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Bolten S, Ralyea RD, Lott TT, Orsi RH, Martin NH, Wiedmann M, Trmcic A. Utilizing whole genome sequencing to characterize Listeria spp. persistence and transmission patterns in a farmstead dairy processing facility and its associated farm environment. J Dairy Sci 2024:S0022-0302(24)00995-0. [PMID: 39004131 DOI: 10.3168/jds.2024-24789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/14/2024] [Indexed: 07/16/2024]
Abstract
Farmstead dairy processing facilities may be particularly susceptible to Listeria spp. contamination due to the close physical proximity of their processing environments (PE) to associated dairy farm environments (FE). In this case study, we supported the implementation of interventions focused on improving (i) cleaning and sanitation efficacy, (ii) hygienic zoning, and (iii) sanitary equipment/facility design and maintenance in a farmstead dairy processing facility, and evaluated their impact on Listeria spp. detection in the farmstead's PE over 1 year. Detection of Listeria spp. in the farmstead's PE was numerically reduced from 50% to 7.5% after 1 year of intervention implementation, suggesting that these interventions were effective at improving Listeria spp. control. In addition, environmental samples were also collected from the farmstead's FE to evaluate the risk of the FE as a potential source of Listeria spp. in the PE. Overall, detection of Listeria spp. was higher in samples collected from the FE (75%, 27/36) compared with samples collected from the PE (24%, 29/120). Whole genome sequencing (WGS) performed on select isolates collected from the PE and FE supported the identification of 6 clusters (range of 3 to 15 isolates per cluster) that showed ≤ 50 high quality single nucleotide polymorphism (hqSNP) differences. Of these 6 clusters, 3 (i.e., clusters 2, 4, and 5) contained isolates that were collected from both the PE and FE, suggesting that transmission between these 2 environments was likely. Moreover, all cluster 2 isolates represented a clonal complex (CC) of L. monocytogenes commonly associated with dairy farm environmental reservoirs (i.e., CC666), which may support that the farmstead's FE represented an upstream source of the cluster 2 isolates that were found in the PE. Overall, our data underscore that, while the FE can represent a potential upstream source of Listeria spp. contamination in a farmstead dairy processing facility, implementation of targeted interventions can help effectively minimize Listeria spp. contamination in the PE.
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Affiliation(s)
- Samantha Bolten
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY, 14853; Food Safety Laboratory, Department of Food Science, Cornell University, Ithaca, NY, 14853
| | - Robert D Ralyea
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY, 14853
| | - Timothy T Lott
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY, 14853
| | - Renato H Orsi
- Food Safety Laboratory, Department of Food Science, Cornell University, Ithaca, NY, 14853
| | - Nicole H Martin
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY, 14853
| | - Martin Wiedmann
- Food Safety Laboratory, Department of Food Science, Cornell University, Ithaca, NY, 14853
| | - Aljosa Trmcic
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY, 14853.
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2
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Bolten S, Lott TT, Ralyea RD, Gianforte A, Trmcic A, Orsi RH, Martin NH, Wiedmann M. Intensive Environmental Sampling and Whole Genome Sequence-based Characterization of Listeria in Small- and Medium-sized Dairy Facilities Reveal Opportunities for Simplified and Size-appropriate Environmental Monitoring Strategies. J Food Prot 2024; 87:100254. [PMID: 38417482 DOI: 10.1016/j.jfp.2024.100254] [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: 12/14/2023] [Revised: 02/17/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
Small- and medium-sized dairy processing facilities (SMDFs) may face unique challenges with respect to controlling Listeria in their processing environments, e.g., due to limited resources. The aim of this study was to implement and evaluate environmental monitoring programs (EMPs) for Listeria control in eight SMDFs in a ∼1-year longitudinal study; this included a comparison of pre-operation (i.e., after cleaning and sanitation and prior to production) and mid-operation (i.e., at least 4 h into production) sampling strategies. Among 2,072 environmental sponge samples collected across all facilities, 272 (13%) were positive for Listeria. Listeria prevalence among pre- and mid-operation samples (15% and 17%, respectively), was not significantly different. Whole genome sequencing (WGS) performed on select isolates to characterize Listeria persistence patterns revealed repeated isolation of closely related Listeria isolates (i.e., ≤20 high-quality single nucleotide polymorphism [hqSNP] differences) in 5/8 facilities over >6 months, suggesting Listeria persistence and/or reintroduction was relatively common among the SMDFs evaluated here. WGS furthermore showed that for 41 sites where samples collected pre- and mid-operation were positive for Listeria, Listeria isolates obtained were highly related (i.e., ≤10 hqSNP differences), suggesting that pre-operation sampling alone may be sufficient and more effective for detecting sites of Listeria persistence. Importantly, our data also showed that only 1/8 of facilities showed a significant decrease in Listeria prevalence over 1 year, indicating continued challenges with Listeria control in at least some SMDFs. We conclude that options for simplified Listeria EMPs (e.g., with a focus on pre-operation sampling, which allows for more rapid identification of likely persistence sites) may be valuable for improved Listeria control in SMDFs.
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Affiliation(s)
- Samantha Bolten
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853, USA; Food Safety Laboratory, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Timothy T Lott
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Robert D Ralyea
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Anika Gianforte
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Aljosa Trmcic
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Renato H Orsi
- Food Safety Laboratory, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Nicole H Martin
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Martin Wiedmann
- Food Safety Laboratory, Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
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3
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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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4
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Bardsley CA, Orsi RH, Clark S, Murphy CM, McEntire JC, Wiedmann M, Strawn LK. Role of Whole Genome Sequencing in Assessing Resident and Transient Listeria monocytogenes in a Produce Packinghouse. J Food Prot 2024; 87:100201. [PMID: 38036175 DOI: 10.1016/j.jfp.2023.100201] [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: 06/23/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/02/2023]
Abstract
Whole genome sequencing (WGS) is a powerful tool that may be used to assist in identifying Listeria contamination sources and movement within environments, and to assess persistence. This study investigated sites in a produce packinghouse where Listeria had been historically isolated; and aimed to characterize dispersal patterns and identify cases of transient and resident Listeria. Environmental swab samples (n = 402) were collected from 67 sites at two time-points on three separate visits. Each sample was tested for Listeria, and Listeria isolates were characterized by partial sigB sequencing to determine species and allelic type (AT). Representative isolates from the three most common L. monocytogenes ATs (n = 79) were further characterized by WGS. Of the 144 Listeria species positive samples (35.8%), L. monocytogenes was the most prevalent species. L. monocytogenes was often coisolated with another species of Listeria. WGS identified cases of sporadic and continued reintroduction of L. monocytogenes from the cold storages into the packinghouse and demonstrated cases of L. monocytogenes persistence over 2 years in cold storages, drains, and on a forklift. Nine distinct clusters were found in this study. Two clusters showed evidence of persistence. Isolates in these two clusters (N = 11, with one historical isolate) were obtained predominantly and over multiple samplings from cold storages, with sporadic movement to sites in the packing area, suggesting residence in cold storages with opportunistic dispersal within the packinghouse. The other seven clusters demonstrated evidence of transient Listeria, as isolation was sporadic over time and space during the packing season. Our data provide important insights into likely L. monocytogenes harborage points and transfer in a packinghouse, which is key to root cause analysis. While results support Listeria spp. as a suitable indicator organism for environmental monitoring surveys, findings were unable to establish a specific species as an index organism for L. monocytogenes. Findings also suggest long-term persistence with substantial SNP diversification, which may assist in identifying potential contamination sources and implementing control measures.
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Affiliation(s)
- Cameron A Bardsley
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA 24061, USA
| | - Renato H Orsi
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Shelley Clark
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Claire M Murphy
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA 24061, USA
| | | | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Laura K Strawn
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA 24061, USA.
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Shikov AE, Savina IA, Nizhnikov AA, Antonets KS. Recombination in Bacterial Genomes: Evolutionary Trends. Toxins (Basel) 2023; 15:568. [PMID: 37755994 PMCID: PMC10534446 DOI: 10.3390/toxins15090568] [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: 08/08/2023] [Revised: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
Bacterial organisms have undergone homologous recombination (HR) and horizontal gene transfer (HGT) multiple times during their history. These processes could increase fitness to new environments, cause specialization, the emergence of new species, and changes in virulence. Therefore, comprehensive knowledge of the impact and intensity of genetic exchanges and the location of recombination hotspots on the genome is necessary for understanding the dynamics of adaptation to various conditions. To this end, we aimed to characterize the functional impact and genomic context of computationally detected recombination events by analyzing genomic studies of any bacterial species, for which events have been detected in the last 30 years. Genomic loci where the transfer of DNA was detected pertained to mobile genetic elements (MGEs) housing genes that code for proteins engaged in distinct cellular processes, such as secretion systems, toxins, infection effectors, biosynthesis enzymes, etc. We found that all inferences fall into three main lifestyle categories, namely, ecological diversification, pathogenesis, and symbiosis. The latter primarily exhibits ancestral events, thus, possibly indicating that adaptation appears to be governed by similar recombination-dependent mechanisms.
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Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Iuliia A. Savina
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
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6
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Finn L, Onyeaka H, O’Neill S. Listeria monocytogenes Biofilms in Food-Associated Environments: A Persistent Enigma. Foods 2023; 12:3339. [PMID: 37761048 PMCID: PMC10529182 DOI: 10.3390/foods12183339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Listeria monocytogenes (LM) is a bacterial pathogen responsible for listeriosis, a foodborne illness associated with high rates of mortality (20-30%) and hospitalisation. It is particularly dangerous among vulnerable groups, such as newborns, pregnant women and the elderly. The persistence of this organism in food-associated environments for months to years has been linked to several devastating listeriosis outbreaks. It may also result in significant costs to food businesses and economies. Currently, the mechanisms that facilitate LM persistence are poorly understood. Unravelling the enigma of what drives listerial persistence will be critical for developing more targeted control and prevention strategies. One prevailing hypothesis is that persistent strains exhibit stronger biofilm production on abiotic surfaces in food-associated environments. This review aims to (i) provide a comprehensive overview of the research on the relationship between listerial persistence and biofilm formation from phenotypic and whole-genome sequencing (WGS) studies; (ii) to highlight the ongoing challenges in determining the role biofilm development plays in persistence, if any; and (iii) to propose future research directions for overcoming these challenges.
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Affiliation(s)
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, UK
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Worley JN, Crothers JW, Wolfgang WJ, Venkata SLG, Hoffmann M, Jayeola V, Klompas M, Allard M, Bry L. Prospective Genomic Surveillance Reveals Cryptic MRSA Outbreaks with Local to International Origins among NICU Patients. J Clin Microbiol 2023; 61:e0001423. [PMID: 37022157 PMCID: PMC10204624 DOI: 10.1128/jcm.00014-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/19/2023] [Indexed: 04/07/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) infections cause substantive morbidity and mortality in neonates. Using publicly available resources from the National Center of Biotechnology Information (NCBI) and Food and Drug Administration's (FDA) GalaxyTrakr pipeline, we illustrate the dynamics of MRSA colonization and infection in neonates. Over 217 days of prospective surveillance, analyses revealed concurrent MRSA transmission chains affecting 11 of 17 MRSA-colonized patients (65%), with two clusters that demonstrated intervals of more than a month among the appearance of isolates. All MRSA infected neonates (n = 3) showed previous colonization with the infecting strain. GalaxyTrakr clustering of the NICU strains, in the context of 21,521 international isolates deposited in NCBI's Pathogen Detection Resource, revealed NICU isolates to be distinct from adult MRSA strains seen locally and internationally. Clustering of the NICU strains within an international context enhanced the resolution of strain clusters and supported the rule-out of suspected, local transmission events within the NICU. Analyses also identified sequence type 1535 isolates, emergent in the Middle East, carrying a unique SCCmec with fusC and aac(6')-Ie/aph(2'')-1a that provided a multidrug-resistant phenotype. NICU genomic pathogen surveillance, leveraging public repositories and outbreak detection tools, supports rapid identification of cryptic MRSA clusters, and can inform infection prevention interventions for this vulnerable patient population. Results demonstrate that sporadic infections in the NICU may be indicative of hidden chains of asymptomatic transmission best identified with sequenced-based approaches.
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Affiliation(s)
- Jay N. Worley
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Jessica W. Crothers
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, Vermont, USA
- Translational Global Infectious Disease Research Center, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - William J. Wolfgang
- Wadsworth Center, Division of Infectious Diseases, New York State Department of Health, Albany, New York, USA
| | - Sai Laxmi Gubbala Venkata
- Wadsworth Center, Division of Infectious Diseases, New York State Department of Health, Albany, New York, USA
| | - Maria Hoffmann
- Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Victor Jayeola
- Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Michael Klompas
- Department of Population Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Marc Allard
- Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Clinical Microbiology Laboratory, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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8
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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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9
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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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Sugar Modification of Wall Teichoic Acids Determines Serotype-Dependent Strong Biofilm Production in Listeria monocytogenes. Microbiol Spectr 2022; 10:e0276922. [PMID: 36190419 PMCID: PMC9603678 DOI: 10.1128/spectrum.02769-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Biofilm production is responsible for persistent food contamination by Listeria monocytogenes, threatening food safety and public health. Human infection and food contamination with L. monocytogenes are caused primarily by serotypes 1/2a, 1/2b, and 4b. However, the association of biofilm production with phylogenic lineage and serotype has not yet been fully understood. In this study, we measured the levels of biofilm production in 98 clinical strains of L. monocytogenes at 37°C, 25°C, and 4°C. The phylogenetic clusters grouped by core genome multilocus sequence typing (cgMLST) exhibited association between biofilm production and phylogenetic lineage and serotype. Whereas clusters 1 and 3 consisting of serotype 4b strains exhibited weak biofilm production, clusters 2 (serotype 1/2b) and 4 (serotype 1/2a) were composed of strong biofilm formers. Particularly, cluster 2 (serotype 1/2b) strains exhibited the highest levels of biofilm production at 37°C, and the levels of biofilm production of cluster 4 (serotype 1/2a) strains were significantly elevated at all tested temperatures. Pan-genome analysis identified 22 genes unique to strong biofilm producers, most of which are related to the synthesis and modification of teichoic acids. Notably, a knockout mutation of the rml genes related to the modification of wall teichoic acids with l-rhamnose, which is specific to serogroup 1/2, significantly reduced the level of biofilm production by preventing biofilm maturation. Here, the results of our study show that biofilm production in L. monocytogenes is related to phylogeny and serotype and that the modification of wall teichoic acids with l-rhamnose is responsible for serotype-specific strong biofilm formation in L. monocytogenes. IMPORTANCE Biofilm formation on the surface of foods or food-processing facilities by L. monocytogenes is a serious food safety concern. Here, our data demonstrate that the level of biofilm production differs among serotypes 1/2a, 1/2b, and 4b depending on the temperature. Furthermore, sugar decoration of bacterial cell walls with l-rhamnose is responsible for strong biofilm production in serotypes 1/2a and 1/2b, commonly isolated from foods and listeriosis cases. The findings in this study improve our understanding of the association of biofilm production with phylogenetic lineage and serotype in L. monocytogenes.
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11
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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: 0] [Impact Index Per Article: 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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Di Renzo L, De Angelis ME, Torresi M, Di Lollo V, Di Teodoro G, Averaimo D, Defourny SVP, Di Giacinto F, Profico C, Olivieri V, Pomilio F, Cammà C, Ferri N, Di Francesco G. First Report of Septicaemic Listeriosis in a Loggerhead Sea Turtle (Caretta caretta) Stranded along the Adriatic Coast: Strain Detection and Sequencing. Animals (Basel) 2022; 12:ani12182364. [PMID: 36139224 PMCID: PMC9495059 DOI: 10.3390/ani12182364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Although there are increasing reports on the prevalence of Listeria monocytogenes in wild species, this is the first case of listeriosis in sea turtle. An adult female Caretta caretta was rescued after being stranded alive along the coast of the Abruzzo region (Italy) in summer 2021. The turtle died in 6 days due to respiratory failure. The necropsy showed widespread organ lesions, such as yellow foci of necrosis in many organs, gastrointestinal erosions, pericarditis, and granulomatous pneumonia. Microbiological and histological analyses were performed on several organs. Listeria monocytogenes was isolated from multiple organs, indicating a case of septicaemic listeriosis, and the genome was sequenced and characterized. All the colonies analysed belonged to the same strain serogroup IVb, ST388, and CC388.
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Affiliation(s)
- Ludovica Di Renzo
- Istituto Zooprofilattico Sperimentale (IZS) dell’Abruzzo e Molise “G. Caporale”, 64100 Teramo, TE, Italy
- Centro Studi Cetacei Onlus, Centro Recupero e Riabilitazione Tartarughe Marine “L.Cagnolaro”, 65125 Pescara, PE, Italy
- Correspondence: ; Tel.: +39-08613321
| | | | - Marina Torresi
- Istituto Zooprofilattico Sperimentale (IZS) dell’Abruzzo e Molise “G. Caporale”, 64100 Teramo, TE, Italy
| | - Valeria Di Lollo
- Istituto Zooprofilattico Sperimentale (IZS) dell’Abruzzo e Molise “G. Caporale”, 64100 Teramo, TE, Italy
| | - Giovanni Di Teodoro
- Istituto Zooprofilattico Sperimentale (IZS) dell’Abruzzo e Molise “G. Caporale”, 64100 Teramo, TE, Italy
| | - Daniela Averaimo
- Istituto Zooprofilattico Sperimentale (IZS) dell’Abruzzo e Molise “G. Caporale”, 64100 Teramo, TE, Italy
| | | | - Federica Di Giacinto
- Istituto Zooprofilattico Sperimentale (IZS) dell’Abruzzo e Molise “G. Caporale”, 64100 Teramo, TE, Italy
| | - Chiara Profico
- Istituto Zooprofilattico Sperimentale (IZS) dell’Abruzzo e Molise “G. Caporale”, 64100 Teramo, TE, Italy
- Centro Studi Cetacei Onlus, Centro Recupero e Riabilitazione Tartarughe Marine “L.Cagnolaro”, 65125 Pescara, PE, Italy
| | - Vincenzo Olivieri
- Centro Studi Cetacei Onlus, Centro Recupero e Riabilitazione Tartarughe Marine “L.Cagnolaro”, 65125 Pescara, PE, Italy
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale (IZS) dell’Abruzzo e Molise “G. Caporale”, 64100 Teramo, TE, Italy
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale (IZS) dell’Abruzzo e Molise “G. Caporale”, 64100 Teramo, TE, Italy
| | - Nicola Ferri
- Istituto Zooprofilattico Sperimentale (IZS) dell’Abruzzo e Molise “G. Caporale”, 64100 Teramo, TE, Italy
| | - Gabriella Di Francesco
- Istituto Zooprofilattico Sperimentale (IZS) dell’Abruzzo e Molise “G. Caporale”, 64100 Teramo, TE, Italy
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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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Phenotypic characterization and analysis of complete genomes of two distinct strains of the proposed species "L. swaminathanii". Sci Rep 2022; 12:9137. [PMID: 35650389 PMCID: PMC9159981 DOI: 10.1038/s41598-022-13119-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/27/2022] [Indexed: 11/29/2022] Open
Abstract
Recently, a new Listeria species, “Listeria swaminathanii”, was proposed. Here, we phenotypically and genotypically characterize two additional strains that were previously obtained from soil samples and compare the results to the type strain. Complete genomes for both strains were assembled from hybrid Illumina and Nanopore sequencing reads and annotated. Further genomic analysis including average nucleotide identity (ANI) and detection of mobile genetic elements and genes of interest (e.g., virulence-associated) were conducted. The strains showed 98.7–98.8% ANI with the type strain. The UTK C1-0015 genome contained a partial monocin locus and a plasmid, while the UTK C1-0024 genome contained a full monocin locus and a prophage. Phenotypic characterization consistent with those performed on the proposed type strain was conducted to assess consistency of phenotypes across a greater diversity of the proposed species (n = 3 instead of n = 1). Only a few findings were notably different from those of the type strain, such as catalase activity, glycerol metabolism, starch metabolism, and growth at 41 °C. This study further expands our understanding of this newly proposed sensu stricto Listeria species.
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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: 18] [Impact Index Per Article: 9.0] [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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Chiaverini A, Guidi F, Torresi M, Acciari VA, Centorotola G, Cornacchia A, Centorame P, Marfoglia C, Blasi G, Di Domenico M, Migliorati G, Roussel S, Pomilio F, Sevellec Y. Phylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Listeria monocytogenes Outbreak. Front Microbiol 2021; 12:750065. [PMID: 34803971 PMCID: PMC8600327 DOI: 10.3389/fmicb.2021.750065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/13/2021] [Indexed: 12/24/2022] Open
Abstract
From May 2015 to March 2016, a severe outbreak due to Listeria monocytogenes ST7 strain occurred in Central Italy and caused 24 confirmed clinical cases. The epidemic strain was deeply investigated using whole-genome sequencing (WGS) analysis. In the interested area, the foodborne outbreak investigation identified a meat food-producing plant contaminated by the outbreak strain, carried by pork-ready-to-eat products. In the same region, in March 2018, the epidemic strain reemerged causing one listeriosis case in a 10-month-old child. The aim of this study was to investigate the phylogeny of the epidemic and reemergent strains over time and to compare them with a closer ST7 clone, detected during the outbreak and with different pulsed-field gel electrophoresis (PFGE) profiles, in order to identify genomic features linked to the persistence and the reemergence of the outbreak. An approach combining phylogenetic analysis and genome-wide association study (GWAS) revealed that the epidemic and reemergent clones were genetically closer to the ST7 clone with different PFGE profiles and strictly associated with the pork production chain. The repeated detection of both clones was probably correlated with (i) the presence of truly persistent clones and the repeated introduction of new ones and (ii) the contribution of prophage genes in promoting the persistence of the epidemic clones. Despite that no significant genomic differences were detected between the outbreak and the reemergent strain, the two related clones detected during the outbreak can be differentiated by transcriptional factor and phage genes associated with the phage LP-114.
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Affiliation(s)
- Alexandra Chiaverini
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Fabrizia Guidi
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche "Togo Rosati", Perugia, Italy
| | - Marina Torresi
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Vicdalia Aniela Acciari
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Gabriella Centorotola
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Alessandra Cornacchia
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Patrizia Centorame
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Cristina Marfoglia
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Giuliana Blasi
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche "Togo Rosati", Perugia, Italy
| | - Marco Di Domenico
- National Reference Centre for Whole Genome Sequencing of Microbial Pathogens Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Giacomo Migliorati
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Sophie Roussel
- Laboratoire de Sécurité des Aliments, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Université PARIS-EST, Maisons-Alfort, France
| | - Francesco Pomilio
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Yann Sevellec
- Laboratoire de Sécurité des Aliments, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Université PARIS-EST, Maisons-Alfort, France
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Genomic Analysis of Prophages Recovered from Listeria monocytogenes Lysogens Found in Seafood and Seafood-Related Environment. Microorganisms 2021; 9:microorganisms9071354. [PMID: 34206706 PMCID: PMC8303350 DOI: 10.3390/microorganisms9071354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 11/23/2022] Open
Abstract
A prophage is a phage-related sequence that is integrated into a bacterial chromosome. Prophages play an important role in bacterial evolution, survival, and persistence. To understand the impact of Listeria prophages on their host genome organizations, this work sequenced two L. monocytogenes strains (134LM and 036LM), previously identified as lysogens by mitomycin C induction. Draft genomes were generated with assembly sizes of 2,953,877 bp and 3,000,399 bp. One intact prophage (39,532 bp) was inserted into the comK gene of the 134LM genome. Two intact prophages (48,684 bp and 39,488 bp) were inserted in tRNA-Lys and elongation-factor genes of the 036LM genome. The findings confirmed the presence of three corresponding induced phages previously obtained by mitomycin C induction. Comparative genomic analysis of three prophages obtained in the newly sequenced lysogens with 61 prophages found in L. monocytogenes genomes, available in public databases, identified six major clusters using whole genome-based phylogenetic analysis. The results of the comparative genomic analysis of the prophage sequences provides knowledge about the diversity of Listeria prophages and their distribution among Listeria genomes in diverse environments, including different sources or geographical regions. In addition, the prophage sequences and their insertion sites contribute to the genomic diversity of L. monocytogenes genomes. These data of prophage sequences, prophage insertion sites, and prophage sequence comparisons, together with ANIb confirmation, could be useful for L. monocytogenes classification by prophages. One potential development could be refinement of prophage typing tools for monitoring or surveillance of L. monocytogenes contamination and transmission.
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da Silva DAL, de Melo Tavares R, Camargo AC, Yamatogi RS, De Martinis ECP, Nero LA. Biofilm growth by Listeria monocytogenes on stainless steel and expression of biofilm-related genes under stressing conditions. World J Microbiol Biotechnol 2021; 37:119. [PMID: 34131813 DOI: 10.1007/s11274-021-03092-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/11/2021] [Indexed: 12/01/2022]
Abstract
This research was carried out to investigate the differences in adhesion and growth during biofilm formation of L. monocytogenes from different sources and clonal complexes. Biofilm by L. monocytogenes (isolates CLIST 441 and 7: both lineage I, serotype 1/2b, CC3; isolates 19 and 508: both lineage II, serotype 1/2c, CC9) was grown on stainless steel coupons under different stressing conditions (NaCl, curing salts and quaternary ammonium compounds-QAC), to determine the expression of different genes involved in biofilm formation and stress response. CLIST 441, which carries a premature stop codon (PMSC) in agrC, formed high-density biofilms in the presence of QAC (7.5% w/v) or curing salts (10% w/v). Reverse Transcriptase-qPCR results revealed that L. monocytogenes isolates presented differences in transcriptional profile of genes related to biofilm formation and adaptation to environmental conditions. Our results demonstrated how L. monocytogenes can survive, multiply and form biofilm under adverse conditions related to food processing environments. Differences in transcriptional expression were observed, highlighting the role of regulatory gene networks for particular serotypes under different stress responses.
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Affiliation(s)
- Danilo Augusto Lopes da Silva
- InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Campus Viçosa, Centro, Viçosa, MG, 36570-900, Brazil
| | - Rafaela de Melo Tavares
- InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Campus Viçosa, Centro, Viçosa, MG, 36570-900, Brazil
| | - Anderson Carlos Camargo
- InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Campus Viçosa, Centro, Viçosa, MG, 36570-900, Brazil.,Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Campus Viçosa, Centro, Viçosa, MG, 36570-900, Brazil
| | - Ricardo Seiti Yamatogi
- InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Campus Viçosa, Centro, Viçosa, MG, 36570-900, Brazil
| | - Elaine Cristina Pereira De Martinis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Cafés/n, Vila Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Luís Augusto Nero
- InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Campus Viçosa, Centro, Viçosa, MG, 36570-900, Brazil.
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Sundarram A, Britton BC, Liu J, Desiree K, Ogas R, Lemaster P, Navarrete B, Nowakowski H, Harrod MK, Marks D, Ebner PD, Oliver HF. Lytic Capacity Survey of Commercial Listeria Phage Against Listeria spp. with Varied Genotypic and Phenotypic Characteristics. Foodborne Pathog Dis 2021; 18:413-418. [PMID: 33902330 DOI: 10.1089/fpd.2020.2897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Listeria monocytogenes is regularly isolated from food processing environments and is endemic in some facilities. Bacteriophage have potential as biocontrol strategies for L. monocytogenes. In this study, the lytic capacity of a commercial Listeria phage cocktail was evaluated against a library of 475 Listeria spp. isolates (426 L. monocytogenes and 49 other Listeria spp.) with varied genotypic and phenotypic characteristics. The lytic capacity of the Listeria phages was measured by spot assays where lysis was scored on a scale of 0-3 (0 = no lysis; 1 = slight lysis; 2 = moderate lysis; 3 = confluent lysis). Only 5% of all tested Listeria spp. isolates, including L. monocytogenes, were either moderately or highly susceptible (score 2 or 3) to lysis by Listeria phage when scores were averaged across temperature and phage concentration; 155 of 5700 treatment (multiplicity of infection [MOI] and temperature) and characteristic (genotype, sanitizer tolerance, and attachment capacity) combinations resulted in confluent lysis (score = 3). Odds ratios for susceptibility to lysis were calculated using multinomial logistic regression. The odds of susceptibility to lysis by phage decreased (p < 0.05) if the L. monocytogenes isolate was previously found to persist or if the phage-bacteria culture was incubated at 30°C; neither isolate persistence or temperature was significant (p ≥ 0.05) when all factors were considered. In addition, lytic efficacy varied (p < 0.05) among pulse field gel electrophoresis (PFGE) pulsotypes and may be affected by host MOI (p < 0.05). There was no effect (p > 0.05) of attachment capacity or sanitizer tolerance on phage susceptibility. This study underscores the complexity of using Listeria phage as a biocontrol for Listeria spp. in food processing facilities and highlights that phage susceptibility is most greatly impacted by genotype. Further studies are needed to evaluate these findings within a processing environment.
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Affiliation(s)
- Ajita Sundarram
- Department of Food Science and College of Agriculture, Purdue University, West Lafayette, Indiana, USA
| | - Brianna C Britton
- Department of Food Science and College of Agriculture, Purdue University, West Lafayette, Indiana, USA
| | - Jia Liu
- Department of Animal Sciences, College of Agriculture, Purdue University, West Lafayette, Indiana, USA
| | - Karina Desiree
- Department of Food Science and College of Agriculture, Purdue University, West Lafayette, Indiana, USA
| | - Raeya Ogas
- Department of Food Science and College of Agriculture, Purdue University, West Lafayette, Indiana, USA
| | - Paige Lemaster
- Department of Food Science and College of Agriculture, Purdue University, West Lafayette, Indiana, USA
| | - Brenda Navarrete
- Department of Food Science and College of Agriculture, Purdue University, West Lafayette, Indiana, USA
| | - Haley Nowakowski
- Department of Animal Sciences, College of Agriculture, Purdue University, West Lafayette, Indiana, USA
| | - Mary Kate Harrod
- Department of Animal Sciences, College of Agriculture, Purdue University, West Lafayette, Indiana, USA
| | - Danielle Marks
- Department of Animal Sciences, College of Agriculture, Purdue University, West Lafayette, Indiana, USA
| | - Paul D Ebner
- Department of Animal Sciences, College of Agriculture, Purdue University, West Lafayette, Indiana, USA
| | - Haley F Oliver
- Department of Food Science and College of Agriculture, Purdue University, West Lafayette, Indiana, USA
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Lachtara B, Osek J, Wieczorek K. Molecular Typing of Listeria monocytogenes IVb Serogroup Isolated from Food and Food Production Environments in Poland. Pathogens 2021; 10:pathogens10040482. [PMID: 33921133 PMCID: PMC8071568 DOI: 10.3390/pathogens10040482] [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: 03/03/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/31/2022] Open
Abstract
Listeria monocytogenes is one of the most important foodborne pathogens that may be present in food and in food processing environments. In the present study, 91 L. monocytogenes isolates of serogroup IVb from raw meat, ready-to-eat food and food production environments in Poland were characterized by whole genome sequencing (WGS). The strains were also compared, using core genome multi-locus sequence typing (cgMLST) analysis, with 186 genomes of L. monocytogenes recovered worldwide from food, environments, and from humans with listeriosis. The L. monocytogenes examined belonged to three MLST clonal complexes: CC1 (10; 11.0% isolates), CC2 (70; 76.9%), and CC6 (11; 12.1%). CC1 comprised of two STs (ST1 and ST515) which could be divided into five cgMLST, CC2 covered two STs (ST2 and ST145) with a total of 20 cgMLST types, whereas CC6 consisted of only one ST (ST6) classified as one cgMLST. WGS sequences of the tested strains revealed that they had several pathogenic markers making them potentially hazardous for public health. Molecular comparison of L. monocytogenes strains tested in the present study with those isolated from food and human listeriosis showed a relationship between the isolates from Poland, but not from other countries.
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Palaiodimou L, Fanning S, Fox EM. Genomic insights into persistence of Listeria species in the food processing environment. J Appl Microbiol 2021; 131:2082-2094. [PMID: 33768629 DOI: 10.1111/jam.15089] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/18/2021] [Accepted: 03/21/2021] [Indexed: 12/01/2022]
Abstract
AIMS Listeria species may colonize and persist in food processing facilities for prolonged periods of time, despite hygiene interventions in place. To understand the genetic factors contributing to persistence of Listeria strains, this study undertook a comparative analysis of seven persistent and six presumed non-persistent strains, isolated from a single food processing environment, to identify genetic markers correlating to promoting persistence of Listeria strains, through whole genome sequence analysis. METHODS AND RESULTS A diverse pool of genetic markers relevant to hygiene tolerance was identified, including disinfectant resistance markers qacH, emrC and the efflux cassette bcrABC. Both persistent and presumed non-persistent cohorts encoded a range of stress resistance markers, including heavy metal resistance, oxidative and pH stress, although trends were associated with each cohort (e.g., qacH and cadA1C resistance was more frequently found in persistent isolates). Persistent isolates were more likely to contain mutations associated with attenuated virulence, including a truncated InlA. Plasmids and transposons were widespread between cohorts. CONCLUSIONS Results suggest that no single genetic marker identified was universally responsible for a strain's ability to persist. Persistent strains were more likely to harbour mutation associated with hypovirulence. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides additional insights into the distribution of genetic elements relevant to persistence across Listeria species, as well as strain virulence potential.
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Affiliation(s)
- L Palaiodimou
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - S Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - E M Fox
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
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An Open-Source Program (Haplo-ST) for Whole-Genome Sequence Typing Shows Extensive Diversity among Listeria monocytogenes Isolates in Outdoor Environments and Poultry Processing Plants. Appl Environ Microbiol 2020; 87:AEM.02248-20. [PMID: 33097499 DOI: 10.1128/aem.02248-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/11/2020] [Indexed: 12/28/2022] Open
Abstract
A reliable and standardized classification of Listeria monocytogenes is important for accurate strain identification during outbreak investigations. Current whole-genome sequencing (WGS)-based approaches for strain characterization are either difficult to standardize, rendering them less suitable for data exchange, or are not freely available. Thus, we developed a portable and open-source tool, Haplo-ST, to improve standardization and provide maximum discriminatory potential to WGS data tied to a multilocus sequence typing (MLST) framework. Haplo-ST performs whole-genome MLST (wgMLST) for L. monocytogenes while allowing for data exchangeability worldwide. This tool takes in (i) raw WGS reads as input, (ii) cleans the raw data according to user-specified parameters, (iii) assembles genes across loci by mapping to genes from reference strains, and (iv) assigns allelic profiles to assembled genes and provides a wgMLST subtyping for each isolate. Data exchangeability relies on the tool assigning allelic profiles based on a centralized nomenclature defined by the widely used BIGSdb-Lm database. Tests of Haplo-ST's performance with simulated reads from L. monocytogenes reference strains demonstrated high sensitivity (97.5%), and coverage depths of ≥20× were found to be sufficient for wgMLST profiling. We then used Haplo-ST to characterize and differentiate between two groups of L. monocytogenes isolates derived from the natural environment and poultry processing plants. Phylogenetic reconstruction identified lineages within each group, and no lineage specificity was observed with isolate phenotypes (transient versus persistent) or origins. Genetic differentiation analyses between isolate groups identified 21 significantly differentiated loci, potentially enriched for adaptation and persistence of L. monocytogenes within poultry processing plants.IMPORTANCE We have developed an open-source tool (https://github.com/swarnalilouha/Haplo-ST) that provides allele-based subtyping of L. monocytogenes isolates at the whole-genome level. Along with allelic profiles, this tool also generates allele sequences and identifies paralogs, which is useful for phylogenetic tree reconstruction and deciphering relationships between closely related isolates. More broadly, Haplo-ST is flexible and can be adapted to characterize the genome of any haploid organism simply by installing an organism-specific gene database. Haplo-ST also allows for scalable subtyping of isolates; fewer reference genes can be used for low-resolution typing, whereas higher resolution can be achieved by increasing the number of genes used in the analysis. Our tool enabled clustering of L. monocytogenes isolates into lineages and detection of potential loci for adaptation and persistence in food processing environments. Findings from these analyses highlight the effectiveness of Haplo-ST in subtyping and evaluating relationships among isolates in studies of bacterial population genetics.
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Bansal M, Dhowlaghar N, Nannapaneni R, Kode D, Chang S, Sharma CS, McDaniel C, Kiess A. Decreased biofilm formation by planktonic cells of Listeria monocytogenes in the presence of sodium hypochlorite. Food Microbiol 2020; 96:103714. [PMID: 33494900 DOI: 10.1016/j.fm.2020.103714] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/30/2020] [Accepted: 12/04/2020] [Indexed: 10/22/2022]
Abstract
The objective of this study was to determine if the adaptation at planktonic stage to subinhibitory concentrations (SIC) of sodium hypochlorite (NaOCl) could modulate the biofilm forming ability of five Listeria monocytogenes strains V7, Scott A, FSL-N1-227, FSL F6-154 and ATCC 19116 representing serotypes 1/2a, 4b and 4c. Biofilm formation by NaOCl nonadapted and adapted L. monocytogenes planktonic cells was measured in the presence or absence of SIC of NaOCl. The biofilm formation ability of NaOCl nonadapted and adapted L. monocyotgenes planktonic cells was reduced only in the presence of NaOCl (P < 0.05). Scanning electron microscopy revealed that the continuous exposure of NaOCl induced morphological changes in the L. monocytogenes biofilm structure and reduced its attachment to polystyrene surface. The qRT-PCR results also showed that the subinhibitory NaOCl reduced biofilm formation related gene expression such as motility and quorum sensing signals (P < 0.05). These findings indicate that subinhibitory NaOCl can reduce the ability of L. monocytogenes planktonic cells to form biofilms on polystyrene surface.
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Affiliation(s)
- Mohit Bansal
- Department of Poultry Science, Mississippi State University, MS, 39762, USA
| | - Nitin Dhowlaghar
- Department of Food Science, Nutrition and Health Promotion, Mississippi State University, MS, 39762, USA
| | - Ramakrishna Nannapaneni
- Department of Food Science, Nutrition and Health Promotion, Mississippi State University, MS, 39762, USA.
| | - Divya Kode
- Department of Food Science, Nutrition and Health Promotion, Mississippi State University, MS, 39762, USA
| | - Sam Chang
- Department of Food Science, Nutrition and Health Promotion, Mississippi State University, MS, 39762, USA
| | - Chander S Sharma
- Department of Poultry Science, Mississippi State University, MS, 39762, USA
| | | | - Aaron Kiess
- Department of Poultry Science, Mississippi State University, MS, 39762, USA
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Scaltriti E, Bolzoni L, Vocale C, Morganti M, Menozzi I, Re MC, Pongolini S. Population Structure of Listeria monocytogenes in Emilia-Romagna (Italy) and Implications on Whole Genome Sequencing Surveillance of Listeriosis. Front Public Health 2020; 8:519293. [PMID: 33072691 PMCID: PMC7531028 DOI: 10.3389/fpubh.2020.519293] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 08/13/2020] [Indexed: 11/25/2022] Open
Abstract
The population structure of human isolates of Listeria monocytogenes in Emilia-Romagna, Italy, from 2012 to 2018 was investigated with the aim of evaluating the presence of genomic clusters indicative of possible outbreaks, the proportion of cluster-associated vs. sporadic isolates and different methods and metrics of genomic analysis for use in routine surveillance. In the 2012–2018 period the notification rate of confirmed invasive cases in Emilia-Romagna was 0.91 per 100,000 population per year, more than twice the average rate of EU countries. Out of the total 283 cases, 268 (about 95%) isolates were typed through whole genome sequencing (WGS) for cluster detection with methods based on core-genome multi-locus sequence typing and single nucleotide polymorphisms. Between 66 and 72% of listeriosis cases belonged to genomic clusters which included up to 27 cases and lasted up to 5 years. This proportion of cluster-associated cases is higher than previously estimated in other European studies. Rarefaction analysis, performed by reducing both the number of consecutive years of surveillance considered and the proportion of isolates included in the analysis, suggested that the observed high proportion of cluster-associated cases can be ascribed to the long surveillance duration (7 years) and the high notification and typing rates of this study. Our findings show that a long temporal perspective and high surveillance intensity, intended as both exhaustiveness of the system to report cases and high WGS-typing rate, are critical for sensitive detection of possible outbreaks within a WGS-based surveillance of listeriosis. Furthermore, the power and complexity of WGS interpretation emerged from the integration of genomic and epidemiological information in the investigation of few past outbreaks within the study, indicating that the use of multiple approaches, including the analysis of the accessory genome, is needed to accurately elucidate the population dynamics of Listeria monocytogenes.
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Affiliation(s)
- Erika Scaltriti
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Parma, Italy
| | - Luca Bolzoni
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Parma, Italy
| | - Caterina Vocale
- Operating Unit of Clinical Microbiology, Regional Reference Center for Microbiological Emergencies, St. Orsola-Malpighi Polyclinic, Bologna, Italy
| | - Marina Morganti
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Parma, Italy
| | - Ilaria Menozzi
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Parma, Italy
| | - Maria Carla Re
- Operating Unit of Clinical Microbiology, Regional Reference Center for Microbiological Emergencies, St. Orsola-Malpighi Polyclinic, Bologna, Italy
| | - Stefano Pongolini
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Parma, Italy
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Matle I, Mbatha KR, Madoroba E. A review of Listeria monocytogenes from meat and meat products: Epidemiology, virulence factors, antimicrobial resistance and diagnosis. ACTA ACUST UNITED AC 2020; 87:e1-e20. [PMID: 33054262 PMCID: PMC7565150 DOI: 10.4102/ojvr.v87i1.1869] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022]
Abstract
Listeria monocytogenes is a zoonotic food-borne pathogen that is associated with serious public health and economic implications. In animals, L. monocytogenes can be associated with clinical listeriosis, which is characterised by symptoms such as abortion, encephalitis and septicaemia. In human beings, listeriosis symptoms include encephalitis, septicaemia and meningitis. In addition, listeriosis may cause gastroenteric symptoms in human beings and still births or spontaneous abortions in pregnant women. In the last few years, a number of reported outbreaks and sporadic cases associated with consumption of contaminated meat and meat products with L. monocytogenes have increased in developing countries. A variety of virulence factors play a role in the pathogenicity of L. monocytogenes. This zoonotic pathogen can be diagnosed using both classical microbiological techniques and molecular-based methods. There is limited information about L. monocytogenes recovered from meat and meat products in African countries. This review strives to: (1) provide information on prevalence and control measures of L. monocytogenes along the meat value chain, (2) describe the epidemiology of L. monocytogenes (3) provide an overview of different methods for detection and typing of L. monocytogenes for epidemiological, regulatory and trading purposes and (4) discuss the pathogenicity, virulence traits and antimicrobial resistance profiles of L. monocytogenes.
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Affiliation(s)
- Itumeleng Matle
- Bacteriology Division, Agricultural Research Council - Onderstepoort Veterinary Research, Onderstepoort, Pretoria, South Africa; and, Department of Agriculture and Animal Health, University of South Africa, Science Campus, Florida.
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Characterization of Mobile Genetic Elements Using Long-Read Sequencing for Tracking Listeria monocytogenes from Food Processing Environments. Pathogens 2020; 9:pathogens9100822. [PMID: 33036450 PMCID: PMC7599586 DOI: 10.3390/pathogens9100822] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/26/2020] [Accepted: 10/01/2020] [Indexed: 02/02/2023] Open
Abstract
Recently developed nanopore sequencing technologies offer a unique opportunity to rapidly close the genome and to identify complete sequences of mobile genetic elements (MGEs). In this study, 17 isolates of Listeria monocytogenes (Lm) epidemic clone II (ECII) from seven ready-to-eat meat or poultry processing facilities, not known to be associated with outbreaks, were shotgun sequenced, and among them, five isolates were further subjected to long-read sequencing. Additionally, 26 genomes of Lm ECII isolates associated with three listeriosis outbreaks in the U.S. and South Africa were obtained from the National Center for Biotechnology Information (NCBI) database and analyzed to evaluate if MGEs may be used as a high-resolution genetic marker for identifying and sourcing the origin of Lm. The analyses identified four comK prophages in 11 non-outbreak isolates from four facilities and three comK prophages in 20 isolates associated with two outbreaks that occurred in the U.S. In addition, three different plasmids were identified among 10 non-outbreak isolates and 14 outbreak isolates. Each comK prophage and plasmid was conserved among the isolates sharing it. Different prophages from different facilities or outbreaks had significant genetic variations, possibly due to horizontal gene transfer. Phylogenetic analysis showed that isolates from the same facility or the same outbreak always closely clustered. The time of most recent common ancestor of the Lm ECII isolates was estimated to be in March 1816 with the average nucleotide substitution rate of 3.1 × 10−7 substitutions per site per year. This study showed that complete MGE sequences provide a good signal to determine the genetic relatedness of Lm isolates, to identify persistence or repeated contamination that occurred within food processing environment, and to study the evolutionary history among closely related isolates.
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Muchaamba F, Stephan R, Tasara T. β-Phenylethylamine as a Natural Food Additive Shows Antimicrobial Activity against Listeria monocytogenes on Ready-to-Eat Foods. Foods 2020; 9:E1363. [PMID: 32992828 PMCID: PMC7600551 DOI: 10.3390/foods9101363] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 12/26/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen and a major cause of death associated with bacterial foodborne infections. Control of L. monocytogenes on most ready-to-eat (RTE) foods remains a challenge. The potential use of β-phenylethylamine (PEA) as an organic antimicrobial against L. monocytogenes was evaluated in an effort to develop a new intervention for its control. Using a collection of 62 clinical and food-related isolates we determined the minimum inhibitory concentration (MIC) of PEA against L. monocytogenes in different broth and agar media. Bologna type sausage (lyoner) and smoked salmon were used as food model systems to validate the in vitro findings. PEA had a growth inhibitory and bactericidal effect against L. monocytogenes both in in vitro experiments as well as on lyoner and smoked salmon. The MIC's ranged from 8 to 12.5 mg/mL. Furthermore, PEA also inhibited L. monocytogenes biofilm formation. Based on good manufacturing practices as a prerequisite, the application of PEA to RTE products might be an additional hurdle to limit L. monocytogenes growth thereby increasing food safety.
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Affiliation(s)
- Francis Muchaamba
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, 8057 Zürich, Switzerland; (R.S.); (T.T.)
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Cherifi T, Arsenault J, Pagotto F, Quessy S, Côté JC, Neira K, Fournaise S, Bekal S, Fravalo P. Distribution, diversity and persistence of Listeria monocytogenes in swine slaughterhouses and their association with food and human listeriosis strains. PLoS One 2020; 15:e0236807. [PMID: 32760141 PMCID: PMC7410256 DOI: 10.1371/journal.pone.0236807] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/13/2020] [Indexed: 02/05/2023] Open
Abstract
Listeria monocytogenes is the etiological agent of listeriosis, a major foodborne disease and an important public health concern. Contamination of meat with L. monocytogenes occurs frequently at the slaughterhouse. Our aims were; 1) to investigate the distribution of L. monocytogenes in the processing areas of four swine slaughterhouses; 2) to describe the diversity of L. monocytogenes strains by pulsed-field gel electrophoresis; 3) to identify persistent L. monocytogenes strains and describe their distribution; 4) to investigate the associations between persistence of strains and their following characteristics: detection in food isolates, detection in human clinical isolates, and the presence of benzalkonium chloride (BAC) resistance genes. Various operation areas within the four swine slaughterhouses were sampled on four occasions. A total of 2496 samples were analyzed, and L. monocytogenes was successfully isolated from 243 samples. The proportion of positive samples ranged from 32 to 58% in each slaughterhouse and from 24 to 68% in each operation area. Fifty-eight different pulsotypes were identified and eight pulsotypes, present in samples collected during 4 visits, were considered persistent. The persistent pulsotypes were significantly more likely to be detected in food (P < 0.01, exact χ²) and human clinical cases (P < 0.01, exact χ²), respectively. Among pulsotypes harboring the BAC bcrABC resistance cassette or the emrE multidrug transporter gene, 42.8% were persistent compared to 4.5% for pulsotypes without these resistance genes (P < 0.01, exact χ²). Our study highlights the importance of persistent L. monocytogenes strains in the environmental contamination of slaughterhouses, which may lead to repeated contamination of meat products. It also shows that the presence of disinfectants resistance genes is an important contributing factor.
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Affiliation(s)
- Tamazight Cherifi
- Chaire de recherche en salubrité des viandes, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Centre de recherche en infectiologie porcine et avicole (CRIPA-FQRNT), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Groupe de recherche et d’enseignement en salubrité des aliments (GRESA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- * E-mail: (TC); (PF)
| | - Julie Arsenault
- Centre de recherche en infectiologie porcine et avicole (CRIPA-FQRNT), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Epidemiology of Zoonoses and Public Health Research Unit (GREZOSP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Franco Pagotto
- Listeriosis Reference Service, Microbiology Research Division, Bureau of Microbial Hazards, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Sylvain Quessy
- Chaire de recherche en salubrité des viandes, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Groupe de recherche et d’enseignement en salubrité des aliments (GRESA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Jean-Charles Côté
- Chaire de recherche en salubrité des viandes, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Groupe de recherche et d’enseignement en salubrité des aliments (GRESA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Kersti Neira
- Chaire de recherche en salubrité des viandes, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Centre de recherche en infectiologie porcine et avicole (CRIPA-FQRNT), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Groupe de recherche et d’enseignement en salubrité des aliments (GRESA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | | | - Sadjia Bekal
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Philippe Fravalo
- Chaire de recherche en salubrité des viandes, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Centre de recherche en infectiologie porcine et avicole (CRIPA-FQRNT), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Epidemiology of Zoonoses and Public Health Research Unit (GREZOSP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- * E-mail: (TC); (PF)
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Muchaamba F, Eshwar AK, von Ah U, Stevens MJA, Tasara T. Evolution of Listeria monocytogenes During a Persistent Human Prosthetic Hip Joint Infection. Front Microbiol 2020; 11:1726. [PMID: 32849369 PMCID: PMC7399150 DOI: 10.3389/fmicb.2020.01726] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/01/2020] [Indexed: 11/23/2022] Open
Abstract
Listeria monocytogenes associated prosthetic joint infections (PJI) are a rare but increasing clinical problem of listeriosis. We characterized two isolates of the same L. monocytogenes strain isolated within five years of each other from a recurrent human prosthetic joint infection. The two isolates although clonally identical were phenotypically distinct confirming that the original infection strain had evolved within the human host PJI environment giving rise to a phenotypically distinct variant. The recurrent PJI isolate displayed various phenotypic differences compared to the parental original PJI isolate including diminished growth and carbon source metabolism, as well as altered morphology and increased stress sensitivity. The PJI isolates were both diminished in virulence due to an identical truncation mutation in the major virulence regulator PrfA. Genome wide sequence comparison provided conclusive evidence that the two isolates were identical clonal descendants of the same L. monocytogenes strain that had evolved through acquisition of various single nucleotide polymorphisms (SNPs) as well as insertion and deletion events (InDels) during a persistent human PJI. Acquired genetic changes included a specific mutation causing premature stop codon (PMSC) and truncation of RNAse J1 protein. Based on analysis of this naturally truncated as well as other complete RNAse J1 deletion mutants we show that the long-term survival of this specific L. monocytogenes strain within the prosthetic joint might in part be explained by the rnjA PMSC mutation that diminishes virulence and activation of the host immune system in a zebrafish embryo localized infection model. Overall our analysis of this special natural case provides insights into random mutation events and molecular mechanisms that might be associated with the adaptation and short-term evolution of this specific L. monocytogenes strain within a persistent human PJI environment.
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Affiliation(s)
- Francis Muchaamba
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Athmanya K. Eshwar
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | | | - Marc J. A. Stevens
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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Yang H, Hoffmann M, Allard MW, Brown EW, Chen Y. Microevolution and Gain or Loss of Mobile Genetic Elements of Outbreak-Related Listeria monocytogenes in Food Processing Environments Identified by Whole Genome Sequencing Analysis. Front Microbiol 2020; 11:866. [PMID: 32547499 PMCID: PMC7272582 DOI: 10.3389/fmicb.2020.00866] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/14/2020] [Indexed: 01/03/2023] Open
Abstract
Whole genome sequencing (WGS) analyses have been instrumental in traceback investigations of Listeria monocytogenes (Lm). To demonstrate how long-read sequencing analysis can capture and describe relationships among isolates from clinical, food, and environmental sources, we analyzed 366 long-read- and shotgun-sequenced isolates from 16 Lm outbreak strains associated with cantaloupe, leafy green, stone fruit, caramel apple, mung bean sprout, multiple cheese products, multiple ice cream products, and their production environments. The analyses demonstrated that outbreak strains could be distributed in different areas and zones of food production environments through persistent or repeated contamination. Multi-strain and multi-clone contamination were common. Further, WGS could differentiate among isolates collected at different time points or from different production lines in the same facility, revealing microevolution events in processing environments. Our comparison between complete and shotgun genomes showed that isolates of the same outbreak strain diversified mostly by gain/loss of plasmids and chromosome-borne prophages that constitute 2 to 5% of the chromosome. In contrast, other genes missing in the shotgun genomes were randomly scattered, constituting ~0.5% of the chromosome. Among different outbreak strains of the same CC, most gene-scale differences were due to gain/loss of mobile genetic elements, such as plasmids, chromosome-borne prophages, a Tn916 like transposon, and Listeria Genomic Island 2. The nucleotide variations in the same prophage and the same plasmid shared among isolates of the same outbreak strain were limited, which enabled different WGS tools to unambiguously cluster isolates of the same outbreak strain. In some outbreak strains, correlation between prophage gain/loss and single nucleotide polymorphism (SNP) accumulations in the genome backbone were observed.
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Affiliation(s)
- Helen Yang
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Marc W Allard
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Eric W Brown
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Yi Chen
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
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Wang LYR, Jokinen CC, Laing CR, Johnson RP, Ziebell K, Gannon VPJ. Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada. Microb Genom 2020; 6. [PMID: 32496181 PMCID: PMC7371104 DOI: 10.1099/mgen.0.000376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Verotoxigenic Escherichia coli (VTEC) are food- and water-borne pathogens associated with both sporadic illness and outbreaks of enteric disease. While it is known that cattle are reservoirs of VTEC, little is known about the genomic variation of VTEC in cattle, and whether the variation in genomes reported for human outbreak strains is consistent with individual animal or group/herd sources of infection. A previous study of VTEC prevalence identified serotypes carried persistently by three consecutive cohorts of heifers within a closed herd of cattle. This present study aimed to: (i) determine whether the genomic relatedness of bovine isolates is similar to that reported for human strains associated with single source outbreaks, (ii) estimate the rates of genome change among dominant serotypes over time within a cattle herd, and (iii) identify genomic features of serotypes associated with persistence in cattle. Illumina MiSeq genome sequencing and genotyping based on allelic and single nucleotide variations were completed, while genome change over time was measured using Bayesian evolutionary analysis sampling trees. The accessory genome, including the non-protein-encoding intergenic regions (IGRs), virulence factors, antimicrobial-resistance genes and plasmid gene content of representative persistent and sporadic cattle strains were compared using Fisher’s exact test corrected for multiple comparisons. Herd strains from serotypes O6:H34 (n=22), O22:H8 (n=30), O108:H8 (n=39), O139:H19 (n=44) and O157:H7 (n=106) were readily distinguishable from epidemiologically unrelated strains of the same serotype using a similarity threshold of 10 or fewer allele differences between adjacent nodes. Temporal-cohort clustering within each serotype was supported by date randomization analysis. Substitutions per site per year were consistent with previously reported values for E. coli; however, there was low branch support for these values. Acquisition of the phage-encoded Shiga toxin 2 gene in serotype O22:H8 was observed. Pan-genome analyses identified accessory regions that were more prevalent in persistent serotypes (P≤0.05) than in sporadic serotypes. These results suggest that VTEC serotypes from a specific cattle population are highly clonal with a similar level of relatedness as human single-source outbreak-associated strains, but changes in the genome occur gradually over time. Additionally, elements in the accessory genomes may provide a selective advantage for persistence of VTEC within cattle herds.
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Affiliation(s)
- Lu Ya Ruth Wang
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
| | | | - Chad R Laing
- National Centre for Animal Disease, Canadian Food Inspection Agency, Lethbridge, Alberta, Canada
| | - Roger P Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Victor P J Gannon
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
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Gwida M, Lüth S, El-Ashker M, Zakaria A, El-Gohary F, Elsayed M, Kleta S, Al Dahouk S. Contamination Pathways can Be Traced along the Poultry Processing Chain by Whole Genome Sequencing of Listeria innocua. Microorganisms 2020; 8:microorganisms8030414. [PMID: 32183339 PMCID: PMC7143663 DOI: 10.3390/microorganisms8030414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/06/2020] [Accepted: 03/13/2020] [Indexed: 11/23/2022] Open
Abstract
Foodborne infection with Listeria causes potentially life-threatening disease listeriosis. Listeria monocytogenes is widely recognized as the only species of public health concern, and the closely related species Listeria innocua is commonly used by the food industry as an indicator to identify environmental conditions that allow for presence, growth, and persistence of Listeria spp. in general. In our study, we analyze the occurrence of Listeria spp. in a farm-to-fork approach in a poultry production chain in Egypt and identify bacterial entry gates and transmission systems. Prevalence of Listeria innocua at the three production stages (farm, slaughterhouse, food products) ranged from 11% to 28%. The pathogenic species Listeria monocytogenes was not detected, and Listeria innocua strains under study did not show genetic virulence determinants. However, the close genetic relatedness of Listeria innocua isolates (maximum 63 SNP differences) indicated cross-contamination between all stages from farm to final food product. Based on these results, chicken can be seen as a natural source of Listeria. Last but not least, sanitary measures during production should be reassessed to prevent bacterial contamination from entering the food chain and to consequently prevent human listeriosis infections. For this purpose, surveillance must not be restricted to pathogenic species.
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Affiliation(s)
- Mayada Gwida
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt; (M.G.)
| | - Stefanie Lüth
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
- Institute for Biology, Freie Universität Berlin, Königin-Luise-Straße 1-3, 14195 Berlin, Germany
- Correspondence:
| | - Maged El-Ashker
- Department of Internal Medicine, Infectious and Fish Diseases, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Amira Zakaria
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Fatma El-Gohary
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt; (M.G.)
| | - Mona Elsayed
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt; (M.G.)
| | - Sylvia Kleta
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Sascha Al Dahouk
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
- RWTH Aachen University Hospital, Pauwelsstraße 30, 52074 Aachen, Germany
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Genomic Differences between Listeria monocytogenes EGDe Isolates Reveal Crucial Roles for SigB and Wall Rhamnosylation in Biofilm Formation. J Bacteriol 2020; 202:JB.00692-19. [PMID: 31964697 PMCID: PMC7167478 DOI: 10.1128/jb.00692-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/16/2020] [Indexed: 12/20/2022] Open
Abstract
Biofilms are an important mode of growth in many settings. Here, we looked at small differences in the genomes of the bacterium Listeria monocytogenes isolate EGDe and used them to find out how biofilms form. This important fundamental information may help new treatments to be developed and also highlights the fact that isolates of the same identity often diverge. Listeria monocytogenes is a Gram-positive firmicute that causes foodborne infections, in part due to its ability to use multiple strategies, including biofilm formation, to survive adverse growth conditions. As a potential way to screen for genes required for biofilm formation, we harnessed the ability of bacteria to accumulate mutations in the genome over time, diverging the properties of seemingly identical strains. By sequencing the genomes of four laboratory reference strains of the commonly used L. monocytogenes EGDe, we showed that each isolate contains single nucleotide polymorphisms (SNPs) compared with the reference genome. We discovered that two SNPs, contained in two independent genes within one of the isolates, impacted biofilm formation. Using bacterial genetics and phenotypic assays, we confirmed that rsbU and rmlA influence biofilm formation. RsbU is the upstream regulator of the alternative sigma factor SigB, and mutation of either rsbU or sigB increased biofilm formation. In contrast, deletion of rmlA, which encodes the first enzyme for TDP-l-rhamnose biosynthesis, resulted in a reduction in the amount of biofilm formed. Further analysis of biofilm formation in a strain that still produces TDP-l-rhamnose but which cannot decorate the wall teichoic acid with rhamnose (rmlT mutant) showed that it is the decorated wall teichoic acid that is required for adhesion of the cells to surfaces. Together, these data uncover novel routes by which biofilm formation by L. monocytogenes can be impacted. IMPORTANCE Biofilms are an important mode of growth in many settings. Here, we looked at small differences in the genomes of the bacterium Listeria monocytogenes isolate EGDe and used them to find out how biofilms form. This important fundamental information may help new treatments to be developed and also highlights the fact that isolates of the same identity often diverge.
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Evolution of Listeria monocytogenes in a Food Processing Plant Involves Limited Single-Nucleotide Substitutions but Considerable Diversification by Gain and Loss of Prophages. Appl Environ Microbiol 2020; 86:AEM.02493-19. [PMID: 31900305 PMCID: PMC7054086 DOI: 10.1128/aem.02493-19] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 12/20/2019] [Indexed: 12/23/2022] Open
Abstract
Knowledge about the genetic evolution of L. monocytogenes in food processing facilities over multiple years is generally lacking. This information is critical to interpret WGS findings involving food or food-associated isolates. This study suggests that L. monocytogenes that persists in processing facilities may evolve with a low single-nucleotide mutation rate mostly driven by negative (i.e., purifying) selection but with rapid diversification of prophages. Hence, isolation of L. monocytogenes with few single-nucleotide polymorphism (SNP) differences in different locations (e.g., supplier plants and receiving plants) is possible, highlighting the importance of epidemiological and detailed isolate metadata for interpreting WGS data in traceback investigation. Our study also shows how advanced WGS data analyses can be used to support root cause analysis efforts and may, for example, pinpoint the time when a persistence event started (which then potentially could be linked to facility changes, introduction of new equipment, etc.). Whole-genome sequencing (WGS) is becoming the standard method for subtyping Listeria monocytogenes. Interpretation of WGS data for isolates from foods and associated environments is, however, challenging due to a lack of detailed data on Listeria evolution in processing facilities. Here, we used previously collected WGS data for 40 L. monocytogenes isolates obtained from a cold-smoked salmon processing facility between 1998 and 2015 to probe the L. monocytogenes molecular evolution in this facility, combined with phenotypic assessment of selected isolates. Isolates represented three clusters (1, 2, and 3); cluster 3 isolates (n = 32) were obtained over 18 years. The average mutation rate for cluster 3 was estimated as 1.15 × 10−7 changes per nucleotide per year (∼0.35 changes per genome per year); the most recent common ancestors (MRCAs) of subclusters 3a and 3b were estimated to have occurred around 1958 and 1974, respectively, within the age of the facility, suggesting long-term persistence in this facility. Extensive prophage diversity was observed within subclusters 3a and 3b, which have one shared and six unique prophage profiles for each subcluster (with 16 prophage profiles found among all 40 isolates). The plasmid-borne sanitizer tolerance operon bcrABC was found in all cluster 2 and 3 isolates, while the transposon-borne sanitizer tolerance gene qacH was found in one cluster 1 isolate; presence of these genes was correlated with the ability to survive increased concentrations of sanitizers. Selected isolates showed significant variation in the ability to attach to surfaces, with persistent isolates attaching better than transient isolates at 21°C. IMPORTANCE Knowledge about the genetic evolution of L. monocytogenes in food processing facilities over multiple years is generally lacking. This information is critical to interpret WGS findings involving food or food-associated isolates. This study suggests that L. monocytogenes that persists in processing facilities may evolve with a low single-nucleotide mutation rate mostly driven by negative (i.e., purifying) selection but with rapid diversification of prophages. Hence, isolation of L. monocytogenes with few single-nucleotide polymorphism (SNP) differences in different locations (e.g., supplier plants and receiving plants) is possible, highlighting the importance of epidemiological and detailed isolate metadata for interpreting WGS data in traceback investigation. Our study also shows how advanced WGS data analyses can be used to support root cause analysis efforts and may, for example, pinpoint the time when a persistence event started (which then potentially could be linked to facility changes, introduction of new equipment, etc.).
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López-Alonso V, Ortiz S, Corujo A, Martínez-Suárez JV. Analysis of Benzalkonium Chloride Resistance and Potential Virulence of Listeria monocytogenes Isolates Obtained from Different Stages of a Poultry Production Chain in Spain. J Food Prot 2020; 83:443-451. [PMID: 32053831 DOI: 10.4315/0362-028x.jfp-19-289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 11/12/2019] [Indexed: 01/30/2023]
Abstract
ABSTRACT Listeria monocytogenes can survive in food production facilities and can be transmitted via contamination of food during the various stages of food production. This study was conducted to compile the results of three independent previous studies on the genetic diversity of L. monocytogenes in a poultry production company in Spain and to determine the potential virulence and sanitizer resistance of the strains by using both genotype and phenotype analyses. L. monocytogenes was detected at three production stages: a broiler abattoir, a processing plant, and retail stores marketing fresh poultry products from the same company. These three stages spanned three locations in three provinces of Spain. A set of 347 L. monocytogenes isolates representing 39 subtypes was obtained using pulsed-field gel electrophoresis (PFGE). A total of 28 subtypes (68%) had a full-length internalin A gene, and two subtypes had a phenotype with low potential for virulence because of a mutation in the prfA gene. A total of 32 subtypes (82%) were classified as benzalkonium chloride resistant (BAC-R) and contained the resistance determinant bcrABC (21 subtypes, 54%) or the resistance gene qacH (11 subtypes, 28%). A total of 13 persistent BAC-R subtypes (minimum of 3 months between the first and last sample from with the isolate was recovered) were identified at the abattoir and processing plant. The three production stages shared a unique subtype (PFGE type 1), which had the mutation in the prfA gene and the bcrABC resistance determinant. Whole genome sequencing revealed this subtype to be sequence type 31. Limited genetic diversity was noted in the isolates studied, including some subtypes that were persistent in the environment of the investigated facilities. Given the high prevalence of BAC-R subtypes, these results support the association between resistance to biocides and persistence of L. monocytogenes. HIGHLIGHTS
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Affiliation(s)
- Victoria López-Alonso
- Unidad de Biología Computacional, UFIEC, Instituto de Salud Carlos III, Carretera de Majadahonda a Pozuelo km 2, 28220 Majadahonda, Madrid, Spain
| | - Sagrario Ortiz
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Autovía A-6 km 7.5, 28040 Madrid, Spain
| | - Alfredo Corujo
- Nutreco Food Research Center, Ctra. CM 4004 km 10.5, 45950 Casarrubios del Monte, Toledo, Spain
| | - Joaquín V Martínez-Suárez
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Autovía A-6 km 7.5, 28040 Madrid, Spain.,(ORCID: https://orcid.org/0000-0003-4306-3223 [J.V.M.-S.])
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36
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Palma F, Brauge T, Radomski N, Mallet L, Felten A, Mistou MY, Brisabois A, Guillier L, Midelet-Bourdin G. Dynamics of mobile genetic elements of Listeria monocytogenes persisting in ready-to-eat seafood processing plants in France. BMC Genomics 2020; 21:130. [PMID: 32028892 PMCID: PMC7006209 DOI: 10.1186/s12864-020-6544-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/30/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Listeria monocytogenes Clonal Complexes (CCs) have been epidemiologically associated with foods, especially ready-to-eat (RTE) products for which the most likely source of contamination depends on the occurrence of persisting clones in food-processing environments (FPEs). As the ability of L. monocytogenes to adapt to environmental stressors met in the food chain challenges the efforts to its eradication from FPEs, the threat of persistent strains to the food industry and public health authorities continues to rise. In this study, 94 food and FPEs L. monocytogenes isolates, representing persistent subtypes contaminating three French seafood facilities over 2-6 years, were whole-genome sequenced to characterize their genetic diversity and determine the biomarkers associated with long-term survival in FPEs. RESULTS Food and FPEs isolates belonged to five CCs, comprising long-term intra- and inter-plant persisting clones. Mobile genetic elements (MGEs) such as plasmids, prophages and transposons were highly conserved within CCs, some of which harboured genes for resistance to chemical compounds and biocides used in the processing plants. Some of these genes were found in a 90.8 kbp plasmid, predicted to be" mobilizable", identical in isolates from CC204 and CC155, and highly similar to an 81.6 kbp plasmid from isolates belonging to CC7. These similarities suggest horizontal transfer between isolates, accompanied by deletion and homologous recombination in isolates from CC7. Prophage profiles characterized persistent clonal strains and several prophage-loci were plant-associated. Notably, a persistent clone from CC101 harboured a novel 31.5 kbp genomic island that we named Listeria genomic island 3 (LGI3), composed by plant-associated loci and chromosomally integrating cadmium-resistance determinants cadA1C. CONCLUSIONS Genome-wide analysis indicated that inter- and intra-plant persisting clones harbour conserved MGEs, likely acquired in FPEs and maintained by selective pressures. The presence of closely related plasmids in L. monocytogenes CCs supports the hypothesis of horizontal gene transfer conferring enhanced survival to FPE-associated stressors, especially in hard-to-clean harbourage sites. Investigating the MGEs evolutionary and transmission dynamics provides additional resolution to trace-back potentially persistent clones. The biomarkers herein discovered provide new tools for better designing effective strategies for the removal or reduction of resident L. monocytogenes in FPEs to prevent contamination of RTE seafood.
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Affiliation(s)
- Federica Palma
- ANSES, Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
| | - Thomas Brauge
- ANSES, Laboratory for Food Safety, Boulogne-sur-Mer, France
| | - Nicolas Radomski
- ANSES, Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
| | - Ludovic Mallet
- ANSES, Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
| | - Arnaud Felten
- ANSES, Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
| | - Michel-Yves Mistou
- ANSES, Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
- INRAE, MaIAGE, University Paris-Saclay, Jouy-en-Josas, France
| | - Anne Brisabois
- ANSES, Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
- ANSES, Laboratory for Food Safety, Boulogne-sur-Mer, France
| | - Laurent Guillier
- ANSES, Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
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Kragh ML, Truelstrup Hansen L. Initial Transcriptomic Response and Adaption of Listeria monocytogenes to Desiccation on Food Grade Stainless Steel. Front Microbiol 2020; 10:3132. [PMID: 32038566 PMCID: PMC6987299 DOI: 10.3389/fmicb.2019.03132] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/26/2019] [Indexed: 12/14/2022] Open
Abstract
The foodborne pathogen Listeria monocytogenes survives exposure to a variety of stresses including desiccation in the food industry. Strand-specific RNA sequencing was applied to analyze changes in the transcriptomes of two strains of L. monocytogenes (Lm 568 and Lm 08-5578) during desiccation [15°C, 43% relative humidity (RH)] on food grade stainless steel surfaces over 48 h to simulate a weekend with no food production. Both strains showed similar survival during desiccation with a 1.8-2 Log CFU/cm2 reduction after 48 h. Analysis of differentially expressed (DE) genes (>twofold, adjusted p-value <0.05) revealed that the initial response to desiccation was established after 6 h and remained constant with few new genes being DE after 12, 24, and 48 h. A core of 81 up- and 73 down-regulated DE genes were identified as a shared, strain independent response to desiccation. Among common upregulated genes were energy and oxidative stress related genes e.g., qoxABCD (cytochrome aa3) pdhABC (pyruvate dehydrogenase complex) and mntABCH (manganese transporter). Common downregulated genes related to anaerobic growth, proteolysis and the two component systems lmo1172/lmo1173 and cheA/cheY, which are involved in cold growth and flagellin production, respectively. Both strains upregulated additional genes involved in combatting oxidative stress and reactive oxygen species (ROS), including sod (superoxide dismutase), kat (catalase), tpx (thiol peroxidase) and several thioredoxins including trxAB, lmo2390 and lmo2830. Osmotic stress related genes were also upregulated in both strains, including gbuABC (glycine betaine transporter) and several chaperones clpC, cspA, and groE. Significant strain differences were also detected with the food outbreak strain Lm 08-5578 differentially expressing 1.9 × more genes (726) compared to Lm 568 (410). Unique to Lm 08-5578 was a significant upregulation of the expression of the alternative transcription factor σB and its regulon. A number of long antisense transcripts (lasRNA) were upregulated during desiccation including anti0605, anti0936, anti1846, and anti0777, with the latter controlling flagellum biosynthesis and possibly the downregulation of motility genes observed in both strains. This exploration of the transcriptomes of desiccated L. monocytogenes provides further understanding of how this bacterium encounters and survives the stress faced when exposed to dry conditions in the food industry.
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Hurley D, Luque-Sastre L, Parker CT, Huynh S, Eshwar AK, Nguyen SV, Andrews N, Moura A, Fox EM, Jordan K, Lehner A, Stephan R, Fanning S. Whole-Genome Sequencing-Based Characterization of 100 Listeria monocytogenes Isolates Collected from Food Processing Environments over a Four-Year Period. mSphere 2019; 4:e00252-19. [PMID: 31391275 PMCID: PMC6686224 DOI: 10.1128/msphere.00252-19] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/12/2019] [Indexed: 02/05/2023] Open
Abstract
Listeria monocytogenes is frequently found in foods and processing facilities, where it can persist, creating concerns for the food industry. Its ability to survive under a wide range of environmental conditions enhances the potential for cross-contamination of the final food products, leading to possible outbreaks of listeriosis. In this study, whole-genome sequencing (WGS) was applied as a tool to characterize and track 100 L. monocytogenes isolates collected from three food processing environments. These WGS data from environmental and food isolates were analyzed to (i) assess the genomic diversity of L. monocytogenes, (ii) identify possible source(s) of contamination, cross-contamination routes, and persistence, (iii) detect absence/presence of antimicrobial resistance-encoding genes, (iv) assess virulence genotypes, and (v) explore in vivo pathogenicity of selected L. monocytogenes isolates carrying different virulence genotypes. The predominant L. monocytogenes sublineages (SLs) identified were SL101 (21%), SL9 (17%), SL121 (12%), and SL5 (12%). Benzalkonium chloride (BC) tolerance-encoding genes were found in 62% of these isolates, a value that increased to 73% among putative persistent subgroups. The most prevalent gene was emrC followed by bcrABC, qacH-Tn6188, and qacC. The L. monocytogenes major virulence factor inlA was truncated in 31% of the isolates, and only one environmental isolate (L. monocytogenes CFS086) harbored all major virulence factors, including Listeria pathogenicity island 4 (LIPI-4), which has been shown to confer hypervirulence. A zebrafish embryo infection model showed a low (3%) embryo survival rate for all putatively hypervirulent L. monocytogenes isolates assayed. Higher embryo survival rates were observed following infection with unknown virulence potential (20%) and putatively hypovirulent (53 to 83%) L. monocytogenes isolates showing predicted pathogenic phenotypes inferred from virulence genotypes.IMPORTANCE This study extends current understanding of the genetic diversity among L. monocytogenes from various food products and food processing environments. Application of WGS-based strategies facilitated tracking of this pathogen of importance to human health along the production chain while providing insights into the pathogenic potential for some of the L. monocytogenes isolates recovered. These analyses enabled the grouping of selected isolates into three putative virulence categories according to their genotypes along with informing selection for phenotypic assessment of their pathogenicity using the zebrafish embryo infection model. It has also facilitated the identification of those isolates with genes conferring tolerance to commercially used biocides. Findings from this study highlight the potential for the application of WGS as a proactive tool to support food safety controls as applied to L. monocytogenes.
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Affiliation(s)
- Daniel Hurley
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Laura Luque-Sastre
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Craig T Parker
- Western Regional Research Center, Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Steven Huynh
- Western Regional Research Center, Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Athmanya K Eshwar
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Scott V Nguyen
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Nicholas Andrews
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Alexandra Moura
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Edward M Fox
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Kieran Jordan
- Food Safety Department, Teagasc Food Research Centre, Fermoy, County Cork, Ireland
| | - Angelika Lehner
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
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Cross-resistance to phage infection in Listeria monocytogenes serotype 1/2a mutants. Food Microbiol 2019; 84:103239. [PMID: 31421769 DOI: 10.1016/j.fm.2019.06.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 01/22/2023]
Abstract
Bacteriophage-based biocontrols are one of several tools available to control Listeria monocytogenes in food and food processing environments. The objective of this study was to determine if phage-resistance that has been characterized with a select few Listeria phages would also confer resistance to a diverse collection of over 100 other Listeria phages. We show that some mutations that are likely to emerge in bacteriophage-treated populations of serotype 1/2a L. monocytogenes can lead to cross-resistance against almost all types of characterized Listeria phages. Out of the 120 phages that showed activity against the parental strain, only one could form visible plaques on the mutant strain of L. monocytogenes lacking rhamnose in its wall teichoic acids. An additional two phages showed signs of lytic activity against this mutant strain; although no visible plaques were observed. The findings presented here are consistent with other studies showing mutations conferring phage resistance through loss of rhamnose likely pose the greatest challenge for phage-based biocontrol in serotype 1/2a strains.
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Smith AM, Tau NP, Smouse SL, Allam M, Ismail A, Ramalwa NR, Disenyeng B, Ngomane M, Thomas J. Outbreak of Listeria monocytogenes in South Africa, 2017-2018: Laboratory Activities and Experiences Associated with Whole-Genome Sequencing Analysis of Isolates. Foodborne Pathog Dis 2019; 16:524-530. [PMID: 31062992 PMCID: PMC6653791 DOI: 10.1089/fpd.2018.2586] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In South Africa, a progressive increase in listeriosis cases was noted from mid-June 2017, heralding what was to become the world's largest listeriosis outbreak. A total of 1060 cases were reported for the period January 1, 2017 to July 17, 2018. We describe laboratory activities, experiences, and results of whole-genome sequencing (WGS) analysis of Listeria monocytogenes isolates associated with this outbreak. Bacteria were identified using the VITEK-2 COMPACT 15 microbial identification system. WGS was performed using Illumina MiSeq technology. WGS data were analyzed using CLC Genomics Workbench Software and free-to-use on-line analysis tools/pipelines. Multilocus sequence typing (MLST) showed that 91% of clinical isolates were sequence type 6 (ST6), determining that the outbreak was largely associated with L. monocytogenes ST6. Epidemiological and laboratory findings led to investigation of a large ready-to-eat processed meat production facility in South Africa, named Enterprise Foods. L. monocytogenes ST6 was found in environmental sampling swabs of the production facility and in ready-to-eat processed meat products (including polony, a product similar to bologna sausage) manufactured at the facility. ST6 isolates, sourced at the Enterprise Foods production facility and from Enterprise food products, were shown by single nucleotide polymorphism (SNP) analysis to be highly related to clinical isolates; these nonclinical ST6 isolates showed <10 SNP differences when compared to clinical ST6 isolates. Core-genome MLST showed that clinical ST6 isolates and Enterprise-related ST6 isolates had no more than 4 allele differences between each other, suggestive of a high probability of epidemiological relatedness. WGS data interpreted together with epidemiological data concluded that the source of the listeriosis outbreak was ready-to-eat processed meat products manufactured by Enterprise Foods. Listeriosis has now been added to the South African list of mandatory notifiable medical conditions. Surveillance systems have been strengthened to facilitate prevention and early detection of listeriosis outbreaks.
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Affiliation(s)
- Anthony M Smith
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa.,2 Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nomsa P Tau
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Shannon L Smouse
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- 3 Sequencing Core Facility, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- 3 Sequencing Core Facility, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Ntsieni R Ramalwa
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Bolele Disenyeng
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mimmy Ngomane
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Juno Thomas
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa.,2 Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Jagadeesan B, Baert L, Wiedmann M, Orsi RH. Comparative Analysis of Tools and Approaches for Source Tracking Listeria monocytogenes in a Food Facility Using Whole-Genome Sequence Data. Front Microbiol 2019; 10:947. [PMID: 31143162 PMCID: PMC6521219 DOI: 10.3389/fmicb.2019.00947] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/15/2019] [Indexed: 12/04/2022] Open
Abstract
As WGS is increasingly used by food industry to characterize pathogen isolates, users are challenged by the variety of analysis approaches available, ranging from methods that require extensive bioinformatics expertise to commercial software packages. This study aimed to assess the impact of analysis pipelines (i.e., different hqSNP pipelines, a cg/wgMLST pipeline) and the reference genome selection on analysis results (i.e., hqSNP and allelic differences as well as tree topologies) and conclusion drawn. For these comparisons, whole genome sequences were obtained for 40 Listeria monocytogenes isolates collected over 18 years from a cold-smoked salmon facility and 2 other isolates obtained from different facilities as part of academic research activities; WGS data were analyzed with three hqSNP pipelines and two MLST pipelines. After initial clustering using a k-mer based approach, hqSNP pipelines were run using two types of reference genomes: (i) closely related closed genomes (“closed references”) and (ii) high-quality de novo assemblies of the dataset isolates (“draft references”). All hqSNP pipelines identified similar hqSNP difference ranges among isolates in a given cluster; use of different reference genomes showed minimal impacts on hqSNP differences identified between isolate pairs. Allelic differences obtained by wgMLST showed similar ranges as hqSNP differences among isolates in a given cluster; cgMLST consistently showed fewer differences than wgMLST. However, phylogenetic trees and dendrograms, obtained based on hqSNP and cg/wgMLST data, did show some incongruences, typically linked to clades supported by low bootstrap values in the trees. When a hqSNP cutoff was used to classify isolates as “related” or “unrelated,” use of different pipelines yielded a considerable number of discordances; this finding supports that cut-off values are valuable to provide a starting point for an investigation, but supporting and epidemiological evidence should be used to interpret WGS data. Overall, our data suggest that cgMLST-based data analyses provide for appropriate subtype differentiation and can be used without the need for preliminary data analyses (e.g., k-mer based clustering) or external closed reference genomes, simplifying data analyses needs. hqSNP or wgMLST analyses can be performed on the isolate clusters identified by cgMLST to increase the precision on determining the genomic similarity between isolates.
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Affiliation(s)
- Balamurugan Jagadeesan
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Lausanne, Switzerland
| | - Leen Baert
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Lausanne, Switzerland
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Renato H Orsi
- Department of Food Science, Cornell University, Ithaca, NY, United States
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Characterization of Listeria prophages in lysogenic isolates from foods and food processing environments. PLoS One 2019; 14:e0214641. [PMID: 30934000 PMCID: PMC6443182 DOI: 10.1371/journal.pone.0214641] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 03/18/2019] [Indexed: 12/15/2022] Open
Abstract
Prophages are commonly found in Listeria genomes, potentially enhancing survival or fitness of Listeria spp. Currently, there is still limited information on the distribution of prophages among Listeria isolates of different allelic types and from various sources. In this study, by using mitomycin C induction, prophages were found in 23/144 isolates (16.0%), including 13 L. monocytogenes and 10 Listeria spp. isolates, resulting in 28 and 11 induced phages, respectively. These prophage-carrying isolates (lysogens) were obtained from foods and food-related environments presenting 3 common allelic types (ATs) of L. monocytogenes (lineage I, II and IV), 4 ATs of L. innocua and 1 AT of L. welshimeri. The likelihood of prophage-carrying isolates of L. monocytogenes was 14.4 (95% CI: 4.9–35.4), and 18.5 (95% CI: 4.8–50.2) for Listeria spp. The 39 induced phages were classified into 3 lysis groups by the host range test against 9 major serotypes of L. monocytogenes and 5 species of Listeria. Most phages were host-specific with higher ability to lyse L. monocytogenes serotype 4 than other serotypes. The genome size of phages ranged from 35±2 kb to 50±2 kb and belonged to two common phage families, Myoviridae and Siphoviridae. Restriction analysis classified 19 selected phages into 16 restriction profiles, suggesting highly diverse prophages with at least 16 types. This may contribute to the variation in the genomes of Listeria. Information obtained here provides basic knowledge for further study to understand the overall role of prophages in Listeria, including roles in survival or fitness in foods and food processing environments.
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Naditz AL, Dzieciol M, Wagner M, Schmitz-Esser S. Plasmids contribute to food processing environment-associated stress survival in three Listeria monocytogenes ST121, ST8, and ST5 strains. Int J Food Microbiol 2019; 299:39-46. [PMID: 30953994 DOI: 10.1016/j.ijfoodmicro.2019.03.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/04/2019] [Accepted: 03/27/2019] [Indexed: 12/17/2022]
Abstract
Listeria monocytogenes is a food-borne pathogen responsible for the disease listeriosis and is commonly isolated from food and food production facilities. Many L. monocytogenes strains contain plasmids, though the contributions of plasmids to survival in food production environments are unknown. Three L. monocytogenes ST5, ST8, and ST121 strains containing plasmids, which harbor putative stress response genes, were cured of their plasmids. Wildtype (WT) and plasmid-cured strains were exposed to disinfectant, oxidative, heat, acid, or salt stress. After stress exposure, cells were plated for colony forming unit (CFU) counts to determine survivors. L. monocytogenes WT strains exposed to 0.01% (vol/vol) H2O2, 1% (vol/vol) lactic acid, and 15% (wt/vol) NaCl, pH 5 showed significantly higher counts of survivors compared to the plasmid-cured strains. The number of survivors for the ST5 WT strain exposed to 10 μg/mL benzalkonium chloride (BC) was significantly higher than in the plasmid-cured strain. The ST8 and ST5 strains were exposed to elevated temperature (50° and 55 °C respectively); only the ST5 WT strain had significantly higher numbers of survivors than the plasmid-cured strains. Our data revealed that L. monocytogenes ST5, ST8, and ST121 plasmids contribute to tolerance against elevated temperature, salinity, acidic environments, oxidative stress and disinfectants.
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Affiliation(s)
- Annabel L Naditz
- Department of Animal Science, Iowa State University, Ames, IA, USA; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, USA
| | - Monika Dzieciol
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Martin Wagner
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria; Austrian Competence Center for Feed and Food Quality, Safety and Innovation (FFoQSI), Technopark C, 3430 Tulln, Austria
| | - Stephan Schmitz-Esser
- Department of Animal Science, Iowa State University, Ames, IA, USA; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, USA.
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Characteristics of Listeria Monocytogenes Strains Persisting in a Meat Processing Facility over a 4-Year Period. Pathogens 2019; 8:pathogens8010032. [PMID: 30866522 PMCID: PMC6471029 DOI: 10.3390/pathogens8010032] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/01/2019] [Accepted: 03/03/2019] [Indexed: 02/07/2023] Open
Abstract
Listeria monocytogenes can persist in food production facilities, resulting in serious threats to consumers due to the high mortality associated with listeriosis, especially in the very young, old and pregnant. We subtyped 124 strains of L. monocytogenes isolated from a meat processing facility in Switzerland by serotyping, multi locus sequence typing (MLST) typing and whole genome sequencing. We then analyzed their ability to form biofilms and their resistance to the disinfectants benzalkonium chloride (BC) and peracetic acid (PAA). The genotyping results of the strains showed that several clonal populations of L. monocytogenes belonging to CC9, CC204 and CC121 had persisted in this meat processing facility for at least four years. All of the strains showed biofilm forming capacity comparable to a known high biofilm forming strain. Known efflux pumps for BC were present in CC204, CC9 (brcABC) and CC121 (qacH) strains, while strains from other CC showed very low minimal inhibitory concentrations (MICs) for BC. For PAA, minimal bactericidal concentrations of 1.2–1.6% for 20 min and minimal inhibitory concentrations between 0.1 and 0.2% were observed. These values were close to or above the recommended concentration for use (0.5–1%), suggesting that PAA might be ineffective at controlling L. monocytogenes in this and potentially other meat processing facilities.
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Reimer A, Weedmark K, Petkau A, Peterson CL, Walker M, Knox N, Kent H, Mabon P, Berry C, Tyler S, Tschetter L, Jerome M, Allen V, Hoang L, Bekal S, Clark C, Nadon C, Van Domselaar G, Pagotto F, Graham M, Farber J, Gilmour M. Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria. Microb Genom 2019; 5. [PMID: 30648944 PMCID: PMC6412057 DOI: 10.1099/mgen.0.000237] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The persuasiveness of genomic evidence has pressured scientific agencies to supplement or replace well-established methodologies to inform public health and food safety decision-making. This study of 52 epidemiologically defined Listeria monocytogenes isolates, collected between 1981 and 2011, including nine outbreaks, was undertaken (1) to characterize their phylogenetic relationship at finished genome-level resolution, (2) to elucidate the underlying genetic diversity within an endemic subtype, CC8, and (3) to re-evaluate the genetic relationship and epidemiology of a CC8-delimited outbreak in Canada in 2008. Genomes representing Canadian Listeria outbreaks between 1981 and 2010 were closed and manually annotated. Single nucleotide variants (SNVs) and horizontally acquired traits were used to generate phylogenomic models. Phylogenomic relationships were congruent with classical subtyping and epidemiology, except for CC8 outbreaks, wherein the distribution of SNV and prophages revealed multiple co-evolving lineages. Chronophyletic reconstruction of CC8 evolution indicates that prophage-related genetic changes among CC8 strains manifest as PFGE subtype reversions, obscuring the relationship between CC8 isolates, and complicating the public health interpretation of subtyping data, even at maximum genome resolution. The size of the shared genome interrogated did not change the genetic relationship measured between highly related isolates near the tips of the phylogenetic tree, illustrating the robustness of these approaches for routine public health applications where the focus is recent ancestry. The possibility exists for temporally and epidemiologically distinct events to appear related even at maximum genome resolution, highlighting the continued importance of epidemiological evidence.
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Affiliation(s)
- Aleisha Reimer
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Kelly Weedmark
- 2Health Canada, Bureau of Microbial Hazards, Ottawa, ON, K1A 0K9, Canada
| | - Aaron Petkau
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | | | - Matthew Walker
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Natalie Knox
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Heather Kent
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Philip Mabon
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Chrystal Berry
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Shaun Tyler
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | | | - Morganne Jerome
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Vanessa Allen
- 3Public Health Ontario, Toronto, ON, M5G 1M1, Canada
| | - Linda Hoang
- 4British Columbia Centre for Disease Control, Public Health Microbiology and Reference Laboratory, Vancouver, BC V5Z 4R4, Canada
| | - Sadjia Bekal
- 5Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, H9X 3R5, Canada
| | - Clifford Clark
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Celine Nadon
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | | | - Franco Pagotto
- 2Health Canada, Bureau of Microbial Hazards, Ottawa, ON, K1A 0K9, Canada
| | - Morag Graham
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Jeff Farber
- 6University of Guelph, Guelph, ON, N1G 2W, Canada
| | - Matthew Gilmour
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
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Cherifi T, Carrillo C, Lambert D, Miniaï I, Quessy S, Larivière-Gauthier G, Blais B, Fravalo P. Genomic characterization of Listeria monocytogenes isolates reveals that their persistence in a pig slaughterhouse is linked to the presence of benzalkonium chloride resistance genes. BMC Microbiol 2018; 18:220. [PMID: 30572836 PMCID: PMC6302515 DOI: 10.1186/s12866-018-1363-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/02/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The aim of this study was to characterize the genomes of 30 Listeria monocytogenes isolates collected at a pig slaughterhouse to determine the molecular basis for their persistence. RESULTS Comparison of the 30 L. monocytogenes genomes showed that successive isolates (i.e., persistent types) recovered from thew sampling site could be linked on the basis of single nucleotide variants confined to prophage regions. In addition, our study revealed the presence among these strains of the bcrABC cassette which is known to produce efflux pump-mediated benzalkonium chloride resistance, and which may account for the persistence of these isolates in the slaughterhouse environment. The presence of the bcrABC cassette was confirmed by WGS and PCR and the resistance phenotype was determined by measuring minimum inhibitory concentrations. Furthermore, the BC-resistant strains were found to produce lower amounts of biofilm in the presence of sublethal concentrations of BC. CONCLUSIONS High resolution SNP-based typing and determination of the bcrABC cassette may provide a means of distinguishing between resident and sporadic L. monocytogenes isolates, and this in turn will support better management of this pathogen in the food industry.
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Affiliation(s)
- Tamazight Cherifi
- Chaire de Recherche en Salubrité des Viandes, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Centre de Recherche sur les Maladies Infectieuses Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Groupe de Recherche et D’enseignement En Salubrité Des Aliments, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
| | - Catherine Carrillo
- Food Microbiology Research Team, Canadian Food Inspection Agency, Ottawa, ON Canada
| | - Dominic Lambert
- Food Microbiology Research Team, Canadian Food Inspection Agency, Ottawa, ON Canada
| | - Ilhem Miniaï
- Chaire de Recherche en Salubrité des Viandes, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Centre de Recherche sur les Maladies Infectieuses Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Groupe de Recherche et D’enseignement En Salubrité Des Aliments, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
| | - Sylvain Quessy
- Chaire de Recherche en Salubrité des Viandes, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Centre de Recherche sur les Maladies Infectieuses Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Groupe de Recherche et D’enseignement En Salubrité Des Aliments, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
| | - Guillaume Larivière-Gauthier
- Chaire de Recherche en Salubrité des Viandes, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Centre de Recherche sur les Maladies Infectieuses Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Groupe de Recherche et D’enseignement En Salubrité Des Aliments, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
| | - Burton Blais
- Food Microbiology Research Team, Canadian Food Inspection Agency, Ottawa, ON Canada
| | - Philippe Fravalo
- Chaire de Recherche en Salubrité des Viandes, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Centre de Recherche sur les Maladies Infectieuses Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Groupe de Recherche et D’enseignement En Salubrité Des Aliments, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
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Luque-Sastre L, Fox EM, Jordan K, Fanning S. A Comparative Study of the Susceptibility of Listeria Species to Sanitizer Treatments When Grown under Planktonic and Biofilm Conditions. J Food Prot 2018; 81:1481-1490. [PMID: 30109972 DOI: 10.4315/0362-028x.jfp-17-466] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Listeria species are ubiquitous in nature and can adapt to survive in a variety of niches, including food processing environments. Listeria species that colonize these environments may also have the potential to persist. Food safety strategies designed to manage these niches include regular cleaning and disinfection with proven sanitizers containing biocide-active compounds. Typically, these sanitizers are effective against bacteria growing under planktonic conditions, but their efficacy may be compromised when bacteria are contained in biofilms. The susceptibility of persistent Listeria isolates, i.e., those capable of forming biofilms, to a selection of sanitizers was investigated. A quaternary ammonium compound-based sanitizer was the biocide most effective against planktonic bacteria, with a MIC of 0.0015 to 0.006%. In contrast, ethanol-based sanitizers were the least effective. Although, no triclosan tolerance was observed for planktonic Listeria isolates, triclosan was the only biocide that resulted in a significant biomass reduction. Differences between Listeria species were observed; L. monocytogenes and L. welshimeri biofilms were more tolerant to quaternary ammonium compound-based sanitizers than were L. innocua biofilms. These findings extend our understanding of the application of commonly used sanitizers in the food industry and the efficacy of these sanitizers against Listeria species and their associated biofilms.
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Affiliation(s)
- Laura Luque-Sastre
- 1 Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland (ORCID: http://orcid.org/0000-0002-1922-8836 [S.F.])
| | - Edward M Fox
- 2 CSIRO Agriculture and Food, Werribee, Victoria, Australia; and
| | - Kieran Jordan
- 3 Department of Food Safety, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Séamus Fanning
- 1 Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland (ORCID: http://orcid.org/0000-0002-1922-8836 [S.F.])
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Van Walle I, Björkman JT, Cormican M, Dallman T, Mossong J, Moura A, Pietzka A, Ruppitsch W, Takkinen J. Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015. Euro Surveill 2018; 23:1700798. [PMID: 30131096 PMCID: PMC6205253 DOI: 10.2807/1560-7917.es.2018.23.33.1700798] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/13/2018] [Indexed: 01/01/2023] Open
Abstract
Background and aimThe trend in reported case counts of invasive Listeria monocytogenes (Lm), a potentially severe food-borne disease, has been increasing since 2008. In 2015, 2,224 cases were reported in the European Union/European Economic Area (EU/EEA). We aimed to validate the microbiological and epidemiological aspects of an envisaged EU/EEA-wide surveillance system enhanced by routine whole genome sequencing (WGS). Methods: WGS and core genome multilocus sequence typing (cgMLST) were performed on isolates from 2,726 cases from 27 EU/EEA countries from 2010-15. Results: Quality controls for contamination, mixed Lm cultures and sequence quality classified nearly all isolates with a minimum average coverage of the genome of 55x as acceptable for analysis. Assessment of the cgMLST variation between six different pipelines revealed slightly less variation associated with assembly-based analysis compared to reads-based analysis. Epidemiological concordance, based on 152 isolates from 19 confirmed outbreaks and a cluster cutoff of seven allelic differences, was good (sensitivity > 95% for two cgMLST schemes of 1,748 and 1,701 loci each; PPV 58‒68%). The proportion of sporadic cases was slightly below 50%. Of remaining isolates, around one third were in clusters involving more than one country, often spanning several years. Detection of multi-country clusters was on average several months earlier when pooling the data at EU/EEA level, compared with first detection at national level. Conclusions: These findings provide a good basis for comprehensive EU/EEA-wide, WGS-enhanced surveillance of listeriosis. Time limits should not be used for hypothesis generation during outbreak investigations, but should be for analytical studies.
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Affiliation(s)
- Ivo Van Walle
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | | | | | - Joël Mossong
- Laboratoire national de santé, Dudelange, Luxembourg
| | - Alexandra Moura
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, Biology of Infection Unit, Inserm U1117, Paris, France
| | - Ariane Pietzka
- Österreichische Agentur für Gesundheit und Ernährungssicherheit, Graz/Vienna, Austria
| | - Werner Ruppitsch
- Österreichische Agentur für Gesundheit und Ernährungssicherheit, Graz/Vienna, Austria
| | - Johanna Takkinen
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
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50
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Genome Sequences of Listeria Phages Induced from Lysogenic Isolates of Listeria monocytogenes from Seafood and a Seafood Processing Environment in Thailand. GENOME ANNOUNCEMENTS 2018; 6:6/27/e00546-18. [PMID: 29976605 PMCID: PMC6033974 DOI: 10.1128/genomea.00546-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We report here the complete genome sequences of three Listeria phages (PSU-VKH-LP019, PSU-VKH-LP040, and PSU-VKH-LP041), which were newly induced from lysogenic isolates of Listeria monocytogenes from seafood and a seafood processing environment in Thailand. The three phages show circularly permuted double-stranded DNA genomes with sizes of 38.6, 39.6, and 48.3 kb. We report here the complete genome sequences of three Listeria phages (PSU-VKH-LP019, PSU-VKH-LP040, and PSU-VKH-LP041), which were newly induced from lysogenic isolates of Listeria monocytogenes from seafood and a seafood processing environment in Thailand. The three phages show circularly permuted double-stranded DNA genomes with sizes of 38.6, 39.6, and 48.3 kb.
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