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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sévellec Y, Ascencio E, Douarre PE, Félix B, Gal L, Garmyn D, Guillier L, Piveteau P, Roussel S. Listeria monocytogenes: Investigation of Fitness in Soil Does Not Support the Relevance of Ecotypes. Front Microbiol 2022; 13:917588. [PMID: 35770178 PMCID: PMC9234652 DOI: 10.3389/fmicb.2022.917588] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
Listeria monocytogenes (Lm) is a ubiquitous bacterium that causes the serious foodborne illness listeriosis. Although soil is a primary reservoir and a central habitat for Lm, little information is available on the genetic features underlying the fitness of Lm strains in this complex habitat. The aim of this study was to identify (i) correlations between the strains fitness in soil, their origin and their phylogenetic position (ii) identify genetic markers allowing Lm to survive in the soil. To this end, we assembled a balanced panel of 216 Lm strains isolated from three major ecological compartments (outdoor environment, animal hosts, and food) and from 33 clonal complexes occurring worldwide. The ability of the 216 strains to survive in soil was tested phenotypically. Hierarchical clustering identified three phenotypic groups according to the survival rate (SR): phenotype 1 “poor survivors” (SR < 2%), phenotype 2 “moderate survivors” (2% < SR < 5%) and phenotype 3 “good survivors” (SR > 5%). Survival in soil depended neither on strains’ origin nor on their phylogenetic position. Genome-wide-association studies demonstrated that a greater number of genes specifically associated with a good survival in soil was found in lineage II strains (57 genes) than in lineage I strains (28 genes). Soil fitness was mainly associated with variations in genes (i) coding membrane proteins, transcription regulators, and stress resistance genes in both lineages (ii) coding proteins related to motility and (iii) of the category “phage-related genes.” The cumulative effect of these small genomic variations resulted in significant increase of soil fitness.
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Affiliation(s)
- Yann Sévellec
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Maisons-Alfort, France
| | - Eliette Ascencio
- Agroecologie, AgroSup Dijon, INRAE, Bourgogne Franche-Comté University, Dijon, France
| | - Pierre-Emmanuel Douarre
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health and 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 and Safety (ANSES), Maisons-Alfort, France
| | - Laurent Gal
- Agroecologie, AgroSup Dijon, INRAE, Bourgogne Franche-Comté University, Dijon, France
| | - Dominique Garmyn
- Agroecologie, AgroSup Dijon, INRAE, Bourgogne Franche-Comté University, Dijon, France
| | - Laurent Guillier
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), University of Paris-Est, Maisons-Alfort, France
| | | | - Sophie Roussel
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Maisons-Alfort, France
- *Correspondence: Sophie Roussel,
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Douarre PE, Sévellec Y, Le Grandois P, Soumet C, Bridier A, Roussel S. FepR as a Central Genetic Target in the Adaptation to Quaternary Ammonium Compounds and Cross-Resistance to Ciprofloxacin in Listeria monocytogenes. Front Microbiol 2022; 13:864576. [PMID: 35663878 PMCID: PMC9158494 DOI: 10.3389/fmicb.2022.864576] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/27/2022] [Indexed: 12/05/2022] Open
Abstract
The foodborne pathogen, Listeria monocytogenes, (Lm), frequently undergoes selection pressure associated with the extensive use of disinfectants, such as quaternary ammonium compounds, which are widely used in food processing plants. The repeated exposure to sub-inhibitory biocide concentrations can induce increased tolerance to these compounds, but can also trigger the development of antibiotic resistance, and both increase the risk of food contamination and persistence in food production environments. Although the acquisition of genes can explain biocide tolerance, the genetic mechanisms underlying the adaptive cross-resistance to antibiotics remain unclear. We previously showed that repeated exposure to benzalkonium chloride (BC) and didecyldimethyl ammonium chloride (DDAC) led to reduced susceptibility to ciprofloxacin in Lm strains from diverse sources. Here, we compared the genomes of 16 biocide-adapted and 10 parental strains to identify the molecular mechanisms of fluoroquinolone cross-resistance. A core genome SNP analysis identified various mutations in the transcriptional regulator fepR (lmo2088) for 94% of the adapted strains and mutations in other effectors at a lower frequency. FepR is a local repressor of the MATE fluoroquinolone efflux pump FepA. The impact of the mutations on the structure and function of the protein was assessed by performing in silico prediction and protein homology modeling. Our results show that 75% of the missense mutations observed in fepR are located in the HTH domain of the protein, within the DNA interaction site. These mutations are predicted to reduce the activity of the regulator, leading to the overexpression of the efflux pump responsible for the ciprofloxacin-enhanced resistance.
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Affiliation(s)
- Pierre-Emmanuel Douarre
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Maisons-Alfort, France
| | - Yann Sévellec
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Maisons-Alfort, France
| | - Patricia Le Grandois
- Antibiotics, Biocides, Residues and Resistance Unit, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Fougères, France
| | - Christophe Soumet
- Antibiotics, Biocides, Residues and Resistance Unit, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Fougères, France
| | - Arnaud Bridier
- Antibiotics, Biocides, Residues and Resistance Unit, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Fougères, France
| | - Sophie Roussel
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Maisons-Alfort, France
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Cadel-Six S, Cherchame E, Douarre PE, Tang Y, Felten A, Barbet P, Litrup E, Banerji S, Simon S, Pasquali F, Gourmelon M, Mensah N, Borowiak M, Mistou MY, Petrovska L. The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant Monophasic Salmonella Typhimurium Circulating in Europe. Front Microbiol 2021; 12:651124. [PMID: 34093465 PMCID: PMC8175864 DOI: 10.3389/fmicb.2021.651124] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/16/2021] [Indexed: 01/23/2023] Open
Abstract
The European epidemic monophasic variant of Salmonella enterica serovar Typhimurium (S. 1,4,[5],12:i:-) characterized by the multi locus sequence type ST34 and the antimicrobial resistance ASSuT profile has become one of the most common serovars in Europe (EU) and the United States (US). In this study, we reconstructed the time-scaled phylogeny and evolution of this Salmonella in Europe. The epidemic S. 1,4,[5],12:i:- ST34 emerged in the 1980s by an acquisition of the Salmonella Genomic Island (SGI)-4 at the 3' end of the phenylalanine phe tRNA locus conferring resistance to copper and arsenic toxicity. Subsequent integration of the Tn21 transposon into the fljAB locus gave resistance to mercury toxicity and several classes of antibiotics used in food-producing animals (ASSuT profile). The second step of the evolution occurred in the 1990s, with the integration of mTmV and mTmV-like prophages carrying the perC and/or sopE genes involved in the ability to reduce nitrates in intestinal contents and facilitate the disruption of the junctions of the host intestinal epithelial cells. Heavy metals are largely used as food supplements or pesticide for cultivation of seeds intended for animal feed so the expansion of the epidemic S. 1,4,[5],12:i:- ST34 was strongly related to the multiple-heavy metal resistance acquired by transposons, integrative and conjugative elements and facilitated by the escape until 2011 from the regulatory actions applied in the control of S. Typhimurium in Europe. The genomic plasticity of the epidemic S. 1,4,[5],12:i:- was demonstrated in our study by the analysis of the plasmidome. We were able to identify plasmids harboring genes mediating resistance to phenicols, colistin, and fluoroquinolone and also describe for the first time in six of the analyzed genomes the presence of two plasmids (pERR1744967-1 and pERR2174855-2) previously described only in strains of enterotoxigenic Escherichia coli and E. fergusonii.
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Affiliation(s)
- Sabrina Cadel-Six
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | - Emeline Cherchame
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | | | - Yue Tang
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Arnaud Felten
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | - Pauline Barbet
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | - Eva Litrup
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sangeeta Banerji
- Robert Koch-Institute, Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Sandra Simon
- Robert Koch-Institute, Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Federique Pasquali
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Michèle Gourmelon
- Ifremer, RBE, SGMM, Health, Environment and Microbiology Laboratory, Plouzané, France
| | - Nana Mensah
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Maria Borowiak
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Michel-Yves Mistou
- Université Paris-Saclay, INRAE, Centre International de Ressource Microbienne (CIRM) MaIAGE, Jouy-en-Josas, France
| | - Liljana Petrovska
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
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Douarre PE, Mallet L, Radomski N, Felten A, Mistou MY. Analysis of COMPASS, a New Comprehensive Plasmid Database Revealed Prevalence of Multireplicon and Extensive Diversity of IncF Plasmids. Front Microbiol 2020; 11:483. [PMID: 32265894 PMCID: PMC7105883 DOI: 10.3389/fmicb.2020.00483] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/05/2020] [Indexed: 12/20/2022] Open
Abstract
Plasmids are genetic elements that enable rapid adaptation and evolution by transferring genes conferring selective advantages to their hosts. Conjugative plasmids are predominantly responsible for the global dissemination of antimicrobial resistance, representing an important threat to global health. As the number of plasmid sequences grows exponentially, it becomes critical to depict the global diversity and decipher the distribution of circulating plasmids in the bacterial community. To this end, we created COMPASS, a novel and comprehensive database compiling 12,084 complete plasmids with associated metadata from 1571 distinct species isolated worldwide over more than 100 years. The curation of the database allowed us to identify identical plasmids across different bacteria revealing mainly intraspecies dissemination and rare cases of horizontal transmission. We outlined and analyzed all relevant features, plasmid properties, host range and characterized their replication and mobilization systems. After an exhaustive comparison of PlasmidFinder and MOB-typer, the MOB-typer-based analysis revealed that the current knowledge embedded in the current typing schemes fails to classify all the plasmid sequences collected in COMPASS. We were able to categorize 6828 and 5229 plasmids by replicon and MOB typing, respectively, mostly associated with Proteobacteria and Firmicutes. We then searched for the presence of multiple core genes involved in replication and propagation. Our results showed that 2403 plasmids carried multiple replicons that were distributed in 206 bacterial species. The co-integration of replicon types from different incompatibility (Inc) groups is an adaptive mechanism, which plays an important role in plasmid survival and dissemination by extending their host range. Our results highlight the crucial role of IncF alleles (present in 56% of all multireplicons) and revealed that IncH, IncR, and IncU replicons were also frequently carried in multireplicons. Here, we provided a comprehensive picture of the different IncF subtypes by identifying 20 different profiles in 849 IncF multireplicons, which were mostly associated with Enterobacteriaceae. These results could provide the basis for a novel IncF plasmid nomenclature based on different allelic profiles.
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Affiliation(s)
- Pierre-Emmanuel Douarre
- Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food Safety, Paris, France
| | - Ludovic Mallet
- Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food Safety, Paris, France
| | - Nicolas Radomski
- Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food Safety, Paris, France
| | - Arnaud Felten
- Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food Safety, Paris, France
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Lorenzo-Diaz F, Fernández-Lopez C, Douarre PE, Baez-Ortega A, Flores C, Glaser P, Espinosa M. Streptococcal group B integrative and mobilizable element IMESag-rpsI encodes a functional relaxase involved in its transfer. Open Biol 2017; 6:rsob.160084. [PMID: 27707895 PMCID: PMC5090054 DOI: 10.1098/rsob.160084] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022] Open
Abstract
Streptococcus agalactiae or Group B Streptococcus (GBS) are opportunistic bacteria that can cause lethal sepsis in children and immuno-compromised patients. Their genome is a reservoir of mobile genetic elements that can be horizontally transferred. Among them, integrative and conjugative elements (ICEs) and the smaller integrative and mobilizable elements (IMEs) primarily reside in the bacterial chromosome, yet have the ability to be transferred between cells by conjugation. ICEs and IMEs are therefore a source of genetic variability that participates in the spread of antibiotic resistance. Although IMEs seem to be the most prevalent class of elements transferable by conjugation, they are poorly known. Here, we have studied a GBS-IME, termed IMESag-rpsI, which is widely distributed in GBS despite not carrying any apparent virulence trait. Analyses of 240 whole genomes showed that IMESag-rpsI is present in approximately 47% of the genomes, has a roughly constant size (approx. 9 kb) and is always integrated at a single location, the 3′-end of the gene encoding the ribosomal protein S9 (rpsI). Based on their genetic variation, several IMESag-rpsI types were defined (A–J) and classified in clonal complexes (CCs). CC1 was the most populated by IMESag-rpsI (more than 95%), mostly of type-A (71%). One CC1 strain (S. agalactiae HRC) was deep-sequenced to understand the rationale underlying type-A IMESag-rpsI enrichment in GBS. Thirteen open reading frames were identified, one of them encoding a protein (MobSag) belonging to the broadly distributed family of relaxases MOBV1. Protein MobSag was purified and, by a newly developed method, shown to cleave DNA at a specific dinucleotide. The S. agalactiae HRC-IMESag-rpsI is able to excise from the chromosome, as shown by the presence of circular intermediates, and it harbours a fully functional mobilization module. Further, the mobSag gene encoded by this mobile element is able to promote plasmid transfer among pneumococcal strains, suggesting that MobSag facilitates the spread of IMESag-rpsI and that this spread would explain the presence of the same IMESag-rpsI type in GBS strains belonging to different CCs.
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Affiliation(s)
- Fabian Lorenzo-Diaz
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Av. Astrofísico Francisco Sánchez s/n, 38071 Santa Cruz de Tenerife, Spain Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | | | - Pierre-Emmanuel Douarre
- Institut Pasteur, Unité Ecologie et Evolution de la Résistance aux Antibiotiques, Paris CNRS UMR3525, France
| | - Adrian Baez-Ortega
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Carlos Flores
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Philippe Glaser
- Institut Pasteur, Unité Ecologie et Evolution de la Résistance aux Antibiotiques, Paris CNRS UMR3525, France
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Douarre PE, Sauvage E, Poyart C, Glaser P. Host specificity in the diversity and transfer of lsa resistance genes in group B Streptococcus. J Antimicrob Chemother 2015; 70:3205-13. [PMID: 26410170 DOI: 10.1093/jac/dkv277] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 08/12/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES In group B Streptococcus (GBS), cross-resistance to lincosamides, streptogramin A and pleuromutilins (LSAP) is mediated by the acquisition of lsa genes. Here, we characterized the diversity, mobility and ecology of lsa genes in this species. METHODS lsa variants were systematically identified by BLAST searches in the genomes of 531 GBS strains from different hosts and geographical origins. The associated phenotypes were determined by a microdilution MIC method. Acquisition of resistance genes was deduced from comparative genomics and phylogeny. Their mobility was tested by conjugation experiments. RESULTS lsa(E) and three variants of lsa(C) were identified in GBS strains. Two lsa(C) variants had not been previously reported. All four variants conferred LSAP phenotypes. lsa(E) was located in a multiresistance gene cluster of a single human strain. This gene was transferred by a high-frequency recombination-type mechanism between GBS strains. Two lsa(C) variants are carried in six unrelated human strains by two similar elements specifically integrated in the oriT site of four different classes of integrative and conjugative elements (ICEs). Strikingly, the acquisition of the resistance gene always occurred by the integration of the element into a resident ICE. The third lsa(C) variant was located at the same site in the core genome of 11 genetically distant bovine strains and was likely propagated by horizontal transfer of the corresponding chromosomal region. CONCLUSIONS lsa genes in GBS show distinct host specificities and modes of transfer. In general, their dissemination is mediated by recombination rather than by the transfer of conjugative elements.
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Affiliation(s)
- Pierre-Emmanuel Douarre
- Unité de Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur, 28 Rue du Dr Roux, 75724, Paris, France CNRS, UMR3525, Paris, France
| | - Elisabeth Sauvage
- Unité de Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur, 28 Rue du Dr Roux, 75724, Paris, France CNRS, UMR3525, Paris, France
| | - Claire Poyart
- Unité de Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur, 28 Rue du Dr Roux, 75724, Paris, France Centre National de Référence des Streptocoques, Groupe Hospitalier Paris Centre Cochin-Hôtel Dieu-Broca, Paris, France Institut Cochin, Université Sorbonne Paris Descartes, Paris, France INSERM, U1016, Paris, France
| | - Philippe Glaser
- Unité de Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur, 28 Rue du Dr Roux, 75724, Paris, France CNRS, UMR3525, Paris, France
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8
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Da Cunha V, Davies MR, Douarre PE, Rosinski-Chupin I, Margarit I, Spinali S, Perkins T, Lechat P, Dmytruk N, Sauvage E, Ma L, Romi B, Tichit M, Lopez-Sanchez MJ, Descorps-Declere S, Souche E, Buchrieser C, Trieu-Cuot P, Moszer I, Clermont D, Maione D, Bouchier C, McMillan DJ, Parkhill J, Telford JL, Dougan G, Walker MJ, Holden MTG, Poyart C, Glaser P. Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline. Nat Commun 2014; 5:4544. [PMID: 25088811 PMCID: PMC4538795 DOI: 10.1038/ncomms5544] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 06/27/2014] [Indexed: 11/17/2022] Open
Abstract
Streptococcus agalactiae (Group B Streptococcus, GBS) is a commensal of the digestive and genitourinary tracts of humans that emerged as the leading cause of bacterial neonatal infections in Europe and North America during the 1960s. Due to the lack of epidemiological and genomic data, the reasons for this emergence are unknown. Here we show by comparative genome analysis and phylogenetic reconstruction of 229 isolates that the rise of human GBS infections corresponds to the selection and worldwide dissemination of only a few clones. The parallel expansion of the clones is preceded by the insertion of integrative and conjugative elements conferring tetracycline resistance (TcR). Thus, we propose that the use of tetracycline from 1948 onwards led in humans to the complete replacement of a diverse GBS population by only few TcR clones particularly well adapted to their host, causing the observed emergence of GBS diseases in neonates.
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Affiliation(s)
- Violette Da Cunha
- Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.,CNRS UMR3525, Paris 75015, France.,Institut Pasteur, Bioinformatics platform, Paris 75015, France
| | - Mark R Davies
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 15A, UK.,Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Pierre-Emmanuel Douarre
- Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.,CNRS UMR3525, Paris 75015, France
| | - Isabelle Rosinski-Chupin
- Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.,CNRS UMR3525, Paris 75015, France
| | | | - Sebastien Spinali
- Centre National de Référence des Streptocoques, Hôpitaux Universitaires, Paris Centre Cochin-Hôtel Dieu-Broca, Paris 75014, France
| | - Tim Perkins
- Novartis Vaccines and Diagnostics, Siena 53100, Italy
| | - Pierre Lechat
- Institut Pasteur, Bioinformatics platform, Paris 75015, France
| | - Nicolas Dmytruk
- Centre National de Référence des Streptocoques, Hôpitaux Universitaires, Paris Centre Cochin-Hôtel Dieu-Broca, Paris 75014, France
| | - Elisabeth Sauvage
- Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.,CNRS UMR3525, Paris 75015, France
| | - Laurence Ma
- Institut Pasteur Genomic platform, Paris 75015, France
| | | | - Magali Tichit
- Institut Pasteur Genomic platform, Paris 75015, France
| | - Maria-José Lopez-Sanchez
- Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.,CNRS UMR3525, Paris 75015, France
| | | | - Erika Souche
- Institut Pasteur, Bioinformatics platform, Paris 75015, France
| | - Carmen Buchrieser
- CNRS UMR3525, Paris 75015, France.,Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris 75015, France
| | - Patrick Trieu-Cuot
- Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.,CNRS ERL3526, Paris 75015, France
| | - Ivan Moszer
- Institut Pasteur, Bioinformatics platform, Paris 75015, France
| | - Dominique Clermont
- Institut Pasteur, Collection de l'Institut Pasteur (CIP), Paris 75015, France
| | | | | | - David J McMillan
- QIMR Berghofer Medical Research Institute, Brisbane, 7006 Queensland, Australia.,Inflammation and Healing Research Cluster, University of the Sunshine Coast, Sippy Downs, 4556 Queensland, Australia
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 15A, UK
| | | | - Gordan Dougan
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 15A, UK
| | - Mark J Walker
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland, Australia
| | | | | | - Claire Poyart
- Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.,Centre National de Référence des Streptocoques, Hôpitaux Universitaires, Paris Centre Cochin-Hôtel Dieu-Broca, Paris 75014, France.,Institut Cochin, Université Sorbonne Paris Descartes, Paris 75014, France.,INSERM, U1016, Paris 75014, France
| | - Philippe Glaser
- Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.,CNRS UMR3525, Paris 75015, France.,Institut Pasteur, Bioinformatics platform, Paris 75015, France
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Jones S, Douarre PE, O'Leary J, Corcoran D, O'Mahony J, Lucey B. Validation of a norovirus multiplex real-time RT-PCR assay for the detection of norovirus GI and GII from faeces samples. Br J Biomed Sci 2011; 68:116-9. [PMID: 21950202 DOI: 10.1080/09674845.2011.11730337] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Norovirus is a leading cause of infectious non-bacterial gastroenteritis. The virus is highly contagious and has multiple modes of transmission, presenting a growing challenge to hospital-based healthcare. In this study, a total of 120 stool samples are tested for the presence of norovirus GI and GII by the Roche two-step Lightcycler 2.0 assay incorporating primers and probes produced by TIB Molbiol, and the results are compared with results from the National Virus Reference Laboratory. The Roche/TIB Molbiol assay produced 51 positive results and 69 negative results. Discrepancy analysis was performed for six conflicting results using a second real-time polymerase chain reaction (PCR) assay (Roche/TIB Molbiol) and this confirmed that four of the five discrepant positive results were true positives. A single discrepant negative result generated by the Roche assay remained negative using the second assay. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated to be 98%, 98.6%, 98.0% and 98.6%, respectively. Melting curve analysis was used to differentiate genogroups I and II and this showed that 92% of strains belonged to genogroup II.
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Affiliation(s)
- S Jones
- Department of Medical Microbiology, Cork University Hospital, Ireland
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