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Mateva G, Pedersen K, Sørensen G, Asseva G, Daskalov H, Petrov P, Kantardjiev T, Alexandar I, Löfström C. Use of multiple-locus variable-number of tandem repeats analysis (MLVA) to investigate genetic diversity of Salmonella enterica subsp. enterica serovar Typhimurium isolates from human, food, and veterinary sources. Microbiologyopen 2018; 7:e00528. [PMID: 28836358 PMCID: PMC5822324 DOI: 10.1002/mbo3.528] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/28/2017] [Accepted: 07/04/2017] [Indexed: 11/27/2022] Open
Abstract
Salmonella enterica subspecies enterica serovar Typhimurium is the most common zoonotic pathogen in Bulgaria. To allow efficient outbreak investigations and surveillance in the food chain, accurate and discriminatory methods for typing are needed. This study evaluated the use of multiple-locus variable-number of tandem repeats analysis (MLVA) and compared results with antimicrobial resistance (AMR) determinations for 100 S. Typhimurium strains isolated in Bulgaria during 2008-2012 (50 veterinary/food and 50 human isolates). Results showed that isolates were divided into 80 and 34 groups using MLVA and AMR, respectively. Simpson's index of diversity was determined to 0.994 ± 0.003 and 0.945 ± 0.012. The most frequently encountered MLVA profiles were 3-11-9-NA-211 (n = 5); 3-12-9-NA-211 (n = 3); 3-12-11-21-311 (n = 3); 3-17-10-NA-311 (n = 3); 2-20-9-7-212 (n = 3); and 2-23-NA-NA-111 (n = 3). No clustering of isolates related to susceptibility/resistance to antimicrobials, source of isolation, or year of isolation was observed. Some MLVA types were found in both human and veterinary/food isolates, indicating a possible route of transmission. A majority (83%) of the isolates were found to be resistant against at least one antimicrobial and 44% against ≥4 antimicrobials. Further studies are needed to verify MLVA usefulness over a longer period of time and with more isolates, including outbreak strains.
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Affiliation(s)
- Gergana Mateva
- National Diagnostic Research Veterinary InstituteSofiaBulgaria
| | - Karl Pedersen
- National Veterinary InstituteTechnical University of DenmarkFrederiksberg CDenmark
- National Food InstituteTechnical University of DenmarkSøborgDenmark
| | - Gitte Sørensen
- National Food InstituteTechnical University of DenmarkSøborgDenmark
| | - Galina Asseva
- National Center of Infectious and Parasitic DiseasesSofiaBulgaria
| | - Hristo Daskalov
- National Diagnostic Research Veterinary InstituteSofiaBulgaria
| | - Petar Petrov
- National Center of Infectious and Parasitic DiseasesSofiaBulgaria
| | | | - Irina Alexandar
- Institute of Molecular BiologyBulgarian Academy of SciencesSofiaBulgaria
| | - Charlotta Löfström
- National Food InstituteTechnical University of DenmarkSøborgDenmark
- Agrifood and BioscienceRISE Research Institutes of SwedenLundSweden
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Apablaza P, Brevik ØJ, Mjøs S, Valdebenito S, Ilardi P, Battaglia J, Dalsgaard I, Nylund A. Variable Number of Tandem Repeats (VNTR) analysis of Flavobacterium psychrophilum from salmonids in Chile and Norway. BMC Vet Res 2015; 11:150. [PMID: 26168788 PMCID: PMC4501049 DOI: 10.1186/s12917-015-0469-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 07/06/2015] [Indexed: 11/22/2022] Open
Abstract
Background Flavobacterium psychrophilum causes serious fish diseases such RTFS and BCWD, affecting the aquaculture industry worldwide. Commercial vaccines are not available and control of the disease depends on the use of antibiotics. Reliable methods for detection and identification of different isolates of this bacterium could play an important role in the development of good management strategies. The aim of this study was to identify genetic markers for discrimination between isolates. A selection of eight VNTRs from 53 F. psychrophilum isolates from Norway, Chile, Denmark and Scotland were analyzed. The results were compared with previous work on the same pathogen using MLST for genetic differentiation. Results The VNTR analysis gave a separation between the F. psychrophilum isolates supporting the results of previous MLST work. A higher diversity was found among the Chilean isolates compared to those from Norway, which suggests a more homogenous reservoir in Norway. Transgenerational transmission of F. psychrophilum from other countries, exporting salmon embryos to Chile, may explain the differences in diversity. The same transmission mechanisms could also explain the wide geographical distribution of identical isolates in Norway. But, this could also be a result of movement of smolts and embryos. The selected VNTRs are stable genetic markers and no variation was observed after several passages on agar plates at different temperatures. Conclusions These VNTRs are important additions for genotyping of F. psychrophilum isolates. Future studies on VNTRs of F. psychrophilum should include isolates from more host species from a wider geographical area. To get a more robust genotyping the VNTRs should be used in concert with MLST. Future studies of isolates with high and low virulence should focus on identifying virulence markers using VTNRs and MLST. Electronic supplementary material The online version of this article (doi:10.1186/s12917-015-0469-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patricia Apablaza
- Fish Diseases Research Group, Department of Biology, University of Bergen, P.O. 7803, N-5020, Bergen, Norway.
| | - Øyvind J Brevik
- Fish Diseases Research Group, Department of Biology, University of Bergen, P.O. 7803, N-5020, Bergen, Norway.
| | - Svein Mjøs
- Nofima, Kjerreidviken 16, 5141, Fyllingsdalen, Bergen, Norway.
| | | | - Pedro Ilardi
- Veterquímica, Camino Melipilla 5641, Cerrillos, Santiago, Chile.
| | - Juan Battaglia
- Veterquímica, Camino Melipilla 5641, Cerrillos, Santiago, Chile.
| | - Inger Dalsgaard
- National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark.
| | - Are Nylund
- Fish Diseases Research Group, Department of Biology, University of Bergen, P.O. 7803, N-5020, Bergen, Norway.
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PCR-based detection and molecular characterization of shiga toxin-producing Escherichia coli strains in a routine microbiology laboratory over 16 years. J Clin Microbiol 2014; 52:3156-63. [PMID: 24920783 DOI: 10.1128/jcm.00453-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) is a heterogeneous group of bacteria causing disease ranging from asymptomatic carriage and mild infection to hemolytic uremic syndrome (HUS). Here, we describe patients with STEC infection and characterize the STEC strains detected in our laboratory by use of PCR for stx1, stx2, and eae from 1996 through 2011. Patient information was collected from referral forms and from the Norwegian Surveillance System for Communicable Diseases. STEC isolates were characterized with respect to serogroup or serotype, selected potential virulence genes, and multilocus variable-number tandem-repeat analysis (MLVA) genotype. STEC strains were isolated from 138 (1.09%) of 12,651 patients tested. STEC strains of serogroups O26, O103, O121, O145, and O157 were the most frequent. These serogroups, except non-sorbitol-fermenting O157, were also the most frequent among the 11 patients (all ≤5 years old) who developed HUS. Twenty-four STEC strains were classified as being HUS associated based on an epidemiological link to a HUS case, including an MLVA genotype identical to that of the STEC strain. The age of the patient (≤5 years) and the genes eae and stx2a were significantly associated with HUS-associated STEC (P < 0.05 for each parameter), while stx1 was associated with non-HUS-associated STEC (P < 0.05). All of the potential virulence genes analyzed, except ehxA, were significantly more frequent among HUS-associated than non-HUS-associated strains (P < 0.05 for each gene). However, these genes were also present in some non-HUS-associated STEC strains and could therefore not reliably differentiate between HUS-associated and non-HUS-associated STEC strains.
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Saleh-Lakha S, Allen VG, Li J, Pagotto F, Odumeru J, Taboada E, Lombos M, Tabing KC, Blais B, Ogunremi D, Downing G, Lee S, Gao A, Nadon C, Chen S. Subtyping of a large collection of historical Listeria monocytogenes strains from Ontario, Canada, by an improved multilocus variable-number tandem-repeat analysis (MLVA). Appl Environ Microbiol 2013; 79:6472-80. [PMID: 23956391 PMCID: PMC3811218 DOI: 10.1128/aem.00759-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/06/2013] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes is responsible for severe and often fatal food-borne infections in humans. A collection of 2,421 L. monocytogenes isolates originating from Ontario's food chain between 1993 and 2010, along with Ontario clinical isolates collected from 2004 to 2010, was characterized using an improved multilocus variable-number tandem-repeat analysis (MLVA). The MLVA method was established based on eight primer pairs targeting seven variable-number tandem-repeat (VNTR) loci in two 4-plex fluorescent PCRs. Diversity indices and amplification rates of the individual VNTR loci ranged from 0.38 to 0.92 and from 0.64 to 0.99, respectively. MLVA types and pulsed-field gel electrophoresis (PFGE) patterns were compared using Comparative Partitions analysis involving 336 clinical and 99 food and environmental isolates. The analysis yielded Simpson's diversity index values of 0.998 and 0.992 for MLVA and PFGE, respectively, and adjusted Wallace coefficients of 0.318 when MLVA was used as a primary subtyping method and 0.088 when PFGE was a primary typing method. Statistical data analysis using BioNumerics allowed for identification of at least 8 predominant and persistent L. monocytogenes MLVA types in Ontario's food chain. The MLVA method correctly clustered epidemiologically related outbreak strains and separated unrelated strains in a subset analysis. An MLVA database was established for the 2,421 L. monocytogenes isolates, which allows for comparison of data among historical and new isolates of different sources. The subtyping method coupled with the MLVA database will help in effective monitoring/prevention approaches to identify environmental contamination by pathogenic strains of L. monocytogenes and investigation of outbreaks.
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Affiliation(s)
- S. Saleh-Lakha
- Laboratory Services Division, University of Guelph, Guelph, Ontario, Canada
| | - V. G. Allen
- Public Health Ontario (PHO), Toronto, Ontario, Canada
| | - J. Li
- Laboratory Services Division, University of Guelph, Guelph, Ontario, Canada
| | - F. Pagotto
- Listeriosis Reference Service, Health Canada, Ottawa, Ontario, Canada
| | - J. Odumeru
- Ontario Ministry of the Environment (MOE), Etobicoke, Ontario, Canada
| | - E. Taboada
- Public Health Agency of Canada, Lethbridge, Alberta, Canada
| | - M. Lombos
- Public Health Ontario (PHO), Toronto, Ontario, Canada
| | - K. C. Tabing
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - B. Blais
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - D. Ogunremi
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - G. Downing
- Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA), Guelph, Ontario, Canada
| | - S. Lee
- Laboratory Services Division, University of Guelph, Guelph, Ontario, Canada
| | - A. Gao
- Laboratory Services Division, University of Guelph, Guelph, Ontario, Canada
| | - C. Nadon
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - S. Chen
- Laboratory Services Division, University of Guelph, Guelph, Ontario, Canada
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Zhou K, Aertsen A, Michiels CW. The role of variable DNA tandem repeats in bacterial adaptation. FEMS Microbiol Rev 2013; 38:119-41. [PMID: 23927439 DOI: 10.1111/1574-6976.12036] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/13/2013] [Accepted: 07/26/2013] [Indexed: 01/05/2023] Open
Abstract
DNA tandem repeats (TRs), also designated as satellite DNA, are inter- or intragenic nucleotide sequences that are repeated two or more times in a head-to-tail manner. Because TR tracts are prone to strand-slippage replication and recombination events that cause the TR copy number to increase or decrease, loci containing TRs are hypermutable. An increasing number of examples illustrate that bacteria can exploit this instability of TRs to reversibly shut down or modulate the function of specific genes, allowing them to adapt to changing environments on short evolutionary time scales without an increased overall mutation rate. In this review, we discuss the prevalence and distribution of inter- and intragenic TRs in bacteria and the mechanisms of their instability. In addition, we review evidence demonstrating a role of TR variations in bacterial adaptation strategies, ranging from immune evasion and tissue tropism to the modulation of environmental stress tolerance. Nevertheless, while bioinformatic analysis reveals that most bacterial genomes contain a few up to several dozens of intra- and intergenic TRs, only a small fraction of these have been functionally studied to date.
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Affiliation(s)
- Kai Zhou
- Department of Microbial and Molecular Systems (M²S), Faculty of Bioscience Engineering, Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
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Multiple-locus variable-number tandem-repeat analysis in genotyping Yersinia enterocolitica strains from human and porcine origins. J Clin Microbiol 2013; 51:2154-9. [PMID: 23637293 DOI: 10.1128/jcm.00710-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sporadic and epidemiologically linked Yersinia enterocolitica strains (n = 379) isolated from fecal samples from human patients, tonsil or fecal samples from pigs collected at slaughterhouses, and pork samples collected at meat stores were genotyped using multiple-locus variable-number tandem-repeat analysis (MLVA) with six loci, i.e., V2A, V4, V5, V6, V7, and V9. In total, 312 different MLVA types were found. Similar types were detected (i) in fecal samples collected from human patients over 2 to 3 consecutive years, (ii) in samples from humans and pigs, and (iii) in samples from pigs that originated from the same farms. Among porcine strains, we found farm-specific MLVA profiles. Variations in the numbers of tandem repeats from one to four for variable-number tandem-repeat (VNTR) loci V2A, V5, V6, and V7 were observed within a farm. MLVA was applicable for serotypes O:3, O:5,27, and O:9 and appeared to be a highly discriminating tool for distinguishing sporadic and outbreak-related strains. With long-term use, interpretation of the results became more challenging due to variations in more-discriminating loci, as was observed for strains originating from pig farms. Additionally, we encountered unexpectedly short V2A VNTR fragments and sequenced them. According to the sequencing results, updated guidelines for interpreting V2A VNTR results were prepared.
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Haugum K, Lindstedt BA, Løbersli I, Kapperud G, Brandal LT. Identification of the anti-terminator qO111:H)- gene in Norwegian sorbitol-fermenting Escherichia coli O157:NM. FEMS Microbiol Lett 2012; 329:102-10. [PMID: 22268961 DOI: 10.1111/j.1574-6968.2012.02505.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/10/2012] [Accepted: 01/13/2012] [Indexed: 11/30/2022] Open
Abstract
Sorbitol-fermenting Escherichia coli O157:NM (SF O157) is an emerging pathogen suggested to be more virulent than nonsorbitol-fermenting Escherichia coli O157:H7 (NSF O157). Important virulence factors are the Shiga toxins (stx), encoded by stx1 and/or stx2 located within prophages integrated in the bacterial genome. The stx genes are expressed from p(R) (') as a late protein, and anti-terminator activity from the Q protein is necessary for read through of the late terminator t(R) (') and activation of p(R) (') . We investigated the regulation of stx2(EDL933) expression at the genomic level in 17 Norwegian SF O157. Sequencing of three selected SF O157 strains revealed that the anti-terminator q gene and genes upstream of stx2(EDL933) were identical or similar to the ones observed in the E. coli O111:H- strain AP010960, but different from the ones observed in the NSF O157 strain EDL933 (AE005174). This suggested divergent stx2(EDL933) -encoding bacteriophages between NSF O157 and the SF O157 strains (FR874039-41). Furthermore, different DNA structures were detected in the SF O157 strains, suggesting diversity among bacteriophages also within the SF O157 group. Further investigations are needed to elucidate whether the q(O111:H) (-) gene observed in all our SF O157 contributes to the increased virulence seen in SF O157 compared to NSF O157. An assay for detecting q(O111:H) (-) was developed.
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Affiliation(s)
- Kjersti Haugum
- Department of Foodborne Infections, The Norwegian Institute of Public Health, Oslo, Norway
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