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Halbedel S, Wamp S, Lachmann R, Holzer A, Pietzka A, Ruppitsch W, Wilking H, Flieger A. High density genomic surveillance and risk profiling of clinical Listeria monocytogenes subtypes in Germany. Genome Med 2024; 16:115. [PMID: 39375806 PMCID: PMC11457394 DOI: 10.1186/s13073-024-01389-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 09/24/2024] [Indexed: 10/09/2024] Open
Abstract
BACKGROUND Foodborne infections such as listeriosis caused by the bacterium Listeria monocytogenes represent a significant public health concern, particularly when outbreaks affect many individuals over prolonged time. Systematic collection of pathogen isolates from infected patients, whole genome sequencing (WGS) and phylogenetic analyses allow recognition and termination of outbreaks after source identification and risk profiling of abundant lineages. METHODS We here present a multi-dimensional analysis of > 1800 genome sequences from clinical L. monocytogenes isolates collected in Germany between 2018 and 2021. Different WGS-based subtyping methods were used to determine the population structure with its main phylogenetic sublineages as well as for identification of disease clusters. Clinical frequencies of materno-foetal and brain infections and in vitro infection experiments were used for risk profiling of the most abundant sublineages. These sublineages and large disease clusters were further characterised in terms of their genetic and epidemiological properties. RESULTS The collected isolates covered 62% of all notified cases and belonged to 188 infection clusters. Forty-two percent of these clusters were active for > 12 months, 60% generated cases cross-regionally, including 11 multinational clusters. Thirty-seven percent of the clusters were caused by sequence type (ST) ST6, ST8 and ST1 clones. ST1 was identified as hyper- and ST8, ST14, ST29 as well as ST155 as hypovirulent, while ST6 had average virulence potential. Inactivating mutations were found in several virulence and house-keeping genes, particularly in hypovirulent STs. CONCLUSIONS Our work presents an in-depth analysis of the genomic characteristics of L. monocytogenes isolates that cause disease in Germany. It supports prioritisation of disease clusters for epidemiological investigations and reinforces the need to analyse the mechanisms underlying hyper- and hypovirulence.
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Affiliation(s)
- Sven Halbedel
- FG11 Division of Enteropathogenic Bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Burgstrasse 37, Wernigerode, D-38855, Germany.
- Institute for Medical Microbiology and Hospital Hygiene, Otto Von Guericke University Magdeburg, Leipziger Strasse 44, Magdeburg, 39120, Germany.
| | - Sabrina Wamp
- FG11 Division of Enteropathogenic Bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Burgstrasse 37, Wernigerode, D-38855, Germany
| | - Raskit Lachmann
- FG35 - Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Seestrasse 10, Berlin, 13353, Germany
| | - Alexandra Holzer
- FG35 - Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Seestrasse 10, Berlin, 13353, Germany
| | - Ariane Pietzka
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Beethovenstraße 6, Graz, 8010, Austria
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Währingerstrasse 25a, Vienna, 1090, Austria
| | - Hendrik Wilking
- FG35 - Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Seestrasse 10, Berlin, 13353, Germany
| | - Antje Flieger
- FG11 Division of Enteropathogenic Bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Burgstrasse 37, Wernigerode, D-38855, Germany.
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Lambrechts K, Rip D. Listeria monocytogenes in the seafood industry: Exploring contamination sources, outbreaks, antibiotic susceptibility and genetic diversity. Microbiologyopen 2024; 13:e70003. [PMID: 39420711 DOI: 10.1002/mbo3.70003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 09/01/2024] [Accepted: 09/26/2024] [Indexed: 10/19/2024] Open
Abstract
Fish and seafood are rich sources of protein, vitamins, and minerals, significantly contributing to individual health. A global increase in consumption has been observed. Listeria monocytogenes is a known problem in food processing environments and is found in various seafood forms, including raw, smoked, salted, and ready-to-eat. Without heat treatment and given L. monocytogenes' ability to multiply under refrigerated conditions, consuming seafood poses a substantial health hazard, particularly to immunocompromised individuals. Numerous global outbreaks of listeriosis have been linked to various fish products, underscoring the importance of studying L. monocytogenes. Different strains exhibit varying disease-causing abilities, making it crucial to understand and monitor the organism's virulence and resistance aspects for food safety. This paper aims to highlight the genetic diversity of L. monocytogenes found in fish products globally and to enhance understanding of contamination routes from raw fish to the final product.
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Affiliation(s)
- Karlene Lambrechts
- Department of Food Science, Stellenbosch University, Matieland, South Africa
| | - Diane Rip
- Department of Food Science, Stellenbosch University, Matieland, South Africa
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3
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Lambrechts K, Gouws P, Rip D. Genetic diversity of Listeria monocytogenes from seafood products, its processing environment, and clinical origin in the Western Cape, South Africa using whole genome sequencing. AIMS Microbiol 2024; 10:608-643. [PMID: 39219753 PMCID: PMC11362271 DOI: 10.3934/microbiol.2024029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/08/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
Listeria monocytogenes is a concern in seafood and its food processing environment (FPE). Several outbreaks globally have been linked to various types of seafood. Genetic profiling of L. monocytogenes is valuable to track bacterial contamination throughout the FPE and in understanding persistence mechanisms, with limited studies from South Africa. Forty-six L. monocytogenes isolates from origins: Fish/seafood products (n = 32) (salmon, smoked trout, fresh hake, oysters), the FPE (n = 6), and clinical (n = 8) were included in this study. Lineage typing, antibiotic susceptibility testing, and screening for two genes (bcrABC and emrC) conferring sanitizer tolerance was conducted. The seafood and FPE isolates originated from seven different factories processing various seafood products with undetermined origin. All clinical isolates were categorized as lineage I, and seafood and FPE isolates were mostly categorized into lineage II (p < 0.01). Seafood and FPE isolates (53%) carried the bcrABC gene cassette and one fish isolate, the emrC gene. A subset, n = 24, was grouped into serotypes, sequence types (STs), and clonal complexes (CCs) with whole genome sequencing (WGS). Eight CCs and ten STs were identified. All clinical isolates belonged to serogroup 4b, hypervirulent CC1. CC121 was the most prevalent in isolates from food and the FPE. All isolates carried Listeria pathogenicity islands (LIPI) 1 and 2. LIPI-3 and LIPI-4 were found in certain isolates. We identified genetic determinants linked to enhanced survival in the FPE, including stress survival islets (SSI) and genes conferring tolerance to sanitizers. SSI-1 was found in 44% isolates from seafood and the FPE. SSI-2 was found in all the ST121 seafood isolates. Isolates (42%) harbored transposon Tn1688_qac (ermC), conferring tolerance to quaternary ammonium compounds. Five plasmids were identified in 13 isolates from seafood and the FPE. This is the first One Health study reporting on L. monocytogenes genetic diversity, virulence and resistance profiles from various types of seafood and its FPE in South Africa.
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Affiliation(s)
| | | | - Diane Rip
- Department of Food Science, Stellenbosch University, 7602, South Africa
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4
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Feodorova VA, Zaitsev SS, Khizhnyakova MA, Lavrukhin MS, Saltykov YV, Zaberezhny AD, Larionova OS. Complete genome of the Listeria monocytogenes strain AUF, used as a live listeriosis veterinary vaccine. Sci Data 2024; 11:643. [PMID: 38886393 PMCID: PMC11183264 DOI: 10.1038/s41597-024-03440-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 05/28/2024] [Indexed: 06/20/2024] Open
Abstract
Listeria monocytogenes (Lm) is a highly pathogenic bacterium that can cause listeriosis, a relatively rare food-borne infectious disease that affects farm, domestic, wild animals and humans as well. The infected livestock is the frequent sources of Lm. Vaccination is one of the methods of controlling listeriosis in target farm animals to prevent Lm-associated food contamination. Here we report the complete sequence of the Lm strain AUF attenuated from a fully-virulent Lm strain by ultraviolet irradiation, successfully used since the 1960s as a live whole-cell veterinary vaccine. The de novo assembled genome consists of a circular chromosome of 2,942,932 bp length, including more than 2,800 CDSs, 17 pseudogenes, 5 antibiotic resistance genes, and 56/92 virulence genes. Two wild Lm strains, the EGD and the 10403S that is also used in cancer Immunotherapy, were the closest homologs for the Lm strain AUF. Although all three strains belonged to different sequence types (ST), namely ST12, ST85, and ST1538, they were placed in the same genetic lineage II, CC7.
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Affiliation(s)
- Valentina A Feodorova
- Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia.
- Department for Microbiology and Biotechnology, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia.
| | - Sergey S Zaitsev
- Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia
| | - Mariya A Khizhnyakova
- Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia
| | - Maxim S Lavrukhin
- Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia
| | - Yury V Saltykov
- Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia
| | - Alexey D Zaberezhny
- All-Russian Scientific Research and Technological Institute of Biological Industry, Biocombinat, Moscow, Russia
| | - Olga S Larionova
- Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia
- Department for Microbiology and Biotechnology, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia
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Lagarde J, Feurer C, Denis M, Douarre PE, Piveteau P, Roussel S. Listeria monocytogenes prevalence and genomic diversity along the pig and pork production chain. Food Microbiol 2024; 119:104430. [PMID: 38225039 DOI: 10.1016/j.fm.2023.104430] [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: 04/07/2023] [Revised: 11/10/2023] [Accepted: 11/19/2023] [Indexed: 01/17/2024]
Abstract
The facultative intracellular bacterium Listeria monocytogenes (L. monocytogenes) is the causative agent of listeriosis, a severe invasive illness. This ubiquitous species is widely distributed in the environment, but infection occurs almost exclusively through ingestion of contaminated food. The pork production sector has been heavily affected by a series of L. monocytogenes-related foodborne outbreaks in the past around the world. Ready-to-eat (RTE) pork products represent one of the main food sources for strong-evidence listeriosis outbreaks. This pathogen is known to be present throughout the entire pig and pork production chain. Some studies hypothesized that the main source of contamination in final pork products was either living pigs or the food-processing environment. A detailed genomic picture of L. monocytogenes can provide a renewed understanding of the routes of contamination from pig farms to the final products. This review provides an overview of the prevalence, the genomic diversity and the genetic background linked to virulence of L. monocytogenes along the entire pig and pork production chain, from farm to fork.
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Affiliation(s)
- Jean Lagarde
- ANSES, Salmonella and Listeria Unit (USEL), University of Paris-Est, Maisons-Alfort Laboratory for Food Safety, 14 rue Pierre et Marie Curie, 94700, Maisons-Alfort, France; INRAE, Unit of Process Optimisation in Food, Agriculture and the Environment (UR OPAALE), 17 avenue de Cucillé, 35000, Rennes, France
| | - Carole Feurer
- IFIP, The French Pig and Pork Institute, Department of Fresh and Processed Meat, La Motte au Vicomte, 35650, Le Rheu, France
| | - Martine Denis
- ANSES, Unit of Hygiene and Quality of Poultry and Pork Products (UHQPAP), Ploufragan-Plouzané-Niort Laboratory, 31 rue des fusillés, 22440, Ploufragan, France
| | - Pierre-Emmanuel Douarre
- ANSES, Salmonella and Listeria Unit (USEL), University of Paris-Est, Maisons-Alfort Laboratory for Food Safety, 14 rue Pierre et Marie Curie, 94700, Maisons-Alfort, France
| | - Pascal Piveteau
- INRAE, Unit of Process Optimisation in Food, Agriculture and the Environment (UR OPAALE), 17 avenue de Cucillé, 35000, Rennes, France
| | - Sophie Roussel
- ANSES, Salmonella and Listeria Unit (USEL), University of Paris-Est, Maisons-Alfort Laboratory for Food Safety, 14 rue Pierre et Marie Curie, 94700, Maisons-Alfort, France.
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Moura A, Leclercq A, Vales G, Tessaud-Rita N, Bracq-Dieye H, Thouvenot P, Madec Y, Charlier C, Lecuit M. Phenotypic and genotypic antimicrobial resistance of Listeria monocytogenes: an observational study in France. THE LANCET REGIONAL HEALTH. EUROPE 2024; 37:100800. [PMID: 38362545 PMCID: PMC10866989 DOI: 10.1016/j.lanepe.2023.100800] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 02/17/2024]
Abstract
Background Large-scale studies are needed to clarify antimicrobial resistance in the foodborne pathogen Listeria monocytogenes (Lm) and the effectiveness of listeriosis treatment options. Here we examined the antimicrobial resistance patterns in Lm over time and assessed genotype-phenotype concordances. Methods We analyzed 5339 Lm isolates (2908 clinical and 2431 food isolates) collected in France and overseas territories, between 2012 and 2019. Whole genome sequencing was performed for all isolates and antimicrobial resistance profiles inferred from draft assemblies. Antimicrobial susceptibility towards 22 antimicrobials was determined for all clinical isolates, and in food isolates with acquired resistance genes. Findings All tested isolates were resistant to at least 3 different classes of antimicrobials, consistent with Lm intrinsic traits. Acquired antimicrobial resistance in Lm was rare (2.23% isolates) and more prevalent in food (mainly lineage II) compared to clinical isolates (mainly lineage I) (3.74% vs 0.98%, p < 0.0001), and in isolates with disinfectants or stress resistance traits (e.g. bcrABC, 20.20% vs 7.20%, p < 0.0001), suggesting co-selection of resistance in food-production environments. Acquired antimicrobial resistance could be predicted from genomes with high accuracy (>99%), except for ciprofloxacin. Acquired antimicrobial phenotypes were towards tetracyclines (mostly due to tetM), trimethoprim (dfrD), lincosamides (lnuG), macrolides (ermB, mphB) and phenicols (fexA). Interpretation The reference treatment for listeriosis (aminopenicillins/aminoglycosides) remains effective, with no acquired resistance observed. Continuous surveillance of antimicrobial resistance in clinical and food isolates is crucial to detect the emergence of novel resistance. Funding Institut Pasteur, INSERM, Santé Publique France, Investissement d'Avenir program Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases' (ANR-10-LABX-62-IBEID).
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Affiliation(s)
- Alexandra Moura
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre Listeria, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, 75015, Paris, France
| | - Alexandre Leclercq
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre Listeria, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, 75015, Paris, France
| | - Guillaume Vales
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre Listeria, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, 75015, Paris, France
| | - Nathalie Tessaud-Rita
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre Listeria, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, 75015, Paris, France
| | - Hélène Bracq-Dieye
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre Listeria, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, 75015, Paris, France
| | - Pierre Thouvenot
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre Listeria, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, 75015, Paris, France
| | - Yoann Madec
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, 75015, Paris, France
| | - Caroline Charlier
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre Listeria, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, 75015, Paris, France
| | - Marc Lecuit
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre Listeria, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, 75015, Paris, France
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, 75006, Paris, France
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Møretrø T, Wagner E, Heir E, Langsrud S, Fagerlund A. Genomic analysis of Listeria monocytogenes CC7 associated with clinical infections and persistence in the food industry. Int J Food Microbiol 2024; 410:110482. [PMID: 37977076 DOI: 10.1016/j.ijfoodmicro.2023.110482] [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: 05/07/2023] [Revised: 11/03/2023] [Accepted: 11/05/2023] [Indexed: 11/19/2023]
Abstract
Listeria monocytogenes clonal complex 7 (CC7), belonging to lineage II, is the most common subtype among clinical listeriosis isolates in Norway, and is also commonly found in Norwegian food industry and outdoor environments. In the present study, the relative prevalence of CCs among clinical isolates of L. monocytogenes in European countries during 2010-2015 was determined. Then, phylogenomic and comparative genomic analyses was performed for 115 Norwegian and 255 international reference genomes from various sources, to examine potential explanations underlying the high prevalence of CC7 among Norwegian listeriosis cases. Selected isolates were also compared using in vitro virulence assays. The results showed a high relative prevalence of CC7 in clinical isolates from Norway and the neighboring Nordic countries Sweden and Finland. In contrast to in most other European countries, lineage II dominated among clinical isolates in these countries. Phylogenetic analysis of the 370 CC7 isolates separated the genomes into four clades, with the majority of Norwegian isolates (69 %) clustered in one of these clades, estimated to have diverged from the other clades around year 1830. The Norwegian isolates within this clade were widely distributed in different habitats; several (poultry) meat processing factories, a salmon processing plant, in nature, farms, and slugs, and among human clinical isolates. In particular, one pervasive CC7 clone was found across three poultry processing plants and one salmon processing plant, and also included three clinical isolates. All analysed CC7 isolates harbored the same set of 72 genes involved in both general and specific stress responses. Divergence was observed for plasmid-encoded genes including genes conferring resistance against arsenic (Tn554-arsCBADR), cadmium (cadA1C1 and cadA2C2), and the biocide benzalkonium chloride (bcrABC). No significant difference in prevalence of these genes was seen between isolates from different habitats or sources. Virulence attributes were highly conserved among the CC7 isolates. In vitro virulence studies of five representative CC7 isolates revealed a virulence potential that, in general, was not significantly lower than that of the control strain EGDe, with isolate-dependent differences that could not be correlated with genetic determinants. The study shows that CC7 is widespread in Norway, and that a pervasive CC7 clone was present in food processing plants. The study highlights the importance of CC7 and lineage II strains in causing listeriosis and shows that more research is needed to understand the reasons behind geographical differences in CC prevalence.
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Affiliation(s)
- Trond Møretrø
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, N-1430 Aas, Norway.
| | - Eva Wagner
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, N-1430 Aas, Norway
| | - Even Heir
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, N-1430 Aas, Norway
| | - Solveig Langsrud
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, N-1430 Aas, Norway
| | - Annette Fagerlund
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, N-1430 Aas, Norway
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8
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Pracser N, Zaiser A, Ying HMK, Pietzka A, Wagner M, Rychli K. Diverse Listeria monocytogenes in-house clones are present in a dynamic frozen vegetable processing environment. Int J Food Microbiol 2024; 410:110479. [PMID: 37977080 DOI: 10.1016/j.ijfoodmicro.2023.110479] [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: 07/07/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023]
Abstract
Listeria (L.) monocytogenes is of global concern for food safety as the listeriosis-causing pathogen is widely distributed in the food processing environments, where it can survive for a long time. Frozen vegetables contaminated with L. monocytogenes were recently identified as the source of two large listeriosis outbreaks in the EU and US. So far, only a few studies have investigated the occurrence and behavior of Listeria in frozen vegetables and the associated processing environment. This study investigates the occurrence of L. monocytogenes and other Listeria spp. in a frozen vegetable processing environment and in frozen vegetable products. Using whole genome sequencing (WGS), the distribution of sequence types (MLST-STs) and core genome sequence types (cgMLST-CT) of L. monocytogenes were assessed, and in-house clones were identified. Comparative genomic analyses and phenotypical characterization of the different MLST-STs and isolates were performed, including growth ability under low temperatures, as well as survival of freeze-thaw cycles. Listeria were widely disseminated in the processing environment and five in-house clones namely ST451-CT4117, ST20-CT3737, ST8-CT1349, ST8-CT6243, ST224-CT5623 were identified among L. monocytogenes isolates present in environmental swab samples. Subsequently, the identified in-house clones were also detected in product samples. Conveyor belts were a major source of contamination in the processing environment. A wide repertoire of stress resistance markers supported the colonization and survival of L. monocytogenes in the frozen vegetable processing facility. The presence of ArgB was significantly associated with in-house clones. Significant differences were also observed in the growth rate between different MLST-STs at low temperatures (4 °C and 10 °C), but not between in-house and non-in-house isolates. All isolates harbored major virulence genes such as full length InlA and InlB and LIPI-1, yet there were differences between MLST-STs in the genomic content. The results of this study demonstrate that WGS is a strong tool for tracing contamination sources and transmission routes, and for identifying in-house clones. Further research targeting the co-occurring microbiota and the presence of biofilms is needed to fully understand the mechanism of colonization and persistence in a food processing environment.
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Affiliation(s)
- Nadja Pracser
- FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, 3430 Tulln, Austria.
| | - Andreas Zaiser
- Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Hui Min Katharina Ying
- Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Ariane Pietzka
- Austrian National Reference Laboratory for Listeria monocytogenes, Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Beethovenstrasse 6, 8010 Graz, Austria.
| | - Martin Wagner
- FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, 3430 Tulln, Austria; Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Kathrin Rychli
- Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
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Tirloni E, Centorotola G, Pomilio F, Torresi M, Bernardi C, Stella S. Listeria monocytogenes in ready-to-eat (RTE) delicatessen foods: Prevalence, genomic characterization of isolates and growth potential. Int J Food Microbiol 2024; 410:110515. [PMID: 38064894 DOI: 10.1016/j.ijfoodmicro.2023.110515] [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: 09/12/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023]
Abstract
This study investigated Listeria monocytogenes prevalence and count in 132 ready-to-eat (RTE) delicatessen samples belonging to different categories (starters with/without mayonnaise pasta/rice-based courses, meat/fish-based main courses) produced by an Italian industry. Whole Genome Sequencing characterized the isolates to map the pathogen circulation. Moreover, the growth potential of L. monocytogenes in the most contaminated product was investigated by a challenge test. L. monocytogenes was detected in 23 samples, giving an estimated prevalence of 17.4 %. Starters with mayonnaise showed a very high prevalence (56.7 %), showing the role of the sauce in the diffusion of the pathogen within the plant. A total of 49 isolates were obtained; they belonged to two different serogroups, IIb and IIa, and were related to two clonal complexes (CCs) and sequence types (STs) (CC288-ST330 and CC121-ST717), suggesting the possible persistence and circulation of the pathogen within the plant. The results of the challenge test showed a limited ability to grow in the selected product thanks to the presence of lactic microflora.
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Affiliation(s)
- E Tirloni
- Department of Veterinary Medicine and Animal Sciences, University of Milan, via dell'Università 6, 26900 Lodi, Italy.
| | - G Centorotola
- IZSAM, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, via Campo Boario, Teramo 64100, Italy
| | - F Pomilio
- IZSAM, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, via Campo Boario, Teramo 64100, Italy
| | - M Torresi
- IZSAM, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, via Campo Boario, Teramo 64100, Italy
| | - C Bernardi
- Department of Veterinary Medicine and Animal Sciences, University of Milan, via dell'Università 6, 26900 Lodi, Italy
| | - S Stella
- Department of Veterinary Medicine and Animal Sciences, University of Milan, via dell'Università 6, 26900 Lodi, Italy
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Cheng J, Wu S, Ye Q, Gu Q, Zhang Y, Ye Q, Lin R, Liang X, Liu Z, Bai J, Zhang J, Chen M, Wu Q. A novel multiplex PCR based method for the detection of Listeria monocytogenes clonal complex 8. Int J Food Microbiol 2024; 409:110475. [PMID: 37976619 DOI: 10.1016/j.ijfoodmicro.2023.110475] [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: 06/07/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
Listeria monocytogenes is an important foodborne pathogen worldwide, which could cause listeriosis with a 20-30 % fatality rate in immunocompromised individuals. Listeria monocytogenes MLST clonal complex (CC) 8 strain is a common clone in food and clinical cases. The aim of this study was to develop multiplex PCR (mPCR) and high-resolution melting (HRM) qPCR to simultaneously detect L. monocytogenes CC8 and the other L. monocytogenes strains based on pan-genome analysis. A novel multiplex PCR and HRM qPCR targeted for the genes LM5578_1180 (specific for CC8) and LM5578_2262 (for L. monocytogenes) were developed. The specificity of this multiplex PCR and HRM qPCR were verified with other CCs of L. monocytogenes and other species strains. The detection limit of this multiplex PCR and HRM qPCR is 2.1 × 103 CFU/mL and 2.1 × 100 CFU/mL, respectively. This multiplex PCR and HRM qPCR could accurately detect CC8 strains with the interference of different ratios of L. monocytogenes CC9, CC87, CC121, CC155, and L. innocua strains. Subsequently, the detection ability of mPCR and HRM qPCR were also evaluated in spiked samples. The mPCR method could successfully detect 6.2 × 103 CFU/mL of CC8 L. monocytogenes after 6 h enrichment while the multiplex HRM qPCR method could successfully detect 6.2 × 104 CFU/mL of CC8 L. monocytogenes after 3 h enrichment. The feasibility of these methods were satisfactory in terms of sensitivity, specificity, and efficiency after evaluating 12 mushroom samples and was consistent with that of the National Standard Detection Method (GB4789.30-2016). In conclusion, the developed assays could be applied for rapid screening and detection of L. monocytogenes CC8 strains both in food and food production environments, providing accurate results to adopt monitoring measures to improve microbiological safety.
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Affiliation(s)
- Jianheng Cheng
- College of Food, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qihui Gu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Ying Zhang
- College of Food, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qinglei Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Ruoqin Lin
- College of Food, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xinwen Liang
- College of Food, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Zihao Liu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jianling Bai
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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11
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Koutsoumanis K, Allende A, Bolton D, Bover‐Cid S, Chemaly M, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Fox E, Gosling R(B, Gil BM, Møretrø T, Stessl B, da Silva Felício MT, Messens W, Simon AC, Alvarez‐Ordóñez A. Persistence of microbiological hazards in food and feed production and processing environments. EFSA J 2024; 22:e8521. [PMID: 38250499 PMCID: PMC10797485 DOI: 10.2903/j.efsa.2024.8521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024] Open
Abstract
Listeria monocytogenes (in the meat, fish and seafood, dairy and fruit and vegetable sectors), Salmonella enterica (in the feed, meat, egg and low moisture food sectors) and Cronobacter sakazakii (in the low moisture food sector) were identified as the bacterial food safety hazards most relevant to public health that are associated with persistence in the food and feed processing environment (FFPE). There is a wide range of subtypes of these hazards involved in persistence in the FFPE. While some specific subtypes are more commonly reported as persistent, it is currently not possible to identify universal markers (i.e. genetic determinants) for this trait. Common risk factors for persistence in the FFPE are inadequate zoning and hygiene barriers; lack of hygienic design of equipment and machines; and inadequate cleaning and disinfection. A well-designed environmental sampling and testing programme is the most effective strategy to identify contamination sources and detect potentially persistent hazards. The establishment of hygienic barriers and measures within the food safety management system, during implementation of hazard analysis and critical control points, is key to prevent and/or control bacterial persistence in the FFPE. Once persistence is suspected in a plant, a 'seek-and-destroy' approach is frequently recommended, including intensified monitoring, the introduction of control measures and the continuation of the intensified monitoring. Successful actions triggered by persistence of L. monocytogenes are described, as well as interventions with direct bactericidal activity. These interventions could be efficient if properly validated, correctly applied and verified under industrial conditions. Perspectives are provided for performing a risk assessment for relevant combinations of hazard and food sector to assess the relative public health risk that can be associated with persistence, based on bottom-up and top-down approaches. Knowledge gaps related to bacterial food safety hazards associated with persistence in the FFPE and priorities for future research are provided.
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12
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Mejía L, Espinosa-Mata E, Freire AL, Zapata S, González-Candelas F. Listeria monocytogenes, a silent foodborne pathogen in Ecuador. Front Microbiol 2023; 14:1278860. [PMID: 38179446 PMCID: PMC10764610 DOI: 10.3389/fmicb.2023.1278860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/23/2023] [Indexed: 01/06/2024] Open
Abstract
Listeria monocytogenes is a foodborne pathogen that can produce serious, even fatal, infections. Among other foods, it can be found in unpasteurized dairy and ready-to-eat products. Surveillance of L. monocytogenes is of great interest since sources of infection are difficult to determine due to the long incubation period, and because the symptoms of listeriosis are similar to other diseases. We performed a genomic study of L. monocytogenes isolated from fresh cheeses and clinical samples from Ecuador. Sixty-five isolates were evaluated and sequenced, 14 isolates from cheese samples and 20 from clinical listeriosis cases from the National Institute of National Institute of Public Health Research, and 31 isolates from artisanal cheese samples from 8 provinces. All isolates exhibited heterogeneous patterns of the presence of pathogenicity islands. All isolates exhibited at least 4 genes from LIPI-1, but all references (26 L. monocytogenes closed genomes available in the NCBI database) showed the complete island, which encompasses 5 genes but is present in only two Ecuadorian isolates. Most isolates lacked gene actA. Genes from LIPI-2 were absent in all isolates. LIPI-3 and LIPI-4 were present in only a few references and isolates. With respect to the stress survival islets, our samples either presented SSI-1 or SSI-F2365, except for one isolate that presented SSI-F2365 and also one gene from SSI-1. None of the samples presented SSI-2. The predominant ST (sequence type) was ST2 (84.62% 55/65), and the only ST found in food (93.33% 42/45) and clinical samples (65% 13/20). Isolates were not grouped according to their sampling origin, date, or place in a phylogenetic tree obtained from the core alignment. The presence of ST2 in food and clinical samples, with high genomic similarity, suggests a foodborne infection risk linked to the consumption of fresh cheeses in Ecuador.
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Affiliation(s)
- Lorena Mejía
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Institute for Integrative Systems Biology, University of Valencia, Valencia, Spain
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Valencia, Spain
| | - Estefanía Espinosa-Mata
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Ana Lucía Freire
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Sonia Zapata
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Fernando González-Candelas
- Institute for Integrative Systems Biology, University of Valencia, Valencia, Spain
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Valencia, Spain
- CIBER (Centro de Investigación Biomédica en Red) in Epidemiology and Public Health, Valencia, Spain
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13
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Tibbs-Cortes BW, Schultz DL, Schmitz-Esser S. Closed genome sequences of two Listeria monocytogenes ST121 strains. Microbiol Resour Announc 2023; 12:e0075023. [PMID: 37768047 PMCID: PMC10586163 DOI: 10.1128/mra.00750-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
We performed Oxford Nanopore and Illumina sequencing to generate accurate, closed genomes for the Listeria monocytogenes strains 6179 and L58-55. The new assemblies were generally similar to the previous Illumina-based assemblies, but additional rRNA operons and repeat regions were identified in the new assembly for strain 6179.
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Affiliation(s)
- Bienvenido W. Tibbs-Cortes
- Department of Animal Science, Iowa State University, Ames, Iowa, USA
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, USA
| | - Dylan L. Schultz
- Department of Animal Science, Iowa State University, Ames, Iowa, USA
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, USA
| | - Stephan Schmitz-Esser
- Department of Animal Science, Iowa State University, Ames, Iowa, USA
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, USA
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14
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Centorotola G, Ziba MW, Cornacchia A, Chiaverini A, Torresi M, Guidi F, Cammà C, Bowa B, Mtonga S, Magambwa P, D’Alterio N, Scacchia M, Pomilio F, Muuka G. Listeria monocytogenes in ready to eat meat products from Zambia: phenotypical and genomic characterization of isolates. Front Microbiol 2023; 14:1228726. [PMID: 37711697 PMCID: PMC10498467 DOI: 10.3389/fmicb.2023.1228726] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023] Open
Abstract
The contamination of ready to eat foods (RTE) products due to Listeria monocytogenes could compromise the products safety becoming a great risk for the consumers. The high presence of L. monocytogenes in RTE products has been described worldwide, but few data are available about these products from African countries. The aims of this study were to report the presence of L. monocytogenes in Zambian RTE products, providing genomic characterization and data on similarity with African circulating strains using whole genome sequencing (WGS). A total of 304 RTE products, produced by different Zambian manufacturers, were purchased at retail, from major supermarkets located in Lusaka, Zambia, comprising 130 dairy and 174 meat products. L. monocytogenes was detected only in 18 (10.3%) RTE meat products of the 174 samples tested. The MLST analysis grouped the 18 L. monocytogenes isolates in 7 clonal complexes (CCs): CC1 (n = 5), CC2 (n = 4), CC9 (n = 4), CC5 (n = 2), CC121 (n = 1), CC155 (n = 1), and CC3 (n = 1). According to the cgMLST results, several clusters were detected, in particular belonging to hyper-virulent clones CC1 and CC2. Regarding the virulence factors, a complete L. monocytogenes Pathogenicity Island 3 (LIPI-3) was present both in the CC1 and CC3, in addition to LIPI-1. Several resistance genes and mobile genetic elements were detected, including Stress Islands, the bcrABC cassette and Tn6188_qac transposon, plasmids and intact prophages. Despite being a first preliminary work with a limited number of samples and isolates, this study helped to increase existing knowledge on contaminated RTE products in Zambia, confirming the presence of hyper-virulent L. monocytogenes CCs, which could play an important role in human diseases, posing a public health concern for consumers.
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Affiliation(s)
- Gabriella Centorotola
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Maureen Wakwamba Ziba
- Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka, Zambia
| | - Alessandra Cornacchia
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Alexandra Chiaverini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Marina Torresi
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Fabrizia Guidi
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Benson Bowa
- Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka, Zambia
| | - Samson Mtonga
- Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka, Zambia
| | - Phelly Magambwa
- Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka, Zambia
| | - Nicola D’Alterio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Massimo Scacchia
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Geoffrey Muuka
- Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka, Zambia
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15
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Liao J, Guo X, Li S, Anupoju SMB, Cheng RA, Weller DL, Sullivan G, Zhang H, Deng X, Wiedmann M. Comparative genomics unveils extensive genomic variation between populations of Listeria species in natural and food-associated environments. ISME COMMUNICATIONS 2023; 3:85. [PMID: 37598265 PMCID: PMC10439904 DOI: 10.1038/s43705-023-00293-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/21/2023]
Abstract
Comprehending bacterial genomic variation linked to distinct environments can yield novel insights into mechanisms underlying differential adaptation and transmission of microbes across environments. Gaining such insights is particularly crucial for pathogens as it benefits public health surveillance. However, the understanding of bacterial genomic variation is limited by a scarcity of investigations in genomic variation coupled with different ecological contexts. To address this limitation, we focused on Listeria, an important bacterial genus for food safety that includes the human pathogen L. monocytogenes, and analyzed a large-scale genomic dataset collected by us from natural and food-associated environments across the United States. Through comparative genomics analyses on 449 isolates from the soil and 390 isolates from agricultural water and produce processing facilities representing L. monocytogenes, L. seeligeri, L. innocua, and L. welshimeri, we find that the genomic profiles strongly differ by environments within each species. This is supported by the environment-associated subclades and differential presence of plasmids, stress islands, and accessory genes involved in cell envelope biogenesis and carbohydrate transport and metabolism. Core genomes of Listeria species are also strongly associated with environments and can accurately predict isolation sources at the lineage level in L. monocytogenes using machine learning. We find that the large environment-associated genomic variation in Listeria appears to be jointly driven by soil property, climate, land use, and accompanying bacterial species, chiefly representing Actinobacteria and Proteobacteria. Collectively, our data suggest that populations of Listeria species have genetically adapted to different environments, which may limit their transmission from natural to food-associated environments.
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Affiliation(s)
- Jingqiu Liao
- Department of Food Science, Cornell University, Ithaca, NY, USA.
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA.
| | - Xiaodong Guo
- Department of Food Science, Cornell University, Ithaca, NY, USA
| | - Shaoting Li
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | | | - Rachel A Cheng
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, USA
| | - Daniel L Weller
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, USA
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
| | | | - Hailong Zhang
- Department of Business Information Technology, Virginia Tech, Blacksburg, VA, USA
| | - Xiangyu Deng
- Center for Food Safety, University of Georgia, Griffin, GA, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, USA
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16
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Halbedel S, Sperle I, Lachmann R, Kleta S, Fischer MA, Wamp S, Holzer A, Lüth S, Murr L, Freitag C, Espenhain L, Stephan R, Pietzka A, Schjørring S, Bloemberg G, Wenning M, Al Dahouk S, Wilking H, Flieger A. Large Multicountry Outbreak of Invasive Listeriosis by a Listeria monocytogenes ST394 Clone Linked to Smoked Rainbow Trout, 2020 to 2021. Microbiol Spectr 2023; 11:e0352022. [PMID: 37036341 PMCID: PMC10269727 DOI: 10.1128/spectrum.03520-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 03/17/2023] [Indexed: 04/11/2023] Open
Abstract
Whole-genome sequencing (WGS) has revolutionized surveillance of infectious diseases. Disease outbreaks can now be detected with high precision, and correct attribution of infection sources has been improved. Listeriosis, caused by the bacterium Listeria monocytogenes, is a foodborne disease with a high case fatality rate and a large proportion of outbreak-related cases. Timely recognition of listeriosis outbreaks and precise allocation of food sources are important to prevent further infections and to promote public health. We report the WGS-based identification of a large multinational listeriosis outbreak with 55 cases that affected Germany, Austria, Denmark, and Switzerland during 2020 and 2021. Clinical isolates formed a highly clonal cluster (called Ny9) based on core genome multilocus sequence typing (cgMLST). Routine and ad hoc investigations of food samples identified L. monocytogenes isolates from smoked rainbow trout filets from a Danish producer grouping with the Ny9 cluster. Patient interviews confirmed consumption of rainbow trout as the most likely infection source. The Ny9 cluster was caused by a MLST sequence type (ST) ST394 clone belonging to molecular serogroup IIa, forming a distinct clade within molecular serogroup IIa strains. Analysis of the Ny9 genome revealed clpY, dgcB, and recQ inactivating mutations, but phenotypic characterization of several virulence-associated traits of a representative Ny9 isolate showed that the outbreak strain had the same pathogenic potential as other serogroup IIa strains. Our report demonstrates that international food trade can cause multicountry outbreaks that necessitate cross-border outbreak collaboration. It also corroborates the relevance of ready-to-eat smoked fish products as causes for listeriosis. IMPORTANCE Listeriosis is a severe infectious disease in humans and characterized by an exceptionally high case fatality rate. The disease is transmitted through consumption of food contaminated by the bacterium Listeria monocytogenes. Outbreaks of listeriosis often occur but can be recognized and stopped through implementation of whole-genome sequencing-based pathogen surveillance systems. We here describe the detection and management of a large listeriosis outbreak in Germany and three neighboring countries. This outbreak was caused by rainbow trout filet, which was contaminated by a L. monocytogenes clone belonging to sequence type ST394. This work further expands our knowledge on the genetic diversity and transmission routes of an important foodborne pathogen.
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Affiliation(s)
- Sven Halbedel
- FG11–Division of Enteropathogenic bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
- Institute for Medical Microbiology and Hospital Hygiene, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Ida Sperle
- FG35–Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
- Postgraduate Training for Applied Epidemiology (PAE), Robert Koch Institute, Berlin, Germany
- ECDC Fellowship Program, Field Epidemiology path (EPIET), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Raskit Lachmann
- FG35–Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Sylvia Kleta
- National Reference Laboratory for Listeria monocytogenes, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Martin A. Fischer
- FG11–Division of Enteropathogenic bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Sabrina Wamp
- FG11–Division of Enteropathogenic bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Alexandra Holzer
- FG35–Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Stefanie Lüth
- National Reference Laboratory for Listeria monocytogenes, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Larissa Murr
- State Institute for Food, Food Hygiene and Cosmetics, Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Christin Freitag
- Institute for Food of Animal Origin, Rhineland–Palatinate State Investigation Office, Koblenz, Germany
| | - Laura Espenhain
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Ariane Pietzka
- Austrian Agency for Health and Food Safety, Graz, Austria
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Guido Bloemberg
- Swiss National Center for Enteropathogenic Bacteria and Listeria, Institute for Food Safety and Hygiene, University of Zurich, Switzerland
| | - Mareike Wenning
- State Institute for Food, Food Hygiene and Cosmetics, Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Sascha Al Dahouk
- National Reference Laboratory for Listeria monocytogenes, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Hendrik Wilking
- FG35–Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Antje Flieger
- FG11–Division of Enteropathogenic bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
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17
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Wiktorczyk-Kapischke N, Skowron K, Wałecka-Zacharska E. Genomic and pathogenicity islands of Listeria monocytogenes-overview of selected aspects. Front Mol Biosci 2023; 10:1161486. [PMID: 37388250 PMCID: PMC10300472 DOI: 10.3389/fmolb.2023.1161486] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023] Open
Abstract
Listeria monocytogenes causes listeriosis, a disease characterized by a high mortality rate (up to 30%). Since the pathogen is highly tolerant to changing conditions (high and low temperature, wide pH range, low availability of nutrients), it is widespread in the environment, e.g., water, soil, or food. L. monocytogenes possess a number of genes that determine its high virulence potential, i.e., genes involved in the intracellular cycle (e.g., prfA, hly, plcA, plcB, inlA, inlB), response to stress conditions (e.g., sigB, gadA, caspD, clpB, lmo1138), biofilm formation (e.g., agr, luxS), or resistance to disinfectants (e.g., emrELm, bcrABC, mdrL). Some genes are organized into genomic and pathogenicity islands. The islands LIPI-1 and LIPI-3 contain genes related to the infectious life cycle and survival in the food processing environment, while LGI-1 and LGI-2 potentially ensure survival and durability in the production environment. Researchers constantly have been searching for new genes determining the virulence of L. monocytogenes. Understanding the virulence potential of L. monocytogenes is an important element of public health protection, as highly pathogenic strains may be associated with outbreaks and the severity of listeriosis. This review summarizes the selected aspects of L. monocytogenes genomic and pathogenicity islands, and the importance of whole genome sequencing for epidemiological purposes.
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Affiliation(s)
- Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Ewa Wałecka-Zacharska
- Department of Food Hygiene and Consumer Health, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
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Guidi F, Centorotola G, Chiaverini A, Iannetti L, Schirone M, Visciano P, Cornacchia A, Scattolini S, Pomilio F, D’Alterio N, Torresi M. The Slaughterhouse as Hotspot of CC1 and CC6 Listeria monocytogenes Strains with Hypervirulent Profiles in an Integrated Poultry Chain of Italy. Microorganisms 2023; 11:1543. [PMID: 37375045 PMCID: PMC10305255 DOI: 10.3390/microorganisms11061543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
In Europe, very few studies are available regarding the diversity of Listeria monocytogenes (L. monocytogenes) clonal complexes (CCs) and sequence types (ST) in poultry and on the related typing of isolates using whole genome sequencing (WGS). In this study, we used a WGS approach to type 122 L. monocytogenes strains isolated from chicken neck skin samples collected in two different slaughterhouses of an integrated Italian poultry company. The studied strains were classified into five CCs: CC1-ST1 (21.3%), CC6-ST6 (22.9%), CC9-ST9 (44.2%), CC121-ST121 (10.6%) and CC193-ST193 (0.8%). CC1 and CC6 strains presented a virulence gene profile composed of 60 virulence genes and including the Listeria Pathogenicity Island 3, aut_IVb, gltA and gltB. According to cgMLST and SNPs analysis, long-term persistent clusters belonging to CC1 and CC6 were found in one of the two slaughterhouses. The reasons mediating the persistence of these CCs (up to 20 months) remain to be elucidated, and may involve the presence and the expression of stress response and environmental adaptation genes including heavy metals resistance genes (cadAC, arsBC, CsoR-copA-copZ), multidrug efflux pumps (mrpABCEF, EmrB, mepA, bmrA, bmr3, norm), cold-shock tolerance (cspD) and biofilm-formation determinants (lmo0673, lmo2504, luxS, recO). These findings indicated a serious risk of poultry finished products contamination with hypervirulent L. monocytogenes clones and raised concern for the consumer health. In addition to the AMR genes norB, mprF, lin and fosX, ubiquitous in L. monocytogenes strains, we also identified parC for quinolones, msrA for macrolides and tetA for tetracyclines. Although the phenotypical expression of these AMR genes was not tested, none of them is known to confer resistance to the primary antibiotics used to treat listeriosis The obtained results increase the data on the L. monocytogenes clones circulating in Italy and in particular in the poultry chain.
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Affiliation(s)
- Fabrizia Guidi
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Gabriella Centorotola
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Alexandra Chiaverini
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Luigi Iannetti
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Maria Schirone
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini, 1, 64100 Teramo, Italy; (M.S.); (P.V.)
| | - Pierina Visciano
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini, 1, 64100 Teramo, Italy; (M.S.); (P.V.)
| | - Alessandra Cornacchia
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Silvia Scattolini
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Nicola D’Alterio
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Marina Torresi
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
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Molecular typing and genome sequencing allow the identification of persistent Listeria monocytogenes strains and the tracking of the contamination source in food environments. Int J Food Microbiol 2023; 386:110025. [PMID: 36436413 DOI: 10.1016/j.ijfoodmicro.2022.110025] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/08/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
The presence of Listeria monocytogenes (Lm) in the food processing environment (facilities and products) is a challenging problem in food safety management. Lm is one of the main causes of mortality in foodborne infections, and the trend is continuously increasing. In this study, a collection of 323 Lm strain isolates recovered from food matrices and food industry environments (surfaces and equipment) over four years from 80 food processing facilities was screened using a restriction site-associated tag sequencing (2b-RAD) typing approach developed for Lm. Thirty-six different restriction site-associated DNA (RAD) types (RTs) were identified, most of which correspond to lineage II. RT1, the most represented genotype in our collection and already reported as one of the most prevalent genotypes in the food environment, was significantly associated with meat processing facilities. The sequencing of the genomes of strains belonging to the same RT and isolated in the same facility in different years revealed several clusters of persistence. The definition of the persistent strains (PSs) allowed the identification of the potential source of contamination in the incoming raw meat that is introduced in the facility to be processed. The slaughterhouses, which, according to the European Union (EU) regulation, are not inspected for the presence of Lm could be hotspots for the persistence of Lm PSs.
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20
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Xu J, Wu S, Liu M, Xiao Z, Peng Y, He H. Prevalence and contamination patterns of Listeria monocytogenes in Pleurotus eryngii (king oyster mushroom) production plants. Front Microbiol 2023; 14:1064575. [PMID: 36778843 PMCID: PMC9912299 DOI: 10.3389/fmicb.2023.1064575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/03/2023] [Indexed: 01/29/2023] Open
Abstract
Listeria monocytogenes is a major foodborne pathogen that is well-known for its high mortality rate upon infection. In recent years, the edible mushroom has also been found to be an important source of L. monocytogenes, but the contamination sources in Pleurotus eryngii (the king oyster mushroom) were unclear. In this study, a total of 203 edible mushrooms and environmental samples from four P. eryngii production plants were obtained. As a result, 29 samples (14.3%) were positive for L. monocytogenes, including eight mushroom samples (13.3%, 8/60) and 21 associated environmental samples (14.7%, 21/143). The contamination of L. monocytogenes in plants A and B was more severe and was likely to originate from the mycelium stimulation machine. The isolates belonged to serogroups II.1 (4b-4d-4e), I.1 (1/2a-3a), and I.2 (1/2c-3c), and multilocus sequence typing (MLST) revealed that these L. monocytogenes strains belonged to five different sequence types (ST3, ST121, ST9, ST87, and ST224). The ST121 and ST3 isolates were only found in plants A and B, respectively. The isolates were carried by hly (29/29, 100%), inlB (23/29, 79.3%), inlA (29/29, 100%), inlC (29/29, 100%), inlJ (29/29, 100%), actA (19/29, 65.5%), iap (29/29, 100%), plcA (26/29, 100%), plcB (29/29, 100%), prfA (27/29, 93.1%), and mpl (29/29, 100%). Further study of inlA sequencing showed that 65.5% of strains (19/29) contained full-length InlA that was required for host cell invasion, whereas the mutation led to premature stop codons (PMSCs) at position 492 (type 6) on inlA alleles. All isolates in this survey were sensitive to gentamicin, kanamycin, sulbactam/ampicillin, trimethoprim-sulfamethoxazole, tetracycline, and doxycycline. The drug with the highest resistance is rifampicin (37.9%), followed by penicillin (24.1%) and ciprofloxacin (10.3%). Most multiply resistant strains are isolated from raw materials and equipment of the P. eryngii processing lines. Our study reflects the contamination patterns and potential risk of L. monocytogenes infection in P. eryngii production plants. The persistence of specific L. monocytogenes isolates (such as ST121 and ST3) may assist with contamination. In accordance with these results, the control of L. monocytogenes should focus on the environmental materials, especially in the mycelium stimulation stage. However, effective Listeria monitoring programs will allow for the improved development of Listeria control measures to minimize cross-contamination in the processing of P. eryngii.
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Affiliation(s)
- Jiang Xu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China,*Correspondence: Shi Wu,
| | - Ming Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Zitian Xiao
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yangyang Peng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Huanqing He
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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21
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Lakicevic B, Jankovic V, Pietzka A, Ruppitsch W. Wholegenome sequencing as the gold standard approach for control of Listeria monocytogenes in the food chain. J Food Prot 2023; 86:100003. [PMID: 36916580 DOI: 10.1016/j.jfp.2022.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 10/05/2022] [Accepted: 10/19/2022] [Indexed: 12/23/2022]
Abstract
Listeria monocytogenes has been implicated in numerous outbreaks and related deaths of listeriosis. In food production, L. monocytogenes occurs in raw food material and above all, through postprocessing contamination. The use of next-generation sequencing technologies such as whole-genome sequencing (WGS) facilitates foodborne outbreak investigations, pathogen source tracking and tracing geographic distributions of different clonal complexes, routine microbiological/epidemiological surveillance of listeriosis, and quantitative microbial risk assessment. WGS can also be used to predict various genetic traits related to virulence, stress, or antimicrobial resistance, which can be of great benefit for improving food safety management as well as public health.
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Affiliation(s)
- Brankica Lakicevic
- Department for Microbiological and Molecular-biological Testing, Institute of Meat Hygiene and Technology, Belgrade, Serbia.
| | - Vesna Jankovic
- Department for Microbiological and Molecular-biological Testing, Institute of Meat Hygiene and Technology, Belgrade, Serbia
| | - Ariane Pietzka
- Institute of Medical Microbiology and Hygiene/National Reference Laboratory for Listeria Division for Public Health, Austrian Agency for Health and Food Safety, Graz, Austria
| | - Werner Ruppitsch
- Institute of Medical Microbiology and Hygiene Division for Public Health, Austrian Agency for Health and Food Safety, Vienna, Austria
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22
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Cardenas-Alvarez MX, Zeng H, Webb BT, Mani R, Muñoz M, Bergholz TM. Comparative Genomics of Listeria monocytogenes Isolates from Ruminant Listeriosis Cases in the Midwest United States. Microbiol Spectr 2022; 10:e0157922. [PMID: 36314928 PMCID: PMC9769944 DOI: 10.1128/spectrum.01579-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022] Open
Abstract
Ruminants are a well-known reservoir for Listeria monocytogenes. In addition to asymptomatic carriage of the pathogen, ruminants can also acquire listeriosis and develop clinical manifestations in the form of neurologic or fetal infections, similar to those occurring in humans. Genomic characterization of ruminant listeriosis cases in Europe have identified lineage 1 and 2 strains associated with infection, as well as clonal complexes (CCs) that are commonly isolated from human cases of listeriosis; however, there is little information on the diversity of L. monocytogenes from ruminant listeriosis in the United States. In this study, we characterized and compared 73 L. monocytogenes isolates from ruminant listeriosis cases from the Midwest and the Upper Great Plains collected from 2015 to 2020. Using whole-genome sequence data, we classified the isolates and identified key virulence factors, stress-associated genes, and mobile genetic elements within our data set. Our isolates belonged to three different lineages: 31% to lineage 1, 53% to lineage 2, and 15% to lineage 3. Lineage 1 and 3 isolates were associated with neurologic infections, while lineage 2 showed a greater frequency of fetal infections. Additionally, the presence of mobile elements, virulence-associated genes, and stress and antimicrobial resistance genes was evaluated. These genetic elements are responsible for most of the subgroup-specific features and may play a key role in the spread of hypervirulent clones, including the spread of hypervirulent CC1 clone commonly associated with disease in humans, and may explain the increased frequency of certain clones in the area. IMPORTANCE Listeria monocytogenes affects humans and animals, causing encephalitis, septicemia, and abortions, among other clinical outcomes. Ruminants such as cattle, goats, and sheep are the main carriers contributing to the maintenance and dispersal of this pathogen in the farm environment. Contamination of food products from farms is of concern not only because many L. monocytogenes genotypes found there are associated with human listeriosis but also as a cause of significant economic losses when livestock and food products are affected. Ruminant listeriosis has been characterized extensively in Europe; however, there is limited information about the genetic diversity of these cases in the United States. Identification of subgroups with a greater ability to spread may facilitate surveillance and management of listeriosis and contribute to a better understanding of the genome diversity of this pathogen, providing insights into the molecular epidemiology of ruminant listeriosis in the region.
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Affiliation(s)
- Maria X. Cardenas-Alvarez
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Hui Zeng
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, Michigan, USA
| | - Brett T. Webb
- Veterinary Diagnostic Laboratory, North Dakota State University, Fargo, North Dakota, USA
| | - Rinosh Mani
- Veterinary Diagnostic Laboratory, Michigan State University, Lansing, Michigan, USA
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Teresa M. Bergholz
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, Michigan, USA
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23
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Li X, Shi X, Song Y, Yao S, Li K, Shi B, Sun J, Liu Z, Zhao W, Zhao C, Wang J. Genetic diversity, antibiotic resistance, and virulence profiles of Listeria monocytogenes from retail meat and meat processing. Food Res Int 2022; 162:112040. [DOI: 10.1016/j.foodres.2022.112040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/30/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022]
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24
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Song Z, Ji S, Wang Y, Luo L, Wang Y, Mao P, Li L, Jiang H, Ye C. The population structure and genetic diversity of Listeria monocytogenes ST9 strains based on genomic analysis. Front Microbiol 2022; 13:982220. [PMID: 36425025 PMCID: PMC9680904 DOI: 10.3389/fmicb.2022.982220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/22/2022] [Indexed: 05/29/2024] Open
Abstract
Listeria monocytogenes is a ubiquitous foodborne pathogen causing both invasive and non-invasive listeriosis. Sequence type (ST) 9 strains is common in food and food processing environments. In this study, the whole-genome sequences (WGS) of 207 ST9 isolates from different sources, geographical locations (14 countries), and isolated years were analyzed. The ST9 isolates were divided into three clusters after phylogenetic analysis; 67.63% of ST9 isolates contained putative plasmids with different sizes and genomic structure, the putative prophages inserted in the chromosome at ten hotspots, and seven types of premature stop codon (PMSC) mutations in inlA were found in 81.86% of the ST9 isolates. In addition, 78.26% of ST9 isolates harbored Tn554-like elements carrying arsenic resistance genes. All the ST9 isolates conservatively contained environment-resistance genes on the chromosome. This analysis of population structures and features of ST9 isolates was aimed to help develop effective strategies to control this prevalent pathogen in the food chain.
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Affiliation(s)
- Zexuan Song
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shunshi Ji
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yan Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lijuan Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Yiqian Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Pan Mao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lingling Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huaying Jiang
- Department of Clinical Laboratory, People's Hospital of Xindu District, Chengdu, China
| | - Changyun Ye
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
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Murr L, Huber I, Pavlovic M, Guertler P, Messelhaeusser U, Weiss M, Ehrmann M, Tuschak C, Bauer H, Wenning M, Busch U, Bretschneider N. Whole-Genome Sequence Comparisons of Listeria monocytogenes Isolated from Meat and Fish Reveal High Inter- and Intra-Sample Diversity. Microorganisms 2022; 10:2120. [PMID: 36363712 PMCID: PMC9698462 DOI: 10.3390/microorganisms10112120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/15/2022] [Accepted: 10/21/2022] [Indexed: 09/10/2024] Open
Abstract
Interpretation of whole-genome sequencing (WGS) data for foodborne outbreak investigations is complex, as the genetic diversity within processing plants and transmission events need to be considered. In this study, we analyzed 92 food-associated Listeria monocytogenes isolates by WGS-based methods. We aimed to examine the genetic diversity within meat and fish production chains and to assess the applicability of suggested thresholds for clustering of potentially related isolates. Therefore, meat-associated isolates originating from the same samples or processing plants as well as fish-associated isolates were analyzed as distinct sets. In silico serogrouping, multilocus sequence typing (MLST), core genome MLST (cgMLST), and pangenome analysis were combined with screenings for prophages and genetic traits. Isolates of the same subtypes (cgMLST types (CTs) or MLST sequence types (STs)) were additionally compared by SNP calling. This revealed the occurrence of more than one CT within all three investigated plants and within two samples. Analysis of the fish set resulted in predominant assignment of isolates from pangasius catfish and salmon to ST2 and ST121, respectively, potentially indicating persistence within the respective production chains. The approach not only allowed the detection of distinct subtypes but also the determination of differences between closely related isolates, which need to be considered when interpreting WGS data for surveillance.
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Affiliation(s)
- Larissa Murr
- Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany
- TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany
| | - Melanie Pavlovic
- Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany
| | - Patrick Guertler
- Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany
| | - Ute Messelhaeusser
- Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany
| | - Manuela Weiss
- Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany
| | - Matthias Ehrmann
- TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Christian Tuschak
- Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany
| | - Hans Bauer
- Bavarian Health and Food Safety Authority (LGL), 91058 Erlangen, Germany
| | - Mareike Wenning
- Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany
| | - Ulrich Busch
- Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany
| | - Nancy Bretschneider
- Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany
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26
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Mafuna T, Matle I, Magwedere K, Pierneef RE, Reva ON. Comparative Genomics of Listeria Species Recovered from Meat and Food Processing Facilities. Microbiol Spectr 2022; 10:e0118922. [PMID: 36066257 PMCID: PMC9604131 DOI: 10.1128/spectrum.01189-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/12/2022] [Indexed: 12/30/2022] Open
Abstract
Listeria species (spp.) are contaminants that can survive in food, on equipment, and on food processing premises if appropriate hygiene measures are not used. Homologous stress tolerance genes, virulence gene clusters such as the prfA cluster, and clusters of internalin genes that contribute to the pathogenic potential of the strains can be carried by both pathogenic and nonpathogenic Listeria spp. To enhance understanding of the genome evolution of virulence and virulence-associated properties, a comparative genome approach was used to analyze 41 genome sequences belonging to L. innocua and L. welshimeri isolated from food and food processing facilities. Genetic determinants responsible for disinfectant and stress tolerance were identified, including the efflux cassette bcrABC and Tn6188_qac_1 disinfectant resistance determinant, and stress survival islets. These disinfectant-resistant genes were more frequently found in L. innocua (12%) than in L. welshimeri (2%). Several isolates representing the presumed nonpathogenic L. innocua still carried virulence-associated genes, including LGI2, LGI3, LIPI-3, and LIPI-4 which were absent in all L. welshimeri isolates. The mobile genetic elements identified were plasmids (pLGUG1 and J1776) and prophages (PHAGE_Lister_vB_LmoS_188, PHAGE_Lister_LP_030_3, PHAGE_Lister_A118, PHAGE_Lister_B054, and PHAGE_Lister_vB_LmoS_293). The results suggest that the presumed nonpathogenic isolates especially L. innocua can carry genes relevant to the strain's virulence and stress tolerance in the food and food processing facilities. IMPORTANCE This study provides genomic insights into the recently expanded genus in order to gain valuable information about the evolution of the virulence and stress tolerance properties of the genus Listeria and the distribution of these genetic elements pertinent to the pathogenic potential across Listeria spp. and clonal lineages in South Africa (SA).
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Affiliation(s)
- T. Mafuna
- Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - I. Matle
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa
| | - K. Magwedere
- Directorate of Veterinary Public Health, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
| | - R. E. Pierneef
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - O. N. Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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27
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Whole-Genome Sequencing-Based Characterization of
Listeria
Isolates from Produce Packinghouses and Fresh-Cut Facilities Suggests Both Persistence and Reintroduction of Fully Virulent L. monocytogenes. Appl Environ Microbiol 2022; 88:e0117722. [PMID: 36286532 PMCID: PMC9680643 DOI: 10.1128/aem.01177-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The contamination of ready-to-eat produce with Listeria monocytogenes (LM) can often be traced back to environmental sources in processing facilities and packinghouses. To provide an improved understanding of Listeria sources and transmission in produce operations, we performed whole-genome sequencing (WGS) of LM (n = 169) and other Listeria spp. (n = 107) obtained from 13 produce packinghouses and three fresh-cut produce facilities. Overall, a low proportion of LM isolates (9/169) had inlA premature stop codons, and a large proportion (83/169) had either or both of the LIPI-3 or LIPI-4 operons, which have been associated with hypervirulence. The further analysis of the WGS data by operation showed a reisolation (at least 2 months apart) of highly related isolates (<10 hqSNP differences) in 7/16 operations. Two operations had highly related strains reisolated from samples that were collected at least 1 year apart. The identification of isolates collected during preproduction (i.e., following sanitation but before the start of production) that were highly related to isolates collected during production (i.e., after people or products have entered and begun moving through the operation) provided evidence that some strains were able to survive standard sanitation practices. The identification of closely related isolates (<20 hqSNPs differences) in different operations suggests that cross-contamination between facilities or introductions from common suppliers may also contribute to Listeria transmission. Overall, our data suggest that the majority of LM isolates collected from produce operations are fully virulent and that both persistence and reintroduction may lead to the repeat isolation of closely related Listeria in produce operations. IMPORTANCEListeria monocytogenes is of particular concern to the produce industry due to its frequent presence in natural environments as well as its ability to survive in packinghouses and fresh-cut processing facilities over time. The use of whole-genome sequencing, which provides high discriminatory power for the characterization of Listeria isolates, along with detailed source data (isolation date and sample location) shows that the presence of Listeria in produce operations appears to be due to random and continued reintroduction as well as to the persistence of highly related strains in both packinghouses and fresh-cut facilities. These findings indicate the importance of using high-resolution characterization approaches for root cause analyses of Listeria contamination issues. In cases of repeat isolation of closely related Listeria in a given facility, both persistence and reintroduction need to be considered as possible root causes.
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Anast JM, Etter AJ, Schmitz‐Esser S. Comparative analysis of Listeria monocytogenes plasmid transcriptomes reveals common and plasmid-specific gene expression patterns and high expression of noncoding RNAs. Microbiologyopen 2022; 11:e1315. [PMID: 36314750 PMCID: PMC9484302 DOI: 10.1002/mbo3.1315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 11/09/2022] Open
Abstract
Recent research demonstrated that some Listeria monocytogenes plasmids contribute to stress survival. However, only a few studies have analyzed gene expression patterns of L. monocytogenes plasmids. In this study, we identified four previously published stress-response-associated transcriptomic data sets which studied plasmid-harboring L. monocytogenes strains but did not include an analysis of the plasmid transcriptomes. The four transcriptome data sets encompass three distinct plasmids from three different L. monocytogenes strains. Differential gene expression analysis of these plasmids revealed that the number of differentially expressed (DE) L. monocytogenes plasmid genes ranged from 30 to 45 with log2 fold changes of -2.2 to 6.8, depending on the plasmid. Genes often found to be DE included the cadmium resistance genes cadA and cadC, a gene encoding a putative NADH peroxidase, the putative ultraviolet resistance gene uvrX, and several uncharacterized noncoding RNAs (ncRNAs). Plasmid-encoded ncRNAs were consistently among the highest expressed genes. In addition, one of the data sets utilized the same experimental conditions for two different strains harboring distinct plasmids. We found that the gene expression patterns of these two L. monocytogenes plasmids were highly divergent despite the identical treatments. These data suggest plasmid-specific gene expression responses to environmental stimuli and differential plasmid regulation mechanisms between L. monocytogenes strains. Our findings further our understanding of the dynamic expression of L. monocytogenes plasmid-encoded genes in diverse environmental conditions and highlight the need to expand the study of L. monocytogenes plasmid genes' functions.
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Affiliation(s)
- Justin M. Anast
- Department of Animal ScienceIowa State UniversityAmesIowaUSA
- Interdepartmental Microbiology Graduate ProgramIowa State UniversityAmesIowaUSA
| | - Andrea J. Etter
- Department of Nutrition and Food SciencesThe University of VermontBurlingtonVermontUSA
| | - Stephan Schmitz‐Esser
- Department of Animal ScienceIowa State UniversityAmesIowaUSA
- Interdepartmental Microbiology Graduate ProgramIowa State UniversityAmesIowaUSA
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Shen J, Zhang G, Yang J, Zhao L, Jiang Y, Guo D, Wang X, Zhi S, Xu X, Dong Q, Wang X. Prevalence, antibiotic resistance, and molecular epidemiology of Listeria monocytogenes isolated from imported foods in China during 2018 to 2020. Int J Food Microbiol 2022; 382:109916. [PMID: 36126498 DOI: 10.1016/j.ijfoodmicro.2022.109916] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 04/19/2022] [Accepted: 09/02/2022] [Indexed: 10/14/2022]
Abstract
A total of 1797 imported food samples collected during 2018 to 2020 were investigated for Listeria monocytogenes. Antibiotic susceptibility tests and whole genome sequencing analysis were performed for the obtained isolates. The overall prevalence of L. monocytogenes was 5.62 %; the highest prevalence was observed for pork (13.65 %), followed by fish (6.25 %), sheep casing (6.06 %), chicken (3.61 %), and beef (2.06 %). Geographical differences in prevalence were also observed for pork. Resistance to oxacillin (39.33 %) and clindamycin (16.85 %) was common, whereas resistance rates for other antibiotics were relatively low, ranging from 0 % to 6.74 %. Pork and fish isolates showed resistance to more antibiotics than beef isolates. Tetracycline and chloramphenicol resistance phenotypes strongly correlated with genotypes. The predominant serogroup was 1/2a, 3a, at 44.44 %, while the percentages of three other serogroups were similar and relatively lower, from 17.28 % to 19.75 %. Significant genetic differences were observed among lineage I and II isolates. LIPI-3 was carried by 19.75 % (16/81) of isolates and LIPI-4 by 6.17 % (5/81); all were lineage I. The stress survival island was present in 31.03 % (9/29) of lineage I and 83.02 % (44/53) of lineage II. Benzalkonium chloride tolerance genes were carried by 10.34 % (3/29) of lineage I and 23.08 % (12/52) of lineage II isolates. A total of 25 sequence types (STs) were identified, among which one was novel; ST9 and ST121 were the most prevalent. Disparate distribution of STs among food types was observed, and geographical and food related characteristics were also found for some STs. Hypervirulent STs, such as ST1, ST4 and ST6, belonged to 4b,4e,4e; carried LIPI-3 and/or LIPI-4; and some even were ECI or ECII; while only one carried SSI or BC tolerance genes. In contrast, hypo-virulent STs such as ST9 and ST121 carried SSI and BC tolerance genes, while none had LIPI-3/LIPI-4. Certain STs were detected frequently from a particular food of a particular country for a long time, indicating more attention should be given to these special persistent isolates. These findings are valuable for source tracking, prevention and control of L. monocytogenes in the global food chain.
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Affiliation(s)
- Jinling Shen
- Technology Center for Animal Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai 200135, China
| | - Guodong Zhang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA
| | - Jielin Yang
- Technology Center for Animal Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai 200135, China
| | - Lina Zhao
- Technology Center for Animal Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai 200135, China
| | - Yuan Jiang
- Technology Center for Animal Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai 200135, China; Jiangsu Collaborative Innovation Center of Meat Production and Processing, Nanjing 210095, China.
| | - Dehua Guo
- Technology Center for Animal Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai 200135, China
| | - Xuan Wang
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Shuai Zhi
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Xuebin Xu
- Shanghai Centers for Disease Prevention and Control, Shanghai 200336, China
| | - Qingli Dong
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xiang Wang
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
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Osek J, Lachtara B, Wieczorek K. Listeria monocytogenes in foods-From culture identification to whole-genome characteristics. Food Sci Nutr 2022; 10:2825-2854. [PMID: 36171778 PMCID: PMC9469866 DOI: 10.1002/fsn3.2910] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/06/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen, which is able to persist in the food production environments. The presence of these bacteria in different niches makes them a potential threat for public health. In the present review, the current information on the classical and alternative methods used for isolation and identification of L. monocytogenes in food have been described. Although these techniques are usually simple, standardized, inexpensive, and are routinely used in many food testing laboratories, several alternative molecular-based approaches for the bacteria detection in food and food production environments have been developed. They are characterized by the high sample throughput, a short time of analysis, and cost-effectiveness. However, these methods are important for the routine testing toward the presence and number of L. monocytogenes, but are not suitable for characteristics and typing of the bacterial isolates, which are crucial in the study of listeriosis infections. For these purposes, novel approaches, with a high discriminatory power to genetically distinguish the strains during epidemiological studies, have been developed, e.g., whole-genome sequence-based techniques such as NGS which provide an opportunity to perform comparison between strains of the same species. In the present review, we have shown a short description of the principles of microbiological, alternative, and modern methods of detection of L. monocytogenes in foods and characterization of the isolates for epidemiological purposes. According to our knowledge, similar comprehensive papers on such subject have not been recently published, and we hope that the current review may be interesting for research communities.
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Affiliation(s)
- Jacek Osek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Beata Lachtara
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Kinga Wieczorek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
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Pervasive Listeria monocytogenes Is Common in the Norwegian Food System and Is Associated with Increased Prevalence of Stress Survival and Resistance Determinants. Appl Environ Microbiol 2022; 88:e0086122. [PMID: 36005805 PMCID: PMC9499026 DOI: 10.1128/aem.00861-22] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
To investigate the diversity, distribution, persistence, and prevalence of stress survival and resistance genes of Listeria monocytogenes clones dominating in food processing environments in Norway, genome sequences from 769 L. monocytogenes isolates from food industry environments, foods, and raw materials (512 of which were sequenced in the present study) were subjected to whole-genome multilocus sequence typing (wgMLST), single-nucleotide polymorphism (SNP), and comparative genomic analyses. The data set comprised isolates from nine meat and six salmon processing facilities in Norway collected over a period of three decades. The most prevalent clonal complex (CC) was CC121, found in 10 factories, followed by CC7, CC8, and CC9, found in 7 factories each. Overall, 72% of the isolates were classified as persistent, showing 20 or fewer wgMLST allelic differences toward an isolate found in the same factory in a different calendar year. Moreover, over half of the isolates (56%) showed this level of genetic similarity toward an isolate collected from a different food processing facility. These were designated as pervasive strains, defined as clusters with the same level of genetic similarity as persistent strains but isolated from different factories. The prevalence of genetic determinants associated with increased survival in food processing environments, including heavy metal and biocide resistance determinants, stress response genes, and inlA truncation mutations, showed a highly significant increase among pervasive isolates but not among persistent isolates. Furthermore, these genes were significantly more prevalent among the isolates from food processing environments compared to in isolates from natural and rural environments (n = 218) and clinical isolates (n = 111) from Norway. IMPORTANCEListeria monocytogenes can persist in food processing environments for months to decades and spread through the food system by, e.g., contaminated raw materials. Knowledge of the distribution and diversity of L. monocytogenes is important in outbreak investigations and is essential to effectively track and control this pathogen in the food system. The present study presents a comprehensive overview of the prevalence of persistent clones and of the diversity of L. monocytogenes in Norwegian food processing facilities. The results demonstrate extensive spread of highly similar strains throughout the Norwegian food system, in that 56% of the 769 collected isolates from food processing factories belonged to clusters of L. monocytogenes identified in more than one facility. These strains were associated with an overall increase in the prevalence of plasmids and determinants of heavy metal and biocide resistance, as well as other genetic elements associated with stress survival mechanisms and persistence.
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Persistence of Listeria monocytogenes ST5 in Ready-to-Eat Food Processing Environment. Foods 2022; 11:foods11172561. [PMID: 36076746 PMCID: PMC9454991 DOI: 10.3390/foods11172561] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/05/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
Most human listeriosis is foodborne, and ready-to-eat (RET) foods contaminated by Listeria monocytogenes during processing are found to be common vehicles. In this study, a total of four L. monocytogens STs (ST5, ST121, ST120, and ST2) have been identified in two RTE food plants from 2019 to 2020 in Shanghai, China. The L. monocytogenes ST5 was predominant in one RTE food processing plant, and it persists in the RTE meat processing plant with continued clone transmission. The genetic features of the four STs isolates were different. ST5 and ST121 had the three genes clpL, mdrL, and lde; however, ST120 and ST2 had two genes except for clpL. SSI-1was present in ST5, ST121, and ST120. Additionally, SSI-2 was present only in the ST121 isolates. ST120 had all six biofilm-forming associated genes (actA, prfA, lmo0673, recO, lmo2504 and luxS). The ST2 isolate had only three biofilm-forming associated genes, which were prfA, lmo0673, and recO. The four ST isolates had different biofilm formation abilities at different stages. The biofilm formation ability of ST120 was significantly higher when grown for one day. However, the biofilm formation ability of ST120 reduced significantly after growing for four days. In contrast, the biofilm formation ability of ST5 and ST121 increased significantly. These results suggested that ST5 and ST121 had stronger ability to adapt to stressful environments. Biofilms formed by all four STs grown over four days can be sanitized entirely by a disinfectant concentration of 500 mg/L. Additionally, only ST5 and ST121 biofilm cells survived in sub-lethal concentrations of chlorine-containing disinfectant. These results suggested that ST5 and ST121 were more resistant to chlorine-containing disinfectants. These results indicated that the biofilm formation ability of L. monocytogenes isolates changed at different stages. Additionally, the persistence in food processing environments might be verified by the biofilm formation, stress resistance, etc. Alternatively, these results underlined that disinfectants should be used at lethal concentrations. More attention should be paid to ST5 and ST121, and stronger surveillance should be taken to prevent and control the clonal spread of L. monocytogenes isolates in food processing plants in Shanghai.
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Wu J, NicAogáin K, McAuliffe O, Jordan K, O’Byrne C. Phylogenetic and Phenotypic Analyses of a Collection of Food and Clinical Listeria monocytogenes Isolates Reveal Loss of Function of Sigma B from Several Clonal Complexes. Appl Environ Microbiol 2022; 88:e0005122. [PMID: 35481758 PMCID: PMC9128516 DOI: 10.1128/aem.00051-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/17/2022] [Indexed: 12/14/2022] Open
Abstract
To understand the molecular mechanisms that contribute to the stress responses of the important foodborne pathogen Listeria monocytogenes, we collected 139 strains (meat, n = 25; dairy, n = 10; vegetable, n = 8; seafood, n = 14; mixed food, n = 4; and food processing environments, n = 78), mostly isolated in Ireland, and subjected them to whole-genome sequencing. These strains were compared to 25 Irish clinical isolates and 4 well-studied reference strains. Core genome and pan-genome analysis confirmed a highly clonal and deeply branched population structure. Multilocus sequence typing showed that this collection contained a diverse range of strains from L. monocytogenes lineages I and II. Several groups of isolates with highly similar genome content were traced to single or multiple food business operators, providing evidence of strain persistence or prevalence, respectively. Phenotypic screening assays for tolerance to salt stress and resistance to acid stress revealed variants within several clonal complexes that were phenotypically distinct. Five of these phenotypic outliers were found to carry mutations in the sigB operon, which encodes the stress-inducible sigma factor sigma B. Transcriptional analysis confirmed that three of the strains that carried mutations in sigB, rsbV, or rsbU had reduced SigB activity, as predicted. These strains exhibited increased tolerance to salt stress and displayed decreased resistance to low pH stress. Overall, this study shows that loss-of-function mutations in the sigB operon are comparatively common in field isolates, probably reflecting the cost of the general stress response to reproductive fitness in this pathogen. IMPORTANCE The bacterial foodborne pathogen Listeria monocytogenes frequently contaminates various categories of food products and is able to cause life-threatening infections when ingested by humans. Thus, it is important to control the growth of this bacterium in food by understanding the mechanisms that allow its proliferation under suboptimal conditions. In this study, intraspecies heterogeneity in stress response was observed across a collection consisting of mainly Irish L. monocytogenes isolates. Through comparisons of genome sequence and phenotypes observed, we identified three strains with impairment of the general stress response regulator SigB. Two of these strains are used widely in food challenge studies for evaluating the growth potential of L. monocytogenes. Given that loss of SigB function is associated with atypical phenotypic properties, the use of these strains in food challenge studies should be re-evaluated.
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Affiliation(s)
- Jialun Wu
- Bacterial Stress Response Group, Microbiology, School of Biological and Chemical Sciences, National University of Ireland, Galway, Ireland
| | - Kerrie NicAogáin
- Bacterial Stress Response Group, Microbiology, School of Biological and Chemical Sciences, National University of Ireland, Galway, Ireland
| | | | - Kieran Jordan
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Conor O’Byrne
- Bacterial Stress Response Group, Microbiology, School of Biological and Chemical Sciences, National University of Ireland, Galway, Ireland
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Osek J, Lachtara B, Wieczorek K. Listeria monocytogenes - How This Pathogen Survives in Food-Production Environments? Front Microbiol 2022; 13:866462. [PMID: 35558128 PMCID: PMC9087598 DOI: 10.3389/fmicb.2022.866462] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/04/2022] [Indexed: 12/13/2022] Open
Abstract
The foodborne pathogen Listeria monocytogenes is the causative agent of human listeriosis, a severe disease, especially dangerous for the elderly, pregnant women, and newborns. Although this infection is comparatively rare, it is often associated with a significant mortality rate of 20-30% worldwide. Therefore, this microorganism has an important impact on food safety. L. monocytogenes can adapt, survive and even grow over a wide range of food production environmental stress conditions such as temperatures, low and high pH, high salt concentration, ultraviolet lights, presence of biocides and heavy metals. Furthermore, this bacterium is also able to form biofilm structures on a variety of surfaces in food production environments which makes it difficult to remove and allows it to persist for a long time. This increases the risk of contamination of food production facilities and finally foods. The present review focuses on the key issues related to the molecular mechanisms of the pathogen survival and adaptation to adverse environmental conditions. Knowledge and understanding of the L. monocytogenes adaptation approaches to environmental stress factors will have a significant influence on the development of new, efficient, and cost-effective methods of the pathogen control in the food industry, which is critical to ensure food production safety.
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Affiliation(s)
- Jacek Osek
- Department of Hygiene of Food of Animal Origin, National Veterinary Research Institute, Puławy, Poland
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Prevalence and Clonal Diversity of over 1,200 Listeria monocytogenes Isolates Collected from Public Access Waters near Produce Production Areas on the Central California Coast during 2011 to 2016. Appl Environ Microbiol 2022; 88:e0035722. [PMID: 35377164 DOI: 10.1128/aem.00357-22] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A 5-year survey of public access surface waters in an agricultural region of the Central California Coast was done to assess the prevalence of the foodborne pathogen Listeria monocytogenes. In nature, L. monocytogenes lives as a saprophyte in soil and water, which are reservoirs for contamination of preharvest produce. Moore swabs were deployed biweekly in lakes, ponds, streams, and rivers during 2011 to 2016. L. monocytogenes was recovered in 1,224 of 2,922 samples, resulting in 41.9% prevalence. Multiple subtypes were isolated from 97 samples, resulting in 1,323 L. monocytogenes isolates. Prevalence was higher in winter and spring and after rain events in some waterways. Over 84% of the isolates were serotype 4b. Whole-genome sequencing was done on 1,248 isolates, and in silico multilocus sequence typing revealed 74 different sequence types (STs) and 39 clonal complexes (CCs). The clones most isolated, CC639, CC183, and CC1, made up 27%, 19%, and 13%, respectively, of the sequenced isolates. Other types were CC663, CC6, CC842, CC4, CC2, CC5, and CC217. All sequenced isolates contained intact copies of core L. monocytogenes virulence genes, and pathogenicity islands LIPI-3 and LIPI-4 were identified in 73% and 63%, respectively, of the sequenced isolates. The virulence factor internalin A was predicted to be intact in all but four isolates, while genes important for sanitizer and heavy metal resistance were found in <5% of the isolates. These waters are not used for crop irrigation directly, but they are available to wildlife and can flood fields during heavy rains. IMPORTANCE Listeria monocytogenes serotype 4b and 1/2a strains are implicated in most listeriosis, and hypervirulent listeriosis stems from strains containing pathogenicity islands LIPI-3 and LIPI-4. The waters and sediments in the Central California Coast agricultural region contain widespread and diverse L. monocytogenes populations, and all the isolates contain intact virulence genes. Emerging clones CC183 and CC639 were the most abundant clones, and major clones CC1, CC4, and CC6 were well represented. CC183 was responsible for three produce-related outbreaks in the last 7 years. Most of the isolates in the survey differ from those of lesser virulence that are often isolated from foods and food processing plants because they contain genes encoding an intact virulence factor, internalin A, and most did not contain genes for sanitizer and heavy metal resistance. This isolate collection is important for understanding L. monocytogenes populations in agricultural and natural regions.
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Cheng Y, Dong Q, Liu Y, Liu H, Zhang H, Wang X. Systematic review of Listeria monocytogenes from food and clinical samples in Chinese mainland from 2010 to 2019. FOOD QUALITY AND SAFETY 2022. [DOI: 10.1093/fqsafe/fyac021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Listeria monocytogenes, a foodborne pathogen, can cause human listeriosis. Listeriosis is a potentially fatal gastrointestinal illness, which is closely related to the spread of food to humans. We review the literature published during 2010 to 2019 to better understand the prevalence of L. monocytogenes in food products, incidence of human listeriosis, and their characteristics in Chinese mainland. We found the main sequence types (STs) strains from foods are similar globally, and the prevalence of L. monocytogenes from raw meat was the highest among all food products. The most common STs in food products and clinical cases were ST9 (serogroup Ⅰ.2) strains and ST87 (serogroup Ⅱ.2) strains, respectively. The ST87 strains being the most common STs of clinical cases might be related to the exist of Listeria pathogenicity islands 4 genes and Chinese eating habits for ready to eat foods, among which the prevalence of ST87 strain was the highest in ready to eat food. Therefore, more research should be conducted to explore the reasons for the L. monocytogenes isolates differences in food and clinic sources. Meanwhile, more research should be conducted to explore the reasons for differences among the L. monocytogenes isolates in food and clinical sources.
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Lourenco A, Linke K, Wagner M, Stessl B. The Saprophytic Lifestyle of Listeria monocytogenes and Entry Into the Food-Processing Environment. Front Microbiol 2022; 13:789801. [PMID: 35350628 PMCID: PMC8957868 DOI: 10.3389/fmicb.2022.789801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Listeria monocytogenes is an environmentally adapted saprophyte that can change into a human and animal bacterial pathogen with zoonotic potential through several regulatory systems. In this review, the focus is on the occurrence of Listeria sensu stricto and sensu lato in different ecological niches, the detection methods, and their analytical limitations. It also highlights the occurrence of L. monocytogenes genotypes in the environment (soil, water, and wildlife), reflects on the molecular determinants of L. monocytogenes for the saprophytic lifestyle and the potential for antibiotic resistance. In particular, the strain-specific properties with which some genotypes circulate in wastewater, surface water, soil, wildlife, and agricultural environments are of particular interest for the continuously updating risk analysis.
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Affiliation(s)
- Antonio Lourenco
- Department of Food Biosciences, Teagasc Food Research Centre, Co. Cork, Ireland
- Unit for Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Kristina Linke
- Unit for Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Martin Wagner
- Unit for Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- Austrian Competence Center for Feed and Food Quality, Safety and Innovation, Tulln, Austria
| | - Beatrix Stessl
- Unit for Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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Lachtara B, Wieczorek K, Osek J. Genetic Diversity and Relationships of Listeria monocytogenes Serogroup IIa Isolated in Poland. Microorganisms 2022; 10:532. [PMID: 35336111 PMCID: PMC8951407 DOI: 10.3390/microorganisms10030532] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 02/05/2023] Open
Abstract
In the present study, 100 L. monocytogenes isolates of serogroup IIa from food and food production environments in Poland were characterized towards the presence of virulence, resistance, and stress response genes using whole-genome sequencing (WGS). The strains were also molecularly typed and compared with multi-locus sequence typing (MLST) and core genome MLST analyses. The present isolates were grouped into 6 sublineages (SLs), with the most prevalent SL155 (33 isolates), SL121 (32 isolates), and SL8 (28 isolates) and classified into six clonal complexes, with the most prevalent CC155 (33 strains), CC121 (32 isolates), and CC8 (28 strains). Furthermore, the strains were grouped to eight sequence types, with the most prevalent ST155 (33 strains), ST121 (30 isolates), and ST8 (28; strains) followed by 60 cgMLST types (CTs). WGS data showed the presence of several virulence genes or putative molecular markers playing a role in pathogenesis of listeriosis and involved in survival of L. monocytogenes in adverse environmental conditions. Some of the present strains were molecularly closely related to L. monocytogenes previously isolated in Poland. The results of the study showed that food and food production environments may be a source of L. monocytogenes of serogroup IIa with pathogenic potential.
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Affiliation(s)
| | | | - Jacek Osek
- Department of Hygiene of Food of Animal Origin, National Veterinary Research Institute, 24-100 Pulawy, Poland; (B.L.); (K.W.)
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Chen T, Orsi RH, Chen R, Gunderson M, Roof S, Wiedmann M, Childs-Sanford SE, Cummings KJ. Characterization of Listeria monocytogenes isolated from wildlife in central New York. Vet Med Sci 2022; 8:1319-1329. [PMID: 35113496 PMCID: PMC9122436 DOI: 10.1002/vms3.758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Background Listeria monocytogenes (Lm) present in farming soil and food‐processing facilities threatens food safety, but little is known about the carriage of Lm by wildlife. Objectives We estimated the prevalence of faecal Lm shedding among wildlife admitted to a veterinary medical teaching hospital in central New York and characterized a subset of the Lm isolates. Methods Wildlife samples were collected between May 2018 and December 2019. We characterized the Lm isolates by assessing the growth at three temperatures approximating the body temperatures of reptiles (25°C), mammals (37°C), and birds (42°C) and identifying genotypic characteristics related to transmission and virulence. Results The apparent prevalence of faecal Lm shedding was 5.6% [18/324; 95% confidence interval (CI), 3.3%–8.6%]. Among 13 isolates that represented two lineages and 11 clonal complexes, three and five isolates were grouped into the same SNP clusters with human clinical isolates and environmental isolates, respectively. However, specific SNP difference data showed that Lm from wildlife was generally not closely related (>22 SNP differences) to Lm from human clinical sources and the food‐processing environment. While the stress response locus SSI‐2 was absent, SSI‐1 was found in four isolates. Virulence genes prfA, plcA, hly, mpl, actA, plcB, inlA, inlB, inlC, inlE, inlH, inlJ, and inlK were present, without any premature stop codons, in all isolates. Virulence loci Listeria pathogenicity island 3 (LIPI‐3) and LIPI‐4, which have been linked to hypervirulence, and inlG were found in four, three, and seven isolates, respectively. Conclusions Wildlife represents a potential reservoir for genetically diverse and putatively hypervirulent Lm strains. No statistically significant association between growth parameters and hosts was observed. However, compared to lineage I isolates, lineage II isolates showed significantly (p < 0.05) faster growth at 25°C and significantly slower growth at 42°C, suggesting that wildlife Lm isolates that belong to lineages I and II differ in their ability to grow at 25°C and 42°C.
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Affiliation(s)
- Tong Chen
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Renato H Orsi
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Ruixi Chen
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Maureen Gunderson
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Sherry Roof
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Sara E Childs-Sanford
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, NY, USA
| | - Kevin J Cummings
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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Chen Y, Simonetti T, Peter K, Jin Q, Brown E, LaBorde LF, Macarisin D. Genetic Diversity of Listeria monocytogenes Isolated From Three Commercial Tree Fruit Packinghouses and Evidence of Persistent and Transient Contamination. Front Microbiol 2022; 12:756688. [PMID: 35082763 PMCID: PMC8784831 DOI: 10.3389/fmicb.2021.756688] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/13/2021] [Indexed: 12/20/2022] Open
Abstract
Whole genome analysis was performed on 501 isolates obtained from a previous survey which recovered 139 positive environmental sponge samples (i.e., up to 4 isolates per sample) from a total of 719 samples collected at 40 standardized sites in 3 commercial apple packinghouse facilities (i.e., P1, P2, and P3) over 3 successive seasons in a single production year. After excluding duplicated isolates, the data from 156 isolates revealed the clonal diversity of L. monocytogenes and allowed the detection of transient contamination, persistent contamination, and cross-area transmission events. Facility P2 with the poorest sanitary conditions had the least diversity (Shannon's index of 0.38). P2 contained a Clonal Complex (CC) 554, serogroup IVb-v1 strain that persisted throughout the year and spread across the entire facility, a singleton Sequence Type (ST) 1003, lineage III strain that persisted through two seasons and spread across two areas of the facility, and 3 other clones from transient contaminations. P1 and P3, facilities with better sanitary conditions, had much higher diversity (i.e., 15 clones with a Shannon's index of 2.49 and 10 clones with a Shannon's index of 2.10, respectively) that were the result of transient contamination. Facilities P1 and P3 had the highest incidence (43.1%) of lineage III isolates, followed by lineage I (31.3%) and lineage II (25.5%) isolates. Only 1 isolate in the three facilities contained a premature stop codon in virulence gene inlA. Fourteen samples yielded 2-3 clones per sample, demonstrating the importance of choosing appropriate methodologies and selecting a sufficient number of isolates per sample for studying L. monocytogenes diversity. Only 1 isolate, belonging to CC5 and from facility P3, contained a known plasmid, and this was also the only isolate containing benzalkonium chloride tolerance genes. The persistent CC554 strain did not exhibit stronger sanitizer resistance than other isolates and did not contain any confirmed molecular determinants of L. monocytogenes stress resistance that were differentially present in other isolates, such as genes involved in sanitizer tolerance, heavy metal resistance, biofilm-forming, stress survival islet 1 (SSI-1), stress survival islet 2 (SSI-2) or Listeria genomic island (LGI2).
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Affiliation(s)
- Yi Chen
- Center for Food Safety and Applied Nutrition, Food and Drug Administration (FDA), College Park, MD, United States
| | - Tobin Simonetti
- Department of Food Science, Pennsylvania State University, University Park, PA, United States
| | - Kari Peter
- Fruit Research and Extension Center, Pennsylvania State University, University Park, PA, United States
| | - Qing Jin
- Center for Food Safety and Applied Nutrition, Food and Drug Administration (FDA), College Park, MD, United States
| | - Eric Brown
- Center for Food Safety and Applied Nutrition, Food and Drug Administration (FDA), College Park, MD, United States
| | - Luke F LaBorde
- Department of Food Science, Pennsylvania State University, University Park, PA, United States
| | - Dumitru Macarisin
- Center for Food Safety and Applied Nutrition, Food and Drug Administration (FDA), College Park, MD, United States
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Muchaamba F, Eshwar AK, Stevens MJA, Stephan R, Tasara T. Different Shades of Listeria monocytogenes: Strain, Serotype, and Lineage-Based Variability in Virulence and Stress Tolerance Profiles. Front Microbiol 2022; 12:792162. [PMID: 35058906 PMCID: PMC8764371 DOI: 10.3389/fmicb.2021.792162] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/11/2021] [Indexed: 12/30/2022] Open
Abstract
Listeria monocytogenes is a public health and food safety challenge due to its virulence and natural stress resistance phenotypes. The variable distribution of L. monocytogenes molecular subtypes with respect to food products and processing environments and among human and animal clinical listeriosis cases is observed. Sixty-two clinical and food-associated L. monocytogenes isolates were examined through phenome and genome analysis. Virulence assessed using a zebrafish infection model revealed serotype and genotype-specific differences in pathogenicity. Strains of genetic lineage I serotype 4b and multilocus sequence type clonal complexes CC1, CC2, CC4, and CC6 grew and survived better and were more virulent than serotype 1/2a and 1/2c lineage II, CC8, and CC9 strains. Hemolysis, phospholipase activity, and lysozyme tolerance profiles were associated with the differences observed in virulence. Osmotic stress resistance evaluation revealed serotype 4b lineage I CC2 and CC4 strains as more osmotolerant, whereas serotype 1/2c lineage II CC9 strains were more osmo-sensitive than others. Variable tolerance to the widely used quaternary ammonium compound benzalkonium chloride (BC) was observed. Some outbreak and sporadic clinical case associated strains demonstrated BC tolerance, which might have contributed to their survival and transition in the food-processing environment facilitating food product contamination and ultimately outbreaks or sporadic listeriosis cases. Genome comparison uncovered various moderate differences in virulence and stress associated genes between the strains indicating that these differences in addition to gene expression regulation variations might largely be responsible for the observed virulence and stress sensitivity phenotypic differences. Overall, our study uncovered strain and genotype-dependent variation in virulence and stress resilience among clinical and food-associated L. monocytogenes isolates with potential public health risk implications. The extensive genome and phenotypic data generated provide a basis for developing improved Listeria control strategies and policies.
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Affiliation(s)
- Francis Muchaamba
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Athmanya K Eshwar
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Marc J A Stevens
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
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Lakicevic BZ, Den Besten HMW, De Biase D. Landscape of Stress Response and Virulence Genes Among Listeria monocytogenes Strains. Front Microbiol 2022; 12:738470. [PMID: 35126322 PMCID: PMC8811131 DOI: 10.3389/fmicb.2021.738470] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/30/2021] [Indexed: 12/23/2022] Open
Abstract
The pathogenic microorganism Listeria monocytogenes is ubiquitous and responsible for listeriosis, a disease with a high mortality rate in susceptible people. It can persist in different habitats, including the farm environment, the food production environments, and in foods. This pathogen can grow under challenging conditions, such as low pH, low temperatures, and high salt concentrations. However, L. monocytogenes has a high degree of strain divergence regarding virulence potential, environmental adaption, and stress response. This review seeks to provide the reader with an up-to-date overview of clonal and serotype-specific differences among L. monocytogenes strains. Emphasis on the genes and genomic islands responsible for virulence and resistance to environmental stresses is given to explain the complex adaptation among L. monocytogenes strains. Moreover, we highlight the use of advanced diagnostic technologies, such as whole-genome sequencing, to fine-tune quantitative microbiological risk assessment for better control of listeriosis.
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Affiliation(s)
- Brankica Z. Lakicevic
- Institute of Meat Hygiene and Technology, Belgrade, Serbia
- *Correspondence: Brankica Z. Lakicevic,
| | | | - Daniela De Biase
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
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43
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A novel multiplex PCR method for simultaneous identification of hypervirulent Listeria monocytogenes clonal complex 87 and CC88 strains in China. Int J Food Microbiol 2022; 366:109558. [DOI: 10.1016/j.ijfoodmicro.2022.109558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 11/20/2022]
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Lake FB, van Overbeek LS, Baars JJP, Koomen J, Abee T, den Besten HMW. Genomic characteristics of Listeria monocytogenes isolated during mushroom (Agaricus bisporus) production and processing. Int J Food Microbiol 2021; 360:109438. [PMID: 34715483 DOI: 10.1016/j.ijfoodmicro.2021.109438] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/21/2022]
Abstract
Listeria monocytogenes is a foodborne pathogen ubiquitously found in nature and which has been isolated from food and food processing environments. This study aimed to characterize L. monocytogenes strains isolated from the production and processing environments of frozen sliced mushrooms (Agaricus bisporus). An analysis was executed along the mushroom processing chain including one mushroom grower and two mushroom processing factories. A total of 153 L. monocytogenes strains were isolated, which could be grouped in three PCR serogroups, namely, serogroup 1/2a-3a (39.2%), serogroup 1/2b-3b-7 (34.0%) and serogroup 4b-4d-4e (26.8%). A selection of 44 L. monocytogenes strains isolated from the processing environment after cleaning and disinfection (C&D) and from frozen sliced mushrooms was genotyped by whole genome sequencing (WGS), because these strains pose a potential risk for product contamination after C&D and for human consumption. Multilocus sequence typing (MLST) revealed 11 clonal complexes (CCs), with strains belonging to CC1, CC4, CC37 and CC87 being detected in both processing factories. Comparative WGS analysis of the 44 strains showed the presence of Listeria pathogenicity island 1 (LIPI-1) with a disrupted version of actA in all CC1, CC4, CC5, CC59 strains, and all but one CC224 strains. Notably, both inlA and inlB were detected as full-length loci in every strain, except for inlA in a CC6 strain that harbored a three amino acid deletion. LIPI-3 was detected in all CC1, CC4, CC6 and CC224 strains, while LIPI-4 was detected in all CC4 and CC87 strains. In addition, antibiotic susceptibility tests showed susceptibility towards fourteen antibiotics tested. The bcrABC operon was found in one CC5 strain, that showed a higher tolerance towards benzalkonium chloride than any other strain tested with confluent growth till 12.5 μg/ml for the CC5 strain compared to 2.5 μg/ml for the other strains. This study highlights that the ecology of L. monocytogenes in the frozen sliced mushroom production chain is highly diverse, and shows the importance of hygienic measures to control L. monocytogenes along the frozen sliced mushroom production chain.
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Affiliation(s)
- Frank B Lake
- Food Microbiology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Leo S van Overbeek
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Johan J P Baars
- Plant Breeding, Wageningen Plant Research, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Jeroen Koomen
- Food Microbiology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Heidy M W den Besten
- Food Microbiology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
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Maggio F, Rossi C, Chiaverini A, Ruolo A, Orsini M, Centorame P, Acciari VA, Chaves López C, Salini R, Torresi M, Serio A, Pomilio F, Paparella A. Genetic relationships and biofilm formation of Listeria monocytogenes isolated from the smoked salmon industry. Int J Food Microbiol 2021; 356:109353. [PMID: 34411997 DOI: 10.1016/j.ijfoodmicro.2021.109353] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 11/24/2022]
Abstract
Among pathogens, L. monocytogenes has the capability to persist on Food Processing Environment (FPE), first of all posing safety issues, then economic impact on productivity. The aim of this work was to determine the influence of biofilm forming-ability and molecular features on the persistence of 19 Listeria monocytogenes isolates obtained from FPE, raw and processed products of a cold-smoked salmon processing plant. To verify the phenotypic and genomic correlations among the isolates, different analyses were employed: serotyping, Clonal Complex (CC), core genome Multi-Locus Sequence Typing (cgMLST) and Single Nucleotide Polymorphisms (SNPs) clustering, and evaluation of the presence of virulence- and persistence-associated genes. From our results, the biofilm formation was significantly higher (*P < 0.05) at 37 °C, compared to 30 and 12 °C, suggesting a temperature-dependent behaviour. Moreover, the biofilm-forming ability showed a strain-specific trend, not correlated with CC or with strains persistence. Instead, the presence of internalin (inL), Stress Survival Islet (SSI) and resistance to erythromycin (ermC) genes was correlated with the ability to produce biofilms. Our data demonstrate that the genetic profile influences the adhesion capacity and persistence of L. monocytogenes in food processing plants and could be the result of environmental adaptation in response to the external selective pressure.
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Affiliation(s)
- Francesca Maggio
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, 64100 Teramo, TE, Italy
| | - Chiara Rossi
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, 64100 Teramo, TE, Italy
| | - Alexandra Chiaverini
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, TE, Italy
| | - Anna Ruolo
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, TE, Italy
| | - Massimiliano Orsini
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, TE, Italy; Department of Risk Analysis and Public Health Surveillance, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Patrizia Centorame
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, TE, Italy
| | - Vicdalia A Acciari
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, TE, Italy
| | - Clemencia Chaves López
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, 64100 Teramo, TE, Italy
| | - Romolo Salini
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, TE, Italy
| | - Marina Torresi
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, TE, Italy
| | - Annalisa Serio
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, 64100 Teramo, TE, Italy.
| | - Francesco Pomilio
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, TE, Italy
| | - Antonello Paparella
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, 64100 Teramo, TE, Italy
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Anast JM, Schmitz-Esser S. Certain Listeria monocytogenes plasmids contribute to increased UVC ultraviolet light stress. FEMS Microbiol Lett 2021; 368:6367057. [PMID: 34498664 PMCID: PMC8457643 DOI: 10.1093/femsle/fnab123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/07/2021] [Indexed: 01/20/2023] Open
Abstract
Listeria monocytogenes is the causative agent of the highly fatal foodborne disease listeriosis and can persist in food production environments. Recent research highlights the involvement of L. monocytogenes plasmids in different stress response mechanisms, which contribute to its survival in food production facilities. Ultraviolet (UV) light in the UVC spectrum (200–280 nm) is used in food production to control microbial contamination. Although plasmid-encoded UV resistance mechanisms have been described in other bacteria, no research indicates that L. monocytogenes plasmids contribute to the UV stress response. The plasmids of L. monocytogenes strains 6179, 4KSM and R479a are genetically distinct and were utilized to study the roles of plasmids in the UV response. Wild-type and plasmid-cured variant cells were grown to logarithmic or late-stationary phase, plated on agar plates and exposed to UVC for 60 or 90 s, and colony-forming units (CFUs) were determined. CFUs of 6179 and 4KSM, bearing pLM6179 and p4KSM, respectively, were significantly (P-value < 0.05) higher than those of the plasmid-cured strains in both logarithmic and stationary phases. No difference in survival was observed for the R479a strain. Our data show for the first time that certain L. monocytogenes plasmids contribute to the survival of UVC light stress.
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Affiliation(s)
- Justin M Anast
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.,Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Stephan Schmitz-Esser
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.,Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, USA
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Sun Q, Cai S, Cheng J, Zhang Y, Lin R, Ye Q, Xue L, Zeng H, Lei T, Zhang S, Luo X, Wu K, Wu Q, Chen M, Zhang J. Distribution, contamination routes, and seasonal influence of persistent Listeria monocytogenes in a commercial fresh Hypsizigus marmoreus production facility. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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48
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Unrath N, McCabe E, Macori G, Fanning S. Application of Whole Genome Sequencing to Aid in Deciphering the Persistence Potential of Listeria monocytogenes in Food Production Environments. Microorganisms 2021; 9:1856. [PMID: 34576750 PMCID: PMC8464834 DOI: 10.3390/microorganisms9091856] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 01/26/2023] Open
Abstract
Listeria monocytogenes is the etiological agent of listeriosis, a foodborne illness associated with high hospitalizations and mortality rates. This bacterium can persist in food associated environments for years with isolates being increasingly linked to outbreaks. This review presents a discussion of genomes of Listeria monocytogenes which are commonly regarded as persisters within food production environments, as well as genes which are involved in mechanisms aiding this phenotype. Although criteria for the detection of persistence remain undefined, the advent of whole genome sequencing (WGS) and the development of bioinformatic tools have revolutionized the ability to find closely related strains. These advancements will facilitate the identification of mechanisms responsible for persistence among indistinguishable genomes. In turn, this will lead to improved assessments of the importance of biofilm formation, adaptation to stressful conditions and tolerance to sterilizers in relation to the persistence of this bacterium, all of which have been previously associated with this phenotype. Despite much research being published around the topic of persistence, more insights are required to further elucidate the nature of true persistence and its implications for public health.
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Affiliation(s)
- Natalia Unrath
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, D04 N2E5 Dublin, Ireland; (N.U.); (E.M.); (G.M.)
| | - Evonne McCabe
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, D04 N2E5 Dublin, Ireland; (N.U.); (E.M.); (G.M.)
- Department of Microbiology, St. Vincent’s University Hospital, D04 T6F4 Dublin, Ireland
| | - Guerrino Macori
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, D04 N2E5 Dublin, Ireland; (N.U.); (E.M.); (G.M.)
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, D04 N2E5 Dublin, Ireland; (N.U.); (E.M.); (G.M.)
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49
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Centorotola G, Guidi F, D’Aurizio G, Salini R, Di Domenico M, Ottaviani D, Petruzzelli A, Fisichella S, Duranti A, Tonucci F, Acciari VA, Torresi M, Pomilio F, Blasi G. Intensive Environmental Surveillance Plan for Listeria monocytogenes in Food Producing Plants and Retail Stores of Central Italy: Prevalence and Genetic Diversity. Foods 2021; 10:foods10081944. [PMID: 34441721 PMCID: PMC8392342 DOI: 10.3390/foods10081944] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Listeria monocytogenes (Lm) can persist in food processing environments (FPEs), surviving environmental stresses and disinfectants. We described an intensive environmental monitoring plan performed in Central Italy and involving food producing plants (FPPs) and retail grocery stores (RSs). The aim of the study was to provide a snapshot of the Lm circulation in different FPEs during a severe listeriosis outbreak, using whole genome sequencing (WGS) to investigate the genetic diversity of the Lm isolated, evaluating their virulence and stress resistance profiles. A total of 1217 samples were collected in 86 FPEs with 12.0% of positive surfaces at FPPs level and 7.5% at RSs level; 133 Lm isolates were typed by multilocus sequencing typing (MLST) and core genome MLST (cgMLST). Clonal complex (CC) 121 (25.6%), CC9 (22.6%), CC1 (11.3%), CC3 (10.5%), CC191 (4.5%), CC7 (4.5%) and CC31 (3.8%) were the most frequent MLST clones. Among the 26 cgMLST clusters obtained, 5 of them persisted after sanitization and were re-isolated during the follow-up sampling. All the CC121 harboured the Tn6188_qac gene for tolerance to benzalkonium chloride and the stress survival islet SSI-2. The CC3, CC7, CC9, CC31 and CC191 carried the SSI-1. All the CC9 and CC121 strains presented a premature stop codon in the inlA gene. In addition to the Lm Pathogenicity Island 1 (LIPI-1), CC1, CC3 and CC191 harboured the LIPI-3. The application of intensive environmental sampling plans for the detection and WGS analysis of Lm isolates could improve surveillance and early detection of outbreaks.
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Affiliation(s)
- Gabriella Centorotola
- Laboratorio Nazionale di Riferimento Per Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, via Campo Boario, 64100 Teramo, Italy; (G.C.); (V.A.A.); (M.T.); (F.P.)
| | - Fabrizia Guidi
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, via Gaetano Salvemini, 1, 06126 Perugia, Italy; (D.O.); (A.P.); (S.F.); (A.D.); (F.T.); (G.B.)
- Correspondence: or ; Tel.: +39-075-3431
| | - Guglielmo D’Aurizio
- ARS P.F. Prevenzione Veterinaria e Sicurezza Alimentare, Regione Marche, via Don Gioia, 8, 60122 Ancona, Italy;
| | - Romolo Salini
- Centro Operativo Veterinario Per l’Epidemiologia, Programmazione, Informazione e Analisi del Rischio (COVEPI), National Reference Center for Veterinary Epidemiology, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, via Campo Boario, 64100 Teramo, Italy;
| | - Marco Di Domenico
- Centro di Referenza Nazionale Per Sequenze Genomiche di Microrganismi Patogeni, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, via Campo Boario, 64100 Teramo, Italy;
| | - Donatella Ottaviani
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, via Gaetano Salvemini, 1, 06126 Perugia, Italy; (D.O.); (A.P.); (S.F.); (A.D.); (F.T.); (G.B.)
| | - Annalisa Petruzzelli
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, via Gaetano Salvemini, 1, 06126 Perugia, Italy; (D.O.); (A.P.); (S.F.); (A.D.); (F.T.); (G.B.)
| | - Stefano Fisichella
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, via Gaetano Salvemini, 1, 06126 Perugia, Italy; (D.O.); (A.P.); (S.F.); (A.D.); (F.T.); (G.B.)
| | - Anna Duranti
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, via Gaetano Salvemini, 1, 06126 Perugia, Italy; (D.O.); (A.P.); (S.F.); (A.D.); (F.T.); (G.B.)
| | - Franco Tonucci
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, via Gaetano Salvemini, 1, 06126 Perugia, Italy; (D.O.); (A.P.); (S.F.); (A.D.); (F.T.); (G.B.)
| | - Vicdalia Aniela Acciari
- Laboratorio Nazionale di Riferimento Per Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, via Campo Boario, 64100 Teramo, Italy; (G.C.); (V.A.A.); (M.T.); (F.P.)
| | - Marina Torresi
- Laboratorio Nazionale di Riferimento Per Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, via Campo Boario, 64100 Teramo, Italy; (G.C.); (V.A.A.); (M.T.); (F.P.)
| | - Francesco Pomilio
- Laboratorio Nazionale di Riferimento Per Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, via Campo Boario, 64100 Teramo, Italy; (G.C.); (V.A.A.); (M.T.); (F.P.)
| | - Giuliana Blasi
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, via Gaetano Salvemini, 1, 06126 Perugia, Italy; (D.O.); (A.P.); (S.F.); (A.D.); (F.T.); (G.B.)
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Mafuna T, Matle I, Magwedere K, Pierneef RE, Reva ON. Whole Genome-Based Characterization of Listeria monocytogenes Isolates Recovered From the Food Chain in South Africa. Front Microbiol 2021; 12:669287. [PMID: 34276601 PMCID: PMC8283694 DOI: 10.3389/fmicb.2021.669287] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/28/2021] [Indexed: 11/30/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen which has the ability to adapt and survive in food and food processing facilities where it can persist for years. In this study, a total of 143 L. monocytogenes isolates in South Africa (SA) were characterized for their strain’s genetic relatedness, virulence profiles, stress tolerance and resistance genes associated with L. monocytogenes. The Core Genome Multilocus Sequence Typing (cgMLST) analysis revealed that the most frequent serogroups were IVb and IIa; Sequence Types (ST) were ST204, ST2, and ST1; and Clonal Complexes (CC) were CC204, CC1, and CC2. Examination of genes involved in adaptation and survival of L. monocytogenes in SA showed that ST1, ST2, ST121, ST204, and ST321 are well adapted in food processing environments due to the significant over-representation of Benzalkonium chloride (BC) resistance genes (bcrABC cassette, ermC, mdrL and Ide), stress tolerance genes (SSI-1 and SSI-2), Prophage (φ) profiles (LP_101, vB LmoS 188, vB_LmoS_293, and B054 phage), plasmids profiles (N1-011A, J1776, and pLM5578) and biofilm formation associated genes. Furthermore, the L. monocytogenes strains that showed hyper-virulent potential were ST1, ST2 and ST204, and hypo-virulent were ST121 and ST321 because of the presence and absence of major virulence factors such as LIPI-1, LIPI-3, LIPI-4 and the internalin gene family members including inlABCEFJ. The information provided in this study revealed that hyper-virulent strains ST1, ST2, and ST204 could present a major public health risk due to their association with meat products and food processing environments in SA.
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Affiliation(s)
- Thendo Mafuna
- Agricultural Research Council, Biotechnology Platform, Private Bag X05, Onderstepoort, South Africa.,Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
| | - Itumeleng Matle
- Bacteriology Division, Agricultural Research Council: Onderstepoort Veterinary Research, Pretoria, South Africa
| | - Kudakwashe Magwedere
- Directorate of Veterinary Public Health, Department of Agriculture, Forestry and Fisheries, Private Bag X138, Pretoria, South Africa
| | - Rian E Pierneef
- Agricultural Research Council, Biotechnology Platform, Private Bag X05, Onderstepoort, South Africa
| | - Oleg N Reva
- Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
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