1
|
Sabol A, Joung YJ, VanTubbergen C, Ale J, Ribot EM, Trees E. Assessment of Genetic Stability During Serial In Vitro Passage and In Vivo Carriage. Foodborne Pathog Dis 2021; 18:894-901. [PMID: 34520233 DOI: 10.1089/fpd.2021.0029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this study, our objective was to evaluate the genetic stability of foodborne bacterial pathogens during serial passage in vitro and persistent in vivo carriage. Six strains of Listeria, Campylobacter, Escherichia, Salmonella, and Vibrio were serially passaged 20 times. Three colonies were picked for whole-genome sequencing (WGS) from passes P0, P5, P10, P15, and P20. In addition, isolates of Salmonella and Escherichia from three patients with persistent infections were sequenced. Genetic stability was evaluated in terms of variations detected in high-quality single-nucleotide polymorphism (hqSNP), core genome multilocus sequence typing (cgMLST), seven-gene MLST, and determinants encoding serotype, antimicrobial resistance (AMR), and virulence. During serial passage, increasing diversity was observed in Listeria, Salmonella, and Vibrio as measured by hqSNPs (from median of 0 SNPs to median of 3-5 SNPs, depending on the organism) and to a lesser extent with cgMLST (from median of 0 alleles to median of 0-5 alleles), while Escherichia and Campylobacter genomes showed minimal variation. The serotype, AMR, and virulence markers remained stable in all organisms. Isolates from persistent infections lasting up to 10 weeks remained genetically stable. However, isolates from a persistent Salmonella enterica ser. Montevideo infection spanning 9 years showed early heterogeneity leading to the emergence of one predominant genotype that continued to evolve over the years, including gains and losses of AMR markers. While the hqSNP and cgMLST variation observed during the serial passage was minimal, culture passages should be limited to as few times as possible before WGS. Our WGS data show that in vivo carriage lasting for a few weeks did not appear to alter the genotype. Longer persistent infections spanning for years, particularly in the presence of selective pressure, may cause changes in the genotype making it challenging to differentiate persistent infections from reinfections.
Collapse
Affiliation(s)
- Ashley Sabol
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yoo Jin Joung
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Jerdie Ale
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Efrain M Ribot
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Eija Trees
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| |
Collapse
|
2
|
Ung A, Baidjoe AY, Van Cauteren D, Fawal N, Fabre L, Guerrisi C, Danis K, Morand A, Donguy MP, Lucas E, Rossignol L, Lefèvre S, Vignaud ML, Cadel-Six S, Lailler R, Jourdan-Da Silva N, Le Hello S. Disentangling a complex nationwide Salmonella Dublin outbreak associated with raw-milk cheese consumption, France, 2015 to 2016. ACTA ACUST UNITED AC 2020; 24. [PMID: 30670140 PMCID: PMC6344836 DOI: 10.2807/1560-7917.es.2019.24.3.1700703] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
On 18 January 2016, the French National Reference Centre for Salmonella reported to Santé publique France an excess of Salmonella enterica serotype Dublin (S. Dublin) infections. We investigated to identify the source of infection and implement control measures. Whole genome sequencing (WGS) and multilocus variable-number tandem repeat analysis (MLVA) were performed to identify microbiological clusters and links among cases, animal and food sources. Clusters were defined as isolates with less than 15 single nucleotide polymorphisms determined by WGS and/or with identical MLVA pattern. We compared different clusters of cases with other cases (case–case study) and controls recruited from a web-based cohort (case–control study) in terms of food consumption. We interviewed 63/83 (76%) cases; 2,914 controls completed a questionnaire. Both studies’ findings indicated that successive S. Dublin outbreaks from different sources had occurred between November 2015 and March 2016. In the case–control study, cases of distinct WGS clusters were more likely to have consumed Morbier (adjusted odds ratio (aOR): 14; 95% confidence interval (CI): 4.8–42) or Vacherin Mont d’Or (aOR: 27; 95% CI: 6.8–105), two bovine raw-milk cheeses. Based on these results, the Ministry of Agriculture launched a reinforced control plan for processing plants of raw-milk cheeses in the production region, to prevent future outbreaks.
Collapse
Affiliation(s)
- Aymeric Ung
- These authors contributed equally to this article and share first authorship.,European Programme for Intervention Epidemiology Training (EPIET), European Centre of Disease Prevention and Control (ECDC), Stockholm, Sweden.,Santé publique France (SpFrance), the French national public health agency, Saint-Maurice, France
| | - Amrish Y Baidjoe
- Institut Pasteur, Enteric Bacterial Pathogens Unit, National Reference Center (NRC) for E. coli, Shigella and Salmonella, Paris, France.,European Programme for Public Health Microbiology Training (EUPHEM), European Centre of Disease Prevention and Control (ECDC), Stockholm, Sweden.,These authors contributed equally to this article and share first authorship
| | - Dieter Van Cauteren
- Santé publique France (SpFrance), the French national public health agency, Saint-Maurice, France
| | - Nizar Fawal
- Institut Pasteur, Enteric Bacterial Pathogens Unit, National Reference Center (NRC) for E. coli, Shigella and Salmonella, Paris, France
| | - Laetitia Fabre
- Institut Pasteur, Enteric Bacterial Pathogens Unit, National Reference Center (NRC) for E. coli, Shigella and Salmonella, Paris, France
| | - Caroline Guerrisi
- Sorbonne Université, UPMC, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Kostas Danis
- European Programme for Intervention Epidemiology Training (EPIET), European Centre of Disease Prevention and Control (ECDC), Stockholm, Sweden.,Santé publique France (SpFrance), the French national public health agency, Saint-Maurice, France
| | - Anne Morand
- French Directorate General for Food (DGAL), Ministry of Agriculture and Food, Paris, France
| | - Marie-Pierre Donguy
- French Directorate General for Food (DGAL), Ministry of Agriculture and Food, Paris, France
| | - Etienne Lucas
- Santé publique France (SpFrance), the French national public health agency, Saint-Maurice, France
| | - Louise Rossignol
- Sorbonne Université, UPMC, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Sophie Lefèvre
- Institut Pasteur, Enteric Bacterial Pathogens Unit, National Reference Center (NRC) for E. coli, Shigella and Salmonella, Paris, France
| | - Marie-Léone Vignaud
- Université Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Sabrina Cadel-Six
- Université Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Renaud Lailler
- Université Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Nathalie Jourdan-Da Silva
- These authors contributed equally to this article and share last authorship.,Santé publique France (SpFrance), the French national public health agency, Saint-Maurice, France
| | - Simon Le Hello
- These authors contributed equally to this article and share last authorship.,Institut Pasteur, Enteric Bacterial Pathogens Unit, National Reference Center (NRC) for E. coli, Shigella and Salmonella, Paris, France
| |
Collapse
|
3
|
Ajayi A, Smith SI, Kalpy JC, Bode-Sojobi IO, René YK, Adeleye AI. Molecular diversity and antibiotic resistance gene profile of Salmonella enterica serovars isolated from humans and food animals in Lagos, Nigeria. Acta Microbiol Immunol Hung 2019; 66:509-527. [PMID: 31658835 DOI: 10.1556/030.66.2019.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Outbreaks of Salmonellosis remain a major public health problem globally. This study determined the diversity and antibiotic resistance gene profile of Salmonella enterica serovars isolated from humans and food animals. Using standard methods, Salmonella spp. were isolated from fecal samples, profiled for antimicrobial susceptibility and resistance genes. Seventy-one Salmonella isolates were recovered from both humans and food animals comprising cattle, sheep, and chicken. Forty-four serovars were identified, with dominant Salmonella Budapest (31.8%). Rare serovars were present in chicken (S. Alfort, S. Wichita, S. Linton, S. Ealing, and S. Ebrie) and humans (S. Mowanjum, S. Huettwillen, S. Limete, and S. Chagoua). Sixty-eight percent of isolates were sensitive to all test antibiotics, while the highest rate of resistance was to nalidixic acid (16.9%; n = 12), followed by ciprofloxacin (11.3%; n = 8) and tetracycline (9.9%; n = 8). Five isolates (7%) were multidrug-resistant and antimicrobial resistance genes coding resistance to tetracycline (tetA), beta-lactam (blaTEM), and quinolone/fluoroquinolone (qnrB and qnrS) were detected. Evolutionary analysis of gyrA gene sequences of human and food animal Salmonella isolates revealed variations but are evolutionarily interconnected. Isolates were grouped into four clades with S. Budapest isolate from cattle clustering with S. Budapest isolated from chicken, whereas S. Essen isolated from sheep and chicken was grouped into a clade. Diverse S. enterica serovars with high antibiotic resistance profile are ubiquitous in food animals; hence, there is a need for surveillance and prudent use of antibiotics in human and veterinary medicine.
Collapse
Affiliation(s)
- Abraham Ajayi
- 1 Department of Microbiology, University of Lagos, Akoka, Nigeria
| | - Stella Ifeanyi Smith
- 2 Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Julien Coulibaly Kalpy
- 3 Laboratoire de Bactériologie et Virologie Institut Pasteur de Côte d’Ivoire, Centre Nationale de Référence de Salmonella, Paris, France
| | | | - Yao Kouamé René
- 3 Laboratoire de Bactériologie et Virologie Institut Pasteur de Côte d’Ivoire, Centre Nationale de Référence de Salmonella, Paris, France
| | | |
Collapse
|
4
|
High similarity and high frequency of virulence genes among Salmonella Dublin strains isolated over a 33-year period in Brazil. Braz J Microbiol 2019; 51:497-509. [PMID: 31701384 DOI: 10.1007/s42770-019-00156-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/07/2019] [Indexed: 12/14/2022] Open
Abstract
Salmonella Dublin is a strongly adapted serovar that causes enteritis and/or systemic disease with high rates of mortality in cattle and occasionally infects humans. Despite the importance of this serovar, there is a lack of studies in Brazil. The aim of this study was to characterize the genetic diversity of 112 S. Dublin strains isolated from humans and animals in Brazil by CRISPR and CRISPR-MVLST and the relatedness among strains by MLST. In addition, the frequency of some important virulence genes was verified. The strains studied belonged to nine different sequence types, being all of them single- or double-locus variants of the ST10. CRISPR discriminated the strains into 69 subtypes with a similarity ≥ 84.4% and CRISPR-MVLST into 72 subtypes with a similarity ≥ 84.7%. The virulence genes ratB, lpfA, mgtC, avrA, sopB, sopE2, sifA, sseA, ssrA, csgA, fliC, and sinH were found in all the strains studied, while spvB, spvC, sodCl, rpoS, sipA, sipD, invA, and hilA were detected in ≥ 93.7% of the strains. In conclusion, the high similarity among the strains reinforces the clonal nature of the strains of this serovar that may have descended from a common ancestor that little differed over 33 years in Brazil. CRISPR and CRISPR-MVLST showed to be good alternatives to type S. Dublin strains. MLST suggested that S. Dublin strains from Brazil were phylogenetically related to strains from other parts of the globe. Moreover, the high frequency of virulence genes among the strains studied reinforces the capacity of S. Dublin to cause invasive diseases.
Collapse
|
5
|
Vilela FP, Frazão MR, Rodrigues DP, Costa RG, Casas MRT, Fernandes SA, Falcão JP, Campioni F. Genetic diversity, anti-microbial resistance, plasmid profile and frequency of the Vi antigen inSalmonellaDublin strains isolated in Brazil. Zoonoses Public Health 2017; 65:e34-e43. [DOI: 10.1111/zph.12407] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Indexed: 12/26/2022]
Affiliation(s)
- F. P. Vilela
- Faculdade de Odontologia de Ribeirão Preto - USP; Ribeirão Preto SP Brasil
| | - M. R. Frazão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas; Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP; Ribeirão Preto SP Brasil
| | | | - R. G. Costa
- Fundação Oswaldo Cruz - FIOCRUZ; Rio de Janeiro RJ Brasil
| | - M. R. T. Casas
- Centro de Bacteriologia; Instituto Adolfo Lutz; São Paulo SP Brasil
| | - S. A. Fernandes
- Centro de Bacteriologia; Instituto Adolfo Lutz; São Paulo SP Brasil
| | - J. P. Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas; Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP; Ribeirão Preto SP Brasil
| | - F. Campioni
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas; Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP; Ribeirão Preto SP Brasil
| |
Collapse
|
6
|
Vignaud ML, Cherchame E, Marault M, Chaing E, Le Hello S, Michel V, Jourdan-Da Silva N, Lailler R, Brisabois A, Cadel-Six S. MLVA for Salmonella enterica subsp. enterica Serovar Dublin: Development of a Method Suitable for Inter-Laboratory Surveillance and Application in the Context of a Raw Milk Cheese Outbreak in France in 2012. Front Microbiol 2017; 8:295. [PMID: 28289408 PMCID: PMC5326744 DOI: 10.3389/fmicb.2017.00295] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/13/2017] [Indexed: 11/17/2022] Open
Abstract
Salmonella enterica subspecies enterica serovar Dublin (S. Dublin) figures among the most frequently isolated Salmonella strains in humans in France. This serovar may affect production and animal health mainly in cattle herds with corresponding high economic losses. Given that the current gold standard method, pulsed-field gel electrophoresis (PFGE), provides insufficient discrimination for epidemiological investigations, we propose a standard operating procedure in this study for multiple-locus variable number tandem repeat analysis (MLVA) of S. Dublin, suitable for inter-laboratory surveillance. An in silico analysis on the genome of S. Dublin strains CT_02021853 was performed to identify appropriate microsatellite regions. Of 21 VNTR loci screened, six were selected and 401 epidemiologically unrelated and related strains, isolated from humans, food and animals were analyzed to assess performance criteria such as typeability, discriminatory power and epidemiological concordance. The MLVA scheme developed was applied to an outbreak involving Saint-Nectaire cheese for which investigations were conducted in France in 2012, making it possible to discriminate between epidemiologically related strains and sporadic case strains, while PFGE assigned only a single profile. The six loci selected were sequenced on a large set of strains to determine the sequence of the repeated units and flanking regions, and their stability was evaluated in vivo through the analysis of the strains investigated from humans, food and the farm environment during the outbreak. The six VNTR selected were found to be stable and the discriminatory power of the MLVA method developed was calculated to be 0.954 compared with that for PFGE, which was only 0.625. Twenty-four reference strains were selected from the 401 examined strains in order to represent most of the allele diversity observed for each locus. This reference set can be used to harmonize MLVA results and allow data exchange between laboratories. This original MLVA protocol could be used easily and routinely for monitoring of serovar Dublin isolates and for conducting outbreak investigations.
Collapse
Affiliation(s)
- Marie-Léone Vignaud
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food SafetyMaisons-Alfort, France
| | - Emeline Cherchame
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food SafetyMaisons-Alfort, France
| | - Muriel Marault
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food SafetyMaisons-Alfort, France
| | - Emilie Chaing
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food SafetyMaisons-Alfort, France
| | - Simon Le Hello
- French National Reference Center for E. coli, Shigella and Salmonella, Institut PasteurParis, France
| | - Valerie Michel
- Department of Dairy Products, Center of Expertise for the Food IndustryLa Roche-sur-Foron, France
| | | | - Renaud Lailler
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food SafetyMaisons-Alfort, France
| | - Anne Brisabois
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food SafetyMaisons-Alfort, France
| | - Sabrina Cadel-Six
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food SafetyMaisons-Alfort, France
| |
Collapse
|
7
|
Kjeldsen MK, Torpdahl M, Pedersen K, Nielsen EM. Development and comparison of a generic multiple-locus variable-number tandem repeat analysis with pulsed-field gel electrophoresis for typing of Salmonella enterica subsp. enterica. J Appl Microbiol 2016; 119:1707-17. [PMID: 26440858 DOI: 10.1111/jam.12965] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/10/2015] [Accepted: 09/17/2015] [Indexed: 11/28/2022]
Abstract
AIMS Salmonella enterica subsp. enterica causes salmonellosis in humans and animals. Serovar-specific multiple-locus variable-number tandem repeat analysis (MLVA) is widely used for Salmonella surveillance; however, isolates have to be serotyped prior to MLVA typing and only the most common serovars can be typed. We developed a MLVA scheme for high-discriminatory typing of Salmonella. METHODS AND RESULTS Sixty-six unique VNTRs were investigated and the polymorphisms of seven promising VNTRs were evaluated with a panel 163 diverse isolates of 14 serotypes of significance for human health. Five VNTRs were selected for MLVA analysis. The discriminatory power was evaluated within serovars by 163 isolates and MLVA yielded 79 genotypes (DI of 0·9790) and pulsed-field gel electrophoresis (PFGE) revealed 87 genotypes (DI of 0·9989). MLVA divided each serotype into 2-8 different profiles and identified six pairs of outbreak-related strains. CONCLUSIONS The technique showed a high-discriminatory power within most serotypes comparable with or better than that of PFGE. SIGNIFICANCE AND IMPACT OF THE STUDY This MLVA assay makes it possible to use a single typing method for Salmonella surveillance and outbreak investigations. This allows inexpensive and fast surveillance for laboratories without resources for both serotyping and molecular typing, e.g. PFGE or sequence-based methods, and thereby improve the effectiveness of epidemiological investigations of Salmonella infections globally.
Collapse
Affiliation(s)
- M K Kjeldsen
- The Unit for Foodborne Infections, Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark.,National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - M Torpdahl
- The Unit for Foodborne Infections, Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - K Pedersen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - E M Nielsen
- The Unit for Foodborne Infections, Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| |
Collapse
|
8
|
Ktari S, Ksibi B, Gharsallah H, Mnif B, Maalej S, Rhimi F, Hammami A. Molecular epidemiological characteristics ofSalmonella entericaserovars Enteritidis, Typhimurium and Livingstone strains isolated in a Tunisian university hospital. APMIS 2015; 124:194-200. [DOI: 10.1111/apm.12484] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/22/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Sonia Ktari
- Laboratory of Microbiology; Faculté de Medecine Sfax; Centre Hospitalier Universitaire Habib Bourguiba; Sfax Tunisia
| | - Boutheina Ksibi
- Laboratory of Microbiology; Faculté de Medecine Sfax; Centre Hospitalier Universitaire Habib Bourguiba; Sfax Tunisia
| | - Houda Gharsallah
- Laboratory of Microbiology; Faculté de Medecine Sfax; Centre Hospitalier Universitaire Habib Bourguiba; Sfax Tunisia
| | - Basma Mnif
- Laboratory of Microbiology; Faculté de Medecine Sfax; Centre Hospitalier Universitaire Habib Bourguiba; Sfax Tunisia
| | - Sonda Maalej
- Laboratory of Microbiology; Faculté de Medecine Sfax; Centre Hospitalier Universitaire Habib Bourguiba; Sfax Tunisia
| | - Fouzia Rhimi
- Laboratory of Microbiology; Faculté de Medecine Sfax; Centre Hospitalier Universitaire Habib Bourguiba; Sfax Tunisia
| | - Adnene Hammami
- Laboratory of Microbiology; Faculté de Medecine Sfax; Centre Hospitalier Universitaire Habib Bourguiba; Sfax Tunisia
| |
Collapse
|
9
|
Whole genome sequencing provides an unambiguous link between Salmonella Dublin outbreak strain and a historical isolate. Epidemiol Infect 2015; 144:576-81. [PMID: 26165314 DOI: 10.1017/s0950268815001636] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Salmonella enterica subsp. enterica serovar Dublin is an uncommon cause of human salmonellosis; however, a relatively high proportion of cases are associated with invasive disease. The serotype is associated with cattle. A geographically diffuse outbreak of S. Dublin involving nine patients occurred in Ireland in 2013. The source of infection was not identified. Typing of outbreak associated isolates by pulsed-field gel electrophoresis (PFGE) was of limited value because PFGE has limited discriminatory power for S. Dublin. Whole genome sequencing (WGS) showed conclusively that the isolates were closely related to each other, to an apparently unrelated isolate from 2011 and distinct from other isolates that were not readily distinguishable by PFGE.
Collapse
|
10
|
Lienemann T, Kyyhkynen A, Halkilahti J, Haukka K, Siitonen A. Characterization of Salmonella Typhimurium isolates from domestically acquired infections in Finland by phage typing, antimicrobial susceptibility testing, PFGE and MLVA. BMC Microbiol 2015; 15:131. [PMID: 26129826 PMCID: PMC4487797 DOI: 10.1186/s12866-015-0467-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 06/17/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salmonella enterica spp. enterica serotype Typhimurium (STM) is the most common agent of domestically acquired salmonellosis in Finland. Subtyping methods which allow the characterization of STM are essential for effective laboratory-based STM surveillance and for recognition of outbreaks. This study describes the diversity of Finnish STM isolates using phage typing, antimicrobial susceptible testing, pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem repeat analysis (MLVA), and compares the discriminatory power and the concordance of these methods. RESULTS A total of 375 sporadic STM isolates were analysed. The isolates were divided into 31 definite phage (DT) types, dominated by DT1 (47 % of the isolates), U277 (9 % of the isolates) and DT104 (8 % of the isolates). Of all the isolates, 62 % were susceptible to all the 12 antimicrobials tested and 11 % were multidrug resistant. Subtyping resulted in 83 different XbaI-PFGE profiles and 111 MLVA types. The three most common XbaI-PFGE profiles (STYM1, STYM7 and STYM8) and one MLVA profile with three single locus variants accounted for 56 % and 49 % of the STM isolates, respectively. The studied isolates showed a genetic similarity of more than 70 % by XbaI-PFGE. In MLVA, 71 % of the isolates lacked STTR6 and 77 % missed STTR10p loci. Nevertheless, the calculated Simpson's diversity index for XbaI-PFGE was 0.829 (95 % CI 0.792-0.865) and for MLVA 0.867 (95 % CI 0.835-0.898). However, the discriminatory power of the 5-loci MLVA varied among the phage types. The highest concordance of the results was found between XbaI-PFGE and phage typing (adjusted Wallace coefficient was 0.833 and adjusted Rand coefficient was 0.627). CONCLUSIONS In general, the calculated discriminatory power was higher for genotyping methods (MLVA and XbaI-PFGE) than for phenotyping methods (phage typing). Overall, comparable diversity indices were calculated for PFGE and MLVA (both DI > 0.8). However, MLVA was phage type dependent providing better discrimination of the most common phage types. Furthermore, 5-loci MLVA was a less laborious method and easier to interpret than XbaI-PFGE. Thus, the laboratory-based surveillance of the Finnish human STM infections has been conducted with a combination of phage typing, antimicrobial susceptibility testing and 5-loci MLVA since January 2014.
Collapse
Affiliation(s)
- Taru Lienemann
- Bacterial Infections Unit, National Institute for Health and Welfare, P.O. BOX 30, 00271, Helsinki, Finland.
| | - Aino Kyyhkynen
- Bacterial Infections Unit, National Institute for Health and Welfare, P.O. BOX 30, 00271, Helsinki, Finland.
| | - Jani Halkilahti
- Bacterial Infections Unit, National Institute for Health and Welfare, P.O. BOX 30, 00271, Helsinki, Finland.
| | - Kaisa Haukka
- Bacterial Infections Unit, National Institute for Health and Welfare, P.O. BOX 30, 00271, Helsinki, Finland.
- Department of Food and Environmental Sciences, Division of Microbiology, University of Helsinki, P.O. BOX 56, 00014, Helsinki, Finland.
| | - Anja Siitonen
- Bacterial Infections Unit, National Institute for Health and Welfare, P.O. BOX 30, 00271, Helsinki, Finland.
| |
Collapse
|
11
|
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.
Collapse
|