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Andrews N, McCabe E, Wall P, Buckley JF, Fanning S. Validating the Utility of Multilocus Variable Number Tandem-repeat Analysis (MLVA) as a Subtyping Strategy to Monitor Listeria monocytogenes In-built Food Processing Environments. J Food Prot 2023; 86:100147. [PMID: 37619693 DOI: 10.1016/j.jfp.2023.100147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Listeria monocytogenes is a serious human pathogen and an enduring challenge to control for the ready-to-eat food processing industry. Cost-effective tools that can be deployed by commercial or in-house laboratories to rapidly investigate and resolve contamination events in the built food processing environment are of value to the food industry. Multilocus variable number tandem-repeat analysis (MLVA) is a molecular subtyping method, which along with other same-generation methods such as pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) is being superseded in disease tracking and outbreak investigations by whole-genome sequencing (WGS). In this paper, it is demonstrated that MLVA can continue to play a valuable role as a valid, fast, simple, and cost-effective method to identify and track Listeria monocytogenes subtypes in factory environments, with the method being highly congruent with MLST. Although MLVA does not have the discriminatory power of WGS to identify truly persistent clones, with careful interpretation of results alongside isolate metadata, it remains a powerful tool in situations and locations where WGS may not be readily available to food business operators.
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Affiliation(s)
- Nicholas Andrews
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Evonne McCabe
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Patrick Wall
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - James F Buckley
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland; Institute for Global Food Security, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT5 6AG, United Kingdom.
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Wu Y, Yu Y, Hua L, Wei Y, Gan Y, Chenia HY, Wang Y, Xie X, Wang J, Liu M, Shao G, Xiong Q, Feng Z. Genotyping and biofilm formation of Mycoplasma hyopneumoniae and their association with virulence. Vet Res 2022; 53:95. [PMCID: PMC9673451 DOI: 10.1186/s13567-022-01109-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/13/2022] [Indexed: 11/19/2022] Open
Abstract
AbstractMycoplasma hyopneumoniae, the causative agent of swine respiratory disease, demonstrates differences in virulence. However, factors associated with this variation remain unknown. We herein evaluated the association between differences in virulence and genotypes as well as phenotype (i.e., biofilm formation ability). Strains 168 L, RM48, XLW-2, and J show low virulence and strains 232, 7448, 7422, 168, NJ, and LH show high virulence, as determined through animal challenge experiments, complemented with in vitro tracheal mucosa infection tests. These 10 strains with known virulence were then subjected to classification via multilocus sequence typing (MLST) with three housekeeping genes, P146-based genotyping, and multilocus variable-number tandem-repeat analysis (MLVA) of 13 loci. MLST and P146-based genotyping identified 168, 168 L, NJ, and RM48 as the same type and clustered them in a single branch. MLVA assigned a different sequence type to each strain. Simpson’s index of diversity indicates a higher discriminatory ability for MLVA. However, no statistically significant correlation was found between genotypes and virulence. Furthermore, we investigated the correlation between virulence and biofilm formation ability. The strains showing high virulence demonstrate strong biofilm formation ability, while attenuated strains show low biofilm formation ability. Pearson correlation analysis revealed a significant positive correlation between biofilm formation ability and virulence. To conclude, there was no association between virulence and our genotyping data, but virulence was found to be significantly associated with the biofilm formation ability of M. hyopneumoniae.
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Dangel A, Berger A, Messelhäußer U, Konrad R, Hörmansdorfer S, Ackermann N, Sing A. Genetic diversity and delineation of Salmonella Agona outbreak strains by next generation sequencing, Bavaria, Germany, 1993 to 2018. ACTA ACUST UNITED AC 2020; 24. [PMID: 31064635 PMCID: PMC6505185 DOI: 10.2807/1560-7917.es.2019.24.18.1800303] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background In 2017, a food-borne Salmonella Agona outbreak caused by infant milk products from a French supplier occurred in Europe. Simultaneously, S. Agona was detected in animal feed samples in Bavaria. Aim Using next generation sequencing (NGS) and three data analysis methods, this study’s objectives were to verify clonality of the Bavarian feed strains, rule out their connection to the outbreak, explore the genetic diversity of Bavarian S. Agona isolates from 1993 to 2018 and compare the analysis approaches employed, for practicality and ability to delineate outbreaks caused by the genetically monomorphic Agona serovar. Methods In this observational retrospective study, three 2017 Bavarian feed isolates were compared to a French outbreak isolate and 48 S. Agona isolates from our strain collections. The later included human, food, feed, veterinary and environmental isolates, of which 28 were epidemiologically outbreak related. All isolates were subjected to NGS and analysed by: (i) a publicly available species-specific core genome multilocus sequence typing (cgMLST) scheme, (ii) single nucleotide polymorphism phylogeny and (iii) an in-house serovar-specific cgMLST scheme. Using additional international S. Agona outbreak NGS data, the cluster resolution capacity of the two cgMLST schemes was assessed. Results We could prove clonality of the feed isolates and exclude their relation to the French outbreak. All approaches confirmed former Bavarian epidemiological clusters. Conclusion Even for S. Agona, species-level cgMLST can produce reasonable resolution, being standardisable by public health laboratories. For single samples or homogeneous sample sets, higher resolution by serovar-specific cgMLST or SNP genotyping can facilitate outbreak investigations.
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Affiliation(s)
- Alexandra Dangel
- These authors contributed equally to this article.,Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | - Anja Berger
- These authors contributed equally to this article.,Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | - Ute Messelhäußer
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | - Regina Konrad
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | | | - Nikolaus Ackermann
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | - Andreas Sing
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
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Di Marcantonio L, Janowicz A, Zilli K, Romantini R, Bilei S, Paganico D, Persiani T, Di Donato G, Di Giannatale E. Genomic Comparison of Salmonella Enteritidis Strains Isolated from Laying Hens and Humans in the Abruzzi Region during 2018. Pathogens 2020; 9:E349. [PMID: 32380662 PMCID: PMC7281747 DOI: 10.3390/pathogens9050349] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/29/2020] [Accepted: 05/01/2020] [Indexed: 11/16/2022] Open
Abstract
Salmonellosis is a major cause of bacterial foodborne infection. Since 2016, an increased number of cases of gastroenteritis caused by Salmonella enterica serovar Enteritidis linked to eggs produced in Poland has been reported in Europe. In Italy, S. Enteritidis is one of the three most commonly reported serotypes, associated mainly with the consumption of contaminated eggs and derived products. In our work, we analysed 61 strains of S. Enteritidis obtained from humans and farms in the Abruzzi region, Italy, in 2018. We used Multiple-Loci Variable-Number Tandem Repeat (VNTR) analysis (MLVA)-based typing and Whole-Genome Sequencing (WGS) tools to identify closely related strains and perform cluster analysis. We found two clusters of genetically similar strains. The first one was present in the local farms and isolated from human cases and had single-linkage distance of no more than two core genes and less than five Single-Nucleotide Polymorphisms (SNPs). The second cluster contained strains isolated from humans and from a dessert (tiramisù) sample that shared identical core genome and were assigned the same SNP address. Cluster 2 isolates were found to be genetically similar to an S. Enteritidis strain from a multi-country outbreak linked to Polish eggs.
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Affiliation(s)
- Lisa Di Marcantonio
- Bacteriology and Diary Production Hygiene department, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise ‘G. Caporale’, Campo Boario, 64100 Teramo, Italy; (A.J.); (K.Z.); (R.R.); (D.P.); (T.P.); (E.D.G.)
| | - Anna Janowicz
- Bacteriology and Diary Production Hygiene department, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise ‘G. Caporale’, Campo Boario, 64100 Teramo, Italy; (A.J.); (K.Z.); (R.R.); (D.P.); (T.P.); (E.D.G.)
| | - Katiuscia Zilli
- Bacteriology and Diary Production Hygiene department, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise ‘G. Caporale’, Campo Boario, 64100 Teramo, Italy; (A.J.); (K.Z.); (R.R.); (D.P.); (T.P.); (E.D.G.)
| | - Romina Romantini
- Bacteriology and Diary Production Hygiene department, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise ‘G. Caporale’, Campo Boario, 64100 Teramo, Italy; (A.J.); (K.Z.); (R.R.); (D.P.); (T.P.); (E.D.G.)
| | - Stefano Bilei
- Food Microbiology department, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Via Appia Nuova 1411, 00178 Rome, Italy;
| | - Daniela Paganico
- Bacteriology and Diary Production Hygiene department, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise ‘G. Caporale’, Campo Boario, 64100 Teramo, Italy; (A.J.); (K.Z.); (R.R.); (D.P.); (T.P.); (E.D.G.)
| | - Tiziana Persiani
- Bacteriology and Diary Production Hygiene department, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise ‘G. Caporale’, Campo Boario, 64100 Teramo, Italy; (A.J.); (K.Z.); (R.R.); (D.P.); (T.P.); (E.D.G.)
| | - Guido Di Donato
- Epidemiology and Risk Analysis department, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise ‘G. Caporale’, Campo Boario, 64100 Teramo, Italy;
| | - Elisabetta Di Giannatale
- Bacteriology and Diary Production Hygiene department, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise ‘G. Caporale’, Campo Boario, 64100 Teramo, Italy; (A.J.); (K.Z.); (R.R.); (D.P.); (T.P.); (E.D.G.)
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Alegbeleye OO, Sant’Ana AS. Pathogen subtyping tools for risk assessment and management of produce-borne outbreaks. Curr Opin Food Sci 2020. [DOI: 10.1016/j.cofs.2020.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Wei X, You L, Wang D, Huang H, Li S, Wang D. Antimicrobial resistance and molecular genotyping of Salmonella enterica serovar Enteritidis clinical isolates from Guizhou province of Southwestern China. PLoS One 2019; 14:e0221492. [PMID: 31546249 PMCID: PMC6756847 DOI: 10.1371/journal.pone.0221492] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/07/2019] [Indexed: 11/23/2022] Open
Abstract
Salmonella enterica serovar Enteritidis (S. Enteritidis) is the most common and essential serotype that causes salmonellosis in Guizhou province. This study aimed to investigate the antimicrobial resistance (AMR) and molecular genotyping of 79 S. Enteritidis clinical isolates from 2011 to 2016 in Guizhou, China. Antimicrobial resistance and minimum inhibitory concentrations (MICs) of S. Enteritidis clinical isolates were detected by micro broth dilution method against ten classes 16 antimicrobial agents, and molecular genotyping were examined by pulsed-field gel electrophoresis (PFGE) and multiple-locus variable-number tandem repeat analysis (MLVA). All (100%) isolates showed resistance to at least one antimicrobial. Resistance to nalidixic acid (98.7%) was the highest, followed by sulfamethoxazole (87.3%) and ampicillin (77.2%). The majority of isolates (92.4%) showed decreased susceptibility to ciprofloxacin. Resistance to the third and fourth-generation cephalosporins was observed. Twenty-six AMR profiles were observed, and the predominant AMR profile was ampicillin-streptomycin-sulfamethoxazole-amoxicillin/clavulanic acid-nalidixic acid. A high burden of multidrug resistance (MDR) (81.0%) was found. Seventy-nine S. Enteritidis isolates were divided into 33 different pulsotypes (PTs), and the most frequent PT was PT18. Twenty-six different MLVA types (MTs) were generated with seven VNTR loci analysis of these isolates. The dominant PTs and MTs were persistent during 2011-2016. S. Enteritidis clinical isolates showed higher genetic diversity using PFGE combined with MLVA grouped into 60 PT-MT genotypes. No correlation was observed between genotypes, AMR profiles and geographic location. These data revealed the characteristics of AMR and molecular genotyping of S. Enteritidis clinical isolates in Guizhou province. These results highlight that strengthening the AMR and molecular genotyping surveillance is essential to prevent and control salmonellosis in Guizhou. PFGE combined with MLVA should be powerful tools for the molecular genotyping of S. Enteritidis isolates.
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Affiliation(s)
- Xiaoyu Wei
- Laboratory of Bacterial Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Lv You
- Laboratory of Bacterial Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Dan Wang
- Institute of Communicable Disease Control and Prevention, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - He Huang
- Institute of Communicable Disease Control and Prevention, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Shijun Li
- Laboratory of Bacterial Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Dingming Wang
- Institute of Communicable Disease Control and Prevention, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
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Mikkelä A, Ranta J, Tuominen P. A Modular Bayesian Salmonella Source Attribution Model for Sparse Data. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2019; 39:1796-1811. [PMID: 30893499 PMCID: PMC6849795 DOI: 10.1111/risa.13310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 06/09/2023]
Abstract
Several statistical models for salmonella source attribution have been presented in the literature. However, these models have often been found to be sensitive to the model parameterization, as well as the specifics of the data set used. The Bayesian salmonella source attribution model presented here was developed to be generally applicable with small and sparse annual data sets obtained over several years. The full Bayesian model was modularized into three parts (an exposure model, a subtype distribution model, and an epidemiological model) in order to separately estimate unknown parameters in each module. The proposed model takes advantage of the consumption and overall salmonella prevalence of the studied sources, as well as bacteria typing results from adjacent years. The latter were used for a smoothed estimation of the annual relative proportions of different salmonella subtypes in each of the sources. The source-specific effects and the salmonella subtype-specific effects were included in the epidemiological model to describe the differences between sources and between subtypes in their ability to infect humans. The estimation of these parameters was based on data from multiple years. Finally, the model combines the total evidence from different modules to proportion human salmonellosis cases according to their sources. The model was applied to allocate reported human salmonellosis cases from the years 2008 to 2015 to eight food sources.
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Affiliation(s)
- Antti Mikkelä
- Risk Assessment UnitFinnish Food AuthorityHelsinkiFinland
| | - Jukka Ranta
- Risk Assessment UnitFinnish Food AuthorityHelsinkiFinland
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Siira L, MacDonald E, Holmbakken GM, Sundar T, Meyer-Myklestad L, Lange H, Brandal LT, Naseer U, Johannessen GS, Bergsjø B, Espenhain L, Vold L, Nygård K. Increasing incubation periods during a prolonged monophasic Salmonella Typhimurium outbreak with environmental contamination of a commercial kitchen at Oslo Airport, Norway, 2017. Euro Surveill 2019; 24:1900207. [PMID: 31456559 PMCID: PMC6712930 DOI: 10.2807/1560-7917.es.2019.24.34.1900207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/13/2019] [Indexed: 11/20/2022] Open
Abstract
In September 2017, a cluster of monophasic Salmonella Typhimurium isolates was identified at the National Reference Laboratory for Enteropathogenic Bacteria in Norway. We investigated the cluster to identify the source and implement control measures. We defined a case as a person with laboratory-confirmed salmonellosis with the outbreak strain multiple locus variable-number tandem repeat analysis type. We conducted descriptive epidemiological and environmental investigations and performed whole genome sequencing (WGS) with core and accessory genome multilocus sequence typing of all isolates from cases or the environment connected with this outbreak. We identified 21 cases, residing in 10 geographically dispersed counties, all of whom had consumed food or drinks from a café at Oslo Airport. Case distribution by date of symptom onset suggested that a point source was introduced in mid-August followed by continued environmental contamination. The incubation periods ranged 0-16 days and increased as the outbreak progressed, likely due to increasingly low-dose exposure as control measures were implemented. WGS confirmed an identical cluster type-944 in all cases and six environmental specimens from the café. Control measures, including temporary closure and kitchen refurbishment, failed to eliminate the environmental source. We recommend strengthened hygiene measures for established environmental contamination during an outbreak.
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Affiliation(s)
- Lotta Siira
- Norwegian Institute of Public Health, Oslo, Norway
- European Program for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
| | | | | | - Tom Sundar
- Municipality of Nannestad, Akershus, Norway
| | | | - Heidi Lange
- Norwegian Institute of Public Health, Oslo, Norway
| | | | - Umaer Naseer
- Norwegian Institute of Public Health, Oslo, Norway
| | | | | | - Laura Espenhain
- Norwegian Institute of Public Health, Oslo, Norway
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
| | - Line Vold
- Norwegian Institute of Public Health, Oslo, Norway
| | - Karin Nygård
- Norwegian Institute of Public Health, Oslo, Norway
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Neoh HM, Tan XE, Sapri HF, Tan TL. Pulsed-field gel electrophoresis (PFGE): A review of the "gold standard" for bacteria typing and current alternatives. INFECTION GENETICS AND EVOLUTION 2019; 74:103935. [PMID: 31233781 DOI: 10.1016/j.meegid.2019.103935] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/18/2019] [Accepted: 06/20/2019] [Indexed: 12/01/2022]
Abstract
Pulsed-field gel electrophoresis (PFGE) is considered the "gold standard" for bacteria typing. The method involves enzyme restriction of bacteria DNA, separation of the restricted DNA bands using a pulsed-field electrophoresis chamber, followed by clonal assignment of bacteria based on PFGE banding patterns. Various PFGE protocols have been developed for typing different bacteria, leading it to be one of the most widely used methods for phylogenetic studies, food safety surveillance, infection control and outbreak investigations. On the other hand, as PFGE is lengthy and labourious, several PCR-based typing methods can be used as alternatives for research purposes. Recently, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and whole genome sequencing (WGS) have also been proposed for bacteria typing. In fact, as WGS provides more information, such as antimicrobial resistance and virulence of the tested bacteria in comparison to PFGE, more and more laboratories are currently transitioning from PFGE to WGS for bacteria typing. Nevertheless, PFGE will remain an affordable and relevant technique for small laboratories and hospitals in years to come.
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Affiliation(s)
- Hui-Min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia.
| | - Xin-Ee Tan
- Department of Infection and Immunity, School of Medicine, Jichi Medical University, Japan
| | - Hassriana Fazilla Sapri
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Malaysia
| | - Toh Leong Tan
- Department of Emergency Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Malaysia
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Pijnacker R, Dallman TJ, Tijsma ASL, Hawkins G, Larkin L, Kotila SM, Amore G, Amato E, Suzuki PM, Denayer S, Klamer S, Pászti J, McCormick J, Hartman H, Hughes GJ, Brandal LCT, Brown D, Mossong J, Jernberg C, Müller L, Palm D, Severi E, Gołębiowska J, Hunjak B, Owczarek S, Le Hello S, Garvey P, Mooijman K, Friesema IHM, van der Weijden C, van der Voort M, Rizzi V, Franz E. An international outbreak of Salmonella enterica serotype Enteritidis linked to eggs from Poland: a microbiological and epidemiological study. THE LANCET. INFECTIOUS DISEASES 2019; 19:778-786. [PMID: 31133519 DOI: 10.1016/s1473-3099(19)30047-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 01/17/2019] [Accepted: 01/17/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Salmonella spp are a major cause of food-borne outbreaks in Europe. We investigated a large multi-country outbreak of Salmonella enterica serotype Enteritidis in the EU and European Economic Area (EEA). METHODS A confirmed case was defined as a laboratory-confirmed infection with the outbreak strains of S Enteritidis based on whole-genome sequencing (WGS), occurring between May 1, 2015, and Oct 31, 2018. A probable case was defined as laboratory-confirmed infection with S Enteritidis with the multiple-locus variable-number tandem repeat analysis outbreak profile. Multi-country epidemiological, trace-back, trace-forward, and environmental investigations were done. We did a case-control study including confirmed and probable cases and controls randomly sampled from the population registry (frequency matched by age, sex, and postal code). Odds ratios (ORs) for exposure rates between cases and controls were calculated with unmatched univariable and multivariable logistic regression. FINDINGS 18 EU and EEA countries reported 838 confirmed and 371 probable cases. 509 (42%) cases were reported in 2016, after which the number of cases steadily increased. The case-control study results showed that cases more often ate in food establishments than did controls (OR 3·4 [95% CI 1·6-7·3]), but no specific food item was identified. Recipe-based food trace-back investigations among cases who ate in food establishments identified eggs from Poland as the vehicle of infection in October, 2016. Phylogenetic analysis identified two strains of S Enteritidis in human cases that were subsequently identified in salmonella-positive eggs and primary production premises in Poland, confirming the source of the outbreak. After control measures were implemented, the number of cases decreased, but increased again in March, 2017, and the increase continued into 2018. INTERPRETATION This outbreak highlights the public health value of multi-country sharing of epidemiological, trace-back, and microbiological data. The re-emergence of cases suggests that outbreak strains have continued to enter the food chain, although changes in strain population dynamics and fewer cases indicate that control measures had some effect. Routine use of WGS in salmonella surveillance and outbreak response promises to identify and stop outbreaks in the future. FUNDING European Centre for Disease Prevention and Control; Directorate General for Health and Food Safety, European Commission; and National Public Health and Food Safety Institutes of the authors' countries (see Acknowledgments for full list).
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Affiliation(s)
- Roan Pijnacker
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, Netherlands.
| | | | - Aloys S L Tijsma
- Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, Netherlands
| | | | | | - Saara M Kotila
- European Centre for Disease Prevention and Control, Solna, Sweden
| | - Giusi Amore
- European Food Safety Authority, Parma, Italy
| | - Ettore Amato
- Rapid Alert System for Food and Feed, Directorate-General for Health and Food Safety, European Commission, Brussels, Belgium
| | - Pamina M Suzuki
- Crisis Management in Food, Directorate-General for Health and Food Safety, European Commission, Brussels, Belgium
| | - Sarah Denayer
- National Institute for Public Health (Sciensano), Elsene, Belgium
| | - Sofieke Klamer
- National Institute for Public Health (Sciensano), Elsene, Belgium
| | - Judit Pászti
- National Centre for Epidemiology, Budapest, Hungary
| | | | | | | | | | - Derek Brown
- Scottish Salmonella, Shigella, and Clostridium difficile Reference Laboratory, Glasgow, UK
| | - Joël Mossong
- National Health Laboratory, Dudelange, Luxembourg
| | | | | | - Daniel Palm
- European Centre for Disease Prevention and Control, Solna, Sweden
| | - Ettore Severi
- European Centre for Disease Prevention and Control, Solna, Sweden
| | | | | | | | | | | | - Kirsten Mooijman
- European Union Reference Laboratory for Salmonella, Bilthoven, Netherlands
| | - Ingrid H M Friesema
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, Netherlands
| | - Coen van der Weijden
- Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, Netherlands
| | - Menno van der Voort
- Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, Netherlands
| | | | - Eelco Franz
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, Netherlands
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Investigation of Salmonella Enteritidis outbreaks in South Africa using multi-locus variable-number tandem-repeats analysis, 2013-2015. BMC Infect Dis 2017; 17:661. [PMID: 28969587 PMCID: PMC5625639 DOI: 10.1186/s12879-017-2751-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/19/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salmonella enterica serovar Enteritidis (Salmonella Enteritidis) has become a significant pathogen in South Africa, and the need for improved molecular surveillance of this pathogen has become important. Over the years, multi-locus variable-number tandem-repeats analysis (MLVA) has become a valuable molecular subtyping technique for Salmonella, particularly for highly homogenic serotypes such as Salmonella Enteritidis. This study describes the use of MLVA in the molecular epidemiological investigation of outbreak isolates in South Africa. METHODS Between the years 2013 and 2015, the Centre for Enteric Diseases (CED) received 39 Salmonella Enteritidis isolates from seven foodborne illness outbreaks, which occurred in six provinces. MLVA was performed on all isolates. RESULTS Three MLVA profiles (MLVA profiles 21, 22 and 28) were identified among the 39 isolates. MLVA profile 28 accounted for 77% (30/39) of the isolates. Isolates from a single outbreak were grouped into a single MLVA profile. A minimum spanning tree (MST) created from the MLVA data showed a close relationship between MLVA profiles 21, 22 and 28, with a single VNTR locus difference between them. CONCLUSIONS MLVA has proven to be a reliable method for the molecular epidemiological investigation of Salmonella Enteritidis outbreaks in South Africa. These foodborne outbreaks emphasize the importance of the One Health approach as an essential component for combating the spread of zoonotic pathogens such as Salmonella Enteritidis.
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Jensen MBF, Schjørring S, Björkman JT, Torpdahl M, Litrup E, Nielsen EM, Niskanen T. External quality assessment for molecular typing of Salmonella 2013-2015: performance of the European national public health reference laboratories. Eur J Clin Microbiol Infect Dis 2017; 36:1923-1932. [PMID: 28573470 PMCID: PMC5602099 DOI: 10.1007/s10096-017-3015-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/12/2017] [Indexed: 11/24/2022]
Abstract
We report the results of three consecutive External Quality Assessments (EQAs) for molecular subtyping of Salmonella to assess the performance of the European national public health reference laboratories (NPHRLs). The EQA included the molecular typing methods used for European enhanced surveillance of human Salmonella infections: pulsed field gel electrophoresis (PFGE), including gel analysis by the use of the software BioNumerics, and 5-locus multiple locus variable number of tandem repeat analysis (MLVA) for serovar Typhimurium. The participation in the PFGE laboratory part was higher (27/35) than in the gel analysis (19/35) and MLVA (15/35), suggestive of the need for capacity building in methods requiring specialized equipment (MLVA) or software (gel analysis). The majority (25/27) of the participating NPHRLs produced inter-laboratory comparable PFGE gel(s). Two laboratories continued to produce low-quality gels and should have additional technical assistance in the future. In particular, two gel quality evaluation parameters, measuring "image acquisition and running conditions" and "bands", were identified to cause gel quality problems throughout the EQAs. Despite the high number of laboratories participating in the PFGE laboratory part, the participation in gel analysis was low, although increasing. In the MLVA part, the NPHRLs correctly assigned 96% (405/420) allelic profiles according to the nomenclature. In conclusion, the EQAs identified critical parameters for unsuccessful performance and helped to offer assistance to those laboratories that needed it most. The assessments supported the development of quality in molecular typing and promoted the harmonization of subtyping methods used for EU/EEA-wide surveillance of human Salmonella infections.
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Affiliation(s)
- M B F Jensen
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark
| | - S Schjørring
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark
- European Programme for Public Health Microbiology Training, European Centre for Disease Prevention and Control (ECDC), Granits väg 8, 171 65, Solna, Stockholm, Sweden
| | - J T Björkman
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark
| | - M Torpdahl
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark
| | - E Litrup
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark
| | - E M Nielsen
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark.
| | - T Niskanen
- European Centre for Disease Prevention and Control (ECDC), Granits väg 8, 171 65, Solna, Stockholm, Sweden
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