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Russini V, De Marchis ML, Sampieri C, Onorati C, Zucchitta P, De Santis P, Varcasia BM, De Santis L, Chiaverini A, Gattuso A, Vestri A, Gasperetti L, Condoleo R, Palla L, Bossù T. Exploratory Genomic Marker Analysis of Virulence Patterns in Listeria monocytogenes Human and Food Isolates. Foods 2025; 14:1669. [PMID: 40428449 PMCID: PMC12110734 DOI: 10.3390/foods14101669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2025] [Revised: 04/30/2025] [Accepted: 05/06/2025] [Indexed: 05/29/2025] Open
Abstract
Listeria monocytogenes causes listeriosis, a severe foodborne disease with high mortality. Contamination with it poses significant risks to food safety and public health. Notably, genetic characteristic differences exist between strains causing human infections and those found in routine food inspections. This study examined the genotypic factors influencing the pathogenicity of L. monocytogenes, focusing on virulence gene profiles and key integrity genes like inlA to explain these divergences. The dataset included 958 strains isolated from human, food, and environmental samples. Whole-genome sequencing identified virulence genes, and principal component analysis (PCA) examined 92 virulence genes and inlA integrity to uncover potentially pathogenic patterns. The results highlight differences in virulence characteristics between strains of different origins. The integrity of inlA and genes such as inlD, inlG, and inlL were pivotal to pathogenicity. Strains with premature stop codons (PMSCs) in inlA, associated with reduced virulence, accounted for a low percentage of human cases but over 30% of food isolates. Sequence types (STs) like ST121, ST580, and ST199 showed unique profiles, while ST9, dominant in food, occasionally caused human cases, posing risks to vulnerable individuals. This research highlights the complexity of the pathogenicity of L. monocytogenes and emphasizes the importance of genomic surveillance for effective risk assessment.
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Affiliation(s)
- Valeria Russini
- UOC Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy (P.D.S.); (B.M.V.); (R.C.); (T.B.)
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy; (A.V.); (L.P.)
| | - Maria Laura De Marchis
- UOC Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy (P.D.S.); (B.M.V.); (R.C.); (T.B.)
| | - Cinzia Sampieri
- UOC Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy (P.D.S.); (B.M.V.); (R.C.); (T.B.)
| | - Cinzia Onorati
- UOC Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy (P.D.S.); (B.M.V.); (R.C.); (T.B.)
| | - Piero Zucchitta
- UOC Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy (P.D.S.); (B.M.V.); (R.C.); (T.B.)
| | - Paola De Santis
- UOC Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy (P.D.S.); (B.M.V.); (R.C.); (T.B.)
| | - Bianca Maria Varcasia
- UOC Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy (P.D.S.); (B.M.V.); (R.C.); (T.B.)
| | - Laura De Santis
- UOC Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy (P.D.S.); (B.M.V.); (R.C.); (T.B.)
| | - Alexandra Chiaverini
- National Reference Laboratory (LNR) for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), 64100 Teramo, Italy;
| | - Antonietta Gattuso
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Annarita Vestri
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy; (A.V.); (L.P.)
| | - Laura Gasperetti
- UOT Toscana Nord, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 56123 Pisa, Italy;
| | - Roberto Condoleo
- UOC Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy (P.D.S.); (B.M.V.); (R.C.); (T.B.)
| | - Luigi Palla
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy; (A.V.); (L.P.)
| | - Teresa Bossù
- UOC Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy (P.D.S.); (B.M.V.); (R.C.); (T.B.)
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Lüth S, Fuchs J, Deneke C. Compatibility of whole-genome sequencing data from Illumina and Ion Torrent technologies in genome comparison analysis of Listeria monocytogenes. Microb Genom 2025; 11:001389. [PMID: 40310451 PMCID: PMC12046094 DOI: 10.1099/mgen.0.001389] [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: 01/09/2025] [Accepted: 02/28/2025] [Indexed: 05/02/2025] Open
Abstract
Whole-genome sequencing (WGS) has become the key approach for molecular surveillance of Listeria monocytogenes. Genome comparison analysis can reveal transmission routes that cannot be found with classic epidemiology. A widespread standard for use in genome comparison analysis involves data from short-read sequencing, generated on Illumina or Ion Torrent devices. To date, little is known about the compatibility of data from both platforms. This knowledge is essential when it comes to the central analysis of data, for example, in the case of outbreaks. We used WGS data from 47 L. monocytogenes isolates of the strain collection of the German National Reference Laboratory for L. monocytogenes, generated on either Illumina or Ion Torrent devices, to analyse the impact of the sequencing technology on downstream analyses. In our study, only the assembler SPAdes delivered qualitatively comparable results. In the gene-based core genome multilocus sequence typing (cgMLST), the same-strain allele discrepancy between the platforms was 14.5 alleles on average, which is well above the threshold of 7 alleles routinely used for cluster detection in L. monocytogenes. An application of a strict frameshift filter in cgMLST analysis could push the mean discrepancy below this threshold but reduced discriminatory power. The impact of the platform on the read-based single nucleotide polymorphism analysis was lower than that on the cgMLST. Overall, it was possible to improve compatibility in various ways, but perfect compatibility could not be achieved.
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Affiliation(s)
- Stefanie Lüth
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Jannika Fuchs
- Chemical and Veterinary Investigation Office (CVUA) Karlsruhe, Weißenburger Str. 3, 76187 Karlsruhe, Germany
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
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Slavinska A, Jauneikaite E, Meškytė U, Kirkliauskienė A, Misevič A, Petrutienė A, Kuisiene N. Genomic characterization of Listeria monocytogenes isolated from normally sterile human body fluids in Lithuania from 2016 to 2021. Microb Genom 2025; 11. [PMID: 40392696 DOI: 10.1099/mgen.0.001410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2025] Open
Abstract
Listeria monocytogenes is a saprophytic gram-positive bacterium and opportunistic foodborne pathogen that can cause listeriosis in humans. The incidence of listeriosis has been rising globally and, despite antimicrobial treatment, the mortality rates associated with the most severe forms of listeriosis such as sepsis, meningitis and meningoencephalitis remain high. The notification of listeriosis in humans is mandatory in Lithuania, and up to 20 cases are reported annually. However, no studies have described the detailed virulence and antimicrobial susceptibility profiles of any clinical L. monocytogenes strains in Lithuania. Accordingly, this study aimed to describe the antibiotic susceptibility of invasive L. monocytogenes and perform in-depth characterization of strains isolated from patients with neuroinfections through whole-genome sequencing. A total of 70 isolates were collected, mostly from infected patients aged 65 or older, between 2016 and 2021 : 41 (58.6%) from blood, 19 (27.1%) from cerebrospinal fluid, 5 (7.1%) from wounds, 1 (1.4%) from pleural fluid and 1 (1.4%) from a brain abscess. Two phylogenetic lineages were identified-I (n = 16/70, 22.9%) and II (n = 54/70, 77.1%)-along with three serogroups-IIa (n = 53/70, 75.7%), IVb (n = 16/70, 22.9%), and IIc (n = 1/70, 1.4%). Genomic analysis of 20 isolates showed a high level of diversity with seven genotypes: ST6 (n = 6), ST155 (n = 5), ST8 (n = 4), ST504 (n = 2) and singletons for ST37, ST451 and ST2. Phylogenetic analysis clustered these isolates into two clades defined by serogroups IVb and IIa. Notably, five isolates were clustered tightly together (difference of 6-48 core SNPs from reference and 0, 4 or 44 SNPs from each other) with ST155, previously reported in a European outbreak. Comparison with publicly available L. monocytogenes genomes did not identify unique clusters or genotypes. No acquired antimicrobial resistance genes were identified. Our study highlights the complementary value of whole-genome sequencing in routine PCR-based surveillance in Lithuania. This is the first study to characterize and compare genomes for L. monocytogenes associated with neuroinfections in Lithuania using whole-genome sequencing. The retrospective detection of the ST155 clone underscores the need for a review and strengthening of epidemiological surveillance strategies in clinical and non-clinical settings in Lithuania.
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Affiliation(s)
- Anželika Slavinska
- Department of Microbiology and Biotechnology, Institute of Biosciences of Vilnius University Life Sciences Centre, 10257 Vilnius, Lithuania
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - Ugnė Meškytė
- Department of Microbiology and Biotechnology, Institute of Biosciences of Vilnius University Life Sciences Centre, 10257 Vilnius, Lithuania
| | - Agnė Kirkliauskienė
- Faculty of Medicine, Institute of Biomedical science, Vilnius University, 03101 Vilnius, Lithuania
| | - Adam Misevič
- Faculty of Medicine, Institute of Biomedical science, Vilnius University, 03101 Vilnius, Lithuania
| | - Aurelija Petrutienė
- Department of Clinical Investigations of the National Public Health Surveillance Laboratory, 10210 Vilnius, Lithuania
| | - Nomeda Kuisiene
- Department of Microbiology and Biotechnology, Institute of Biosciences of Vilnius University Life Sciences Centre, 10257 Vilnius, Lithuania
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Andersson P, Dougall S, Mercoulia K, Horan KA, Seemann T, Lacey JA, Hoang T, Leong LEX, Speers D, Cooley L, Kennedy K, Baird R, Graham R, Wang Q, Levy A, Menouhos D, Sherry NL, Ballard SA, Sintchenko V, Jennison AV, Howden BP. Effects of Decentralized Sequencing on National Listeria monocytogenes Genomic Surveillance, Australia, 2016-2023. Emerg Infect Dis 2025; 31:89-97. [PMID: 40359100 PMCID: PMC12078541 DOI: 10.3201/eid3113.241357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2025] Open
Abstract
We assessed turnaround times in the national Listeria monocytogenes genomic surveillance system in Australia before and after decentralized sequencing. Using 1,204 samples collected during 2016-2023, we observed statistically significant reductions in median time from sample collection to issuance of national genomic surveillance report to 26 days, despite sample numbers doubling in 2022 and 2023. During 2016-2018, all jurisdictions referred samples to the National Listeria Reference Laboratory for sequencing and analysis, but as jurisdictional sequencing capacity increased, 4 jurisdictions transitioned to sequencing their own samples and referring sequence data to the national laboratory. One jurisdiction had well-established genomics capacity, transitioned without noticeable disruption, and continued to improve. Another 3 jurisdictions initially had increased turnaround times, highlighting the need for defined sequence referral mechanisms. Overall, timeliness and throughput improved, and sequencing decentralization strengthened Australia's genomic surveillance system while maintaining timeliness. The practices described could be beneficial and achievable in other countries.
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Chrzastek K, Seal BS, Kulkarni A, Kapczynski DR. Whole-Genome Shotgun Sequencing from Chicken Clinical Tracheal Samples for Bacterial and Novel Bacteriophage Identification. Vet Sci 2025; 12:162. [PMID: 40005922 PMCID: PMC11861695 DOI: 10.3390/vetsci12020162] [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: 01/06/2025] [Revised: 01/30/2025] [Accepted: 02/05/2025] [Indexed: 02/27/2025] Open
Abstract
A whole-genome shotgun sequencing (sWGS) approach was applied to chicken clinical tracheal swab samples during metagenomics investigations to identify possible microorganisms among poultry with respiratory diseases. After applying shotgun sequencing, Ornithobacterium rhinotracheale (ORT) and a putative prophage candidate were found in one of the swab samples. A multi-locus sequence typing (MLST) scheme of the ORT genome involved the adk, aroE, fumC, gdhA, pgi, and pmi genes. Antibiotic resistant analysis demonstrated tetracycline-resistan t ribosomal protection protein, tetQ, the aminoglycoside-(3)-acetyltransferase IV gene, aminoglycoside antibiotic inactivation and macrolide resistance, and the ermX gene in the ORT genome. A putative prophage candidate was predicted using Prophage Hunter and PHAST, while BLAST analyses were utilized to identify genes encoding bacteriophage proteins. Interestingly, genes encoding endolysins were detected in bacteriophage genomes. The gene products encoded in the prophage sequence were most closely related to bacteriophages in the N4-like family among the Authographiviridae in the Caudovirales. This study demonstrates the potential of sWGS for the rapid detection and characterization of etiologic agents found in clinical samples.
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Affiliation(s)
- Klaudia Chrzastek
- Exotic and Emerging Avian Diseases Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture (USDA), 934 College Station Road, Athens, GA 30605, USA
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Bruce S. Seal
- Biology Program, Oregon State University—Cascades, 1500 SW Chandler Avenue, Bend, OR 97702, USA;
| | - Arun Kulkarni
- Georgia Poultry Laboratory Network, 3235 Abit Massey Way, Gainesville, GA 30507, USA;
| | - Darrell R. Kapczynski
- Exotic and Emerging Avian Diseases Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture (USDA), 934 College Station Road, Athens, GA 30605, USA
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Merda D, Vila-Nova M, Bonis M, Boutigny AL, Brauge T, Cavaiuolo M, Cunty A, Regnier A, Sayeb M, Vingadassalon N, Yvon C, Chesnais V. Unraveling the impact of genome assembly on bacterial typing: a one health perspective. BMC Genomics 2024; 25:1059. [PMID: 39516732 PMCID: PMC11545336 DOI: 10.1186/s12864-024-10982-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 10/30/2024] [Indexed: 11/16/2024] Open
Abstract
BACKGROUND In the context of pathogen surveillance, it is crucial to ensure interoperability and harmonized data. Several surveillance systems are designed to compare bacteria and identify outbreak clusters based on core genome MultiLocus Sequence Typing (cgMLST). Among the different approaches available to generate bacterial cgMLST, our research used an assembly-based approach (chewBBACA tool). METHODS Simulations of short-read sequencing were conducted for 5 genomes of 27 pathogens of interest in animal, plant, and human health to evaluate the repeatability and reproducibility of cgMLST. Various quality parameters, such as read quality and depth of sequencing were applied, and several read simulations and genome assemblies were repeated using three tools: SPAdes, Unicycler and Shovill. In vitro sequencing were also used to evaluate assembly impact on cgMLST results, for six bacterial species: Bacillus thuringiensis, Listeria monocytogenes, Salmonella enterica, Staphylococcus aureus, Vibrio parahaemolyticus and Xylella fastidiosa. RESULTS The results highlighted variability in cgMLST, which not only related to the assembly tools, but also induced by the intrinsic composition of the genomes themselves. This variability observed in simulated sequencing was further validated with real data for six of the bacterial pathogens studied. CONCLUSION This highlights that the intrinsic genome composition affects assembly and resulting cgMLST profiles, and that variability in bioinformatics tools can induce a bias in cgMLST profiles. In conclusion, we propose that the completeness of cgMLST schemes should be considered when clustering strains.
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Affiliation(s)
- Déborah Merda
- Université Paris Est, ANSES, Laboratory for Food Safety, SPAAD unit, Maisons-Alfort, F-94701, France.
| | - Meryl Vila-Nova
- Université Paris Est, ANSES, Laboratory for Food Safety, SPAAD unit, Maisons-Alfort, F-94701, France
| | - Mathilde Bonis
- Université Paris Est, ANSES, Laboratory for Food Safety, SBCL unit, Maisons-Alfort, F-94701, France
| | - Anne-Laure Boutigny
- ANSES, Plant Health Laboratory, Bacteriology Virology GMO Unit, 7 rue Jean Dixméras, Angers cedex 01, 49044, France
| | - Thomas Brauge
- ANSES, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit (B3PA), Boulevard du Bassin Napoléon, Boulogne-sur-Mer, France
| | - Marina Cavaiuolo
- Université Paris Est, ANSES, Laboratory for Food Safety, SBCL unit, Maisons-Alfort, F-94701, France
| | - Amandine Cunty
- ANSES, Plant Health Laboratory, Bacteriology Virology GMO Unit, 7 rue Jean Dixméras, Angers cedex 01, 49044, France
| | - Antoine Regnier
- ANSES, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit (B3PA), Boulevard du Bassin Napoléon, Boulogne-sur-Mer, France
| | - Maroua Sayeb
- Université Paris Est, ANSES, Laboratory for Food Safety, SEL unit, Maisons-Alfort, F-94701, France
| | - Noémie Vingadassalon
- Université Paris Est, ANSES, Laboratory for Food Safety, SBCL unit, Maisons-Alfort, F-94701, France
| | - Claire Yvon
- Université Paris Est, ANSES, Laboratory for Food Safety, SEL unit, Maisons-Alfort, F-94701, France
| | - Virginie Chesnais
- Université Paris Est, ANSES, Laboratory for Food Safety, SPAAD unit, Maisons-Alfort, F-94701, France
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Belias A, Bolten S, Wiedmann M. Challenges and opportunities for risk- and systems-based control of Listeria monocytogenes transmission through food. Compr Rev Food Sci Food Saf 2024; 23:e70071. [PMID: 39610177 PMCID: PMC11605164 DOI: 10.1111/1541-4337.70071] [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: 11/01/2024] [Revised: 11/05/2024] [Accepted: 11/05/2024] [Indexed: 11/30/2024]
Abstract
Listeria monocytogenes contamination of ready-to-eat (RTE) food products and food-associated built environments (e.g., processing facilities) represents a food safety issue with major public health and business risk implications. A number of factors make L. monocytogenes control a particular challenge, including (i) its frequent presence in different environments, (ii) its propensity for establishing persistence in food-associated environments, (iii) its ability to grow under a variety of stressful conditions, and (iv) its ability to cause severe illness, particularly in immunocompromised individuals and pregnant people. Key sources of L. monocytogenes contamination of RTE foods are food-associated built environments. However, raw materials can also be an important source, particularly for products without a "kill step" (e.g., fresh produce, raw dairy products, cold-smoked seafood). While certain RTE foods (e.g., deli meats, soft cheeses, produce) have commonly been linked to listeriosis outbreaks, cases, and recalls, a number of factors will influence the specific public health risk a given RTE food represents, including the likelihood of contamination, ability to support L. monocytogenes growth, and consumer-related factors (including consumption by pregnant or immunocompromised individuals). Consequently, a risk-based approach presents the most appropriate strategy to minimize the public health and business impact of L. monocytogenes. Key challenges to control L. monocytogenes include (i) development and implementation of food safety systems that prevent L. monocytogenes persistence in food-associated built environments, (ii) minimizing L. monocytogenes contamination of raw material sources, (iii) implementation of effective root cause analysis procedures, (iv) minimizing L. monocytogenes growth in finished product, and (v) consumer education.
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Affiliation(s)
| | - Samantha Bolten
- Department of Food ScienceCornell UniversityIthacaNew YorkUSA
| | - Martin Wiedmann
- Department of Food ScienceCornell UniversityIthacaNew YorkUSA
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Hati S, Vahora S, Panchal J, Patel S, Patel A, Chauhan H, Sharma K, Sabara P, Shrimali M. Whole genome sequencing (WGS) analysis of antimicrobial resistance (AMR) milk and dairy-derived pathogens from Anand, Gujarat, India. Microb Pathog 2024; 197:107076. [PMID: 39454806 DOI: 10.1016/j.micpath.2024.107076] [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: 09/09/2024] [Revised: 10/21/2024] [Accepted: 10/22/2024] [Indexed: 10/28/2024]
Abstract
This study aimed to evaluate the antimicrobial resistance (AMR) patterns and genomic characteristics of Enterococcus faecalis, Enterococcus faecium, and Staphylococcus aureus strains isolated from dairy products, including buttermilk, curd, ice cream, and sweets, in the Anand region of Gujarat, India. A total of 205 isolates were analysed, with the highest contamination levels found in buttermilk and curd. The bacterial isolates were identified using biochemical tests and advanced Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) mass spectrometry. Antimicrobial susceptibility testing (AST) was performed using the Kirby-Bauer disk diffusion method, following CLSI guidelines, focusing on common antibiotics used for treating dairy-related bacterial infections. Resistance profiles were analysed using WHONET software.s The findings revealed significant multidrug resistance (MDR), particularly among E. faecium and E. faecalis, with over 95 % resistance to key antibiotics, including linezolid, ciprofloxacin, cefpodoxime, and carbapenems. Many strains were classified as MDR, XDR, and PDR. Staphylococcus aureus also exhibited substantial resistance to penicillin and enrofloxacin. whole-genome sequencing (WGS) and phylogenetic analysis to identify AMR determinants and conduct nucleotide sequence alignment. The study identified several antibiotic resistance genes, including LiaF, which regulates the expression of LiaR and LiaS genes. WGS revealed that genes such as GdpD, MprF, and PgsA encode intrinsic resistance determinants, contributing to antibiotic resistance. Additional AMR mechanisms were identified, including ABC transporter efflux pumps and the regulation of resistance genes by LiaR and LiaS. Phylogenetic analysis indicates a close relationship between Enterococcus faecium 640 1352.18624 and Enterococcus durans FB129-CNAB-4 883162.3.
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Affiliation(s)
- Subrota Hati
- Department of Dairy Microbiology, College of Dairy Sciences, Anand, 385505, Kamdhenu University, Gujarat, India.
| | - Shirin Vahora
- Department of Dairy Microbiology, College of Dairy Sciences, Anand, 385505, Kamdhenu University, Gujarat, India
| | - Janki Panchal
- Department of Veterinary Microbiology and Animal Biotechnology, College of Veterinary Sciences & Animal Husbandry, Sardarkrushinagar, 385505, Kamdhenu University, Gujarat, India
| | - Sandip Patel
- Department of Veterinary Microbiology and Animal Biotechnology, College of Veterinary Sciences & Animal Husbandry, Sardarkrushinagar, 385505, Kamdhenu University, Gujarat, India.
| | - Arun Patel
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Anand, 385505, Kamdhenu University, Gujarat, India
| | - Harshad Chauhan
- Department of Veterinary Microbiology and Animal Biotechnology, College of Veterinary Sciences & Animal Husbandry, Sardarkrushinagar, 385505, Kamdhenu University, Gujarat, India
| | - Kishan Sharma
- Department of Veterinary Microbiology and Animal Biotechnology, College of Veterinary Sciences & Animal Husbandry, Sardarkrushinagar, 385505, Kamdhenu University, Gujarat, India
| | - Pritesh Sabara
- Gujarat Biotechnology Research Centre, Department of Science & Technology, Gandhinagar, 382011, Gujarat, India
| | - Mehul Shrimali
- Department of Veterinary Microbiology and Animal Biotechnology, College of Veterinary Sciences & Animal Husbandry, Sardarkrushinagar, 385505, Kamdhenu University, Gujarat, India
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Martins BTF, Camargo AC, Tavares RDM, Nero LA. Relevant foodborne bacteria associated to pork production chain. ADVANCES IN FOOD AND NUTRITION RESEARCH 2024; 113:181-218. [PMID: 40023561 DOI: 10.1016/bs.afnr.2024.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2025]
Abstract
Foodborne diseases affect millions of people globally, resulting in a huge number of hospitalizations and deaths. In this context, laboratory-based research is crucial to identify the major pathogens as well as the relevance of each one for distinct food production chains. Pork meat is very popular, being the most consumed meat in many countries and its inspection at the slaughterhouse is the main component of surveillance to protect consumers. Healthy pigs may carry pathogenic and antibiotic resistant bacteria that can be subsequently transferred to humans through the consumption of contaminated meat. Further, the food processing environment can harbor pathogenic persistent bacteria, representing a risk of cross-contamination to pork meat, demanding strict slaughtering procedures. Among these foodborne bacteria, Salmonella, Yersinia enterocolitica, Escherichia coli, Campylobacter spp., Listeria monocytogenes and Staphylococcus aureus are the most relevant in the pork production chain. Molecular subtyping has been fundamental for pathogen detection and also to track transmission, and nowadays it is a key component of the efforts to prevent and control foodborne diseases. In this chapter, characteristics of these major foodborne bacteria associated to pork meat will be addressed, including their occurrence and importance along the pork production chain, worldwide distribution, typing, as well as control and prevention measures from farm to fork.
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Affiliation(s)
- Bruna Torres Furtado Martins
- InsPOA-Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | - Anderson Carlos Camargo
- InsPOA-Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, MG, Brasil; InovaLeite-Laboratório de Pesquisa em Leites e Derivados, Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | - Rafaela de Melo Tavares
- InsPOA-Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | - Luís Augusto Nero
- InsPOA-Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, MG, Brasil.
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Halbedel S, Wamp S, Lachmann R, Holzer A, Pietzka A, Ruppitsch W, Wilking H, Flieger A. High density genomic surveillance and risk profiling of clinical Listeria monocytogenes subtypes in Germany. Genome Med 2024; 16:115. [PMID: 39375806 PMCID: PMC11457394 DOI: 10.1186/s13073-024-01389-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 09/24/2024] [Indexed: 10/09/2024] Open
Abstract
BACKGROUND Foodborne infections such as listeriosis caused by the bacterium Listeria monocytogenes represent a significant public health concern, particularly when outbreaks affect many individuals over prolonged time. Systematic collection of pathogen isolates from infected patients, whole genome sequencing (WGS) and phylogenetic analyses allow recognition and termination of outbreaks after source identification and risk profiling of abundant lineages. METHODS We here present a multi-dimensional analysis of > 1800 genome sequences from clinical L. monocytogenes isolates collected in Germany between 2018 and 2021. Different WGS-based subtyping methods were used to determine the population structure with its main phylogenetic sublineages as well as for identification of disease clusters. Clinical frequencies of materno-foetal and brain infections and in vitro infection experiments were used for risk profiling of the most abundant sublineages. These sublineages and large disease clusters were further characterised in terms of their genetic and epidemiological properties. RESULTS The collected isolates covered 62% of all notified cases and belonged to 188 infection clusters. Forty-two percent of these clusters were active for > 12 months, 60% generated cases cross-regionally, including 11 multinational clusters. Thirty-seven percent of the clusters were caused by sequence type (ST) ST6, ST8 and ST1 clones. ST1 was identified as hyper- and ST8, ST14, ST29 as well as ST155 as hypovirulent, while ST6 had average virulence potential. Inactivating mutations were found in several virulence and house-keeping genes, particularly in hypovirulent STs. CONCLUSIONS Our work presents an in-depth analysis of the genomic characteristics of L. monocytogenes isolates that cause disease in Germany. It supports prioritisation of disease clusters for epidemiological investigations and reinforces the need to analyse the mechanisms underlying hyper- and hypovirulence.
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Affiliation(s)
- Sven Halbedel
- FG11 Division of Enteropathogenic Bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Burgstrasse 37, Wernigerode, D-38855, Germany.
- Institute for Medical Microbiology and Hospital Hygiene, Otto Von Guericke University Magdeburg, Leipziger Strasse 44, Magdeburg, 39120, Germany.
| | - Sabrina Wamp
- FG11 Division of Enteropathogenic Bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Burgstrasse 37, Wernigerode, D-38855, Germany
| | - Raskit Lachmann
- FG35 - Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Seestrasse 10, Berlin, 13353, Germany
| | - Alexandra Holzer
- FG35 - Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Seestrasse 10, Berlin, 13353, Germany
| | - Ariane Pietzka
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Beethovenstraße 6, Graz, 8010, Austria
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Währingerstrasse 25a, Vienna, 1090, Austria
| | - Hendrik Wilking
- FG35 - Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Seestrasse 10, Berlin, 13353, Germany
| | - Antje Flieger
- FG11 Division of Enteropathogenic Bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Burgstrasse 37, Wernigerode, D-38855, Germany.
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11
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Jashari B, Capitaine K, Bisha B, Stessl B, Blagoevska K, Cana A, Jankuloski D, Félix B. Molecular Characterization of Listeria monocytogenes in the Food Chain of the Republic of Kosovo from 2016 to 2022. Foods 2024; 13:2883. [PMID: 39335812 PMCID: PMC11431155 DOI: 10.3390/foods13182883] [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: 07/22/2024] [Revised: 08/30/2024] [Accepted: 09/06/2024] [Indexed: 09/30/2024] Open
Abstract
The present study describes the genetic characterization of L. monocytogenes strains found in the Republic of Kosovo's food chain. From 2016 to 2022, 995 samples were collected. Overall, 648 samples were from ready-to-eat (RTE) food products, 281 from food products consumed cooked (FPCC), 60 from raw materials, and 6 from environmental samples. Overall, 11.76% (117 out of 995) of the samples were contaminated by L. monocytogenes, comprising 6.33% (41 out of 648) from RTE products, 14.95% (42 out of 281) from FPCC, 55.00% (33 out of 60) from raw materials, and 16.66% (1 out of 6) from environmental samples. All isolates were subjected to molecular serotyping and clonal complex (CC) identification by using real-time PCR, as well as multilocus sequence typing. All isolates were grouped into four molecular serotypes, IIa (34.19%), IIb (3.48%), IIc (32.48%), and IVb (29.91%), as well as Lineage I (33.33%) and Lineage II (66.66%). In total, 14 CCs were identified from 41 RTE isolates; however, CC29 (7), CC2 (6), and CC6 (6) were the most dominant. By contrast, CC9 was by far the most represented CC in both FPCC (21) and RM (14). Moreover, 30 isolates expressed CC1, CC2, CC4, or CC6, which are particularly associated with severe human infections.
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Affiliation(s)
- Besart Jashari
- Food Microbiology, Food and Veterinary Laboratory, Food and Veterinary Agency of Kosovo, Lidhja e Pejës 241, 10000 Pristina, Kosovo
| | - Karine Capitaine
- Laboratory for Food Safety, Salmonella and Listeria Unit, ANSES, European Union Reference Laboratory for L. monocytogenes, University of Paris-Est, 94700 Maisons-Alfort, France
| | - Bledar Bisha
- Department of Animal Science, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY 82071, USA
| | - Beatrix Stessl
- Unit of Food Microbiology, Centre for Food Science and Public Veterinary Health, Clinical Department for Farm Animals and Food Systems Safety, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-2110 Vienna, Austria
| | - Katerina Blagoevska
- Food Institute, Faculty of Veterinary Medicine-Skopje, Ss. Cyril and Methodius University in Skopje, Lazar Pop-Trajkov 5-7, 1000 Skopje, North Macedonia
| | - Armend Cana
- Microbiology Laboratory, University for Business and Technology-Higher Education Institution, Kalabria, 10000 Pristina, Kosovo
| | - Dean Jankuloski
- Food Institute, Faculty of Veterinary Medicine-Skopje, Ss. Cyril and Methodius University in Skopje, Lazar Pop-Trajkov 5-7, 1000 Skopje, North Macedonia
| | - Benjamin Félix
- Laboratory for Food Safety, Salmonella and Listeria Unit, ANSES, European Union Reference Laboratory for L. monocytogenes, University of Paris-Est, 94700 Maisons-Alfort, France
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12
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Rohilla A, Kumar V, Ahire JJ. Unveiling the persistent threat: recent insights into Listeria monocytogenes adaptation, biofilm formation, and pathogenicity in foodborne infections. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2024; 61:1428-1438. [PMID: 38966782 PMCID: PMC11219595 DOI: 10.1007/s13197-023-05918-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 11/28/2023] [Accepted: 12/13/2023] [Indexed: 07/06/2024]
Abstract
Listeriosis is a severe disease caused by the foodborne pathogen Listeria monocytogenes, posing a significant risk to vulnerable populations such as the elderly, pregnant women, and newborns. While relatively uncommon, it has a high global mortality rate of 20-30%. Recent research indicates that smaller outbreaks of the more severe, invasive form of the disease occur more frequently than previously thought, despite the overall stable infection rates of L. monocytogenes over the past 10 years. The ability of L. monocytogenes to form biofilm structures on various surfaces in food production environments contributes to its persistence and challenges in eradication, potentially leading to contamination of food and food production facilities. To address these concerns, this review focuses on recent developments in epidemiology, risk evaluations, and molecular mechanisms of L. monocytogenes survival in adverse conditions and environmental adaptation. Additionally, it covers new insights into strain variability, pathogenicity, mutations, and host vulnerability, emphasizing the important events framework that elucidates the biochemical pathways from ingestion to infection. Understanding the adaptation approaches of L. monocytogenes to environmental stress factors is crucial for the development of effective and affordable pathogen control techniques in the food industry, ensuring the safety of food production.
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Affiliation(s)
- Alka Rohilla
- Institute of Biology Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Vikram Kumar
- Department of Basic and Applied Sciences, National Institute of Food Technology Entrepreneurship and Management, Sonipat, 131028 India
| | - Jayesh J. Ahire
- Dr. Reddy’s Laboratories Limited, Ameerpet, Hyderabad, 500016 India
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13
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Rasoanandrasana S, Rabenandrasana MAN, Ravaoharisoa LM, Randrianaivo N, Rahajamanana VL, Rakotovao-Ravahatra ZD, Moura A, Lecuit M, Rakotovao AL. Clinical and genomic features of a Listeria monocytogenes fatal case of meningitis in Madagascar. Access Microbiol 2024; 6:000764.v3. [PMID: 39045257 PMCID: PMC11261731 DOI: 10.1099/acmi.0.000764.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 06/04/2024] [Indexed: 07/25/2024] Open
Abstract
Listeriosis constitutes a significant public health threat due to its high mortality rate. This study investigates the microbiological and genomic characteristics of Listeria monocytogenes isolates in Madagascar, where listeriosis is a notifiable disease. The analysis focuses on a fatal case of meningeal listeriosis in a 12-year-old child. Genomic analysis revealed a novel cgMLST type (L2-SL8-ST8-CT11697; CC8, serogroup Iia) with typical virulence and antibiotic resistance profiles. These isolates, unique to Madagascar, formed an independent clade in the phylogenetic tree. This study presents the first genomic characterization of Listeria isolates in Madagascar, highlighting the necessity of ongoing genomic surveillance to strengthen listeriosis prevention and control strategies in the region.
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Affiliation(s)
| | | | | | | | | | | | - Alexandra Moura
- Institut Pasteur, Biology of Infection Unit, Université Paris Cité, Inserm U1117, Paris, 75015, France
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre Listeria, Paris, France
| | - Marc Lecuit
- Institut Pasteur, Biology of Infection Unit, Université Paris Cité, Inserm U1117, Paris, 75015, France
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre Listeria, Paris, France
- Division of Infectious Diseases and Tropical Medicine, Institut Imagine, APHP, Necker-Enfants Malades University Hospital, Paris, France
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14
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Lagarde J, Feurer C, Denis M, Douarre PE, Piveteau P, Roussel S. Listeria monocytogenes prevalence and genomic diversity along the pig and pork production chain. Food Microbiol 2024; 119:104430. [PMID: 38225039 DOI: 10.1016/j.fm.2023.104430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 11/10/2023] [Accepted: 11/19/2023] [Indexed: 01/17/2024]
Abstract
The facultative intracellular bacterium Listeria monocytogenes (L. monocytogenes) is the causative agent of listeriosis, a severe invasive illness. This ubiquitous species is widely distributed in the environment, but infection occurs almost exclusively through ingestion of contaminated food. The pork production sector has been heavily affected by a series of L. monocytogenes-related foodborne outbreaks in the past around the world. Ready-to-eat (RTE) pork products represent one of the main food sources for strong-evidence listeriosis outbreaks. This pathogen is known to be present throughout the entire pig and pork production chain. Some studies hypothesized that the main source of contamination in final pork products was either living pigs or the food-processing environment. A detailed genomic picture of L. monocytogenes can provide a renewed understanding of the routes of contamination from pig farms to the final products. This review provides an overview of the prevalence, the genomic diversity and the genetic background linked to virulence of L. monocytogenes along the entire pig and pork production chain, from farm to fork.
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Affiliation(s)
- Jean Lagarde
- ANSES, Salmonella and Listeria Unit (USEL), University of Paris-Est, Maisons-Alfort Laboratory for Food Safety, 14 rue Pierre et Marie Curie, 94700, Maisons-Alfort, France; INRAE, Unit of Process Optimisation in Food, Agriculture and the Environment (UR OPAALE), 17 avenue de Cucillé, 35000, Rennes, France
| | - Carole Feurer
- IFIP, The French Pig and Pork Institute, Department of Fresh and Processed Meat, La Motte au Vicomte, 35650, Le Rheu, France
| | - Martine Denis
- ANSES, Unit of Hygiene and Quality of Poultry and Pork Products (UHQPAP), Ploufragan-Plouzané-Niort Laboratory, 31 rue des fusillés, 22440, Ploufragan, France
| | - Pierre-Emmanuel Douarre
- ANSES, Salmonella and Listeria Unit (USEL), University of Paris-Est, Maisons-Alfort Laboratory for Food Safety, 14 rue Pierre et Marie Curie, 94700, Maisons-Alfort, France
| | - Pascal Piveteau
- INRAE, Unit of Process Optimisation in Food, Agriculture and the Environment (UR OPAALE), 17 avenue de Cucillé, 35000, Rennes, France
| | - Sophie Roussel
- ANSES, Salmonella and Listeria Unit (USEL), University of Paris-Est, Maisons-Alfort Laboratory for Food Safety, 14 rue Pierre et Marie Curie, 94700, Maisons-Alfort, France.
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15
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Di Renzo L, De Angelis ME, Torresi M, Mariani G, Pizzurro F, Mincarelli LF, Esposito E, Oliviero M, Iaccarino D, Di Nocera F, Paduano G, Lucifora G, Cammà C, Ferri N, Pomilio F. Genomic Characterization of Listeria monocytogenes and Other Listeria Species Isolated from Sea Turtles. Microorganisms 2024; 12:817. [PMID: 38674761 PMCID: PMC11052188 DOI: 10.3390/microorganisms12040817] [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: 02/26/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Listeria monocytogenes is a ubiquitous pathogen found both in the environment and food. It can cause listeriosis in a wide range of animals as well as in humans. Investigations on presence, spread and virulence are still limited to terrestrial and human environments. Embracing the One Health Approach, investigating the presence and spread of L. monocytogenes in marine ecosystems and among wildlife, would provide us with useful information for human health. This study investigated the presence of L. monocytogenes and Listeria spp. in two species of sea turtles common in the Mediterranean Sea (Caretta caretta and Chelonia mydas). A total of one hundred and sixty-four carcasses of sea turtles (C. caretta n = 161 and C. mydas n = 3) stranded along the Abruzzo, Molise, Campania, and Calabria coasts, were collected. Brain and fecal samples were taken, enriched, and cultured for the detection of Listeria spp. From the specimens collected, strains of L. monocytogenes (brain n = 1, brain and feces n = 1, multiorgan n = 1 and feces n = 1), L. innocua (feces n = 1 and brain n = 1), and L. ivanovii (brain n = 1) were isolated. Typical colonies were isolated for Whole Genome Sequencing (WGS). Virulence genes, disinfectants/metal resistance, and antimicrobial resistance were also investigated. L. monocytogenes, L. innocua, and L. ivanovii were detected in C. caretta, whilst only L. monocytogenes and L. innocua in C. mydas. Notable among the results is the lack of significant differences in gene distribution between human and sea turtle strains. Furthermore, potentially pathogenic strains of L. monocytogenes were found in sea turtles.
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Affiliation(s)
- Ludovica Di Renzo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
- Centro Studi Cetacei, 65125 Pescara, Italy
| | - Maria Elisabetta De Angelis
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
- Faculty of Bioscience and Agro-Food and Environmental Technology, University of Teramo, 64100 Teramo, Italy
| | - Marina Torresi
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
| | - Giulia Mariani
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
- Faculty of Bioscience and Agro-Food and Environmental Technology, University of Teramo, 64100 Teramo, Italy
| | - Federica Pizzurro
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
| | - Luana Fiorella Mincarelli
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
| | - Emanuele Esposito
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy; (E.E.); (D.I.); (F.D.N.); (G.L.)
| | - Maria Oliviero
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy; (E.E.); (D.I.); (F.D.N.); (G.L.)
| | - Doriana Iaccarino
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy; (E.E.); (D.I.); (F.D.N.); (G.L.)
| | - Fabio Di Nocera
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy; (E.E.); (D.I.); (F.D.N.); (G.L.)
| | | | - Giuseppe Lucifora
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy; (E.E.); (D.I.); (F.D.N.); (G.L.)
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
| | - Nicola Ferri
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
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16
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Pracser N, Zaiser A, Ying HMK, Pietzka A, Wagner M, Rychli K. Diverse Listeria monocytogenes in-house clones are present in a dynamic frozen vegetable processing environment. Int J Food Microbiol 2024; 410:110479. [PMID: 37977080 DOI: 10.1016/j.ijfoodmicro.2023.110479] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023]
Abstract
Listeria (L.) monocytogenes is of global concern for food safety as the listeriosis-causing pathogen is widely distributed in the food processing environments, where it can survive for a long time. Frozen vegetables contaminated with L. monocytogenes were recently identified as the source of two large listeriosis outbreaks in the EU and US. So far, only a few studies have investigated the occurrence and behavior of Listeria in frozen vegetables and the associated processing environment. This study investigates the occurrence of L. monocytogenes and other Listeria spp. in a frozen vegetable processing environment and in frozen vegetable products. Using whole genome sequencing (WGS), the distribution of sequence types (MLST-STs) and core genome sequence types (cgMLST-CT) of L. monocytogenes were assessed, and in-house clones were identified. Comparative genomic analyses and phenotypical characterization of the different MLST-STs and isolates were performed, including growth ability under low temperatures, as well as survival of freeze-thaw cycles. Listeria were widely disseminated in the processing environment and five in-house clones namely ST451-CT4117, ST20-CT3737, ST8-CT1349, ST8-CT6243, ST224-CT5623 were identified among L. monocytogenes isolates present in environmental swab samples. Subsequently, the identified in-house clones were also detected in product samples. Conveyor belts were a major source of contamination in the processing environment. A wide repertoire of stress resistance markers supported the colonization and survival of L. monocytogenes in the frozen vegetable processing facility. The presence of ArgB was significantly associated with in-house clones. Significant differences were also observed in the growth rate between different MLST-STs at low temperatures (4 °C and 10 °C), but not between in-house and non-in-house isolates. All isolates harbored major virulence genes such as full length InlA and InlB and LIPI-1, yet there were differences between MLST-STs in the genomic content. The results of this study demonstrate that WGS is a strong tool for tracing contamination sources and transmission routes, and for identifying in-house clones. Further research targeting the co-occurring microbiota and the presence of biofilms is needed to fully understand the mechanism of colonization and persistence in a food processing environment.
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Affiliation(s)
- Nadja Pracser
- FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, 3430 Tulln, Austria.
| | - Andreas Zaiser
- Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Hui Min Katharina Ying
- Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Ariane Pietzka
- Austrian National Reference Laboratory for Listeria monocytogenes, Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Beethovenstrasse 6, 8010 Graz, Austria.
| | - Martin Wagner
- FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, 3430 Tulln, Austria; Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Kathrin Rychli
- Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
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17
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de Bernardi Schneider A, Su M, Hinrichs AS, Wang J, Amin H, Bell J, Wadford DA, O’Toole Á, Scher E, Perry MD, Turakhia Y, De Maio N, Hughes S, Corbett-Detig R. SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method. Virus Evol 2024; 10:vead085. [PMID: 38361813 PMCID: PMC10868549 DOI: 10.1093/ve/vead085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024] Open
Abstract
With the rapid spread and evolution of SARS-CoV-2, the ability to monitor its transmission and distinguish among viral lineages is critical for pandemic response efforts. The most commonly used software for the lineage assignment of newly isolated SARS-CoV-2 genomes is pangolin, which offers two methods of assignment, pangoLEARN and pUShER. PangoLEARN rapidly assigns lineages using a machine-learning algorithm, while pUShER performs a phylogenetic placement to identify the lineage corresponding to a newly sequenced genome. In a preliminary study, we observed that pangoLEARN (decision tree model), while substantially faster than pUShER, offered less consistency across different versions of pangolin v3. Here, we expand upon this analysis to include v3 and v4 of pangolin, which moved the default algorithm for lineage assignment from pangoLEARN in v3 to pUShER in v4, and perform a thorough analysis confirming that pUShER is not only more stable across versions but also more accurate. Our findings suggest that future lineage assignment algorithms for various pathogens should consider the value of phylogenetic placement.
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Affiliation(s)
- Adriano de Bernardi Schneider
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Michelle Su
- Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jade Wang
- Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA
| | - Helly Amin
- Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA
| | - John Bell
- California Department of Public Health (CDPH), VRDL/COVIDNet, Richmond, CA 94804, USA
| | - Debra A Wadford
- California Department of Public Health (CDPH), VRDL/COVIDNet, Richmond, CA 94804, USA
| | - Áine O’Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Emily Scher
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Marc D Perry
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA 92093, USA
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SD, UK
| | - Scott Hughes
- Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA
| | - Russ Corbett-Detig
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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18
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Andrews N, McCabe E, Wall P, Buckley JF, Fanning S. Validating the Utility of Multilocus Variable Number Tandem-repeat Analysis (MLVA) as a Subtyping Strategy to Monitor Listeria monocytogenes In-built Food Processing Environments. J Food Prot 2023; 86:100147. [PMID: 37619693 DOI: 10.1016/j.jfp.2023.100147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Listeria monocytogenes is a serious human pathogen and an enduring challenge to control for the ready-to-eat food processing industry. Cost-effective tools that can be deployed by commercial or in-house laboratories to rapidly investigate and resolve contamination events in the built food processing environment are of value to the food industry. Multilocus variable number tandem-repeat analysis (MLVA) is a molecular subtyping method, which along with other same-generation methods such as pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) is being superseded in disease tracking and outbreak investigations by whole-genome sequencing (WGS). In this paper, it is demonstrated that MLVA can continue to play a valuable role as a valid, fast, simple, and cost-effective method to identify and track Listeria monocytogenes subtypes in factory environments, with the method being highly congruent with MLST. Although MLVA does not have the discriminatory power of WGS to identify truly persistent clones, with careful interpretation of results alongside isolate metadata, it remains a powerful tool in situations and locations where WGS may not be readily available to food business operators.
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Affiliation(s)
- Nicholas Andrews
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Evonne McCabe
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Patrick Wall
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - James F Buckley
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland; Institute for Global Food Security, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT5 6AG, United Kingdom.
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19
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Charlier C, Noel C, Hafner L, Moura A, Mathiaud C, Pitsch A, Meziane C, Jolly-Sanchez L, de Pontfarcy A, Diamantis S, Bracq-Dieye H, Disson O, Thouvenot P, Valès G, Tessaud-Rita N, Tourdjman M, Leclercq A, Lecuit M. Fatal neonatal listeriosis following L. monocytogenes horizontal transmission highlights neonatal susceptibility to orally acquired listeriosis. Cell Rep Med 2023; 4:101094. [PMID: 37385252 PMCID: PMC10394164 DOI: 10.1016/j.xcrm.2023.101094] [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: 12/29/2022] [Revised: 04/18/2023] [Accepted: 06/02/2023] [Indexed: 07/01/2023]
Abstract
We report a case of fulminant fatal neonatal listeriosis due to horizontal transmission of Listeria monocytogenes (Lm) in a neonatal double room. Genomic analyses reveal a close genetic relationship between clinical isolates, supporting cross-contamination. Oral inoculation experiments in adult and neonatal mice show that neonates are susceptible to a low Lm inoculum and that this susceptibility results from the immaturity of the neonatal gut microbiota. Infected neonates should therefore be isolated for as long as they shed Lm in their feces to avoid horizontal transmission and its dire consequences.
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Affiliation(s)
- Caroline Charlier
- Institut Pasteur, Université Paris Cité, INSERM U1117, Biology of Infection Unit, 75015 Paris, France; Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France; Cochin University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, 75015 Paris, France.
| | - Coralie Noel
- Groupe Hospitalier Sud Ile-de-France, 77000 Melun, France
| | - Lukas Hafner
- Institut Pasteur, Université Paris Cité, INSERM U1117, Biology of Infection Unit, 75015 Paris, France
| | - Alexandra Moura
- Institut Pasteur, Université Paris Cité, INSERM U1117, Biology of Infection Unit, 75015 Paris, France; Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
| | | | - Aurélia Pitsch
- Groupe Hospitalier Sud Ile-de-France, 77000 Melun, France
| | - Chakib Meziane
- Groupe Hospitalier Sud Ile-de-France, 77000 Melun, France
| | | | | | | | - Hélène Bracq-Dieye
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
| | - Olivier Disson
- Institut Pasteur, Université Paris Cité, INSERM U1117, Biology of Infection Unit, 75015 Paris, France
| | - Pierre Thouvenot
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
| | - Guillaume Valès
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
| | - Nathalie Tessaud-Rita
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
| | | | - Alexandre Leclercq
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
| | - Marc Lecuit
- Institut Pasteur, Université Paris Cité, INSERM U1117, Biology of Infection Unit, 75015 Paris, France; Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France; Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, 75015 Paris, France.
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20
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Suominen K, Jaakola S, Salmenlinna S, Simola M, Wallgren S, Hakkinen M, Suokorpi A, Rimhanen-Finne R. Invasive listeriosis in Finland: surveillance and cluster investigations, 2011-2021. Epidemiol Infect 2023; 151:e118. [PMID: 37424309 PMCID: PMC10468812 DOI: 10.1017/s0950268823001073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/16/2023] [Accepted: 06/24/2023] [Indexed: 07/11/2023] Open
Abstract
Foodborne pathogen Listeria monocytogenes may cause serious, life-threatening disease in susceptible persons. We combined data from Finnish national listeriosis surveillance, patient interview responses, and laboratory data of patient samples and compared them to listeria findings from food and food production plants collected as part of outbreak investigations during 2011-2021. The incidence of invasive listeriosis in Finland (1.3/100000 in 2021) is higher than the EU average (0.5/100000 in 2021), and most cases are observed in the elderly with a predisposing condition. Many cases reported consuming high-risk foods as well as improper food storage. Since ongoing patient interviews and whole genome sequencing were introduced, several listeriosis outbreaks were detected and food sources identified. Recommendations about high-risk foods for listeriosis and proper food storage should be better communicated to susceptible people. In Finland, patient interviews and typing and comparing listeria isolates in foods and patient samples are crucial in solving outbreaks and determining measures to control invasive listeriosis.
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Affiliation(s)
- Kristiina Suominen
- Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Sari Jaakola
- Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Saara Salmenlinna
- Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | | | | | | | - Ruska Rimhanen-Finne
- Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
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21
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Pereira E, Conrad A, Tesfai A, Palacios A, Kandar R, Kearney A, Locas A, Jamieson F, Elliot E, Otto M, Kurdilla K, Tijerina M, Son I, Pettengill JB, Chen Y, Fox T, Lane C, Aguillon R, Huffman J, Sheau Fong Low M, Wise M, Edwards L, Bidol S, Blankenship HM, Rosen HE, Leclercq A, Lecuit M, Tourdjman M, Herber H, Singleton LS, Viazis S, Bazaco MC. Multinational Outbreak of Listeria monocytogenes Infections Linked to Enoki Mushrooms Imported from the Republic of Korea 2016-2020. J Food Prot 2023; 86:100101. [PMID: 37169291 PMCID: PMC10947956 DOI: 10.1016/j.jfp.2023.100101] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Keeping the global food supply safe necessitates international collaborations between countries. Health and regulatory agencies routinely communicate during foodborne illness outbreaks, allowing partners to share investigational evidence. A 2016-2020 outbreak of Listeria monocytogenes infections linked to imported enoki mushrooms required a multinational collaborative investigation among the United States, Canada, Australia, and France. Ultimately, this outbreak included 48 ill people, 36 in the United States and 12 in Canada, and was linked to enoki mushrooms sourced from one manufacturer located in the Republic of Korea. Epidemiologic, laboratory, and traceback evidence led to multiple regulatory actions, including extensive voluntary recalls by three firms in the United States and one firm in Canada. In the United States and Canada, the Korean manufacturer was placed on import alert while other international partners provided information about their respective investigations and advised the public not to eat the recalled enoki mushrooms. The breadth of the geographic distribution of this outbreak emphasizes the global reach of the food industry. This investigation provides a powerful example of the impact of national and international coordination of efforts to respond to foodborne illness outbreaks and protect consumers. It also demonstrates the importance of fast international data sharing and collaboration in identifying and stopping foodborne outbreaks in the global community. Additionally, it is a meaningful example of the importance of food sampling, testing, and integration of sequencing results into surveillance databases.
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Affiliation(s)
- Evelyn Pereira
- Food and Drug Administration, College Park, Maryland, USA.
| | - Amanda Conrad
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
| | - Adiam Tesfai
- Food and Drug Administration, College Park, Maryland, USA
| | | | - Rima Kandar
- Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Ashley Kearney
- Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Annie Locas
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Fred Jamieson
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Elisa Elliot
- Food and Drug Administration, College Park, Maryland, USA
| | - Mark Otto
- Food and Drug Administration, College Park, Maryland, USA; Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kerry Kurdilla
- Food and Drug Administration, College Park, Maryland, USA
| | - Mary Tijerina
- Food and Drug Administration, College Park, Maryland, USA
| | - Insook Son
- Food and Drug Administration, College Park, Maryland, USA
| | | | - Yi Chen
- Food and Drug Administration, College Park, Maryland, USA
| | - Teresa Fox
- Food and Drug Administration, College Park, Maryland, USA
| | - Chris Lane
- Food and Drug Administration, College Park, Maryland, USA
| | - Ryan Aguillon
- Food and Drug Administration, College Park, Maryland, USA
| | - Jasmine Huffman
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Matthew Wise
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lauren Edwards
- Michigan Department of Agriculture and Rural Development, USA
| | - Sally Bidol
- Michigan Department of Health and Human Services, USA
| | | | | | - Alexandre Leclercq
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, Paris-F, France; Institut Pasteur, National Reference Centre and WHO Collaborating Centre Listeria, Paris-F, France
| | - Marc Lecuit
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, Paris-F, France; Institut Pasteur, National Reference Centre and WHO Collaborating Centre Listeria, Paris-F, France; Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, Paris-F, France
| | | | - Hubert Herber
- Alert Unit, General Directorate for Competition Policy, Consumer Affairs and Fraud Control, French Ministry for the Economy and Finance, France
| | | | - Stelios Viazis
- Food and Drug Administration, College Park, Maryland, USA
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22
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Brauge T, Leleu G, Hanin A, Capitaine K, Felix B, Midelet G. Genetic population structure of Listeria monocytogenes strains isolated from salmon and trout sectors in France. Heliyon 2023; 9:e18154. [PMID: 37483814 PMCID: PMC10362350 DOI: 10.1016/j.heliyon.2023.e18154] [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] [Received: 04/21/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/25/2023] Open
Abstract
Smoked salmon and smoked trout are ready-to-eat and potentially contaminated with the pathogenic bacterium Listeria monocytogenes making them high risk for the consumer. This raises questions about the presence of hypervirulent or persistent strains in the salmon and trout industries. Knowledge of the genetic diversity of circulating strains in these sectors is essential to evaluate the risk associated with this pathogen and improve food safety. We analyzed the genetic structure of 698 strains of L. monocytogenes isolated from 2006 to 2017 in France, based on their serogroup, lineage and clonal complexes (CCs) determined by Multilocus sequence typing (MLST). Most of the CCs were identified by mapping the strains PFGE profiles and a novel high-throughput real-time PCR method for CC identification. We identified thirteen CCs and one sequence type (ST) with variable distribution in salmon and trout samples (food, environment). The three most prevalent CCs were CC121, CC26 and CC204. Strains from ST191 and CC54 were detected for the first time in these sectors, while less than 0.6% of the isolates belonged to the hyper-virulent CC1, CC6 and CC20. No CC was exclusively associated with the salmon sector. This project allowed us to assess the population diversity of CCs of L. monocytogenes in the salmon and trout industries.
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Affiliation(s)
- Thomas Brauge
- ANSES, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, 62200, Boulogne sur Mer, France
| | - Guylaine Leleu
- ANSES, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, 62200, Boulogne sur Mer, France
| | | | - Karine Capitaine
- ANSES, Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, 94700, Maisons-Alfort, France
| | - Benjamin Felix
- ANSES, Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, 94700, Maisons-Alfort, France
| | - Graziella Midelet
- ANSES, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, 62200, Boulogne sur Mer, France
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23
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Schiavano GF, Guidi F, Pomilio F, Brandi G, Salini R, Amagliani G, Centorotola G, Palma F, Felici M, Lorenzetti C, Blasi G. Listeria monocytogenes Strains Persisting in a Meat Processing Plant in Central Italy: Use of Whole Genome Sequencing and In Vitro Adhesion and Invasion Assays to Decipher Their Virulence Potential. Microorganisms 2023; 11:1659. [PMID: 37512831 PMCID: PMC10383671 DOI: 10.3390/microorganisms11071659] [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: 05/04/2023] [Revised: 06/12/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
In this study, we used both a WGS and an in vitro approach to study the virulence potential of nine Listeria monocytogenes (Lm) strains belonging to genetic clusters persisting in a meat processing plant in Central Italy. The studied clusters belonged to CC1-ST1, CC9-ST9, and CC218-ST2801. All the CC1 and CC218 strains presented the same accessory virulence genes (LIPI-3, gltA, gltB, and aut_IVb). CC1 and CC9 strains presented a gene profile similarity of 22.6% as well as CC9 and CC218 isolates. CC1 and CC218 showed a similarity of 45.2% of the same virulence profile. The hypervirulent strains of lineage I (CC1 and CC218) presented a greater ability to adhere and invade Caco-2 cells than hypovirulent ones (CC9). CC1 strains were significantly more adhesive and invasive compared with CC9 and CC218 strains, although these last CCs presented the same accessory virulence genes. No statistically significant difference was found comparing CC218 with CC9 strains. This study provided for the first time data on the in vitro adhesiveness and invasiveness of CC218-ST2801 and added more data on the virulence characteristics of CC1 and CC9. What we observed confirmed that the ability of Lm to adhere to and invade human cells in vitro is not always decipherable from its virulence gene profile.
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Affiliation(s)
- Giuditta Fiorella Schiavano
- Dipartimento di Studi Umanistici, Università degli Studi di Urbino "Carlo Bo", Via Bramante, 17, 61029 Urbino, Italy
| | - Fabrizia Guidi
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Laboratorio Nazionale di Riferimento per Listeria Monocytogenes, Via Campo Boario, 64100 Teramo, Italy
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Laboratorio Nazionale di Riferimento per Listeria Monocytogenes, Via Campo Boario, 64100 Teramo, Italy
| | - Giorgio Brandi
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino "Carlo Bo", Via Santa Chiara, 27, 61029 Urbino, Italy
| | - Romolo Salini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Centro Operativo Veterinario per l'Epidemiologia, Programmazione, Informazione e Analisi del Rischio (COVEPI), National Reference Center for Veterinary Epidemiology, Via Campo Boario, 64100 Teramo, Italy
| | - Giulia Amagliani
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino "Carlo Bo", Via Santa Chiara, 27, 61029 Urbino, Italy
| | - Gabriella Centorotola
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Laboratorio Nazionale di Riferimento per Listeria Monocytogenes, Via Campo Boario, 64100 Teramo, Italy
| | - Francesco Palma
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino "Carlo Bo", Via Santa Chiara, 27, 61029 Urbino, Italy
| | - Martina Felici
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino "Carlo Bo", Via Santa Chiara, 27, 61029 Urbino, Italy
| | - Cinzia Lorenzetti
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche "Togo Rosati", Via Gaetano Salvemini, 1, 06126 Perugia, Italy
| | - Giuliana Blasi
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche "Togo Rosati", Via Gaetano Salvemini, 1, 06126 Perugia, Italy
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24
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Halbedel S, Sperle I, Lachmann R, Kleta S, Fischer MA, Wamp S, Holzer A, Lüth S, Murr L, Freitag C, Espenhain L, Stephan R, Pietzka A, Schjørring S, Bloemberg G, Wenning M, Al Dahouk S, Wilking H, Flieger A. Large Multicountry Outbreak of Invasive Listeriosis by a Listeria monocytogenes ST394 Clone Linked to Smoked Rainbow Trout, 2020 to 2021. Microbiol Spectr 2023; 11:e0352022. [PMID: 37036341 PMCID: PMC10269727 DOI: 10.1128/spectrum.03520-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 03/17/2023] [Indexed: 04/11/2023] Open
Abstract
Whole-genome sequencing (WGS) has revolutionized surveillance of infectious diseases. Disease outbreaks can now be detected with high precision, and correct attribution of infection sources has been improved. Listeriosis, caused by the bacterium Listeria monocytogenes, is a foodborne disease with a high case fatality rate and a large proportion of outbreak-related cases. Timely recognition of listeriosis outbreaks and precise allocation of food sources are important to prevent further infections and to promote public health. We report the WGS-based identification of a large multinational listeriosis outbreak with 55 cases that affected Germany, Austria, Denmark, and Switzerland during 2020 and 2021. Clinical isolates formed a highly clonal cluster (called Ny9) based on core genome multilocus sequence typing (cgMLST). Routine and ad hoc investigations of food samples identified L. monocytogenes isolates from smoked rainbow trout filets from a Danish producer grouping with the Ny9 cluster. Patient interviews confirmed consumption of rainbow trout as the most likely infection source. The Ny9 cluster was caused by a MLST sequence type (ST) ST394 clone belonging to molecular serogroup IIa, forming a distinct clade within molecular serogroup IIa strains. Analysis of the Ny9 genome revealed clpY, dgcB, and recQ inactivating mutations, but phenotypic characterization of several virulence-associated traits of a representative Ny9 isolate showed that the outbreak strain had the same pathogenic potential as other serogroup IIa strains. Our report demonstrates that international food trade can cause multicountry outbreaks that necessitate cross-border outbreak collaboration. It also corroborates the relevance of ready-to-eat smoked fish products as causes for listeriosis. IMPORTANCE Listeriosis is a severe infectious disease in humans and characterized by an exceptionally high case fatality rate. The disease is transmitted through consumption of food contaminated by the bacterium Listeria monocytogenes. Outbreaks of listeriosis often occur but can be recognized and stopped through implementation of whole-genome sequencing-based pathogen surveillance systems. We here describe the detection and management of a large listeriosis outbreak in Germany and three neighboring countries. This outbreak was caused by rainbow trout filet, which was contaminated by a L. monocytogenes clone belonging to sequence type ST394. This work further expands our knowledge on the genetic diversity and transmission routes of an important foodborne pathogen.
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Affiliation(s)
- Sven Halbedel
- FG11–Division of Enteropathogenic bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
- Institute for Medical Microbiology and Hospital Hygiene, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Ida Sperle
- FG35–Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
- Postgraduate Training for Applied Epidemiology (PAE), Robert Koch Institute, Berlin, Germany
- ECDC Fellowship Program, Field Epidemiology path (EPIET), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Raskit Lachmann
- FG35–Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Sylvia Kleta
- National Reference Laboratory for Listeria monocytogenes, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Martin A. Fischer
- FG11–Division of Enteropathogenic bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Sabrina Wamp
- FG11–Division of Enteropathogenic bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Alexandra Holzer
- FG35–Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Stefanie Lüth
- National Reference Laboratory for Listeria monocytogenes, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Larissa Murr
- State Institute for Food, Food Hygiene and Cosmetics, Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Christin Freitag
- Institute for Food of Animal Origin, Rhineland–Palatinate State Investigation Office, Koblenz, Germany
| | - Laura Espenhain
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Ariane Pietzka
- Austrian Agency for Health and Food Safety, Graz, Austria
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Guido Bloemberg
- Swiss National Center for Enteropathogenic Bacteria and Listeria, Institute for Food Safety and Hygiene, University of Zurich, Switzerland
| | - Mareike Wenning
- State Institute for Food, Food Hygiene and Cosmetics, Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Sascha Al Dahouk
- National Reference Laboratory for Listeria monocytogenes, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Hendrik Wilking
- FG35–Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Antje Flieger
- FG11–Division of Enteropathogenic bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
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25
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Guidi F, Centorotola G, Chiaverini A, Iannetti L, Schirone M, Visciano P, Cornacchia A, Scattolini S, Pomilio F, D’Alterio N, Torresi M. The Slaughterhouse as Hotspot of CC1 and CC6 Listeria monocytogenes Strains with Hypervirulent Profiles in an Integrated Poultry Chain of Italy. Microorganisms 2023; 11:1543. [PMID: 37375045 PMCID: PMC10305255 DOI: 10.3390/microorganisms11061543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
In Europe, very few studies are available regarding the diversity of Listeria monocytogenes (L. monocytogenes) clonal complexes (CCs) and sequence types (ST) in poultry and on the related typing of isolates using whole genome sequencing (WGS). In this study, we used a WGS approach to type 122 L. monocytogenes strains isolated from chicken neck skin samples collected in two different slaughterhouses of an integrated Italian poultry company. The studied strains were classified into five CCs: CC1-ST1 (21.3%), CC6-ST6 (22.9%), CC9-ST9 (44.2%), CC121-ST121 (10.6%) and CC193-ST193 (0.8%). CC1 and CC6 strains presented a virulence gene profile composed of 60 virulence genes and including the Listeria Pathogenicity Island 3, aut_IVb, gltA and gltB. According to cgMLST and SNPs analysis, long-term persistent clusters belonging to CC1 and CC6 were found in one of the two slaughterhouses. The reasons mediating the persistence of these CCs (up to 20 months) remain to be elucidated, and may involve the presence and the expression of stress response and environmental adaptation genes including heavy metals resistance genes (cadAC, arsBC, CsoR-copA-copZ), multidrug efflux pumps (mrpABCEF, EmrB, mepA, bmrA, bmr3, norm), cold-shock tolerance (cspD) and biofilm-formation determinants (lmo0673, lmo2504, luxS, recO). These findings indicated a serious risk of poultry finished products contamination with hypervirulent L. monocytogenes clones and raised concern for the consumer health. In addition to the AMR genes norB, mprF, lin and fosX, ubiquitous in L. monocytogenes strains, we also identified parC for quinolones, msrA for macrolides and tetA for tetracyclines. Although the phenotypical expression of these AMR genes was not tested, none of them is known to confer resistance to the primary antibiotics used to treat listeriosis The obtained results increase the data on the L. monocytogenes clones circulating in Italy and in particular in the poultry chain.
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Affiliation(s)
- Fabrizia Guidi
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Gabriella Centorotola
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Alexandra Chiaverini
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Luigi Iannetti
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Maria Schirone
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini, 1, 64100 Teramo, Italy; (M.S.); (P.V.)
| | - Pierina Visciano
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini, 1, 64100 Teramo, Italy; (M.S.); (P.V.)
| | - Alessandra Cornacchia
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Silvia Scattolini
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Nicola D’Alterio
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
| | - Marina Torresi
- Istituto Zooprofilattico Sperimentale Dell’abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy; (F.G.); (A.C.); (L.I.); (A.C.); (S.S.); (N.D.); (M.T.)
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Abstract
Listeria monocytogenes is a Gram-positive facultative intracellular pathogen that can cause severe invasive infections upon ingestion with contaminated food. Clinically, listerial disease, or listeriosis, most often presents as bacteremia, meningitis or meningoencephalitis, and pregnancy-associated infections manifesting as miscarriage or neonatal sepsis. Invasive listeriosis is life-threatening and a main cause of foodborne illness leading to hospital admissions in Western countries. Sources of contamination can be identified through international surveillance systems for foodborne bacteria and strains' genetic data sharing. Large-scale whole genome studies have increased our knowledge on the diversity and evolution of L. monocytogenes, while recent pathophysiological investigations have improved our mechanistic understanding of listeriosis. In this article, we present an overview of human listeriosis with particular focus on relevant features of the causative bacterium, epidemiology, risk groups, pathogenesis, clinical manifestations, and treatment and prevention.
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Affiliation(s)
- Merel M Koopmans
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Matthijs C Brouwer
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - José A Vázquez-Boland
- Infection Medicine, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, United Kingdom
| | - Diederik van de Beek
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam, the Netherlands
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Duval A, Opatowski L, Brisse S. Defining genomic epidemiology thresholds for common-source bacterial outbreaks: a modelling study. THE LANCET MICROBE 2023; 4:e349-e357. [PMID: 37003286 PMCID: PMC10156608 DOI: 10.1016/s2666-5247(22)00380-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 10/12/2022] [Accepted: 12/09/2022] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Epidemiological surveillance relies on microbial strain typing, which defines genomic relatedness among isolates to identify case clusters and their potential sources. Although predefined thresholds are often applied, known outbreak-specific features such as pathogen mutation rate and duration of source contamination are rarely considered. We aimed to develop a hypothesis-based model that estimates genetic distance thresholds and mutation rates for point-source single-strain food or environmental outbreaks. METHODS In this modelling study, we developed a forward model to simulate bacterial evolution at a specific mutation rate (μ) over a defined outbreak duration (D). From the distribution of genetic distances expected under the given outbreak parameters and sample isolation dates, we estimated a distance threshold beyond which isolates should not be considered as part of the outbreak. We embedded the model into a Markov Chain Monte Carlo inference framework to estimate the most probable mutation rate or time since source contamination, which are both often imprecisely documented. A simulation study validated the model over realistic durations and mutation rates. We then identified and analysed 16 published datasets of bacterial source-related outbreaks; datasets were included if they were from an identified foodborne outbreak and if whole-genome sequence data and collection dates for the described isolates were available. FINDINGS Analysis of simulated data validated the accuracy of our framework in both discriminating between outbreak and non-outbreak cases and estimating the parameters D and μ from outbreak data. Precision of estimation was much higher for high values of D and μ. Sensitivity of outbreak cases was always very high, and specificity in detecting non-outbreak cases was poor for low mutation rates. For 14 of the 16 outbreaks, the classification of isolates as being outbreak-related or sporadic is consistent with the original dataset. Four of these outbreaks included outliers, which were correctly classified as being beyond the threshold of exclusion estimated by our model, except for one isolate of outbreak 4. For two outbreaks, both foodborne Listeria monocytogenes, conclusions from our model were discordant with published results: in one outbreak two isolates were classified as outliers by our model and in another outbreak our algorithm separated food samples into one cluster and human samples into another, whereas the isolates were initially grouped together based on epidemiological and genetic evidence. Re-estimated values of the duration of outbreak or mutation rate were largely consistent with a priori defined values. However, in several cases the estimated values were higher and improved the fit with the observed genetic distance distribution, suggesting that early outbreak cases are sometimes missed. INTERPRETATION We propose here an evolutionary approach to the single-strain conundrum by estimating the genetic threshold and proposing the most probable cluster of cases for a given outbreak, as determined by its particular epidemiological and microbiological properties. This forward model, applicable to foodborne or environmental-source single point case clusters or outbreaks, is useful for epidemiological surveillance and may inform control measures. FUNDING European Union Horizon 2020 Research and Innovation Programme.
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Affiliation(s)
- Audrey Duval
- Epidemiology and Modelling of Bacterial Escape to Antimicrobials Laboratory, Institut Pasteur, Université Paris Cité, Paris, France; Anti-infective Evasion and Pharmacoepidemiology Team, CESP, Université Paris-Saclay, UVSQ, INSERM U1018, Montigny-le-Bretonneux, France; Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Lulla Opatowski
- Epidemiology and Modelling of Bacterial Escape to Antimicrobials Laboratory, Institut Pasteur, Université Paris Cité, Paris, France; Anti-infective Evasion and Pharmacoepidemiology Team, CESP, Université Paris-Saclay, UVSQ, INSERM U1018, Montigny-le-Bretonneux, France
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.
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Adhikari P, Florien N, Gupta S, Kaushal A. Recent Advances in the Detection of Listeria monocytogenes. Infect Dis (Lond) 2023. [DOI: 10.5772/intechopen.109948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Listeria monocytogenes is the third-most severe pathogen causing a yearly outbreak of food poisoning in the world that proliferates widely in the environment. Infants, pregnant mothers, and immuno-compromised people are at high risk. Its ability to grow in both biotic and abiotic environments leads to epidemics that infect 5 out of 10 people annually. Because of the epithelial adhesion (by E-cadherin binding), it can suppress immune cells and thrive in the gastrointestinal tract till the brain through blood flow (E-cadherin). Microbial culture is still used as a gold standard, but takes a long time and often yields false positive results due to incompetence and temperature variations. Therefore, in order to treat it rather than using broad spectrum antibiotics, a standardized time-saving and highly specific technology for early detection is very important. It has been observed that the production of a particular antibody is delaying (so does the detection process) as a result of the inadequate understanding of the pathophysiology of the bacteria. This book chapter provides a brief summary of a pathogen as well as the scientific advances that led to its identification more easily.
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29
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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: 10] [Impact Index Per Article: 5.0] [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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30
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Coipan CE, Friesema IHM, van Hoek AHAM, van den Bosch T, van den Beld M, Kuiling S, Gras LM, Bergval I, Bosch T, Wullings B, van der Voort M, Franz E. New insights into the epidemiology of Listeria monocytogenes - A cross-sectoral retrospective genomic analysis in the Netherlands (2010-2020). Front Microbiol 2023; 14:1147137. [PMID: 37089559 PMCID: PMC10118018 DOI: 10.3389/fmicb.2023.1147137] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/13/2023] [Indexed: 04/25/2023] Open
Abstract
Introduction Listeriosis, caused by infection with Listeria monocytogenes (Lm), is a relatively rare but severe disease with one of the highest mortality rates among bacterial foodborne illnesses. A better understanding on the degree of Lm clustering, the temporal distribution of the clusters, and their association with the various food sources is expected to lead to improved source tracing and risk-based sampling. Methods We investigated the genomic epidemiology of Lm in the Netherlands between 2010 and 2020 by analyzing whole-genome-sequencing (WGS) data of isolates from listerioss patients and food sources from nationwide integrated surveillance and monitoring. WGS data of 756 patient and 770 food/environmental isolates was assessed using core-genome multi-locus sequence typing (cgMLST) with Hamming distance as measure for pairwise distances. Associations of genotype with the epidemiological variables such as patient's age and gender, and systematic use of specific drugs were tested by multinomial logistic regressions. Genetic differentiation of the Lm within and between food categories was calculated based on allele frequencies at the 1701 cgMLST loci in each food category. Results We confirmed previous results that some clonal complexes (CCs) are overrepresented among clinical isolates but could not identify any epidemiological risk factors. The main findings of this study include the observation of a very weak attribution of Lm types to food categories and a much better attribution to the producer level. In addition, we identified a high degree of temporal persistence of food, patient and mixed clusters, with more than half of the clusters spanning over more than 1 year and up to 10 years. Discussion Taken together this would indicate that identifying persistent contamination in food production settings, and producers that process a wide variety of raw food produce, could significantly contribute to lowering the Lm disease burden.
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Affiliation(s)
- Claudia E. Coipan
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- *Correspondence: Claudia E. Coipan,
| | - Ingrid H. M. Friesema
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Angela H. A. M. van Hoek
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | | | - Maaike van den Beld
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Sjoerd Kuiling
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Lapo Mughini Gras
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- Institute for Risk Assessment Sciences (IURAS), Utrecht University, Utrecht, Netherlands
| | - Indra Bergval
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Thijs Bosch
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Bart Wullings
- Wageningen Food Safety Research (WFSR), Wageningen, Netherlands
| | | | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
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Lachmann R, Halbedel S, Lüth S, Holzer A, Adler M, Pietzka A, Al Dahouk S, Stark K, Flieger A, Kleta S, Wilking H. Invasive listeriosis outbreaks and salmon products: a genomic, epidemiological study. Emerg Microbes Infect 2022; 11:1308-1315. [PMID: 35380514 PMCID: PMC9132468 DOI: 10.1080/22221751.2022.2063075] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Invasive listeriosis, caused by Listeria (L.) monocytogenes, is a severe foodborne infection, especially for immunocompromised individuals. The aim of our investigation was the identification and analysis of listeriosis outbreaks in Germany with smoked and graved salmon products as the most likely source of infection using whole-genome sequencing (WGS) and patient interviews. In a national surveillance programme, WGS was used for subtyping and core genome multi locus sequence typing (cgMLST) for cluster detection of L. monocytogenes isolates from listeriosis cases as well as food and environmental samples in Germany. Patient interviews were conducted to complement the molecular typing. We identified 22 independent listeriosis outbreaks occurring between 2010 and 2021 that were most likely associated with the consumption of smoked and graved salmon products. In Germany, 228 cases were identified, of 50 deaths (22%) reported 17 were confirmed to have died from listeriosis. Many of these 22 outbreaks were cross-border outbreaks with further cases in other countries. This report shows that smoked and graved salmon products contaminated with L. monocytogenes pose a serious risk for listeriosis infection in Germany. Interdisciplinary efforts including WGS and epidemiological investigations were essential to identifying the source of infection. Uncooked salmon products are high-risk foods frequently contaminated with L. monocytogenes. In order to minimize the risk of infection for consumers, food producers need to improve hygiene measures and reduce the entry of pathogens into food processing. Furthermore, susceptible individuals should be better informed of the risk of acquiring listeriosis from consuming smoked and graved salmon products.
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Affiliation(s)
- Raskit Lachmann
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Sven Halbedel
- FG11 Division of Enteropathogenic Bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Stefanie Lüth
- German Federal Institute for Risk Assessment, National Reference Laboratory for Listeria Monocytogenes, Berlin, Germany
| | - Alexandra Holzer
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Marlen Adler
- German Federal Institute for Risk Assessment, National Reference Laboratory for Listeria Monocytogenes, Berlin, Germany
| | - Ariane Pietzka
- Austrian Agency for Health and Food Safety, Graz, Austria
| | - Sascha Al Dahouk
- German Federal Institute for Risk Assessment, National Reference Laboratory for Listeria Monocytogenes, Berlin, Germany
| | - Klaus Stark
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Antje Flieger
- FG11 Division of Enteropathogenic Bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Sylvia Kleta
- German Federal Institute for Risk Assessment, National Reference Laboratory for Listeria Monocytogenes, Berlin, Germany
| | - Hendrik Wilking
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
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32
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Whole-Genome Sequencing-Based Characterization of
Listeria
Isolates from Produce Packinghouses and Fresh-Cut Facilities Suggests Both Persistence and Reintroduction of Fully Virulent L. monocytogenes. Appl Environ Microbiol 2022; 88:e0117722. [PMID: 36286532 PMCID: PMC9680643 DOI: 10.1128/aem.01177-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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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Osek J, Lachtara B, Wieczorek K. Listeria monocytogenes in foods-From culture identification to whole-genome characteristics. Food Sci Nutr 2022; 10:2825-2854. [PMID: 36171778 PMCID: PMC9469866 DOI: 10.1002/fsn3.2910] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/06/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen, which is able to persist in the food production environments. The presence of these bacteria in different niches makes them a potential threat for public health. In the present review, the current information on the classical and alternative methods used for isolation and identification of L. monocytogenes in food have been described. Although these techniques are usually simple, standardized, inexpensive, and are routinely used in many food testing laboratories, several alternative molecular-based approaches for the bacteria detection in food and food production environments have been developed. They are characterized by the high sample throughput, a short time of analysis, and cost-effectiveness. However, these methods are important for the routine testing toward the presence and number of L. monocytogenes, but are not suitable for characteristics and typing of the bacterial isolates, which are crucial in the study of listeriosis infections. For these purposes, novel approaches, with a high discriminatory power to genetically distinguish the strains during epidemiological studies, have been developed, e.g., whole-genome sequence-based techniques such as NGS which provide an opportunity to perform comparison between strains of the same species. In the present review, we have shown a short description of the principles of microbiological, alternative, and modern methods of detection of L. monocytogenes in foods and characterization of the isolates for epidemiological purposes. According to our knowledge, similar comprehensive papers on such subject have not been recently published, and we hope that the current review may be interesting for research communities.
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Affiliation(s)
- Jacek Osek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Beata Lachtara
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Kinga Wieczorek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
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Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs. Nat Microbiol 2022; 7:1221-1229. [PMID: 35918422 DOI: 10.1038/s41564-022-01182-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/22/2022] [Indexed: 12/31/2022]
Abstract
Controlling foodborne diseases requires robust outbreak detection and a comprehensive understanding of outbreak dynamics. Here, by integrating large-scale phylogenomic analysis of 3,642 isolates and epidemiological data, we performed 'data-driven' outbreak detection and described the long-term outbreak dynamics of the leading seafood-associated pathogen, Vibrio parahaemolyticus, in Shenzhen, China, over a 17-year period. Contradictory to the widely accepted notion that sporadic patients and independent point-source outbreaks dominated foodborne infections, we found that 71% of isolates from patients grouped into within-1-month clusters that differed by ≤6 single nucleotide polymorphisms, indicating putative outbreaks. Furthermore, we showed that despite the long time spans between clusters, 70% of them were genomically closely related and were inferred to arise from a small number of common sources, which provides evidence that hidden persistent reservoirs generated most of the outbreaks rather than independent point-sources. Phylogeographical analysis further revealed the geographical heterogeneity of outbreaks and identified a coastal district as the potential hotspot of outbreaks and as the hub and major source of cross-district spread events. Our findings provide a comprehensive picture of the long-term spatiotemporal dynamics of foodborne outbreaks and present a different perspective on the major source of foodborne infections, which will inform the design of future disease control strategies.
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Vallejo P, Cilla G, López-Olaizola M, Vicente D, Marimón JM. Epidemiology and Clinical Features of Listeriosis in Gipuzkoa, Spain, 2010-2020. Front Microbiol 2022; 13:894334. [PMID: 35755994 PMCID: PMC9218358 DOI: 10.3389/fmicb.2022.894334] [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: 03/11/2022] [Accepted: 04/29/2022] [Indexed: 12/28/2022] Open
Abstract
Background Listeriosis continues to be one of the most important notifiable foodborne diseases. Nonetheless, in Spain, there are few data on the molecular epidemiology of Listeria monocytogenes infections in recent years. Aim To describe clinical features and the molecular epidemiology of human listeriosis over an 11-year period (2010–2020) in Gipuzkoa, Northern Spain. Methods A total of 111 isolates, all but one from invasive disease, were studied. Serotyping (agglutination and multiplex polymerase chain reaction [PCR]) and multilocus sequence typing were performed for all isolates. Antibiotic susceptibility was assessed by the broth microdilution method. Results The average annual incidence of listeriosis in non-pregnancy-associated cases was 1.55 per 100,000 population, with a 1-month mortality rate of 22.2%. In pregnant women, the average incidence was 0.45 cases per 1,000 pregnancies. Twenty-four sequence types were identified, serotype 4b ST1 (24.3%) being the most frequent followed by 1/2b ST87 (18.9%), which caused two long outbreaks in 2013–2014. A significant association was observed between ST219 and meningitis (p < 0.001). All isolates were susceptible to ampicillin as well as other antibiotics used in listeriosis treatment. Conclusion Despite current control measures, listeriosis continues to be an important cause of mortality in the elderly, preterm birth, and miscarriages in pregnant women. Improvements in the control and diagnosis of listeriosis are needed to reduce the impact of this infection on vulnerable populations.
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Affiliation(s)
- Pedro Vallejo
- Microbiology Department, Osakidetza Basque Health Service, Donostialdea Integrated Health Organization, San Sebastián, Spain.,Department of Preventive Medicine, University of the Basque Country (UPV/EHU), San Sebastián, Spain
| | - Gustavo Cilla
- Microbiology Department, Infectious Diseases Area, Biodonostia Health Research Institute, Vaccine Preventable Diseases Group, Osakidetza Basque Health Service, Donostialdea Integrated Health Organization, San Sebastián, Spain
| | - Maddi López-Olaizola
- Microbiology Department, Osakidetza Basque Health Service, Donostialdea Integrated Health Organization, San Sebastián, Spain
| | - Diego Vicente
- Department of Preventive Medicine, University of the Basque Country (UPV/EHU), San Sebastián, Spain.,Microbiology Department, Infectious Diseases Area, Respiratory Infection and Antimicrobial Resistance Group, Biodonostia Health Research Institute, Osakidetza Basque Health Service, Donostialdea Integrated Health Organization, San Sebastián, Spain
| | - José María Marimón
- Department of Preventive Medicine, University of the Basque Country (UPV/EHU), San Sebastián, Spain.,Microbiology Department, Infectious Diseases Area, Respiratory Infection and Antimicrobial Resistance Group, Biodonostia Health Research Institute, Osakidetza Basque Health Service, Donostialdea Integrated Health Organization, San Sebastián, Spain
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Yan M, Zhou Y, Cao Y, Li Z, Lu X, Pang B, Wang S, Kan B. Salmonella enterica subsp. II serovar 4,5,12:a:- may cause gastroenteritis infections in humans. Gut Microbes 2022; 14:2089007. [PMID: 35734810 PMCID: PMC9235882 DOI: 10.1080/19490976.2022.2089007] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Some serovars of Salmonella are not or rare found to cause salmonellosis in human. In our clinic-based surveillance, three rare Salmonella 4,5,12:a:- strains were recovered from three patients with diarrhea. To explore their genetic and epidemiological characteristics and pathogenesis, we conducted whole-genome sequencing, in vitro invasion assays in mammalian cells, and in vivo virulence assays in an animal model. The three isolates had indistinguishable molecular patterns and similar genome sequences, and clustered together with an isolate from edible fish traded among countries. The isolates had biochemical reactions identical with those of Salmonella subspecies enterica but belonged to subspecies salamae according to genome phylogeny, revealing a new serovar, S. enterica subsp. II serovar 4,5,12:a:-. The strains contained multiple virulence genes, elicited temporary bacteremia and enteritidis and caused cell damage in the mouse liver and cecum. This study provides evidence that this new Salmonella salamae serovar can infect humans and cause clusters of cases, and whole-genome sequencing detection and surveillance of Salmonella can help to accurately define Salmonella classification and clonality, improve diagnosis, facilitate outbreak detection and aid in the source tracing of salmonellosis epidemics.
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Affiliation(s)
- Meiying Yan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Yongming Zhou
- Institute for Acute Communicable Disease Prevention and Control, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yang Cao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Zhenpeng Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Xin Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Bo Pang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Shukun Wang
- Institute for Acute Communicable Disease Prevention and Control, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Beijing, China,CONTACT Biao Kan Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, China
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Raufu IA, Moura A, Vales G, Ahmed OA, Aremu A, Thouvenot P, Tessaud-Rita N, Bracq-Dieye H, Krishnamurthy R, Leclercq A, Lecuit M. Listeria ilorinensis sp. nov., isolated from cow milk cheese in Nigeria. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During microbial assessment of cow milk cheese products in the city of Ilorin, Nigeria, a
Listeria
-like isolate was detected that could not be assigned to any known species. Whole-genome sequence analyses against all currently known 26
Listeria
species confirmed that this isolate constitutes a new taxon within the genus
Listeria
, with highest similarity to
Listeria costaricensis
(average nucleotide identity blast of 82.66%, in silico DNA–DNA hybridization of 28.3%). Phenotypically, it differs from
L. costaricensis
by the inability to ferment sucrose, l-fucose and starch. The absence of haemolysis and
Listeria
pathogenic islands suggest that this novel species is not pathogenic for humans and animals. The name Listeria ilorinensis sp. nov. is proposed, with the type strain CLIP 2019/01311T (=CIP 111875T=DSM 111566T).
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Affiliation(s)
- Ibrahim Adisa Raufu
- Department of Veterinary Microbiology, University of Ilorin, Ilorin, Nigeria
| | - Alexandra Moura
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, Paris, France
| | - Guillaume Vales
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, Paris, France
| | | | - Abdulfatai Aremu
- Department of Veterinary Pharmacology and Toxicology, University of Ilorin, Ilorin, Nigeria
| | - Pierre Thouvenot
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, Paris, France
| | - Nathalie Tessaud-Rita
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, Paris, France
| | - Hélène Bracq-Dieye
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, Paris, France
| | - Ramar Krishnamurthy
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Bardoli, Gujarat State, India
| | - Alexandre Leclercq
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, Paris, France
| | - Marc Lecuit
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
- Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, Necker-Enfants Malades University Hospital, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, Paris, France
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Russini V, Spaziante M, Varcasia BM, Diaconu EL, Paolillo P, Picone S, Brunetti G, Mattia D, De Carolis A, Vairo F, Bossù T, Bilei S, De Marchis ML. A Whole Genome Sequencing-Based Epidemiological Investigation of a Pregnancy-Related Invasive Listeriosis Case in Central Italy. Pathogens 2022; 11:667. [PMID: 35745521 PMCID: PMC9228178 DOI: 10.3390/pathogens11060667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
Listeriosis is currently the fifth most common foodborne disease in Europe. Most cases are sporadic; however, outbreaks have also been reported. Compared to other foodborne infections, listeriosis has a modest incidence but can cause life-threatening complications, especially in elderly or immunocompromised people and pregnant women. In the latter case, the pathology can be the cause of premature birth or spontaneous abortion, especially if the fetus is affected during the first months of gestation. The causative agent of listeriosis, Listeria monocytogenes, is characterized by the innate ability to survive in the environment and in food, even in adverse conditions and for long periods. Ready-to-eat food represents the category most at risk for contracting listeriosis. This study presents the result of an investigation carried out on a case of maternal-fetal transmission of listeriosis which occurred in 2020 in central Italy and which was linked, with a retrospective approach, to other cases residing in the same city of the pregnant woman. Thanks to the use of next-generation sequencing methodologies, it was possible to identify an outbreak of infection, linked to the consumption of ready-to-eat sliced products sold in a supermarket in the investigated city.
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Affiliation(s)
- Valeria Russini
- Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (V.R.); (B.M.V.); (T.B.); (S.B.)
| | - Martina Spaziante
- Regional Service Surveillance and Control for Infectious Diseases (SERESMI), National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (M.S.); (F.V.)
| | - Bianca Maria Varcasia
- Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (V.R.); (B.M.V.); (T.B.); (S.B.)
| | - Elena Lavinia Diaconu
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy;
| | - Piermichele Paolillo
- UO Neonatologia, Patologia Neonatale e Terapia Intensiva Neonatale (TIN), Policlinico Casilino General Hospital, 00169 Rome, Italy; (P.P.); (S.P.)
| | - Simonetta Picone
- UO Neonatologia, Patologia Neonatale e Terapia Intensiva Neonatale (TIN), Policlinico Casilino General Hospital, 00169 Rome, Italy; (P.P.); (S.P.)
| | - Grazia Brunetti
- Pathology-Microbiology Laboratory, Policlinico Casilino General Hospital, 00169 Rome, Italy;
| | - Daniela Mattia
- Dipartimento di Prevenzione, Servizio Veterinario Area B—Igiene Alimenti di Origine Animale (SIOA), ASL Roma 6, 00072 Rome, Italy;
| | - Angela De Carolis
- Dipartimento di Prevenzione, Servizio di Igiene degli Alimenti e della Nutrizione (SIAN), ASL Roma 6, 00044 Rome, Italy;
| | - Francesco Vairo
- Regional Service Surveillance and Control for Infectious Diseases (SERESMI), National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (M.S.); (F.V.)
| | - Teresa Bossù
- Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (V.R.); (B.M.V.); (T.B.); (S.B.)
| | - Stefano Bilei
- Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (V.R.); (B.M.V.); (T.B.); (S.B.)
| | - Maria Laura De Marchis
- Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (V.R.); (B.M.V.); (T.B.); (S.B.)
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Stevens EL, Carleton HA, Beal J, Tillman GE, Lindsey RL, Lauer AC, Pightling A, Jarvis KG, Ottesen A, Ramachandran P, Hintz L, Katz LS, Folster JP, Whichard JM, Trees E, Timme RE, McDERMOTT P, Wolpert B, Bazaco M, Zhao S, Lindley S, Bruce BB, Griffin PM, Brown E, Allard M, Tallent S, Irvin K, Hoffmann M, Wise M, Tauxe R, Gerner-Smidt P, Simmons M, Kissler B, Defibaugh-Chavez S, Klimke W, Agarwala R, Lindsay J, Cook K, Austerman SR, Goldman D, McGARRY S, Hale KR, Dessai U, Musser SM, Braden C. Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States. J Food Prot 2022; 85:755-772. [PMID: 35259246 DOI: 10.4315/jfp-21-437] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/22/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT This multiagency report developed by the Interagency Collaboration for Genomics for Food and Feed Safety provides an overview of the use of and transition to whole genome sequencing (WGS) technology for detection and characterization of pathogens transmitted commonly by food and for identification of their sources. We describe foodborne pathogen analysis, investigation, and harmonization efforts among the following federal agencies: National Institutes of Health; Department of Health and Human Services, Centers for Disease Control and Prevention (CDC) and U.S. Food and Drug Administration (FDA); and the U.S. Department of Agriculture, Food Safety and Inspection Service, Agricultural Research Service, and Animal and Plant Health Inspection Service. We describe single nucleotide polymorphism, core-genome, and whole genome multilocus sequence typing data analysis methods as used in the PulseNet (CDC) and GenomeTrakr (FDA) networks, underscoring the complementary nature of the results for linking genetically related foodborne pathogens during outbreak investigations while allowing flexibility to meet the specific needs of Interagency Collaboration partners. We highlight how we apply WGS to pathogen characterization (virulence and antimicrobial resistance profiles) and source attribution efforts and increase transparency by making the sequences and other data publicly available through the National Center for Biotechnology Information. We also highlight the impact of current trends in the use of culture-independent diagnostic tests for human diagnostic testing on analytical approaches related to food safety and what is next for the use of WGS in the area of food safety. HIGHLIGHTS
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Affiliation(s)
- Eric L Stevens
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Heather A Carleton
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jennifer Beal
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Glenn E Tillman
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Rebecca L Lindsey
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - A C Lauer
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Arthur Pightling
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Karen G Jarvis
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Andrea Ottesen
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Padmini Ramachandran
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Leslie Hintz
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Lee S Katz
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jason P Folster
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jean M Whichard
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Eija Trees
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Ruth E Timme
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Patrick McDERMOTT
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, Maryland 20708
| | - Beverly Wolpert
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Michael Bazaco
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Shaohua Zhao
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, Maryland 20708
| | - Sabina Lindley
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Beau B Bruce
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Patricia M Griffin
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Eric Brown
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Marc Allard
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Sandra Tallent
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Kari Irvin
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Maria Hoffmann
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Matt Wise
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Robert Tauxe
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Peter Gerner-Smidt
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Mustafa Simmons
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Bonnie Kissler
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | | | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Richa Agarwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - James Lindsay
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705
| | - Kimberly Cook
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705
| | - Suelee Robbe Austerman
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Ames, Iowa 50010, USA
| | - David Goldman
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Sherri McGARRY
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Kis Robertson Hale
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Uday Dessai
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Steven M Musser
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Chris Braden
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
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Palma F, Mangone I, Janowicz A, Moura A, Chiaverini A, Torresi M, Garofolo G, Criscuolo A, Brisse S, Di Pasquale A, Cammà C, Radomski N. In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes. BMC Genomics 2022; 23:235. [PMID: 35346021 PMCID: PMC8961897 DOI: 10.1186/s12864-022-08437-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/28/2022] [Indexed: 02/02/2023] Open
Abstract
Background Whole genome sequencing analyzed by core genome multi-locus sequence typing (cgMLST) is widely used in surveillance of the pathogenic bacteria Listeria monocytogenes. Given the heterogeneity of available bioinformatics tools to define cgMLST alleles, our aim was to identify parameters influencing the precision of cgMLST profiles. Methods We used three L. monocytogenes reference genomes from different phylogenetic lineages and assessed the impact of in vitro (i.e. tested genomes, successive platings, replicates of DNA extraction and sequencing) and in silico parameters (i.e. targeted depth of coverage, depth of coverage, breadth of coverage, assembly metrics, cgMLST workflows, cgMLST completeness) on cgMLST precision made of 1748 core loci. Six cgMLST workflows were tested, comprising assembly-based (BIGSdb, INNUENDO, GENPAT, SeqSphere and BioNumerics) and assembly-free (i.e. kmer-based MentaLiST) allele callers. Principal component analyses and generalized linear models were used to identify the most impactful parameters on cgMLST precision. Results The isolate’s genetic background, cgMLST workflows, cgMLST completeness, as well as depth and breadth of coverage were the parameters that impacted most on cgMLST precision (i.e. identical alleles against reference circular genomes). All workflows performed well at ≥40X of depth of coverage, with high loci detection (> 99.54% for all, except for BioNumerics with 97.78%) and showed consistent cluster definitions using the reference cut-off of ≤7 allele differences. Conclusions This highlights that bioinformatics workflows dedicated to cgMLST allele calling are largely robust when paired-end reads are of high quality and when the sequencing depth is ≥40X. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08437-4.
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Lachtara B, Wieczorek K, Osek J. Genetic Diversity and Relationships of Listeria monocytogenes Serogroup IIa Isolated in Poland. Microorganisms 2022; 10:532. [PMID: 35336111 PMCID: PMC8951407 DOI: 10.3390/microorganisms10030532] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 02/05/2023] Open
Abstract
In the present study, 100 L. monocytogenes isolates of serogroup IIa from food and food production environments in Poland were characterized towards the presence of virulence, resistance, and stress response genes using whole-genome sequencing (WGS). The strains were also molecularly typed and compared with multi-locus sequence typing (MLST) and core genome MLST analyses. The present isolates were grouped into 6 sublineages (SLs), with the most prevalent SL155 (33 isolates), SL121 (32 isolates), and SL8 (28 isolates) and classified into six clonal complexes, with the most prevalent CC155 (33 strains), CC121 (32 isolates), and CC8 (28 strains). Furthermore, the strains were grouped to eight sequence types, with the most prevalent ST155 (33 strains), ST121 (30 isolates), and ST8 (28; strains) followed by 60 cgMLST types (CTs). WGS data showed the presence of several virulence genes or putative molecular markers playing a role in pathogenesis of listeriosis and involved in survival of L. monocytogenes in adverse environmental conditions. Some of the present strains were molecularly closely related to L. monocytogenes previously isolated in Poland. The results of the study showed that food and food production environments may be a source of L. monocytogenes of serogroup IIa with pathogenic potential.
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Affiliation(s)
| | | | - Jacek Osek
- Department of Hygiene of Food of Animal Origin, National Veterinary Research Institute, 24-100 Pulawy, Poland; (B.L.); (K.W.)
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Parra-Flores J, Holý O, Bustamante F, Lepuschitz S, Pietzka A, Contreras-Fernández A, Castillo C, Ovalle C, Alarcón-Lavín MP, Cruz-Córdova A, Xicohtencatl-Cortes J, Mancilla-Rojano J, Troncoso M, Figueroa G, Ruppitsch W. Virulence and Antibiotic Resistance Genes in Listeria monocytogenes Strains Isolated From Ready-to-Eat Foods in Chile. Front Microbiol 2022; 12:796040. [PMID: 35299835 PMCID: PMC8921925 DOI: 10.3389/fmicb.2021.796040] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/13/2021] [Indexed: 01/30/2023] Open
Abstract
Listeria monocytogenes is causing listeriosis, a rare but severe foodborne infection. Listeriosis affects pregnant women, newborns, older adults, and immunocompromised individuals. Ready-to-eat (RTE) foods are the most common sources of transmission of the pathogen This study explored the virulence factors and antibiotic resistance in L. monocytogenes strains isolated from ready-to-eat (RTE) foods through in vitro and in silico testing by whole-genome sequencing (WGS). The overall positivity of L. monocytogenes in RTE food samples was 3.1% and 14 strains were isolated. L. monocytogenes ST8, ST2763, ST1, ST3, ST5, ST7, ST9, ST14, ST193, and ST451 sequence types were identified by average nucleotide identity, ribosomal multilocus sequence typing (rMLST), and core genome MLST. Seven isolates had serotype 1/2a, five 1/2b, one 4b, and one 1/2c. Three strains exhibited in vitro resistance to ampicillin and 100% of the strains carried the fosX, lin, norB, mprF, tetA, and tetC resistance genes. In addition, the arsBC, bcrBC, and clpL genes were detected, which conferred resistance to stress and disinfectants. All strains harbored hlyA, prfA, and inlA genes almost thirty-two the showed the bsh, clpCEP, hly, hpt, iap/cwhA, inlA, inlB, ipeA, lspA, mpl, plcA, pclB, oat, pdgA, and prfA genes. One isolate exhibited a type 11 premature stop codon (PMSC) in the inlA gene and another isolate a new mutation (deletion of A in position 819). The Inc18(rep25), Inc18(rep26), and N1011A plasmids and MGEs were found in nine isolates. Ten isolates showed CAS-Type II-B systems; in addition, Anti-CRISPR AcrIIA1 and AcrIIA3 phage-associated systems were detected in three genomes. These virulence and antibiotic resistance traits in the strains isolated in the RTE foods indicate a potential public health risk for consumers.
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Affiliation(s)
- Julio Parra-Flores
- Department of Nutrition and Public Health, Universidad del Bío-Bío, Chillán, Chile
| | - Ondrej Holý
- Science and Research Centre, Faculty of Health Sciences, Palacký University Olomouc, Olomouc, Czechia
| | - Fernanda Bustamante
- Environmental and Public Health Laboratory, Regional Secretariat of the Ministry of Health in Maule, Talca, Chile
| | - Sarah Lepuschitz
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Ariane Pietzka
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | | | - Claudia Castillo
- School of Nutrition and Dietetics, Universidad del Bío-Bío, Chillán, Chile
| | - Catalina Ovalle
- School of Nutrition and Dietetics, Universidad del Bío-Bío, Chillán, Chile
| | | | - Ariadnna Cruz-Córdova
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Juan Xicohtencatl-Cortes
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Jetsi Mancilla-Rojano
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
- Faculty of Medicine, Biological Sciences Graduate Program, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Miriam Troncoso
- Microbiology and Probiotics Laboratory, Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Guillermo Figueroa
- Microbiology and Probiotics Laboratory, Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
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Waddington C, Carey ME, Boinett CJ, Higginson E, Veeraraghavan B, Baker S. Exploiting genomics to mitigate the public health impact of antimicrobial resistance. Genome Med 2022; 14:15. [PMID: 35172877 PMCID: PMC8849018 DOI: 10.1186/s13073-022-01020-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/04/2022] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a major global public health threat, which has been largely driven by the excessive use of antimicrobials. Control measures are urgently needed to slow the trajectory of AMR but are hampered by an incomplete understanding of the interplay between pathogens, AMR encoding genes, and mobile genetic elements at a microbial level. These factors, combined with the human, animal, and environmental interactions that underlie AMR dissemination at a population level, make for a highly complex landscape. Whole-genome sequencing (WGS) and, more recently, metagenomic analyses have greatly enhanced our understanding of these processes, and these approaches are informing mitigation strategies for how we better understand and control AMR. This review explores how WGS techniques have advanced global, national, and local AMR surveillance, and how this improved understanding is being applied to inform solutions, such as novel diagnostic methods that allow antimicrobial use to be optimised and vaccination strategies for better controlling AMR. We highlight some future opportunities for AMR control informed by genomic sequencing, along with the remaining challenges that must be overcome to fully realise the potential of WGS approaches for international AMR control.
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Affiliation(s)
- Claire Waddington
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Megan E Carey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Ellen Higginson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Balaji Veeraraghavan
- Department of Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK. .,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.
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44
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Palacios-Gorba C, Moura A, Gomis J, Leclercq A, Gómez-Martín Á, Bracq-Dieye H, Mocé ML, Tessaud-Rita N, Jiménez-Trigos E, Vales G, García-Muñoz Á, Thouvenot P, García-Roselló E, Lecuit M, Quereda JJ. Ruminant-associated Listeria monocytogenes isolates belong preferentially to dairy-associated hypervirulent clones: a longitudinal study in 19 farms. Environ Microbiol 2021; 23:7617-7631. [PMID: 34863016 DOI: 10.1111/1462-2920.15860] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/24/2021] [Indexed: 01/18/2023]
Abstract
Studies have shown that ruminants constitute reservoirs of Listeria monocytogenes, but little is known about the epidemiology and genetic diversity of this pathogen within farms. Here we conducted a large-scale longitudinal study to monitor Listeria spp. in 19 dairy farms during three consecutive seasons (N = 3251 samples). L. innocua was the most prevalent species, followed by L. monocytogenes. Listeria monocytogenes was detected in 52.6% of farms and more frequently in cattle (4.1%) and sheep (4.5%) than in goat farms (0.2%). Lineage I accounted for 69% of L. monocytogenes isolates. Among animal samples, the most prevalent sublineages (SL) and clonal complexes (CC) were SL1/CC1, SL219/CC4, SL26/CC26 and SL87/CC87, whereas SL666/CC666 was most prevalent in environmental samples. Sixty-one different L. monocytogenes cgMLST types were found, 28% common to different animals and/or surfaces within the same farm and 21% previously reported elsewhere in the context of food and human surveillance. Listeria monocytogenes prevalence was not affected by farm hygiene but by season: higher prevalence was observed during winter in cattle, and during winter and spring in sheep farms. Cows in their second lactation had a higher probability of L. monocytogenes faecal shedding. This study highlights dairy farms as a reservoir for hypervirulent L. monocytogenes.
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Affiliation(s)
- Carla Palacios-Gorba
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Alexandra Moura
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, 75015, France
| | - Jesús Gomis
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Alexandre Leclercq
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, 75015, France
| | - Ángel Gómez-Martín
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Hélène Bracq-Dieye
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, 75015, France
| | - María L Mocé
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Nathalie Tessaud-Rita
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, 75015, France
| | - Estrella Jiménez-Trigos
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Guillaume Vales
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, 75015, France
| | - Ángel García-Muñoz
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Pierre Thouvenot
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, 75015, France
| | - Empar García-Roselló
- Departamento Medicina y Cirugía Animal, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Marc Lecuit
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, 75015, France.,Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, Institut Imagine, APHP, Paris, France
| | - Juan J Quereda
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
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45
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Moura A, Lefrancq N, Wirth T, Leclercq A, Borges V, Gilpin B, Dallman TJ, Frey J, Franz E, Nielsen EM, Thomas J, Pightling A, Howden BP, Tarr CL, Gerner-Smidt P, Cauchemez S, Salje H, Brisse S, Lecuit M, Listeria CC1 Study Group. Emergence and global spread of Listeria monocytogenes main clinical clonal complex. SCIENCE ADVANCES 2021; 7:eabj9805. [PMID: 34851675 PMCID: PMC8635441 DOI: 10.1126/sciadv.abj9805] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
The bacterial foodborne pathogen Listeria monocytogenes clonal complex 1 (Lm-CC1) is the most prevalent clonal group associated with human listeriosis and is strongly associated with cattle and dairy products. Here, we analyze 2021 isolates collected from 40 countries, covering Lm-CC1 first isolation to present days, to define its evolutionary history and population dynamics. We show that Lm-CC1 spread worldwide from North America following the Industrial Revolution through two waves of expansion, coinciding with the transatlantic livestock trade in the second half of the 19th century and the rapid growth of cattle farming and food industrialization in the 20th century. In sharp contrast to its global spread over the past century, transmission chains are now mostly local, with limited inter- and intra-country spread. This study provides an unprecedented insight into L. monocytogenes phylogeography and population dynamics and highlights the importance of genome analyses for a better control of pathogen transmission.
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Affiliation(s)
- Alexandra Moura
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
| | - Noémie Lefrancq
- Institut Pasteur, Université de Paris, Mathematical Modelling of Infectious Diseases Unit, CNRS UMR 2000, Paris, France
| | - Thierry Wirth
- Institut Systématique Evolution Biodiversité (ISYEB),Museum National d’Histoire Naturelle, CNRS, Sorbonne Université, Université des Antilles, EPHE, Paris, France
- PSL University, EPHE, Paris, France
| | - Alexandre Leclercq
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
| | - Vítor Borges
- Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Brent Gilpin
- Christchurch Science Centre, Institute of Environmental Science and Research Limited, Christchurch, New Zealand
| | | | - Joachim Frey
- Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | | | - Juno Thomas
- Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Arthur Pightling
- Biostatistics and Bioinformatics, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Infectious Diseases Department, Austin Health, Heidelberg, Victoria, Australia
| | - Cheryl L. Tarr
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Simon Cauchemez
- Institut Pasteur, Université de Paris, Mathematical Modelling of Infectious Diseases Unit, CNRS UMR 2000, Paris, France
| | - Henrik Salje
- Institut Pasteur, Université de Paris, Mathematical Modelling of Infectious Diseases Unit, CNRS UMR 2000, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Marc Lecuit
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, Paris, France
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46
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Liu YY, Chen CC. A machine learning-based typing scheme refinement for Listeria monocytogenes core genome multilocus sequence typing with high discriminatory power for common source outbreak tracking. PLoS One 2021; 16:e0260293. [PMID: 34797875 PMCID: PMC8604304 DOI: 10.1371/journal.pone.0260293] [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: 07/25/2021] [Accepted: 11/05/2021] [Indexed: 11/18/2022] Open
Abstract
Background As whole-genome sequencing for pathogen genomes becomes increasingly popular, the typing methods of gene-by-gene comparison, such as core genome multilocus sequence typing (cgMLST) and whole-genome multilocus sequence typing (wgMLST), are being routinely implemented in molecular epidemiology. However, some intrinsic problems remain. For example, genomic sequences with varying read depths, read lengths, and assemblers influence the genome assemblies, introducing error or missing alleles into the generated allelic profiles. These errors and missing alleles might create “specious discrepancy” among closely related isolates, thus making accurate epidemiological interpretation challenging. In addition, the rapid growth of the cgMLST allelic profile database can cause problems related to storage and maintenance as well as long query search times. Methods We attempted to resolve these issues by decreasing the scheme size to reduce the occurrence of error and missing alleles, alleviate the storage burden, and improve the query search time. The challenge in this approach is maintaining the typing resolution when using fewer loci. We achieved this by using a popular artificial intelligence technique, XGBoost, coupled with Shapley additive explanations for feature selection. Finally, 370 loci from the original 1701 cgMLST loci of Listeria monocytogenes were selected. Results Although the size of the final scheme (LmScheme_370) was approximately 80% lower than that of the original cgMLST scheme, its discriminatory power, tested for 35 outbreaks, was concordant with that of the original cgMLST scheme. Although we used L. monocytogenes as a demonstration in this study, the approach can be applied to other schemes and pathogens. Our findings might help elucidate gene-by-gene–based epidemiology.
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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
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung, Taiwan
- * E-mail:
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47
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Kubicová Z, Roussel S, Félix B, Cabanová L. Genomic Diversity of Listeria monocytogenes Isolates From Slovakia (2010 to 2020). Front Microbiol 2021; 12:729050. [PMID: 34795648 PMCID: PMC8593459 DOI: 10.3389/fmicb.2021.729050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022] Open
Abstract
Over the past 11 years, the Slovak National Reference Laboratory has collected a panel of 988 Listeria monocytogenes isolates in Slovakia, which were isolated from various food sectors (61%), food-processing environments (13.7%), animals with listeriosis symptoms (21.2%), and human cases (4.1%). We serotyped these isolates by agglutination method, which revealed the highest prevalence (61.1%) of serotype 1/2a and the lowest (4.7%) of serotype 1/2c, although these represented the majority of isolates from the meat sector. The distribution of CCs analyzed on 176 isolates demonstrated that CC11-ST451 (15.3%) was the most prevalent CC, particularly in food (14.8%) and animal isolates (17.5%). CC11-ST451, followed by CC7, CC14, and CC37, were the most prevalent CCs in the milk sector, and CC9 and CC8 in the meat sector. CC11-ST451 is probably widely distributed in Slovakia, mainly in the milk and dairy product sectors, posing a possible threat to public health. Potential persistence indication of CC9 was observed in one meat facility between 2014 and 2018, highlighting its general meat-related distribution and potential for persistence worldwide.
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Affiliation(s)
- Zuzana Kubicová
- State Veterinary and Food Institute (SVFI), Dolny Kubin, Slovakia
| | - Sophie Roussel
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Maisons-Alfort, France
| | - Benjamin Félix
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Maisons-Alfort, France
| | - Lenka Cabanová
- State Veterinary and Food Institute (SVFI), Dolny Kubin, Slovakia
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48
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Maćkiw E, Korsak D, Kowalska J, Felix B, Stasiak M, Kucharek K, Antoszewska A, Postupolski J. Genetic diversity of Listeria monocytogenes isolated from ready-to-eat food products in retail in Poland. Int J Food Microbiol 2021; 358:109397. [PMID: 34536853 DOI: 10.1016/j.ijfoodmicro.2021.109397] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/01/2021] [Accepted: 09/04/2021] [Indexed: 12/22/2022]
Abstract
The study describes the characterization of Listeria monocytogenes isolated from the general 2017-2019 national official control and monitoring sampling program. A total of 60,928 of ready-to-eat (RTE) food products were collected in retail in Poland, while the number of L. monocytogenes contaminated samples was 67 (0.1%). The majority of the strains belonged to molecular serotype IVb followed by IIa, frequently associated with human listeriosis. Furthermore, 61.2% of the isolates were resistant at least to one of the tested antimicrobials: penicillin, ampicillin, meropenem, erythromycin, sulfamethoxazole-trimethoprim, amoxicillin-clavulanic acid, ciprofloxacin, chloramphenicol, gentamicin, vancomycin, tetracycline and rifampicin. Virulence genes inlA, inlC, inlJ and lmo2672 were detected in all of the isolates. In our study the llsX gene (encoding LLS) exhibited 11.6% positivity. The 32 strains were grouped into 12 clonal complexes (CCs) which belong to the major clones that are in circulation in Europe. Among them, seven strains with the cgMLST close relatedness (CC2) were isolated from diverse food sectors, underlining a large circulation of this clone in Poland, most likely from multiple introduction sources. Additionally, two RTE strains CC6 and one CC37 were identified as closely related by cgMLST to two publicly available genomes of clinical strains isolated in Poland in 2012-2013. These results indicate the large strain circulation and point to RTE food products as a potential source of human listeriosis. The present study provided data to capture the contamination status of L. monocytogenes in foods at the retail level in Poland and assess the potential risk of this pathogen for human safety.
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Affiliation(s)
- Elżbieta Maćkiw
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland.
| | - Dorota Korsak
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Joanna Kowalska
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Benjamin Felix
- European Union Reference Laboratory for L. monocytogenes, ANSES, Laboratory for Food Safety, University of Paris-Est, 94700 Maisons-Alfort, France
| | - Monika Stasiak
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Katarzyna Kucharek
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Aleksandra Antoszewska
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Jacek Postupolski
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
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49
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Thomassen GMB, Krych L, Knøchel S, Mehli L. ON-rep-seq as a rapid and cost-effective alternative to whole-genome sequencing for species-level identification and strain-level discrimination of Listeria monocytogenes contamination in a salmon processing plant. Microbiologyopen 2021; 10:e1246. [PMID: 34964295 PMCID: PMC8591450 DOI: 10.1002/mbo3.1246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/19/2021] [Indexed: 12/28/2022] Open
Abstract
Identification, source tracking, and surveillance of food pathogens are crucial factors for the food-producing industry. Over the last decade, the techniques used for this have moved from conventional enrichment methods, through species-specific detection by PCR to sequencing-based methods, whole-genome sequencing (WGS) being the ultimate method. However, using WGS requires the right infrastructure, high computational power, and bioinformatics expertise. Therefore, there is a need for faster, more cost-effective, and more user-friendly methods. A newly developed method, ON-rep-seq, combines the classical rep-PCR method with nanopore sequencing, resulting in a highly discriminating set of sequences that can be used for species identification and also strain discrimination. This study is essentially a real industry case from a salmon processing plant. Twenty Listeria monocytogenes isolates were analyzed both by ON-rep-seq and WGS to identify and differentiate putative L. monocytogenes from a routine sampling of processing equipment and products, and finally, compare the strain-level discriminatory power of ON-rep-seq to different analyzing levels delivered from the WGS data. The analyses revealed that among the isolates tested there were three different strains. The isolates of the most frequently detected strain (n = 15) were all detected in the problematic area in the processing plant. The strain level discrimination done by ON-rep-seq was in full accordance with the interpretation of WGS data. Our findings also demonstrate that ON-rep-seq may serve as a primary screening method alternative to WGS for identification and strain-level differentiation for surveillance of potential pathogens in a food-producing environment.
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Affiliation(s)
| | - Lukasz Krych
- Department of Food ScienceUniversity of CopenhagenFrederiksbergDenmark
| | - Susanne Knøchel
- Department of Food ScienceUniversity of CopenhagenFrederiksbergDenmark
| | - Lisbeth Mehli
- Department of Biotechnology and Food ScienceNorwegian University of Science and Technology (NTNU)TrondheimNorway
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50
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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: 1.0] [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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