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Gana J, Gcebe N, Pierneef RE, Chen Y, Moerane R, Adesiyun AA. Whole Genome Sequence Analysis of Listeria monocytogenes Isolates Obtained from the Beef Production Chain in Gauteng Province, South Africa. Microorganisms 2024; 12:1003. [PMID: 38792832 PMCID: PMC11123765 DOI: 10.3390/microorganisms12051003] [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: 03/27/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
The study used whole-genome sequencing (WGS) and bioinformatics analysis for the genomic characterization of 60 isolates of Listeria monocytogenes obtained from the beef production chain (cattle farms, abattoirs, and retail outlets) in Gauteng province, South Africa. The sequence types (STs), clonal complexes (CCs), and the lineages of the isolates were determined using in silico multilocus sequence typing (MLST). We used BLAST-based analyses to identify virulence and antimicrobial genes, plasmids, proviruses/prophages, and the CRISPR-Cas system. The study investigated any association of the detected genes to the origin in the beef production chain of the L. monocytogenes isolates. Overall, in 60 isolates of Listeria monocytogenes, there were seven STs, six CCs, forty-four putative virulence factors, two resistance genes, one plasmid with AMR genes, and three with conjugative genes, one CRISPR gene, and all 60 isolates were positive for proviruses/prophages. Among the seven STs detected, ST204 (46.7%) and ST2 (21.7%) were the most prominent, with ST frequency varying significantly (p < 0.001). The predominant CC detected were CC2 (21.7%) and CC204 (46.7%) in lineages I and II, respectively. Of the 44 virulence factors detected, 26 (across Listeria Pathogenicity Islands, LIPIs) were present in all the isolates. The difference in the detection frequency varied significantly (p < 0.001). The two AMR genes (fosX and vga(G)) detected were present in all 60 (100%) isolates of L. monocytogenes. The only plasmid, NF033156, was present in three (5%) isolates. A CRISPR-Cas system was detected in six (10%), and all the isolates carried proviruses/prophages. The source and sample type significantly affected the frequencies of STs and virulence factors in the isolates of L. monocytogenes. The presence of fosX and vga(G) genes in all L. monocytogenes isolates obtained from the three industries of the beef production chain can potentially cause therapeutic implications. Our study, which characterized L. monocytogenes recovered from the three levels in the beef production chain, is the first time genomics was performed on this type of data set in the country, and this provides insights into the health implications of Listeria.
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Affiliation(s)
- James Gana
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, Pretoria 0110, South Africa; (J.G.); (R.M.)
- Department of Agricultural Education, Federal College of Education, Kontagora 923101, Niger State, Nigeria
| | - Nomakorinte Gcebe
- Bacteriology Department, Onderstepoort Veterinary Research, Agricultural Research Council, Pretoria 0110, South Africa;
| | - Rian Edward Pierneef
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0001, South Africa;
- Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria 0001, South Africa
- Microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0001, South Africa
| | - Yi Chen
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, 5001 Campus Dr. Room 4E-007/Mailstop HFS-710, College Park, MD 20740, USA;
| | - Rebone Moerane
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, Pretoria 0110, South Africa; (J.G.); (R.M.)
| | - Abiodun Adewale Adesiyun
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, Pretoria 0110, South Africa; (J.G.); (R.M.)
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine 685509, Trinidad and Tobago
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2
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Karlsmose AK, Ivanova M, Kragh ML, Kjeldgaard JS, Otani S, Svendsen CA, Papić B, Zdovc I, Tasara T, Stephan R, Heir E, Langsrud S, Møretrø T, Dalgaard P, Fagerlund A, Hansen LT, Aarestrup FM, Leekitcharoenphon P. A novel metagenomic approach uncovers phage genes as markers for increased disinfectant tolerance in mixed Listeria monocytogenes communities. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 119:105582. [PMID: 38467173 DOI: 10.1016/j.meegid.2024.105582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
Listeria monocytogenes is an important human pathogen with a high mortality rate. Consumption of contaminated ready-to-eat food is the main mode of transmission to humans. Disinfectant-tolerant L. monocytogenes have emerged, which are believed to have increased persistence potential. Elucidating the mechanisms of L. monocytogenes disinfectant tolerance has been the focus of previous studies using pure cultures. A limitation of such approach is the difficulty to identify strains with reduced susceptibility due to inter-strain variation and the need to screen large numbers of strains and genes. In this study, we applied a novel metagenomic approach to detect genes associated with disinfectant tolerance in mixed L. monocytogenes planktonic communities. Two communities, consisting of 71 and 80 isolates each, were treated with the food industry disinfectants benzalkonium chloride (BC, 1.75 mg/L) or peracetic acid (PAA, 38 mg/L). The communities were subjected to metagenomic sequencing and differences in individual gene abundances between biocide-free control communities and biocide-treated communities were determined. A significant increase in the abundance of Listeria phage-associated genes was observed in both communities after treatment, suggesting that prophage carriage could lead to an increased disinfectant tolerance in mixed L. monocytogenes planktonic communities. In contrast, a significant decrease in the abundance of a high-copy emrC-harbouring plasmid pLmN12-0935 was observed in both communities after treatment. In PAA-treated community, a putative ABC transporter previously found to be necessary for L. monocytogenes resistance to antimicrobial agents and virulence, was among the genes with the highest weight for differentiating treated from control samples. The undertaken metagenomic approach in this study can be applied to identify genes associated with increased tolerance to other antimicrobials in mixed bacterial communities.
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Affiliation(s)
- Agnete Kirstine Karlsmose
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mirena Ivanova
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Martin Laage Kragh
- Research Group for Food Microbiology and Hygiene, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jette Sejer Kjeldgaard
- Research Group for Global Capacity Building, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Saria Otani
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christina Aaby Svendsen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Bojan Papić
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Zdovc
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Taurai Tasara
- 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
| | - Even Heir
- Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Solveig Langsrud
- Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Trond Møretrø
- Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Paw Dalgaard
- Research Group for Food Microbiology and Hygiene, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Annette Fagerlund
- Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Lisbeth Truelstrup Hansen
- Research Group for Food Microbiology and Hygiene, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
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Félix B, Capitaine K, Te S, Felten A, Gillot G, Feurer C, van den Bosch T, Torresi M, Sréterné Lancz Z, Delannoy S, Brauge T, Midelet G, Leblanc JC, Roussel S. Identification by High-Throughput Real-Time PCR of 30 Major Circulating Listeria monocytogenes Clonal Complexes in Europe. Microbiol Spectr 2023; 11:e0395422. [PMID: 37158749 PMCID: PMC10269651 DOI: 10.1128/spectrum.03954-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
Listeria monocytogenes is a ubiquitous bacterium that causes a foodborne illness, listeriosis. Most strains can be classified into major clonal complexes (CCs) that account for the majority of outbreaks and sporadic cases in Europe. In addition to the 20 CCs known to account for the majority of human and animal clinical cases, 10 CCs are frequently reported in food production, thereby posing a serious challenge for the agrifood industry. Therefore, there is a need for a rapid and reliable method to identify these 30 major CCs. The high-throughput real-time PCR assay presented here provides accurate identification of these 30 CCs and eight genetic subdivisions within four CCs, splitting each CC into two distinct subpopulations, along with the molecular serogroup of a strain. Based on the BioMark high-throughput real-time PCR system, our assay analyzes 46 strains against 40 real-time PCR arrays in a single experiment. This European study (i) designed the assay from a broad panel of 3,342 L. monocytogenes genomes, (ii) tested its sensitivity and specificity on 597 sequenced strains collected from 24 European countries, and (iii) evaluated its performance in the typing of 526 strains collected during surveillance activities. The assay was then optimized for conventional multiplex real-time PCR for easy implementation in food laboratories. It has already been used for outbreak investigations. It represents a key tool for assisting food laboratories to establish strain relatedness with human clinical strains during outbreak investigations and for helping food business operators by improving their microbiological management plans. IMPORTANCE Multilocus sequence typing (MLST) is the reference method for Listeria monocytogenes typing but is expensive and takes time to perform, from 3 to 5 days for laboratories that outsource sequencing. Thirty major MLST clonal complexes (CCs) are circulating in the food chain and are currently identifiable only by sequencing. Therefore, there is a need for a rapid and reliable method to identify these CCs. The method presented here enables the rapid identification, by real-time PCR, of 30 CCs and eight genetic subdivisions within four CCs, splitting each CC into two distinct subpopulations. The assay was then optimized on different conventional multiplex real-time PCR systems for easy implementation in food laboratories. The two assays will be used for frontline identification of L. monocytogenes isolates prior to whole-genome sequencing. Such assays are of great interest for all food industry stakeholders and public agencies for tracking L. monocytogenes food contamination.
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Affiliation(s)
- Benjamin Félix
- ANSES, European Union Reference Laboratory for Listeria monocytogenes, Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, Maisons-Alfort, France
| | - Karine Capitaine
- ANSES, European Union Reference Laboratory for Listeria monocytogenes, Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, Maisons-Alfort, France
| | - Sandrine Te
- ANSES, European Union Reference Laboratory for Listeria monocytogenes, Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, Maisons-Alfort, France
| | - Arnaud Felten
- ANSES, Ploufragan/Plouzané/Niort Laboratory, Viral Genetics and Bio-Security Unit, Université Européenne de Bretagne, Ploufragan, France
| | | | - Carole Feurer
- IFIP–The French Pig and Pork Institute, Department of Fresh and Processed Meat, Le Rheu, France
| | - Tijs van den Bosch
- Wageningen Food Safety Research, Department of Bacteriology, Molecular Technology and Antimicrobial Resistance, Wageningen, The Netherlands
| | - Marina Torresi
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale” Via Campo Boario, Teramo, Italy
| | - Zsuzsanna Sréterné Lancz
- Microbiological National Reference Laboratory, National Food Chain Safety Office, Food Chain Safety Laboratory Directorate, Budapest, Hungary
| | - Sabine Delannoy
- ANSES, Laboratory for Food Safety, IdentyPath Platform, Maisons-Alfort, France
| | - Thomas Brauge
- ANSES, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Boulogne-sur-Mer, France
| | - Graziella Midelet
- ANSES, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Boulogne-sur-Mer, France
| | - Jean-Charles Leblanc
- ANSES, European Union Reference Laboratory for Listeria monocytogenes, Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, Maisons-Alfort, France
| | - Sophie Roussel
- ANSES, European Union Reference Laboratory for Listeria monocytogenes, Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, Maisons-Alfort, France
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Obaidat MM, AlShehabat IA. High multidrug resistance of Listeria monocytogenes and association with water sources in sheep and goat dairy flocks in Jordan. Prev Vet Med 2023; 215:105922. [PMID: 37084631 DOI: 10.1016/j.prevetmed.2023.105922] [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: 07/21/2022] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 04/23/2023]
Abstract
Listeria monocytogenes is a significant pathogen that causes listeriosis in humans and small ruminants. This study aimed to estimate the prevalence, antimicrobial resistance and risk factors of L. monocytogenes in small dairy ruminants in Jordan. A total of 948 milk samples were collected from 155 sheep and goat flocks across Jordan. L. monocytogenes was isolated from the samples, confirmed and tested for 13 clinically important antimicrobials. Data were also collected on the husbandry practices to identify risk factors for the presence of L. monocytogenes. The results showed that the flock-level prevalence of L. monocytogenes was 20.0% (95% CI; 14.46%-26.99%) and the prevalence in the individual milk samples was 6.43% (95% CI; 4.92%-8.36%). The univariable (UOR=2.65, p = 0.021) and multivariable (AOR=2.49, p = 0.028) analyses showed that using water from municipality pipelines as a water source in the flock reduced L. monocytogenes prevalence. All L. monocytogenes isolates were resistant to at least one antimicrobial. High percentages of the isolates were resistant to ampicillin (83.6%), streptomycin (79.3%), kanamycin (75.0%), quinupristin/dalfopristin (63.8%) and clindamycin (61.2%). About 83.6% of the isolates (94.2% and 75% of the sheep and goat isolates) exhibited multidrug resistance (resistance to ≥3 antimicrobial classes). In addition, the isolates exhibited fifty unique antimicrobial resistance profiles. Thus, it's recommended to restrict the misuse of clinically important antimicrobials and to chlorinate and monitor the water sources in sheep and goat flocks.
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Affiliation(s)
- Mohammad M Obaidat
- Department of Vet. Pathol.and Public Health, Faculty of Veterinary Medicine, Jordan University of Science and Technology, Ar-Ramtha, Irbid, Jordan.
| | - Issa A AlShehabat
- Department of Vet. Pathol.and Public Health, Faculty of Veterinary Medicine, Jordan University of Science and Technology, Ar-Ramtha, Irbid, Jordan
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5
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Schoder D, Pelz A, Paulsen P. Transmission Scenarios of Listeria monocytogenes on Small Ruminant On-Farm Dairies. Foods 2023; 12:foods12020265. [PMID: 36673359 PMCID: PMC9858201 DOI: 10.3390/foods12020265] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 01/11/2023] Open
Abstract
Listeria monocytogenes can cause severe foodborne infections in humans and invasive diseases in different animal species, especially in small ruminants. Infection of sheep and goats can occur via contaminated feed or through the teat canal. Both infection pathways result in direct (e.g., raw milk from an infected udder or fresh cheese produced from such milk) or indirect exposure of consumers. The majority of dairy farmers produces a high-risk product, namely fresh cheese made from raw ewe's and goat's milk. This, and the fact that L. monocytogenes has an extraordinary viability, poses a significant challenge to on-farm dairies. Yet, surprisingly, almost no scientific studies have been conducted dealing with the hygiene and food safety aspects of directly marketed dairy products. L. monocytogenes prevalence studies on small ruminant on-farm dairies are especially limited. Therefore, it was our aim to focus on three main transmission scenarios of this important major foodborne pathogen: (i) the impact of caprine and ovine listerial mastitis; (ii) the significance of clinical listeriosis and outbreak scenarios; and (iii) the impact of farm management and feeding practices.
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Affiliation(s)
- Dagmar Schoder
- Institute of Food Safety, Food Technology and Veterinary Public Health, Unit of Food Microbiology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
- Vétérinaires sans Frontières Austria, Veterinaerplatz 1, 1210 Vienna, Austria
- Correspondence: ; Tel.: +43-1-25077-3520
| | - Alexandra Pelz
- Vétérinaires sans Frontières Austria, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Peter Paulsen
- Institute of Food Safety, Food Technology and Veterinary Public Health, Unit of Food Hygiene and Technology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
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Zaitsev SS, Khizhnyakova MA, Feodorova VA. Retrospective Investigation of the Whole Genome of the Hypovirulent Listeria monocytogenes Strain of ST201, CC69, Lineage III, Isolated from a Piglet with Fatal Neurolisteriosis. Microorganisms 2022; 10:microorganisms10071442. [PMID: 35889161 PMCID: PMC9324732 DOI: 10.3390/microorganisms10071442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/12/2022] [Accepted: 07/15/2022] [Indexed: 02/06/2023] Open
Abstract
Listeria monocytogenes (Lm), the causative agent for both human and animal listeriosis, is considered to be a rare but potentially fatal foodborne pathogen. While Lm strains associated with current cases of human listeriosis are now being intensely investigated, our knowledge of this microorganism which has caused listerial infection in the past is still extremely limited. The objective of this study was a retrospective whole-genome sequence analysis of the Lm collection strain, 4/52-1953, isolated in the middle of the 20th century from a piglet with listerial neuroinfection. The multi-locus sequence typing (MLST) analysis based on seven housekeeping genes (abcZ, bglA, cat, dapE, dat, ldh, and lhkA) showed that the Lm strain 4/52-1953 was assigned to the sequence type 201 (ST201), clonal complex 69 (CC69), and phylogenetic lineage III. The strain 4/52-1953, similarly to other ST201 strains, probably originated from the ST9, CC69 via ST157. At least eight different STs, ST69, ST72, ST130, ST136, ST148, ST469, ST769, and ST202, were identified as the descendants of the first generation and a single one, ST2290, was proved to be the descendant of the second generation. Among them there were strains either associated with some sporadic cases of human and animal listerial infection in the course of more than 60 years worldwide or isolated from food samples, fish and dairy products, or migratory birds. Phylogenetic analysis based on whole genomes of all the Lm strains available in the NCBI GenBank (n = 256) demonstrated that the strain 4/52-1953 belonged to minor Cluster I, represented by lineage III only, while two other major Clusters, II and III, were formed by lineages I and II. In the genome of the strain 4/52-1953, 41 virulence-associated genes, including the Listeria pathogenicity island 1 (LIPI-1), and LIPI-2 represented by two internalin genes, the inlA and inlB genes, and five genes related to antibiotic resistance, were found. These findings can help to make the emergence of both hyper- and hypovirulent variants, including those bearing antibiotic resistance genes, more visible and aid the aims of molecular epidemiology as well.
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Affiliation(s)
- Sergey S Zaitsev
- Federal Research Center for Virology and Microbiology, Branch in Saratov, 410028 Saratov, Russia
| | - Mariya A Khizhnyakova
- Federal Research Center for Virology and Microbiology, Branch in Saratov, 410028 Saratov, Russia
| | - Valentina A Feodorova
- Federal Research Center for Virology and Microbiology, Branch in Saratov, 410028 Saratov, Russia
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Liu YY, Chen CC, Yang CH, Hsieh HY, He JX, Lin HH, Lee CC. LmTraceMap: A Listeria monocytogenes fast-tracing platform for global surveillance. PLoS One 2022; 17:e0267972. [PMID: 35533187 PMCID: PMC9084517 DOI: 10.1371/journal.pone.0267972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/19/2022] [Indexed: 12/02/2022] Open
Abstract
Listeria monocytogenes can cause listeriosis, and people with hypoimmunity such as pregnant women, infants and fetuses are at high risk of invasive infection. Although the incidence of listeriosis is low, the fatality rate is high. Therefore, continual surveillance and rapid epidemiological investigation are crucial for addressing L. monocytogenes. Because of the popularity of next-generation sequencing, obtaining the whole-genome sequence of a bacterium is easy. Several genome-based typing methods are available, and core-genome multilocus sequence typing (cgMLST) is the most recognized methods. Using cgMLST typing to compare L. monocytogenes whole-genome sequences (WGS) with those obtained across distinct regions is beneficial. However, the concern is how to incorporate the powerful cgMLST method into investigations, such as by using source tracing. Herein, we present an easy-to-use web service called–LmTraceMap (http://lmtracemap.cgu.edu.tw/hua_map/test/upload.php; http://120.126.17.192/hua_map/test/upload.php) that can help public-health professionals rapidly trace closely related isolates worldwide and visually inspect them in search results on a world map with labeled epidemiological data. We expect the proposed service to improve the convenience of public health investigations.
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Affiliation(s)
- Yen-Yi Liu
- Department of Public Health, China Medical University, Taichung, Taiwan
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Chien-Hua Yang
- Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Hui-Yi Hsieh
- Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Jia-Xin He
- Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Hao-Hsuan Lin
- Department of Public Health, China Medical University, Taichung, Taiwan
| | - Chi-Ching Lee
- Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Linkou, Taiwan
- Artificial Intelligence Research Center, Chang Gung University, Taoyuan, Taiwan
- * E-mail:
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Chalenko Y, Kolbasova O, Pivova E, Abdulkadieva M, Povolyaeva O, Kalinin E, Kolbasov D, Ermolaeva S. Listeria monocytogenes Invasion Into Sheep Kidney Epithelial Cells Depends on InlB, and Invasion Efficiency Is Modulated by Phylogenetically Defined InlB Isoforms. Front Microbiol 2022; 13:825076. [PMID: 35197955 PMCID: PMC8859113 DOI: 10.3389/fmicb.2022.825076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/05/2022] [Indexed: 11/13/2022] Open
Abstract
The facultative intracellular pathogen Listeria monocytogenes is of major veterinary importance in small ruminants. Nevertheless, details of L. monocytogenes interactions with cells of small ruminants are not fully established. To study the potential of L. monocytogenes to infect sheep cells, we used the finite sheep kidney cell line (shKEC), which was infected with the wild-type L. monocytogenes strain EGDe. The invasion efficiency was 0.015 ± 0.004%. The invasion factor InlB was critically important for invasion, and inlB gene deletion almost prevented L. monocytogenes invasion into shKEC cells. Comparison of the potential of phylogenetically defined InlB isoforms to restore the invasive phenotype of the EGDeΔinlB strain demonstrated that although all InlB isoforms restored invasion of the EGDeΔinlB strain into shKEC cells, the InlB isoforms typical of highly virulent ruminant strains of the clonal complexes CC1 and CC7 were more efficient than isoforms typical of CC2 and CC9 strains (which are less virulent toward ruminants) in supporting invasion. Listeria monocytogenes effectively multiplied with a doubling of time in about 90 min after they entered the sheep cells. Intracellular bacteria moved using the well-known actin polymerization mechanism. Cell-to-cell spreading was restricted to the infection of a few tens of neighboring cells for 7 days. Overall, the obtained results demonstrated that (i) InlB is required for invasion into sheep cells, (ii) InlB isoforms might be important for hypervirulence of certain clonal groups toward ruminants, and (iii) L. monocytogenes effectively multiplies in ovine cells once entered.
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Affiliation(s)
- Yaroslava Chalenko
- Laboratory of Ecology of Pathogenic Bacteria, Gamaleya Research Center of Epidemiology and Microbiology, Moscow, Russia
- Yaroslava Chalenko,
| | - Olga Kolbasova
- Federal Research Center for Virology and Microbiology (FRCVM), Volginsky, Russia
| | - Elena Pivova
- Federal Research Center for Virology and Microbiology (FRCVM), Volginsky, Russia
| | - Mariam Abdulkadieva
- Department of Dusty Plasma, Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow, Russia
| | - Olga Povolyaeva
- Federal Research Center for Virology and Microbiology (FRCVM), Volginsky, Russia
| | - Egor Kalinin
- Laboratory of Ecology of Pathogenic Bacteria, Gamaleya Research Center of Epidemiology and Microbiology, Moscow, Russia
| | - Denis Kolbasov
- Federal Research Center for Virology and Microbiology (FRCVM), Volginsky, Russia
| | - Svetlana Ermolaeva
- Laboratory of Ecology of Pathogenic Bacteria, Gamaleya Research Center of Epidemiology and Microbiology, Moscow, Russia
- Federal Research Center for Virology and Microbiology (FRCVM), Nizhny Novgorod Research Veterinary Institute Branch, Nizhny Novgorod, Russia
- *Correspondence: Svetlana Ermolaeva,
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9
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Papić B, Golob M, Zdovc I, Avberšek J, Pislak Ocepek M, Kušar D. Using whole-genome sequencing to assess the diversity of Paenibacillus larvae within an outbreak and a beekeeping operation. Microb Genom 2021; 7. [PMID: 34860153 PMCID: PMC8767340 DOI: 10.1099/mgen.0.000709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The spore-forming bacterium
Paenibacillus larvae
is the causative agent of American foulbrood (AFB), a devastating disease of honeybees (Apis mellifera). In the present study, we used whole-genome sequencing (WGS) to investigate an extensive outbreak of AFB in northwestern Slovenia in 2019. A total of 59
P
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larvae
isolates underwent WGS, of which 40 originated from a single beekeeping operation, to assess the diversity of
P. larvae
within the beekeeping operation, apiary and colony. By applying a case-specific single-linkage threshold of 34 allele differences (AD), whole-genome multilocus sequence typing (wgMLST) identified two outbreak clusters represented by ERIC II-ST11 clones. All isolates from a single beekeeping operation fell within cluster 1 and the median pairwise AD between them was 10 (range=1–22). The median pairwise AD for apiaries of the same beekeeping operation ranged from 8 to 11 (min.=1, max.=22). For colonies of the same apiary and honey samples from these colonies, the median pairwise AD ranged from 8 to 14 (min.=1, max.=20). The maximum within-cluster distance was 33 pairwise AD for cluster 1 and 44 for cluster 2 isolates. The minimum distance between the outbreak-related and non-related isolates was 37 AD, confirming the importance of associated epidemiological data for delineating outbreak clusters. The observed transmission events could be explained by the activities of honeybees and beekeepers. The present study provides insight into the genetic diversity of
P. larvae
at different levels and thus provides information for future AFB surveillance.
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Affiliation(s)
- Bojan Papić
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, Ljubljana, Slovenia
| | - Majda Golob
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, Ljubljana, Slovenia
| | - Irena Zdovc
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, Ljubljana, Slovenia
| | - Jana Avberšek
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, Ljubljana, Slovenia
| | - Metka Pislak Ocepek
- Institute of Pathology, Wild Animals, Fish and Bees, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, Ljubljana, Slovenia
| | - Darja Kušar
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, Ljubljana, Slovenia
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10
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Genome Typing and Epidemiology of Human Listeriosis in New Zealand, 1999 to 2018. J Clin Microbiol 2021; 59:e0084921. [PMID: 34406797 DOI: 10.1128/jcm.00849-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This study describes the epidemiology of listeriosis in New Zealand between 1999 and 2018 as well as the retrospective whole-genome sequencing (WGS) of 453 Listeria monocytogenes isolates corresponding to 95% of the human cases within this period. The average notified rate of listeriosis was 0.5 cases per 100,000 population, and non-pregnancy-associated cases were more prevalent than pregnancy-associated cases (averages of 19 and 5 cases per annum, respectively). WGS data was assessed using multilocus sequencing typing (MLST), including core-genome and whole-genome MLST (cgMLST and wgMLST, respectively) and single-nucleotide polymorphism (SNP) analysis. Thirty-nine sequence types (STs) were identified, with the most common being ST1 (21.9%), ST4 (13.2%), ST2 (11.3%), ST120 (6.1%), and ST155 (6.4%). A total of 291 different cgMLST types were identified, with the majority (n = 243) of types observed as a single isolate, consistent with the observation that listeriosis is predominately sporadic. Among the 49 cgMLST types containing two or more isolates, 18 cgMLST types were found with 2 to 4 isolates each (50 isolates in total, including three outbreak-associated isolates) that shared low genetic diversity (0 to 2 whole-genome alleles), some of which were dispersed in time or geographical regions. SNP analysis also produced results comparable to those from wgMLST. The low genetic diversity within these clusters suggests a potential common source, but incomplete epidemiological data impaired retrospective epidemiological investigations. Prospective use of WGS analysis together with thorough exposure information from cases could potentially identify future outbreaks more rapidly, including those that may have been undetected for some time over different geographical regions.
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11
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Bespalova TY, Mikhaleva TV, Meshcheryakova NY, Kustikova OV, Matovic K, Dmitrić M, Zaitsev SS, Khizhnyakova MA, Feodorova VA. Novel Sequence Types of Listeria monocytogenes of Different Origin Obtained in the Republic of Serbia. Microorganisms 2021; 9:1289. [PMID: 34204786 PMCID: PMC8231576 DOI: 10.3390/microorganisms9061289] [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: 05/21/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 12/15/2022] Open
Abstract
Listeria monocytogenes, the causative agent of listeriosis, is amongst the major food-borne pathogens in the world that affect mammal species, including humans. This microorganism has been associated with both sporadic episodes and large outbreaks of human listeriosis worldwide, with high mortality rates. In this study, the main sequence types (STs) and clonal complexes (CCs) were investigated in all of the 13 L. monocytogenes strains originating from different sources in the Republic of Serbia in 2004-2019 and that were available in the BIGSdb-Lm database. We found at least 13 STs belonging to the phylogenetic lineages I and II. These strains were represented by ST1/ST3/ST9 of CC1/CC3/CC9, which were common in the majority of the European countries and worldwide, as well as by eight novel STs (ST1232/ST1233/ST1234/ST1235/ST1238/ST1236/ST1237/ST1242) of CC19/CC155/CC5/CC21/CC3/CC315/CC37, and the rare ST32 (clonal complex ST32) and ST734 (CC1), reported in the Republic of Serbia, the EU, for the first time. Our study confirmed the association of CC1 with cases of neuroinfection and abortions among small ruminants, and of CC3 and CC9 with food products of animal origin. The strains isolated in 2019 carried alleles of the internalin genes (inlA/inlB/inlC/inlE) characteristic of the most virulent strains from the hypervirulent CC1. These findings demonstrated the genetic relatedness between L. monocytogenes strains isolated in the Republic of Serbia and worldwide. Our study adds further information about the diversity of the L. monocytogenes genotypes of small ruminants and food products, as the strain distribution in these sources in Serbia had not previously been evaluated.
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Affiliation(s)
- Tatiana Yu. Bespalova
- Federal Research Center for Virology and Microbiology, Branch in Samara, 443013 Samara, Russia; (T.Y.B.); (T.V.M.); (N.Y.M.); (O.V.K.)
| | - Tatiana V. Mikhaleva
- Federal Research Center for Virology and Microbiology, Branch in Samara, 443013 Samara, Russia; (T.Y.B.); (T.V.M.); (N.Y.M.); (O.V.K.)
| | - Nadezhda Yu Meshcheryakova
- Federal Research Center for Virology and Microbiology, Branch in Samara, 443013 Samara, Russia; (T.Y.B.); (T.V.M.); (N.Y.M.); (O.V.K.)
| | - Olga V. Kustikova
- Federal Research Center for Virology and Microbiology, Branch in Samara, 443013 Samara, Russia; (T.Y.B.); (T.V.M.); (N.Y.M.); (O.V.K.)
| | - Kazimir Matovic
- Department for Laboratory Diagnostic, Veterinary Specialized Institute Kraljevo, 36000 Kraljevo, Serbia; (K.M.); (M.D.)
- Department of Food Safety, Veterinary Specialized Institute Kraljevo, 36000 Kraljevo, Serbia
| | - Marko Dmitrić
- Department for Laboratory Diagnostic, Veterinary Specialized Institute Kraljevo, 36000 Kraljevo, Serbia; (K.M.); (M.D.)
- Department of Food Safety, Veterinary Specialized Institute Kraljevo, 36000 Kraljevo, Serbia
| | - Sergey S. Zaitsev
- Federal Research Center for Virology and Microbiology, Branch in Saratov, 410028 Saratov, Russia; (S.S.Z.); (M.A.K.)
| | - Maria A. Khizhnyakova
- Federal Research Center for Virology and Microbiology, Branch in Saratov, 410028 Saratov, Russia; (S.S.Z.); (M.A.K.)
| | - Valentina A. Feodorova
- Federal Research Center for Virology and Microbiology, Branch in Saratov, 410028 Saratov, Russia; (S.S.Z.); (M.A.K.)
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12
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Wang Y, Ji Q, Li S, Liu M. Prevalence and Genetic Diversity of Listeria monocytogenes Isolated From Retail Pork in Wuhan, China. Front Microbiol 2021; 12:620482. [PMID: 33767677 PMCID: PMC7986423 DOI: 10.3389/fmicb.2021.620482] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/15/2021] [Indexed: 11/25/2022] Open
Abstract
Listeria monocytogenes is a ubiquitous bacteria and causative agent of zoonotic listeriosis with high mortality. The consumption of contaminated animal-derived foods has been linked with both epidemic and sporadic listeriosis. In this work, a total of 64 L. monocytogenes isolates from 259 pork samples sold in 11 supermarket chains were identified and characterized by comparative whole-genome analysis. All isolates were delineated into eight clonal complexes (CCs), namely CC2, CC8, CC9, CC11, CC155, CC121, CC204, and CC619, spanning two lineages (I and II) and carrying 3–5 antibiotic-resistant genes (fosX, lnu, mprF, tetM, and dhfR). It is noted that Listeria pathogenicity island (LIPI)-1, LIPI-3, and LIPI-4 were distributed in all ST619 isolates from two supermarket chains that were closely related with clinical isolates (<40 SNP). Some of the isolates from different supermarket chains with 0 SNP difference indicated a common pork supply source. Notably, 57.81% of the strains carried types IB, IIA, or IIIB CRISPR-Cas system, CC121 isolates carried both types IB and IIA CRISPR-Cas systems, Cas proteins of CC155 isolates located between two CRISPR loci, each CC has unique organization of Cas proteins as well as CRISPR loci. CRISPR-Cas system-based subtyping improved discrimination of pork-derived L. monocytogenes isolates. Comparisons at the genome level contributed to understand the genetic diversities and variations among the isolates and provided insights into the genetic makeup and relatedness of these pathogens.
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Affiliation(s)
- Yiqian Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qiang Ji
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Shaowen Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Mei Liu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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13
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Bahrami A, Davis S, Mousavi Khaneghah A, Williams L. The efficiency of technologies used for epidemiological characterization of Listeria monocytogenes isolates : an update. Crit Rev Food Sci Nutr 2020; 62:1079-1091. [PMID: 33092402 DOI: 10.1080/10408398.2020.1835816] [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: 10/23/2022]
Abstract
The characterization of pathogenic bacteria by providing information regarding the identification and source-tracking of the causes of outbreaks is vital for the epidemiological investigations of foodborne diseases. The knowledge of transmission of Listeria monocytogenes (L. monocytogenes) strains from the environment, directly or indirectly (through food processing facilities) to the final food products, due to the complexity of evaluating numerous, affecting parameters is quite limited. The food trade globalization also adds difficulties in tracking the association between the infection occurrence and causative pathogens, aiming to prevent their spread. The occurrence of listeriosis, a notifiable disease throughout the world, can either be sporadic or outbreak-related. Due to the importance of foodborne outbreaks from a public health aspect and its correspondence enormous economic losses, cross-linked surveillance studies regarding the contamination of foods by L. monocytogenes, besides identifying clusters and tracing the sources of infections on an international-scale to prevent and control L. monocytogenes outbreaks sounds very crucial. Contrary to the conventional typing methods, molecular-based techniques, such as whole-genome sequencing, owing to the capacity to discriminate L. monocytogenes strains down to single nucleotide differences, provide an accurate characterization of strains and tracking the causes of outbreaks. However, routinely using molecular-based methods depends on the required improvements in the affordability, proper timing, and preparing reliable, standardized bioinformatics facilities. This work was conducted to critically review the practical potential of diverse typing methods have been used for the characterization of L. monocytogenes and discuss how they might change the future of efforts for control of listeriosis.
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Affiliation(s)
- Akbar Bahrami
- Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural, and Technical State University, North Carolina Research Campus, Kannapolis, North Carolina, USA
| | - Shurrita Davis
- Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural, and Technical State University, North Carolina Research Campus, Kannapolis, North Carolina, USA
| | - Amin Mousavi Khaneghah
- Department of Food Science, Faculty of Food Engineering (FEA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Leonard Williams
- Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural, and Technical State University, North Carolina Research Campus, Kannapolis, North Carolina, USA
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14
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Sharma R, Gal L, Garmyn D, Bisaria VS, Sharma S, Piveteau P. Evidence of Biocontrol Activity of Bioinoculants Against a Human Pathogen, Listeria monocytogenes. Front Microbiol 2020; 11:350. [PMID: 32218775 PMCID: PMC7078112 DOI: 10.3389/fmicb.2020.00350] [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: 12/05/2019] [Accepted: 02/17/2020] [Indexed: 11/13/2022] Open
Abstract
Due to rhizodeposits and various microbial interactions, the rhizosphere is an extremely dynamic system, which provides a conductive niche not only for bacteria beneficial to plants but also for those that might pose a potential threat to humans. The importance of bioinoculants as biocontrol agents to combat phytopathogens has been widely recognized. However, little information exists with respect to their role in inhibiting human pathogens in the rhizosphere. The present study is an attempt to understand the impact of an established bacterial consortium, Azotobacter chroococcum, Bacillus megaterium, and Pseudomonas fluorescens, on the survivability of Listeria monocytogenes in the rhizosphere of Cajanus cajan and Festuca arundinacea. An experiment conducted in Hoagland's medium in the presence of C. cajan demonstrated that the presence of bioinoculants impaired growth of L. monocytogenes compared to that observed in their absence. On the other hand, in the presence of F. arundinacea, no significant differences were observed in the population dynamics of L. monocytogenes in the presence or absence of the bioinoculants. Agar plate assay through cross streak method revealed the inhibition of L. monocytogenes by bioinoculants. Potential bioactive compounds were identified by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). These results suggest that agricultural amendments can act as protective agents against human pathogens while enforcing plant growth promotion.
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Affiliation(s)
- Richa Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Laurent Gal
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne – Franche-Comté, Dijon, France
| | - Dominique Garmyn
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne – Franche-Comté, Dijon, France
| | - V. S. Bisaria
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Pascal Piveteau
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne – Franche-Comté, Dijon, France
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