1
|
Painset A, Björkman JT, Kiil K, Guillier L, Mariet JF, Félix B, Amar C, Rotariu O, Roussel S, Perez-Reche F, Brisse S, Moura A, Lecuit M, Forbes K, Strachan N, Grant K, Møller-Nielsen E, Dallman TJ. LiSEQ - whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe. Microb Genom 2019; 5:e000257. [PMID: 30775964 PMCID: PMC6421348 DOI: 10.1099/mgen.0.000257] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 01/29/2019] [Indexed: 12/20/2022] Open
Abstract
We present the LiSEQ (Listeria SEQuencing) project, funded by the European Food Safety Agency (EFSA) to compare Listeria monocytogenes isolates collected in the European Union from ready-to-eat foods, compartments along the food chain (e.g. food-producing animals, food-processing environments) and humans. In this article, we report the molecular characterization of a selection of this data set employing whole-genome sequencing analysis. We present an overview of the strain diversity observed in different sampled sources, and characterize the isolates based on their virulence and resistance profile. We integrate into our analysis the global L. monocytogenes genome collection described by Moura and colleagues in 2016 to assess the representativeness of the LiSEQ collection in the context of known L. monocytogenes strain diversity.
Collapse
Affiliation(s)
- Anaïs Painset
- Public Health England Gastrointestinal Bacteria Reference Unit, 61 Colindale Avenue, London, NW9 5EQ, UK
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool, Liverpool, UK
| | - Jonas T. Björkman
- Statens Serum Institut, 5 Artillerivej, DK-2300, Copenhagen S, Denmark
| | - Kristoffer Kiil
- Statens Serum Institut, 5 Artillerivej, DK-2300, Copenhagen S, Denmark
| | - Laurent Guillier
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Maisons-Alfort, France
| | - Jean-François Mariet
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Maisons-Alfort, France
| | - Benjamin Félix
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Maisons-Alfort, France
| | - Corinne Amar
- Public Health England Gastrointestinal Bacteria Reference Unit, 61 Colindale Avenue, London, NW9 5EQ, UK
| | - Ovidiu Rotariu
- School of Biological Sciences, The University of Aberdeen, Cruickshank Building. St Machar Drive, Aberdeen, Scotland, AB24 3UU, UK
| | - Sophie Roussel
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Maisons-Alfort, France
| | - Francisco Perez-Reche
- Institute of Complex Systems and Mathematical Biology, SUPA, School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, Scotland, UK
| | | | | | | | - Ken Forbes
- School of Medicine and Dentistry, The University of Aberdeen, Foresterhill, Aberdeen, Scotland, AB25 2ZD, UK
| | - Norval Strachan
- School of Biological Sciences, The University of Aberdeen, Cruickshank Building. St Machar Drive, Aberdeen, Scotland, AB24 3UU, UK
| | - Kathie Grant
- Public Health England Gastrointestinal Bacteria Reference Unit, 61 Colindale Avenue, London, NW9 5EQ, UK
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool, Liverpool, UK
| | | | - Timothy J. Dallman
- Public Health England Gastrointestinal Bacteria Reference Unit, 61 Colindale Avenue, London, NW9 5EQ, UK
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool, Liverpool, UK
| |
Collapse
|
2
|
Abstract
We present a case where Listeria monocytogenes serotype 1/2a was determined to be the causative agent of peritonitis in a patient on automated peritoneal dialysis. The patient, a 53-year-old Caucasian woman from the Faroe Islands was admitted to the National Hospital reporting of constant abdominal pain and a fever. Peritoneal cultures were positive for growth of L. monocytogenes. The patient was successfully treated with oral amoxicillin for 2 weeks and intraperitoneal vancomycin for 3 weeks. To date, the patient has not been readmitted due to peritonitis. The Faroese salmon was the suspected source of infection with L. monocytogenes.
Collapse
Affiliation(s)
| | - Torkil Á Steig
- Medical Department, National Hospital in the Faroe Islands, Tórshavn, Faroe Islands
| | - Jonas T Björkman
- Statens Serum Institut Mikrobiologisk Diagnostik og Virologi, Kobenhavn, Hovedstaden, Denmark
| | - Shahin Gaini
- Medical Department, National Hospital in the Faroe Islands, Tórshavn, Faroe Islands.,Department of Infectious Diseases, Odense Universitetshospital, Odense, Denmark
| |
Collapse
|
3
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
4
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| | | |
Collapse
|
5
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
6
|
Nielsen EM, Björkman JT, Kiil K, Grant K, Dallman T, Painset A, Amar C, Roussel S, Guillier L, Félix B, Rotariu O, Perez‐Reche F, Forbes K, Strachan N. Closing gaps for performing a risk assessment on Listeria monocytogenes in ready‐to‐eat (RTE) foods: activity 3, the comparison of isolates from different compartments along the food chain, and from humans using whole genome sequencing (WGS) analysis. ACTA ACUST UNITED AC 2017. [DOI: 10.2903/sp.efsa.2017.en-1151] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
7
|
Abstract
Denmark has a high incidence of invasive listeriosis (0.9 cases/100,000 population in 2012). We analyzed patient data, clinical outcome, and trends in pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) of Listeria monocytogenes strains isolated in Denmark during 2002-2012. We performed 2-enzyme PFGE and serotyping on 559 isolates and MLST on 92 isolates and identified some correlation between molecular type and clinical outcome and patient characteristics. We found 178 different PFGE types, but isolates from 122 cases belonged to just 2 closely related PFGE types, clonal complex 8 and sequence type 8. These 2 types were the main cause of a peak in incidence of invasive listeriosis during 2005-2009, possibly representing an outbreak or the presence of a highly prevalent clone. However, current typing methods could not fully confirm these possibilities, highlighting the need for more refined discriminatory typing methods to identify outbreaks within frequently occurring L. monocytogenes PFGE types.
Collapse
|
8
|
Moura A, Criscuolo A, Pouseele H, Maury MM, Leclercq A, Tarr C, Björkman JT, Dallman T, Reimer A, Enouf V, Larsonneur E, Carleton H, Bracq-Dieye H, Katz LS, Jones L, Touchon M, Tourdjman M, Walker M, Stroika S, Cantinelli T, Chenal-Francisque V, Kucerova Z, Rocha EPC, Nadon C, Grant K, Nielsen EM, Pot B, Gerner-Smidt P, Lecuit M, Brisse S. Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes. Nat Microbiol 2016; 2:16185. [PMID: 27723724 DOI: 10.1038/nmicrobiol.2016.185] [Citation(s) in RCA: 397] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 08/30/2016] [Indexed: 01/31/2023]
Abstract
Listeria monocytogenes (Lm) is a major human foodborne pathogen. Numerous Lm outbreaks have been reported worldwide and associated with a high case fatality rate, reinforcing the need for strongly coordinated surveillance and outbreak control. We developed a universally applicable genome-wide strain genotyping approach and investigated the population diversity of Lm using 1,696 isolates from diverse sources and geographical locations. We define, with unprecedented precision, the population structure of Lm, demonstrate the occurrence of international circulation of strains and reveal the extent of heterogeneity in virulence and stress resistance genomic features among clinical and food isolates. Using historical isolates, we show that the evolutionary rate of Lm from lineage I and lineage II is low (∼2.5 × 10-7 substitutions per site per year, as inferred from the core genome) and that major sublineages (corresponding to so-called 'epidemic clones') are estimated to be at least 50-150 years old. This work demonstrates the urgent need to monitor Lm strains at the global level and provides the unified approach needed for global harmonization of Lm genome-based typing and population biology.
Collapse
Affiliation(s)
- Alexandra Moura
- National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.,Biology of Infection Unit, Institut Pasteur, 75724 Paris, France.,Inserm U1117, 75015 Paris, France.,Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.,CNRS, UMR 3525, 75015 Paris, France
| | - Alexis Criscuolo
- Institut Pasteur-Hub Bioinformatique et Biostatistique-C3BI, USR 3756 IP CNRS, 75724 Paris, France
| | | | - Mylène M Maury
- National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.,Biology of Infection Unit, Institut Pasteur, 75724 Paris, France.,Inserm U1117, 75015 Paris, France.,Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.,CNRS, UMR 3525, 75015 Paris, France.,Sorbonne Paris Cité, Cellule Pasteur, Paris Diderot University, 75013 Paris, France
| | - Alexandre Leclercq
- National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.,Biology of Infection Unit, Institut Pasteur, 75724 Paris, France
| | - Cheryl Tarr
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | | | | | - Aleisha Reimer
- Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Vincent Enouf
- Pasteur International Bioresources network (PIBnet), Mutualized Microbiology Platform (P2M), Institut Pasteur, 75724 Paris, France
| | - Elise Larsonneur
- Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.,Institut Pasteur-Hub Bioinformatique et Biostatistique-C3BI, USR 3756 IP CNRS, 75724 Paris, France.,CNRS, UMS 3601 IFB-Core, 91198 Gif-sur-Yvette, France
| | - Heather Carleton
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Hélène Bracq-Dieye
- National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.,Biology of Infection Unit, Institut Pasteur, 75724 Paris, France
| | - Lee S Katz
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Louis Jones
- Institut Pasteur-Hub Bioinformatique et Biostatistique-C3BI, USR 3756 IP CNRS, 75724 Paris, France
| | - Marie Touchon
- Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.,CNRS, UMR 3525, 75015 Paris, France
| | | | - Matthew Walker
- Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Steven Stroika
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Thomas Cantinelli
- National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France
| | - Viviane Chenal-Francisque
- National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France
| | - Zuzana Kucerova
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.,CNRS, UMR 3525, 75015 Paris, France
| | - Celine Nadon
- Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | | | | | - Bruno Pot
- Applied-Maths, 9830 Sint-Martens-Latem, Belgium
| | | | - Marc Lecuit
- National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.,Biology of Infection Unit, Institut Pasteur, 75724 Paris, France.,Inserm U1117, 75015 Paris, France.,Sorbonne Paris Cité, Institut Imagine, 75006 Paris, Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Paris Descartes University, 75015 Paris, France
| | - Sylvain Brisse
- Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.,CNRS, UMR 3525, 75015 Paris, France
| |
Collapse
|