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Abdel-Glil MY, Fischer U, Steinhagen D, McCarthy U, Neubauer H, Sprague LD. Phylogenetic Relatedness and Genome Structure of Yersinia ruckeri Revealed by Whole Genome Sequencing and a Comparative Analysis. Front Microbiol 2021; 12:782415. [PMID: 34867924 PMCID: PMC8640586 DOI: 10.3389/fmicb.2021.782415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 09/24/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM), a serious infection that affects global aquaculture with high economic impact. The present study used whole genome sequences to perform a comparative analysis on 10 Y. ruckeri strains and to explore their genetic relatedness to other members of the genus. Y. ruckeri, Yersinia entomophaga, and Yersinia nurmii formed a species complex that constitutes the most basal lineage of the genus. The results showed that the taxonomy of Y. ruckeri strains is better defined by using a core genome alignment and phylogenetic analysis. The distribution of accessory genes in all Yersinia species revealed the presence of 303 distinctive genes in Y. ruckeri. Of these, 169 genes were distributed in 17 genomic islands potentially involved in the pathogenesis of ERM via (1) encoding virulence factors such as Afp18, Yrp1, phage proteins and (2) improving the metabolic capabilities by enhancing utilization and metabolism of iron, amino acids (specifically, arginine and histidine), and carbohydrates. The genome of Y. ruckeri is highly conserved regarding gene structure, gene layout and functional categorization of genes. It contains various components of mobile genetic elements but lacks the CRISPR-Cas system and possesses a stable set of virulence genes possibly playing a critical role in pathogenicity. Distinct virulence plasmids were exclusively restricted to a specific clonal group of Y. ruckeri (CG4), possibly indicating a selective advantage. Phylogenetic analysis of Y. ruckeri genomes revealed the co-presence of multiple genetically distant lineages of Y. ruckeri strains circulating in Germany. Our results also suggest a possible dissemination of a specific group of strains in the United States, Peru, Germany, and Denmark. In conclusion, this study provides new insights into the taxonomy and evolution of Y. ruckeri and contributes to a better understanding of the pathogenicity of ERM in aquaculture. The genomic analysis presented here offers a framework for the development of more efficient control strategies for this pathogen.
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Affiliation(s)
- Mostafa Y Abdel-Glil
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Jena, Germany
| | - Uwe Fischer
- Friedrich-Loeffler-Institut, Institute of Infectiology, Greifswald-Insel Riems, Germany
| | - Dieter Steinhagen
- Fish Disease Research Unit, Institute for Parasitology, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Una McCarthy
- Marine Laboratory, Marine Scotland, Aberdeen, United Kingdom
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Jena, Germany
| | - Lisa D Sprague
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Jena, Germany
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Mourão J, Rebelo A, Ribeiro S, Peixe L, Novais C, Antunes P. Atypical Non-H 2S-Producing Monophasic Salmonella Typhimurium ST3478 Strains from Chicken Meat at Processing Stage Are Adapted to Diverse Stresses. Pathogens 2020; 9:pathogens9090701. [PMID: 32859122 PMCID: PMC7557518 DOI: 10.3390/pathogens9090701] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 07/27/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 01/23/2023] Open
Abstract
Poultry products are still an important cause of Salmonella infections worldwide, with an increasingly reported expansion of less-frequent serotypes or atypical strains that are frequently multidrug-resistant. Nevertheless, the ability of Salmonella to survive antimicrobials promoted in the context of antibiotic reducing/replacing and farming rethinking (e.g., organic acids and copper in feed/biocides) has been scarcely explored. We investigated Salmonella occurrence (conventional and molecular assays) among chicken meat at the processing stage (n = 53 batches/29 farms) and characterized their tolerance to diverse stress factors (antibiotics, copper, acid pH, and peracetic acid). Whole-genome sequencing was used to assess adaptive features and to perform comparative analysis. We found a low Salmonella occurrence (4%) and identified S. Enteritidis/ST11 plus atypical non-H2S-producing S. 1,4,[5],12:i:-/ST3478. The ST3478 presented the ability to grow under diverse stresses (antibiotics, copper, and acid-pH). Comparative genomics among ST3478 isolates showed similar antibiotic/metal resistance gene repertoires and identical nonsense phsA thiosulfate reductase mutations (related to H2S-negative phenotype), besides their close phylogenetic relationship by cgMLST and SNPs. This study alerts for the ongoing national and international spread of an emerging monophasic Salmonella Typhimurium clonal lineage with an enlarged ability to survive to antimicrobials/biocides commonly used in poultry production, being unnoticed by conventional Salmonella detection approaches due to an atypical non-H2S-producing phenotype.
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Affiliation(s)
- Joana Mourão
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Andreia Rebelo
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
- Scientific Area of Environmental Health, School of Health, Polytechnic Institute of Porto, 4200-465 Porto, Portugal
| | - Sofia Ribeiro
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
- ESCMID Food- and Water-borne Infections Study Group (EFWISG), 4010 Basel, Switzerland
| | - Carla Novais
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
- ESCMID Food- and Water-borne Infections Study Group (EFWISG), 4010 Basel, Switzerland
| | - Patrícia Antunes
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
- ESCMID Food- and Water-borne Infections Study Group (EFWISG), 4010 Basel, Switzerland
- Faculty of Nutrition and Food Sciences, University of Porto, 4150-180 Porto, Portugal
- Correspondence: ; Tel.: +351-507-4320
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