern.
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Affiliation(s)
- Ruud H Deurenberg
- Department of Medical Microbiology, Maastricht Infection, University Hospital Maastricht, The Netherlands
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46
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Abstract
We resolved the relationships between 2 pandemic clones of Vibrio cholerae. Using 26 housekeeping genes, we showed that the US Gulf clone, the Australian clone, and 3 El Tor strains isolated before the seventh pandemic were related to the seventh pandemic clone. The sixth pandemic clone was well separated from them.
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Affiliation(s)
- Anna Salim
- University of Sydney, Sydney, New South Wales, Australia
| | - Ruiting Lan
- University of New South Wales, Sydney, New South Wales, Australia
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47
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Bartual SG, Seifert H, Hippler C, Luzon MAD, Wisplinghoff H, Rodríguez-Valera F. Development of a multilocus sequence typing scheme for characterization of clinical isolates of Acinetobacter baumannii. J Clin Microbiol 2005; 43:4382-90. [PMID: 16145081 PMCID: PMC1234098 DOI: 10.1128/jcm.43.9.4382-4390.2005] [Citation(s) in RCA: 477] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In this study a multilocus sequence typing (MLST) scheme for Acinetobacter baumannii was developed and evaluated by using 40 clinical A. baumannii isolates recovered from outbreaks in Spanish and German hospitals during the years 1990 to 2001, as well as isolates from other European hospitals and two DSMZ reference strains of A. baumannii. For comparison, two isolates of Acinetobacter species 13 (sensu Tjernberg and Ursing), two clinical isolates, and three DSMZ strains of A. calcoaceticus (both belonging to the A. calcoaceticus-A. baumannii complex) were also investigated. Primers were designed for conserved regions of housekeeping genes, and 305- to 513-bp internal fragments of seven such genes-gltA, gyrB, gdhB, recA, cpn60, gpi, and rpoD-were sequenced for all strains. The number of alleles at individual loci ranged from 6 to 12, and a total of 20 allelic profiles or sequence types were distinguished among the investigated A. baumannii strains. The MLST data were in high concordance with the epidemiologic typing results generated by pulsed-field gel electrophoresis and amplified fragment length polymorphism fingerprinting. The MLST scheme provides a high level of resolution and an excellent tool for studying the population structure and long-term epidemiology of A. baumannii.
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Affiliation(s)
- Sergio G Bartual
- Division de Microbiologia and Evolutionary Genomics Group, Campus de San Juan, Universidad Miguel Hernandez, San Juan de Alicante, Spain.
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48
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Sukhnanand S, Alcaine S, Warnick LD, Su WL, Hof J, Craver MPJ, McDonough P, Boor KJ, Wiedmann M. DNA sequence-based subtyping and evolutionary analysis of selected Salmonella enterica serotypes. J Clin Microbiol 2005; 43:3688-98. [PMID: 16081897 PMCID: PMC1233967 DOI: 10.1128/jcm.43.8.3688-3698.2005] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
While serotyping and phage typing have been used widely to characterize Salmonella isolates, sensitive subtyping methods that allow for evolutionary analyses are essential for examining Salmonella transmission, ecology, and evolution. A set of 25 Salmonella enterica isolates, representing five clinically relevant serotypes (serotypes Agona, Heidelberg, Schwarzengrund, Typhimurium, and Typhimurium var. Copenhagen) was initially used to develop a multilocus sequence typing (MLST) scheme for Salmonella targeting seven housekeeping and virulence genes (panB, fimA, aceK, mdh, icdA, manB, and spaN). A total of eight MLST types were found among the 25 isolates sequenced. A good correlation between MLST types and Salmonella serotypes was observed; only one serotype Typhimurium var. Copenhagen isolate displayed an MLST type otherwise typical for serotype Typhimurium isolates. Since manB, fimA, and mdh allowed for the highest subtype discrimination among the initial 25 isolates, we chose these three genes to perform DNA sequencing of an additional 41 Salmonella isolates representing a larger diversity of serotypes. This "three-gene sequence typing scheme" allowed discrimination of 25 sequence types (STs) among a total of 66 isolates; STs correlated well with serotypes and allowed within-serotype differentiation for 9 of the 12 serotypes characterized. Phylogenetic analyses showed that serotypes Kentucky and Newport could each be separated into two distinct, statistically well supported evolutionary lineages. Our results show that a three-gene sequence typing scheme allows for accurate serotype prediction and for limited subtype discrimination among clinically relevant serotypes of Salmonella. Three-gene sequence typing also supports the notion that Salmonella serotypes represent both monophyletic and polyphyletic lineages.
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Affiliation(s)
- Sharinne Sukhnanand
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Sam Alcaine
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Lorin D. Warnick
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Wan-Lin Su
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Jessica Hof
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Mary Pat J. Craver
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Patrick McDonough
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Kathryn J. Boor
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Martin Wiedmann
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
- Corresponding author. Mailing address: Department of Food Science, 412 Stocking Hall, Cornell University, Ithaca, NY 14853. Phone: (607) 254-2838. Fax: (607) 254-4868. E-mail:
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49
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Fakhr MK, Nolan LK, Logue CM. Multilocus sequence typing lacks the discriminatory ability of pulsed-field gel electrophoresis for typing Salmonella enterica serovar Typhimurium. J Clin Microbiol 2005; 43:2215-9. [PMID: 15872244 PMCID: PMC1153745 DOI: 10.1128/jcm.43.5.2215-2219.2005] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nontyphoidal salmonellae are among the leading causes of food-borne disease in the United States. Because of the importance of Salmonella enterica in food-borne disease, numerous typing methodologies have been developed. Among the several molecular typing methods, pulsed-field gel electrophoresis (PFGE) is currently considered the "gold standard" technique in typing Salmonella. The aim of this study was to compare the discriminatory power of PFGE to multilocus sequence typing (MLST) in typing Salmonella enterica serovar Typhimurium clinical isolates. A total of 85 Salmonella Typhimurium clinical isolates from cattle were used in this study. PFGE using XbaI was performed on the 85 isolates by the Centers for Disease Control and Prevention method, and data were analyzed using the BioNumerics software package. Fifty PFGE profiles were observed among the isolates, and these grouped into three major clusters. For the MLST analysis, the manB, pduF, glnA, and spaM genes were amplified by PCR from the same 85 isolates. DNA sequencing of these four genes, manB, pduF, glnA, and spaM, showed no genetic diversity among the isolates tested, with a 100% identity in nucleotide sequence. Moreover, the DNA sequences of the aforementioned genes showed 100% identity to the sequence reported in GenBank for the S. enterica serovar Typhimurium LT2 strain. Therefore, MLST, using these genes, lacks the discriminatory power of PFGE for typing Salmonella enterica serovar Typhimurium.
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Affiliation(s)
- Mohamed K Fakhr
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, ND 58105, USA
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Nemoy LL, Kotetishvili M, Tigno J, Keefer-Norris A, Harris AD, Perencevich EN, Johnson JA, Torpey D, Sulakvelidze A, Morris JG, Stine OC. Multilocus sequence typing versus pulsed-field gel electrophoresis for characterization of extended-spectrum beta-lactamase-producing Escherichia coli isolates. J Clin Microbiol 2005; 43:1776-81. [PMID: 15814998 PMCID: PMC1081380 DOI: 10.1128/jcm.43.4.1776-1781.2005] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strains are emerging pathogens. Molecular typing of ESBL-producing E. coli is useful for surveillance purposes, to monitor outbreaks and track nosocomial spread. Although pulsed-field gel electrophoresis (PFGE) is the current "gold standard" for bacterial molecular typing, multilocus sequence typing (MLST) may offer advantages. Forty ESBL-producing E. coli isolates were selected at random from a cohort of intensive care unit patients who had active surveillance perirectal cultures done. PFGE identified 19 unique PFGE types (PT) among the 40 isolates; MLST identified 22 unique sequence types. MLST had greater discriminatory ability than PFGE for ESBL-producing E. coli. Simpson's indices of diversity for PFGE and MLST were 0.895 and 0.956, respectively. There were five clonal complexes (CCs) (isolates with differences of no more than two loci) that each contained multiple PT, but each PT was found in only one CC, indicating genetic consistency within a CC. MLST has clear utility in studies of ESBL-producing E. coli, based on a greater discriminatory ability and reproducibility than PFGE and the ability to a priori define genetically related bacterial strains.
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Affiliation(s)
- Lucia L Nemoy
- Department of Epidemiology and Preventive Medicine, University of Maryland School of Medicine, MSTF Building, Room 9-34, 10 South Pine Street, Baltimore, MD 21201, USA.
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