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Soliani L, Rugna G, Prosperi A, Chiapponi C, Luppi A. Salmonella Infection in Pigs: Disease, Prevalence, and a Link between Swine and Human Health. Pathogens 2023; 12:1267. [PMID: 37887782 PMCID: PMC10610219 DOI: 10.3390/pathogens12101267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
Salmonella is one of the most spread foodborne pathogens worldwide, and Salmonella infections in humans still represent a global health burden. The main source of Salmonella infections in humans is represented by contaminated animal-derived foodstuffs, with pork products being one of the most important players. Salmonella infection in swine is critical not only because it is one of the main causes of economic losses in the pork industry, but also because pigs can be infected by several Salmonella serovars, potentially contaminating the pig meat production chain and thus posing a significant threat to public health globally. As of now, in Europe and in the United States, swine-related Salmonella serovars, e.g., Salmonella Typhimurium and its monophasic variant Salmonella enterica subsp. enterica 1,4,[5],12:i:-, are also frequently associated with human salmonellosis cases. Moreover, multiple outbreaks have been reported in the last few decades which were triggered by the consumption of Salmonella-contaminated pig meat. Throughout the years, changes and evolution across the pork industry may have acted as triggers for new issues and obstacles hindering Salmonella control along the food chain. Gathered evidence reinforces the importance of coordinating control measures and harmonizing monitoring programs for the efficient control of Salmonella in swine. This is necessary in order to manage outbreaks of clinical disease in pigs and also to protect pork consumers by controlling Salmonella subclinical carriage and shedding. This review provides an update on Salmonella infection in pigs, with insights on Salmonella ecology, focusing mainly on Salmonella Choleraesuis, S. Typhimurium, and S. 1,4,[5],12:i:-, and their correlation to human salmonellosis cases. An update on surveillance methods for epidemiological purposes of Salmonella infection in pigs and humans, in a "One Health" approach, will also be reported.
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Affiliation(s)
- Laura Soliani
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna (IZSLER), 25124 Brescia, Italy; (G.R.); (A.P.); (C.C.); (A.L.)
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Ferrari RG, Panzenhagen PHN, Conte-Junior CA. Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking. Front Microbiol 2017; 8:2587. [PMID: 29312260 PMCID: PMC5744012 DOI: 10.3389/fmicb.2017.02587] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/12/2017] [Indexed: 11/13/2022] Open
Abstract
Salmonellosis is one of the most common causes of foodborne infection and a leading cause of human gastroenteritis. Throughout the last decade, Salmonella enterica serotype Typhimurium (ST) has shown an increase report with the simultaneous emergence of multidrug-resistant isolates, as phage type DT104. Therefore, to successfully control this microorganism, it is important to attribute salmonellosis to the exact source. Studies of Salmonella source attribution have been performed to determine the main food/food-production animals involved, toward which, control efforts should be correctly directed. Hence, the election of a ST subtyping method depends on the particular problem that efforts must be directed, the resources and the data available. Generally, before choosing a molecular subtyping, phenotyping approaches such as serotyping, phage typing, and antimicrobial resistance profiling are implemented as a screening of an investigation, and the results are computed using frequency-matching models (i.e., Dutch, Hald and Asymmetric Island models). Actually, due to the advancement of molecular tools as PFGE, MLVA, MLST, CRISPR, and WGS more precise results have been obtained, but even with these technologies, there are still gaps to be elucidated. To address this issue, an important question needs to be answered: what are the currently suitable subtyping methods to source attribute ST. This review presents the most frequently applied subtyping methods used to characterize ST, analyses the major available microbial subtyping attribution models and ponders the use of conventional phenotyping methods, as well as, the most applied genotypic tools in the context of their potential applicability to investigates ST source tracking.
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Affiliation(s)
- Rafaela G. Ferrari
- Molecular and Analytical Laboratory Center, Department of Food Technology, Faculty of Veterinary, Universidade Federal Fluminense, Niterói, Brazil
- Food Science Program, Chemistry Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Pedro H. N. Panzenhagen
- Molecular and Analytical Laboratory Center, Department of Food Technology, Faculty of Veterinary, Universidade Federal Fluminense, Niterói, Brazil
- Food Science Program, Chemistry Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos A. Conte-Junior
- Molecular and Analytical Laboratory Center, Department of Food Technology, Faculty of Veterinary, Universidade Federal Fluminense, Niterói, Brazil
- Food Science Program, Chemistry Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- National Institute of Health Quality Control, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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Peters T, Bertrand S, Björkman JT, Brandal LT, Brown DJ, Erdõsi T, Heck M, Ibrahem S, Johansson K, Kornschober C, Kotila SM, Le Hello S, Lienemann T, Mattheus W, Nielsen EM, Ragimbeau C, Rumore J, Sabol A, Torpdahl M, Trees E, Tuohy A, de Pinna E. Multi-laboratory validation study of multilocus variable-number tandem repeat analysis (MLVA) for Salmonella enterica serovar Enteritidis, 2015. ACTA ACUST UNITED AC 2017; 22:30477. [PMID: 28277220 PMCID: PMC5356433 DOI: 10.2807/1560-7917.es.2017.22.9.30477] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/10/2016] [Indexed: 11/20/2022]
Abstract
Multilocus variable-number tandem repeat analysis (MLVA) is a rapid and reproducible typing method that is an important tool for investigation, as well as detection, of national and multinational outbreaks of a range of food-borne pathogens. Salmonella enterica serovar Enteritidis is the most common Salmonella serovar associated with human salmonellosis in the European Union/European Economic Area and North America. Fourteen laboratories from 13 countries in Europe and North America participated in a validation study for MLVA of S. Enteritidis targeting five loci. Following normalisation of fragment sizes using a set of reference strains, a blinded set of 24 strains with known allele sizes was analysed by each participant. The S. Enteritidis 5-loci MLVA protocol was shown to produce internationally comparable results as more than 90% of the participants reported less than 5% discrepant MLVA profiles. All 14 participating laboratories performed well, even those where experience with this typing method was limited. The raw fragment length data were consistent throughout, and the inter-laboratory validation helped to standardise the conversion of raw data to repeat numbers with at least two countries updating their internal procedures. However, differences in assigned MLVA profiles remain between well-established protocols and should be taken into account when exchanging data.
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Affiliation(s)
| | | | | | | | - Derek J Brown
- Scottish Microbiology Reference Laboratories, Glasgow, United Kingdom
| | - Tímea Erdõsi
- National Center for Epidemiology, Budapest, Hungary
| | - Max Heck
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Salha Ibrahem
- National Institute for Health and Welfare, Helsinki, Finland
| | - Karin Johansson
- European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | | | - Saara M Kotila
- European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | | | - Taru Lienemann
- National Institute for Health and Welfare, Helsinki, Finland
| | | | | | | | | | - Ashley Sabol
- Centers for Disease Control and Prevention, Atlanta, USA
| | | | - Eija Trees
- Centers for Disease Control and Prevention, Atlanta, USA
| | - Alma Tuohy
- University Hospital Galway, Galway, Ireland
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Schjørring S, Niskanen T, Torpdahl M, Björkman JT, Nielsen EM. Evaluation of molecular typing of foodborne pathogens in European reference laboratories from 2012 to 2013. ACTA ACUST UNITED AC 2017; 21:30429. [PMID: 28006653 PMCID: PMC5291138 DOI: 10.2807/1560-7917.es.2016.21.50.30429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 10/05/2016] [Indexed: 11/20/2022]
Abstract
In 2012, the European Centre for Disease Prevention and Control (ECDC) initiated external quality assessment (EQA) schemes for molecular typing including the National Public Health Reference Laboratories in Europe. The overall aim for these EQA schemes was to enhance the European surveillance of food-borne pathogens by evaluating and improving the quality and comparability of molecular typing. The EQAs were organised by Statens Serum Institut (SSI) and included Salmonella enterica subsp. enterica, verocytotoxin-producing Escherichia coli (VTEC) and Listeria monocytogenes. Inter-laboratory comparable pulsed-field gel electrophoresis (PFGE) images were obtained from 10 of 17 of the participating laboratories for Listeria, 15 of 25 for Salmonella, but only nine of 20 for VTEC. Most problems were related to PFGE running conditions and/or incorrect use of image acquisition. Analysis of the gels was done in good accordance with the provided guidelines. Furthermore, we assessed the multilocus variable-number tandem repeat analysis (MLVA) scheme for S. Typhimurium. Of 15 laboratories, nine submitted correct results for all analysed strains, and four had difficulties with one strain only. In conclusion, both PFGE and MLVA are prone to variation in quality, and there is therefore a continuous need for standardisation and validation of laboratory performance for molecular typing methods of food-borne pathogens in the human public health sector.
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Affiliation(s)
- Susanne Schjørring
- Unit of foodborne infections, Department of Microbiology and Infection Control, Statens Serum Institut (SSI), Copenhagen, Denmark.,European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Taina Niskanen
- Food and Waterborne Diseases and Zoonoses Programme, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Mia Torpdahl
- Unit of foodborne infections, Department of Microbiology and Infection Control, Statens Serum Institut (SSI), Copenhagen, Denmark
| | - Jonas T Björkman
- Unit of foodborne infections, Department of Microbiology and Infection Control, Statens Serum Institut (SSI), Copenhagen, Denmark
| | - Eva Møller Nielsen
- Unit of foodborne infections, Department of Microbiology and Infection Control, Statens Serum Institut (SSI), Copenhagen, Denmark
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Salmonella in the pork production chain and its impact on human health in the European Union. Epidemiol Infect 2017; 145:1513-1526. [PMID: 28241896 DOI: 10.1017/s095026881700036x] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Salmonella spp. comprise the second most common food-borne pathogens in the European Union (EU). The role of pigs as carriers of Salmonella has been intensively studied both on farm and at slaughter. Salmonella infection in pigs may cause fever, diarrhoea, prostration and mortality. However, most infected pigs remain healthy carriers, and those infected at the end of the fattening period could pose a threat to human health. Contamination of pig carcasses can occur on the slaughter line, and it is linked to cross-contamination from other carcasses and the presence of Salmonella in the environment. Therefore, Salmonella serovars present on pig carcasses can be different from those detected in the same bathes on the farm. In recent years, S. Typhimurium, S. Derby and S. serotype 4,[5],12:i:- (a monophasic variant of S. Typhimurium) have been the most common serovars to be detected in pigs in EU countries, but S. Rissen, S. Infantis, S. Enteritidis and S. Brandenburg have also been reported. In humans, several cases of salmonellosis have been linked to the consumption of raw or undercooked pork and pork products. Among the main serovars of porcine origin detected in confirmed human cases, S. Typhimurium, the monophasic variant S. 4,[5],12:i:- and S. Derby are certainly the most important.
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A prevalence study ofSalmonellaspp.,Yersiniaspp.,Toxoplasma gondiiand porcine reproductive and respiratory syndrome virus in UK pigs at slaughter. Epidemiol Infect 2015; 144:1538-49. [DOI: 10.1017/s0950268815002794] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
SUMMARYAn abattoir-based study was undertaken between January and May 2013 to estimate the prevalence ofSalmonellaspp. andYersiniaspp. carriage and seroprevalence of antibodies toToxoplasma gondii andporcine reproductive and respiratory syndrome virus (PRRSv) in UK pigs at slaughter. In total, 626 pigs were sampled at 14 abattoirs that together process 80% of the annual UK pig slaughter throughput. Sampling was weighted by abattoir throughput and sampling dates and pig carcasses were randomly selected. Rectal swabs, blood samples, carcass swabs and the whole caecum, tonsils, heart and tongue were collected.Salmonellaspp. was isolated from 30·5% [95% confidence interval (CI) 26·5–34·6] of caecal content samples but only 9·6% (95% CI 7·3–11·9) of carcass swabs, which was significantly lower than in a UK survey in 2006–2007.S.Typhimurium andS.4,[5],12:i:- were the most commonly isolated serovars, followed byS.Derby andS.Bovismorbificans. The prevalence ofYersinia enterocoliticacarriage in tonsils was 28·7% (95% CI 24·8–32·7) whereas carcass contamination was much lower at 1·8% (95% CI 0·7–2·8). The seroprevalence of antibodies toToxoplasma gondiiand PRRSv was 7·4% (95% CI 5·3–9·5) and 58·3% (95% CI 53·1–63·4), respectively. This study provides a comparison to previous abattoir-based prevalence surveys forSalmonellaandYersinia, and the first UK-wide seroprevalence estimates for antibodies toToxoplasmaand PRRSv in pigs at slaughter.
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Wuyts V, Mattheus W, Roosens NHC, Marchal K, Bertrand S, De Keersmaecker SCJ. A multiplex oligonucleotide ligation-PCR as a complementary tool for subtyping of Salmonella Typhimurium. Appl Microbiol Biotechnol 2015. [PMID: 26205523 PMCID: PMC4561068 DOI: 10.1007/s00253-015-6831-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Subtyping below the serovar level is essential for surveillance and outbreak detection and investigation of Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) and its monophasic variant 1,4,[5],12:i:- (S. 1,4,[5],12:i:-), frequent causes of foodborne infections. In an attempt to overcome the intrinsic shortcomings of currently used subtyping techniques, a multiplex oligonucleotide ligation-PCR (MOL-PCR) assay was developed which combines different types of molecular markers in a high-throughput microsphere suspension array. The 52 molecular markers include prophage genes, amplified fragment length polymorphism (AFLP) elements, Salmonella genomic island 1 (SGI1), allantoinase gene allB, MLVA locus STTR10, antibiotic resistance genes, single nucleotide polymorphisms (SNPs) and phase 2 flagellar gene fljB. The in vitro stability of these markers was confirmed in a serial passage experiment. The validation of the MOL-PCR assay for subtyping of S. Typhimurium and S. 1,4,[5],12:i:- on 519 isolates shows that the method is rapid, reproducible, flexible, accessible, easy to use and relatively inexpensive. Additionally, a 100 % typeability and a discriminatory power equivalent to that of phage typing were observed, and epidemiological concordance was assessed on isolates of 2 different outbreaks. Furthermore, a data analysis method is provided so that the MOL-PCR assay allows for objective, computerised data analysis and data interpretation of which the results can be easily exchanged between different laboratories in an international surveillance network.
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Affiliation(s)
- Véronique Wuyts
- Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20 bus 2460, 3001, Leuven, Belgium
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Diffusion and persistence of multidrug resistant Salmonella Typhimurium strains phage type DT120 in southern Italy. BIOMED RESEARCH INTERNATIONAL 2015; 2015:265042. [PMID: 26060815 PMCID: PMC4427771 DOI: 10.1155/2015/265042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 08/29/2014] [Accepted: 09/11/2014] [Indexed: 12/02/2022]
Abstract
Sixty-two multidrug resistant Salmonella enterica serovar Typhimurium strains isolated from 255 clinical strains collected in Southern Italy in 2006–2008 were characterised for antimicrobial resistance genes, pulsotype, and phage type. Most strains (83.9%) were resistant to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline (ACSSuT) encoded in 88.5% by the Salmonella genomic island (SGI1) and in 11.5% by the InH-like integron (blaOXA-30–aadA1) and catA1, sul1, and tet(B) genes. STYMXB.0061 (75%) and DT120 (84.6%) were the prevalent pulsotype and phage type identified in these strains, respectively. Five other resistance patterns were found either in single or in a low number of isolates. The pandemic clone DT104 (ACSSuT encoded by SGI1) has been identified in Italy since 1992, while strains DT120 (ACSSuT encoded by SGI1) have never been previously reported in Italy. In Europe, clinical strains DT120 have been reported from sporadic outbreaks linked to the consumption of pork products. However, none of these strains were STYMXB.0061 and SGI1 positive. The prevalent identification and persistence of DT120 isolates would suggest, in Southern Italy, a phage type shifting of the pandemic DT104 clone pulsotype STYMXB.0061. Additionally, these findings raise epidemiological concern about the potential diffusion of these emerging multidrug resistant (SGI linked) DT120 strains.
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Abstract
Antimicrobial resistance, including multidrug resistance (MDR), is an increasing problem globally. MDR bacteria are frequently detected in humans and animals from both more- and less-developed countries and pose a serious concern for human health. Infections caused by MDR microbes may increase morbidity and mortality and require use of expensive drugs and prolonged hospitalization. Humans may be exposed to MDR pathogens through exposure to environments at health-care facilities and farms, livestock and companion animals, human food, and exposure to other individuals carrying MDR microbes. The Centers for Disease Control and Prevention classifies drug-resistant foodborne bacteria, including Campylobacter, Salmonella Typhi, nontyphoidal salmonellae, and Shigella, as serious threats. MDR bacteria have been detected in both meat and fresh produce. Salmonellae carrying genes coding for resistance to multiple antibiotics have caused numerous foodborne MDR outbreaks. While there is some level of resistance to antimicrobials in environmental bacteria, the widespread use of antibiotics in medicine and agriculture has driven the selection of a great variety of microbes with resistance to multiple antimicrobials. MDR bacteria on meat may have originated in veterinary health-care settings or on farms where animals are given antibiotics in feed or to treat infections. Fresh produce may be contaminated by irrigation or wash water containing MDR bacteria. Livestock, fruits, and vegetables may also be contaminated by food handlers, farmers, and animal caretakers who carry MDR bacteria. All potential sources of MDR bacteria should be considered and strategies devised to reduce their presence in foods. Surveillance studies have documented increasing trends in MDR in many pathogens, although there are a few reports of the decline of certain multidrug pathogens. Better coordination of surveillance programs and strategies for controlling use of antimicrobials need to be implemented in both human and animal medicine and agriculture and in countries around the world.
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Affiliation(s)
- Marjorie E Doyle
- Food Research Institute, University of Wisconsin , Madison, Wisconsin
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Fournier PE, Dubourg G, Raoult D. Clinical detection and characterization of bacterial pathogens in the genomics era. Genome Med 2014; 6:114. [PMID: 25593594 PMCID: PMC4295418 DOI: 10.1186/s13073-014-0114-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The availability of genome sequences obtained using next-generation sequencing (NGS) has revolutionized the field of infectious diseases. Indeed, more than 38,000 bacterial and 5,000 viral genomes have been sequenced to date, including representatives of all significant human pathogens. These tremendous amounts of data have not only enabled advances in fundamental biology, helping to understand the pathogenesis of microorganisms and their genomic evolution, but have also had implications for clinical microbiology. Here, we first review the current achievements of genomics in the development of improved diagnostic tools, including those that are now available in the clinic, such as the design of PCR assays for the detection of microbial pathogens, virulence factors or antibiotic-resistance determinants, or the design of optimized culture media for 'unculturable' pathogens. We then review the applications of genomics to the investigation of outbreaks, either through the design of genotyping assays or the direct sequencing of the causative strains. Finally, we discuss how genomics might change clinical microbiology in the future.
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Affiliation(s)
- Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut hospitalo-universitaire Méditerranée-Infection, Aix-Marseille University, Faculté de Medecine, 27 Blvd Jean Moulin, Marseille, 13385, cedex 5 France
| | - Gregory Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut hospitalo-universitaire Méditerranée-Infection, Aix-Marseille University, Faculté de Medecine, 27 Blvd Jean Moulin, Marseille, 13385, cedex 5 France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut hospitalo-universitaire Méditerranée-Infection, Aix-Marseille University, Faculté de Medecine, 27 Blvd Jean Moulin, Marseille, 13385, cedex 5 France
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Analysis of Salmonella enterica serovar Typhimurium variable-number tandem-repeat data for public health investigation based on measured mutation rates and whole-genome sequence comparisons. J Bacteriol 2014; 196:3036-44. [PMID: 24957617 DOI: 10.1128/jb.01820-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Variable-number tandem repeats (VNTRs) mutate rapidly and can be useful markers for genotyping. While multilocus VNTR analysis (MLVA) is increasingly used in the detection and investigation of food-borne outbreaks caused by Salmonella enterica serovar Typhimurium (S. Typhimurium) and other bacterial pathogens, MLVA data analysis usually relies on simple clustering approaches that may lead to incorrect interpretations. Here, we estimated the rates of copy number change at each of the five loci commonly used for S. Typhimurium MLVA, during in vitro and in vivo passage. We found that loci STTR5, STTR6, and STTR10 changed during passage but STTR3 and STTR9 did not. Relative rates of change were consistent across in vitro and in vivo growth and could be accurately estimated from diversity measures of natural variation observed during large outbreaks. Using a set of 203 isolates from a series of linked outbreaks and whole-genome sequencing of 12 representative isolates, we assessed the accuracy and utility of several alternative methods for analyzing and interpreting S. Typhimurium MLVA data. We show that eBURST analysis was accurate and informative. For construction of MLVA-based trees, a novel distance metric, based on the geometric model of VNTR evolution coupled with locus-specific weights, performed better than the commonly used simple or categorical distance metrics. The data suggest that, for the purpose of identifying potential transmission clusters for further investigation, isolates whose profiles differ at one of the rapidly changing STTR5, STTR6, and STTR10 loci should be collapsed into the same cluster.
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Wuyts V, Mattheus W, De Laminne de Bex G, Wildemauwe C, Roosens NHC, Marchal K, De Keersmaecker SCJ, Bertrand S. MLVA as a tool for public health surveillance of human Salmonella Typhimurium: prospective study in Belgium and evaluation of MLVA loci stability. PLoS One 2013; 8:e84055. [PMID: 24391880 PMCID: PMC3877154 DOI: 10.1371/journal.pone.0084055] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 11/15/2013] [Indexed: 11/19/2022] Open
Abstract
Surveillance of Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is generally considered to benefit from molecular techniques like multiple-locus variable-number of tandem repeats analysis (MLVA), which allow earlier detection and confinement of outbreaks. Here, a surveillance study, including phage typing, antimicrobial susceptibility testing and the in Europe most commonly used 5-loci MLVA on 1,420 S. Typhimurium isolates collected between 2010 and 2012 in Belgium, was used to evaluate the added value of MLVA for public health surveillance. Phage types DT193, DT195, DT120, DT104, DT12 and U302 dominate the Belgian S. Typhimurium population. A combined resistance to ampicillin, streptomycin, sulphonamides and tetracycline (ASSuT) with or without additional resistances was observed for 42.5% of the isolates. 414 different MLVA profiles were detected, of which 14 frequent profiles included 44.4% of the S. Typhimurium population. During a serial passage experiment on selected isolates to investigate the in vitro stability of the 5 MLVA loci, variations over time were observed for loci STTR6, STTR10, STTR5 and STTR9. This study demonstrates that MLVA improves public health surveillance of S. Typhimurium. However, the 5-loci MLVA should be complemented with other subtyping methods for investigation of possible outbreaks with frequent MLVA profiles. Also, variability in these MLVA loci should be taken into account when investigating extended outbreaks and studying dynamics over longer periods.
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Affiliation(s)
- Véronique Wuyts
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIVISP), Brussels, Belgium
| | - Wesley Mattheus
- National Reference Centre for Salmonella and Shigella, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Guillaume De Laminne de Bex
- National Reference Centre for Salmonella and Shigella, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Christa Wildemauwe
- National Reference Centre for Salmonella and Shigella, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Nancy H. C. Roosens
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIVISP), Brussels, Belgium
| | - Kathleen Marchal
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Department of Information Technology, Ghent University, IMinds, Gent, Belgium
| | | | - Sophie Bertrand
- National Reference Centre for Salmonella and Shigella, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
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13
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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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14
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Padmanabhan R, Mishra AK, Raoult D, Fournier PE. Genomics and metagenomics in medical microbiology. J Microbiol Methods 2013; 95:415-24. [PMID: 24200711 DOI: 10.1016/j.mimet.2013.10.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/08/2013] [Accepted: 10/10/2013] [Indexed: 02/06/2023]
Abstract
Over the last two decades, sequencing tools have evolved from laborious time-consuming methodologies to real-time detection and deciphering of genomic DNA. Genome sequencing, especially using next generation sequencing (NGS) has revolutionized the landscape of microbiology and infectious disease. This deluge of sequencing data has not only enabled advances in fundamental biology but also helped improve diagnosis, typing of pathogen, virulence and antibiotic resistance detection, and development of new vaccines and culture media. In addition, NGS also enabled efficient analysis of complex human micro-floras, both commensal, and pathological, through metagenomic methods, thus helping the comprehension and management of human diseases such as obesity. This review summarizes technological advances in genomics and metagenomics relevant to the field of medical microbiology.
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Affiliation(s)
- Roshan Padmanabhan
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Aix-Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, 27 Bd. Jean Moulin, 13005 Marseille, France
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