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Utrarachkij F, Nakajima C, Siripanichgon K, Changkaew K, Thongpanich Y, Pornraungwong S, Suthienkul O, Suzuki Y. Genetic diversity and antimicrobial resistance pattern of Salmonella enterica serovar Enteritidis clinical isolates in Thailand. J Infect Chemother 2016; 22:209-15. [PMID: 26860961 DOI: 10.1016/j.jiac.2015.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/16/2015] [Accepted: 12/18/2015] [Indexed: 10/22/2022]
Abstract
OBJECTIVE To trace the history of antimicrobial resistance in Salmonella enterica serovar Enteritidis (S. Enteritidis, SE) circulating in Thailand, we characterised clinical isolates obtained during 2004-2007. METHODS Antimicrobial resistance profiles, multi-locus variable number tandem repeat analysis (MLVA) types and 3 representative virulence determinants (spvA, sodCI and sopE) were established from SE isolates (n = 192) collected from stool and blood of patients throughout Thailand during the period 2004-2007. RESULTS Resistance was found in SE against 10 out of 11 antimicrobials studied. The highest resistance ratios were observed for nalidixic acid (83.2%), ciprofloxacin (51.1%) and ampicillin (50.5%), and 25.5% were multidrug resistant. Based on five polymorphic tandem repeat loci analysis, MLVA identified 20 distinct types with three closely related predominant types. A significant increase of AMP resistance from 2004 to 2006 was strongly correlated with that of a MLVA type, 5-5-11-7-3. CONCLUSION The usage of antimicrobials in human medicine or farm settings might act as selective pressures and cause the spread of resistant strains. Hence, a strict policy on antimicrobial usage needs to be implemented to achieve the control of resistant SE in Thailand.
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Affiliation(s)
- Fuangfa Utrarachkij
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Chie Nakajima
- Division of Bioresources Hokkaido University, Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan
| | - Kanokrat Siripanichgon
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Kanjana Changkaew
- Division of Bioresources Hokkaido University, Research Center for Zoonosis Control, Sapporo, Japan
| | - Yuwanda Thongpanich
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Srirat Pornraungwong
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Orasa Suthienkul
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand.
| | - Yasuhiko Suzuki
- Division of Bioresources Hokkaido University, Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan.
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Chindelevitch L, Colijn C, Moodley P, Wilson D, Cohen T. ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections. PLoS Comput Biol 2016; 12:e1004475. [PMID: 26829497 PMCID: PMC4734664 DOI: 10.1371/journal.pcbi.1004475] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/22/2015] [Indexed: 11/18/2022] Open
Abstract
Genomic tools have revealed genetically diverse pathogens within some hosts. Within-host pathogen diversity, which we refer to as "complex infection", is increasingly recognized as a determinant of treatment outcome for infections like tuberculosis. Complex infection arises through two mechanisms: within-host mutation (which results in clonal heterogeneity) and reinfection (which results in mixed infections). Estimates of the frequency of within-host mutation and reinfection in populations are critical for understanding the natural history of disease. These estimates influence projections of disease trends and effects of interventions. The genotyping technique MLVA (multiple loci variable-number tandem repeats analysis) can identify complex infections, but the current method to distinguish clonal heterogeneity from mixed infections is based on a rather simple rule. Here we describe ClassTR, a method which leverages MLVA information from isolates collected in a population to distinguish mixed infections from clonal heterogeneity. We formulate the resolution of complex infections into their constituent strains as an optimization problem, and show its NP-completeness. We solve it efficiently by using mixed integer linear programming and graph decomposition. Once the complex infections are resolved into their constituent strains, ClassTR probabilistically classifies isolates as clonally heterogeneous or mixed by using a model of tandem repeat evolution. We first compare ClassTR with the standard rule-based classification on 100 simulated datasets. ClassTR outperforms the standard method, improving classification accuracy from 48% to 80%. We then apply ClassTR to a sample of 436 strains collected from tuberculosis patients in a South African community, of which 92 had complex infections. We find that ClassTR assigns an alternate classification to 18 of the 92 complex infections, suggesting important differences in practice. By explicitly modeling tandem repeat evolution, ClassTR helps to improve our understanding of the mechanisms driving within-host diversity of pathogens like Mycobacterium tuberculosis.
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Affiliation(s)
- Leonid Chindelevitch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- * E-mail:
| | - Caroline Colijn
- Department of Mathematics, Imperial College, London, United Kingdom
| | - Prashini Moodley
- School of Laboratory Medicine and Medical Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Douglas Wilson
- Department of Medicine, Edendale Hospital, Pietermaritzberg, South Africa
- Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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Muellner P, Stärk KDC, Dufour S, Zadoks RN. ‘Next-Generation’ Surveillance: An Epidemiologists’ Perspective on the Use of Molecular Information in Food Safety and Animal Health Decision-Making. Zoonoses Public Health 2015; 63:351-7. [DOI: 10.1111/zph.12230] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Indexed: 01/01/2023]
Affiliation(s)
- P. Muellner
- Epi-interactive; Miramar Wellington New Zealand
- Epi-interactive; Eppingen Germany
| | - K. D. C. Stärk
- Royal Veterinary College; North Mymms UK
- SAFOSO AG; Bern Switzerland
| | - S. Dufour
- Faculté de médecine vétérinaire; Université de Montréal; St-Hyacinthe QC Canada
- Canadian Bovine Mastitis Research Network; St-Hyacinthe QC Canada
| | - R. N. Zadoks
- Institute for Biodiversity, Animal Health and Comparative Medicine; College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow UK
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Hotchkiss EJ, Gilray JA, Brennan ML, Christley RM, Morrison LJ, Jonsson NN, Innes EA, Katzer F. Development of a framework for genotyping bovine-derived Cryptosporidium parvum, using a multilocus fragment typing tool. Parasit Vectors 2015; 8:500. [PMID: 26427625 PMCID: PMC4591062 DOI: 10.1186/s13071-015-1107-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 09/22/2015] [Indexed: 11/23/2022] Open
Abstract
Background There is a need for an integrated genotyping approach for C. parvum; no sufficiently discriminatory scheme to date has been fully validated or widely adopted by veterinary or public health researchers. Multilocus fragment typing (MLFT) can provide good differentiation and is relatively quick and cheap to perform. A MLFT tool was assessed in terms of its typeability, specificity, precision (repeatability and reproducibility), accuracy and ability to genotypically discriminate bovine-derived Cryptosporidium parvum. Methods With the aim of working towards a consensus, six markers were selected for inclusion based on their successful application in previous studies: MM5, MM18, MM19, TP14, MS1 and MS9. Alleles were assigned according to the fragment sizes of repeat regions amplified, as determined by capillary electrophoresis. In addition, a region of the GP60 gene was amplified and sequenced to determine gp60 subtype and this was added to the allelic profiles of the 6 markers to determine the multilocus genotype (MLG). The MLFT tool was applied to 140 C. parvum samples collected in two cross-sectional studies of UK calves, conducted in Cheshire in 2004 (principally dairy animals) and Aberdeenshire/Caithness in 2011 (beef animals). Results Typeability was 84 %. The primers did not amplify tested non-parvum species frequently detected in cattle. In terms of repeatability, within- and between-run fragment sizes showed little variability. Between laboratories, fragment sizes differed but allele calling was reproducible. The MLFT had good discriminatory ability (Simpson’s Index of Diversity, SID, was 0.92), compared to gp60 sequencing alone (SID 0.44). Some markers were more informative than others, with MS1 and MS9 proving monoallelic in tested samples. Conclusions Further inter-laboratory trials are now warranted with the inclusion of human-derived C. parvum samples, allowing progress towards an integrated, standardised typing scheme to enable source attribution and to determine the role of livestock in future outbreaks of human C. parvum.
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Affiliation(s)
- Emily J Hotchkiss
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, EH26 0PZ, UK.
| | - Janice A Gilray
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, EH26 0PZ, UK.
| | - Marnie L Brennan
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.
| | - Robert M Christley
- Institute of Infection and Global Health, University of Liverpool, NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Leahurst Campus CH64 7TE, Liverpool, L69 7BE, UK.
| | - Liam J Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Nicholas N Jonsson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK.
| | - Elizabeth A Innes
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, EH26 0PZ, UK.
| | - Frank Katzer
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, EH26 0PZ, UK.
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Chalker VJ, Pereyre S, Dumke R, Winchell J, Khosla P, Sun H, Yan C, Vink C, Bébéar C. International Mycoplasma pneumoniae typing study: interpretation of M. pneumoniae multilocus variable-number tandem-repeat analysis. New Microbes New Infect 2015; 7:37-40. [PMID: 26236493 PMCID: PMC4501435 DOI: 10.1016/j.nmni.2015.05.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/05/2015] [Accepted: 05/15/2015] [Indexed: 10/29/2022] Open
Abstract
Typing of Mycoplasma pneumoniae by multiple-locus variable-number tandem repeat analysis (MLVA) is increasingly in use. However, no specific internationally agreed guidance is available. Thirty M. pneumoniae DNA samples including serial dilutions of a type strain were sent to six international laboratories to perform MLVA and results were compared. Good correlation was observed, indicating that this methodology can be robustly performed in multiple sites. However, differences due to interpretation of fragment size, repeat sequence identification and repeat numbering led to inconsistency in the final profiles assigned by laboratories. We propose guidelines for interpreting M. pneumoniae MLVA typing and assigning the number of repeats.
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Affiliation(s)
| | - S Pereyre
- USC EA 3671 Mycoplasmal and Chlamydial Infections in Humans, University of Bordeaux, France ; USC EA 3671 Mycoplasmal and Chlamydial Infections in Humans, Institut National de la Recherche Agronomique, Bordeaux, France
| | - R Dumke
- TU Dresden, Medical Faculty Carl Gustav Carus, Institute of Medical Microbiology and Hygiene, Dresden, Germany
| | - J Winchell
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - P Khosla
- Public Health England Colindale, London, UK
| | - H Sun
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - C Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - C Vink
- Erasmus MC-Sophia Children's Hospital, Laboratory of Pediatrics, Rotterdam, The Netherlands
| | - C Bébéar
- USC EA 3671 Mycoplasmal and Chlamydial Infections in Humans, University of Bordeaux, France ; USC EA 3671 Mycoplasmal and Chlamydial Infections in Humans, Institut National de la Recherche Agronomique, Bordeaux, France
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Becker CAM, Thibault FM, Arcangioli MA, Tardy F. Loss of diversity within Mycoplasma bovis isolates collected in France from bovines with respiratory diseases over the last 35 years. INFECTION GENETICS AND EVOLUTION 2015; 33:118-26. [PMID: 25913158 DOI: 10.1016/j.meegid.2015.04.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 11/18/2022]
Abstract
Mycoplasma (M.) bovis has recently emerged as a major, worldwide etiological agent of bovine respiratory diseases leading to huge economic losses mainly due to high morbidity and mortality as well as poor growth rates. The spread of M. bovis infections between different animals, herds, regions or countries has been often reported to be connected to the movement of animals. However, despite recent considerable efforts, no universal subtyping method is yet available to trace M. bovis isolates circulation at an international scale. Moreover in France, the overall population diversity of M. bovis isolates has not been assessed since the early 1990s. This study was conducted to fill in these gaps. The genotypic diversity between sixty isolates collected in France over the last 35 years was assessed using two molecular subtyping methods that addressed either the long-term epidemiological relationships (Multi Locus Sequence Typing, MLST) or the genetic microvariations (Multiple Locus VNTR Analysis, MLVA) between isolates. Phenotypic diversity was also analyzed by using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) to compare the main protein patterns of isolates. All proposed subtyping approaches were optimized and led to the same pattern in the French M. bovis population that consisted of two clusters, the first one comprising isolates collected before 2000 and the second, those collected after 2000. Recent strains were further shown to be more homogeneous than older ones, which is consistent with the spread of a single clone throughout the country. Because this spread was concomitant with the emergence of multiresistant M. bovis isolates, several hypotheses are discussed to explain the homogeneity of M. bovis isolates in France, even though the M. bovis species is fully equipped to generate diversity.
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Affiliation(s)
- Claire A M Becker
- Université de Lyon, VetAgro Sup, UMR Mycoplasmoses des Ruminants, F-69280 Marcy l'Etoile, France; Anses, Laboratoire de Lyon, UMR Mycoplasmoses des Ruminants, F-69364 Lyon Cedex 07, France.
| | - François M Thibault
- Institut de Recherche Biomédicale des Armées, HIA Desgenettes, F-69275 Lyon Cedex 03, France.
| | - Marie-Anne Arcangioli
- Université de Lyon, VetAgro Sup, UMR Mycoplasmoses des Ruminants, F-69280 Marcy l'Etoile, France; Anses, Laboratoire de Lyon, UMR Mycoplasmoses des Ruminants, F-69364 Lyon Cedex 07, France.
| | - Florence Tardy
- Anses, Laboratoire de Lyon, UMR Mycoplasmoses des Ruminants, F-69364 Lyon Cedex 07, France; Université de Lyon, VetAgro Sup, UMR Mycoplasmoses des Ruminants, F-69280 Marcy l'Etoile, France.
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Papadopoulou E, Gale N, Goodchild SA, Cleary DW, Weller SA, Brown T, Bartlett PN. Strain discrimination of Yersinia pestis using a SERS-based electrochemically driven melting curve analysis of variable number tandem repeat sequences. Chem Sci 2015; 6:1846-1852. [PMID: 29449917 PMCID: PMC5701729 DOI: 10.1039/c4sc03084b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/23/2014] [Indexed: 12/05/2022] Open
Abstract
Strain discrimination within genetically highly similar bacteria is critical for epidemiological studies and forensic applications. An electrochemically driven melting curve analysis monitored by SERS has been utilised to reliably discriminate strains of the bacterial pathogen Yersinia pestis, the causative agent of plague. DNA amplicons containing Variable Number Tandem Repeats (VNTRs) were generated from three strains of Y. pestis: CO92, Harbin 35 and Kim. These amplicons contained a 10 base pair VNTR repeated 6, 5, and 4 times in CO92, Harbin 35 and Kim respectively. The assay also included a blocker oligonucleotide comprising 3 repeats of the 10-mer VNTR sequence. The use of the blocker reduced the effective length of the target sequence available to bind to the surface bound probe and significantly improved the sensitivity of the discrimination. The results were consistent during three replicates that were carried out on different days, using different batches of PCR product and different SERS sphere segment void (SSV) substrate. This methodology which combines low cost, speed and sensitivity is a promising alternative to the time consuming current electrophoretic methods.
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Affiliation(s)
- E Papadopoulou
- Chemistry , University of Southampton , Highfield , Southampton SO17 1BJ , UK .
| | - N Gale
- ATDBio Ltd , Chemistry , University of Southampton , Highfield , Southampton SO17 1BJ , UK
| | - S A Goodchild
- DSTL , Wiltshire SP4 0JQ , Salisbury , Porton Down , UK
| | - D W Cleary
- DSTL , Wiltshire SP4 0JQ , Salisbury , Porton Down , UK
| | - S A Weller
- DSTL , Wiltshire SP4 0JQ , Salisbury , Porton Down , UK
| | - T Brown
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , Oxford OX1 3TA , UK
| | - P N Bartlett
- Chemistry , University of Southampton , Highfield , Southampton SO17 1BJ , UK .
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Bertrand S, De Lamine de Bex G, Wildemauwe C, Lunguya O, Phoba MF, Ley B, Jacobs J, Vanhoof R, Mattheus W. Multi locus variable-number tandem repeat (MLVA) typing tools improved the surveillance of Salmonella enteritidis: a 6 years retrospective study. PLoS One 2015; 10:e0117950. [PMID: 25693200 PMCID: PMC4334661 DOI: 10.1371/journal.pone.0117950] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 01/05/2015] [Indexed: 11/18/2022] Open
Abstract
Surveillance of Salmonella enterica subsp. enterica serovar Enteritidis is generally considered to benefit from molecular techniques like multiple-locus variable-number of tandem repeats analysis (MLVA), which allow early detection and confinement of outbreaks. Here, a surveillance study, including phage typing, antimicrobial susceptibility testing and MLVA on 1,535 S. Enteritidis isolates collected between 2007 and 2012, was used to evaluate the added value of MLVA for public health surveillance in Belgium. Phage types PT4, PT8, PT21, PT1, PT6, PT14b, PT28 and PT13 dominate the Belgian S. Enteritidis population. The isolates of S. Enteritidis were most frequently susceptible to all antibiotics tested. 172 different MLVA profiles were detected, of which 9 frequent profiles included 67.2% of the S. Enteritidis population. During a serial passage experiment on selected isolates to investigate the in vitro stability of the 5 MLVA loci, no variations over time were observed indicating that the MLVA profiles were stable. The MLVA profile of isolates originating from different outbreaks in the Democratic Republic of the Congo (DRC) between 2010 and 2011 were distinct from any of the MLVA profiles found in Belgian isolates throughout the six year observational period and demonstrates that MLVA improves public health surveillance of S. Enteritidis. However, MLVA should be complemented with other subtyping methods when investigating outbreaks is caused by the most common MLVA profile.
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Affiliation(s)
- Sophie Bertrand
- National Reference Centre for Salmonellas, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
- * E-mail:
| | - Guillaume De Lamine de Bex
- National Reference Centre for Salmonellas, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Christa Wildemauwe
- National Reference Centre for Salmonellas, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Octavie Lunguya
- Department of Clinical Microbiology, National Institute for Biomedical Research, Kinshasa, The Democratic Republic of Congo
| | - Marie France Phoba
- Department of Clinical Microbiology, National Institute for Biomedical Research, Kinshasa, The Democratic Republic of Congo
| | - Benedikt Ley
- Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Jan Jacobs
- Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Department of Microbiology and Immunology, Faculty of Medicine, University of Leuven, Belgium
| | - Raymond Vanhoof
- National Reference Centre for Salmonellas, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Wesley Mattheus
- National Reference Centre for Salmonellas, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
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Molecular epidemiology of cases of Mycoplasma californicum infection in Japan. Appl Environ Microbiol 2014; 80:7717-24. [PMID: 25281385 DOI: 10.1128/aem.02488-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bovine mastitis due to Mycoplasma californicum is often accompanied by huge economic losses, and the disease spreads very quickly. An appropriate molecular epidemiological analysis is needed to prevent and control infectious disease, but molecular epidemiological analysis methods for M. californicum have not yet been reported. Here we developed a combination of multiple-locus variable-number tandem repeat analysis (MLVA) and pulsed-field gel electrophoresis (PFGE) methods, which are common genotyping methods for various bacteria, for M. californicum. The MLVA is based on four interspersed repeat units that were found in the M. californicum genome data. The MLVA using these repeat units showed sufficient discriminatory power for a molecular epidemiological analysis; i.e., a Hunter-Gaston diversity index (HGDI) of 0.949, against M. californicum strains in Japan and M. californicum strain ATCC 33461. The PFGE for M. californicum also showed sufficient discriminatory power, with an HGDI of 0.985. Strain ATCC 33461 showed MLVA profiles and pulsotypes that differed greatly from those of strains from Japan. These results indicate that MLVA and PFGE are good tools for identifying M. californicum transmission events more accurately. Our combined MLVA and PFGE analysis suggests the persistence of M. californicum infection among herds in a specific area for a long period of time, as well as the movement of cows and heifers accompanying the expansion of M. californicum infection. Failure to identify asymptomatic infected cows is suspected as one of the central causes of the present M. californicum infection scenario in Japan.
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Inter-laboratory comparison of multi-locus variable-number tandem repeat analysis (MLVA) for verocytotoxin-producing Escherichia coli O157 to facilitate data sharing. Epidemiol Infect 2014; 143:104-7. [PMID: 24703302 DOI: 10.1017/s0950268814000739] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Multi-locus variable number tandem repeat analysis (MLVA) is used in clinical and reference laboratories for subtyping verocytotoxin-producing Escherichia coli O157 (VTEC O157). However, as yet there is no common allelic or profile nomenclature to enable laboratories to easily compare data. In this study, we carried out an inter-laboratory comparison of an eight-loci MLVA scheme using a set of 67 isolates of VTEC O157. We found all but two isolates were identical in profile in the two laboratories, and repeat units were homogeneous in size but some were incomplete. A subset of the isolates (n = 17) were sequenced to determine the actual copy number of representative alleles, thereby enabling alleles to be named according to international consensus guidelines. This work has enabled us to realize the potential of MLVA as a portable, highly discriminatory and convenient subtyping method.
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Scientific Opinion on the evaluation of molecular typing methods for major food‐borne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance: Part 1 (evaluation of methods and applications). EFSA J 2013. [DOI: 10.2903/j.efsa.2013.3502] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Eurosurveillance editorial team. Note from the editors: Consensus paper on MLVA development, validation, nomenclature and quality control – an important step forward for molecular typing-based surveillance and outbreak investigation. Euro Surveill 2013. [DOI: 10.2807/1560-7917.es2013.18.35.20570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Larsson JT, Torpdahl M, Møller Nielsen E. Proof-of-concept study for successful inter-laboratory comparison of MLVA results. ACTA ACUST UNITED AC 2013; 18:20566. [PMID: 24008232 DOI: 10.2807/1560-7917.es2013.18.35.20566] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Multiple-locus variable-number of tandem repeats analysis (MLVA) is widely used for typing of pathogens. Methods such as MLVA based on determining DNA fragment size by the use of capillary electrophoresis have an inherent problem as a considerable offset between measured and real (sequenced) lengths is commonly observed. This discrepancy arises from variation within the laboratory set-up used for fragment analysis. To obtain comparable results between laboratories using different set-ups, some form of calibration is a necessity. A simple approach is to use a set of calibration strains with known allele sizes and determine what compensation factors need to be applied under the chosen set-up conditions in order to obtain the correct allele sizes. We present here a proof-of-concept study showing that using such a set of calibration strains makes inter-laboratory comparison possible. In this study, 20 international laboratories analysed 15 test strains using a five-locus Salmonella enterica serovar Typhimurium MLVA scheme. When using compensation factors derived from a calibration set of 33 isolates, 99.4% (1,461/1,470) of the MLVA alleles of the test strains were assigned correctly, compared with 64.8% (952/1,470) without any compensation. After final analysis, 97.3% (286/294) of the test strains were assigned correct MLVA profiles. We therefore recommend this concept for obtaining comparable MLVA results.
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