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Ojiakor A, Gibbs RN, Chen Z, Gao X, Fowler CC. The evolutionary diversification of the Salmonella artAB toxin locus. Front Microbiol 2022; 13:1016438. [PMID: 36504768 PMCID: PMC9732031 DOI: 10.3389/fmicb.2022.1016438] [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: 08/10/2022] [Accepted: 10/07/2022] [Indexed: 11/27/2022] Open
Abstract
Salmonella enterica is a diverse species of bacterial pathogens comprised of >2,500 serovars with variable host ranges and virulence properties. Accumulating evidence indicates that two AB5-type toxins, typhoid toxin and ArtAB toxin, contribute to the more severe virulence properties of the Salmonella strains that encode them. It was recently discovered that there are two distinct types of artAB-like genetic elements in Salmonella: those that encode ArtAB toxins (artAB elements) and those in which the artA gene is degraded and the ArtB homolog, dubbed PltC, serves as an alternative delivery subunit for typhoid toxin (pltC elements). Here, we take a multifaceted approach to explore the evolutionary diversification of artAB-like genetic elements in Salmonella. We identify 7 subtypes of ArtAB toxins and 4 different PltC sequence groups that are distributed throughout the Salmonella genus. Both artAB and pltC are encoded within numerous diverse prophages, indicating a central role for phages in their evolutionary diversification. Genetic and structural analyses revealed features that distinguish pltC elements from artAB and identified evolutionary adaptations that enable PltC to efficiently engage typhoid toxin A subunits. For both pltC and artAB, we find that the sequences of the B subunits are especially variable, particularly amongst amino acid residues that fine tune the chemical environment of their glycan binding pockets. This study provides a framework to delineate the remarkably complex collection of Salmonella artAB/pltC-like genetic elements and provides a window into the mechanisms of evolution for AB5-type toxins.
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Affiliation(s)
- Adaobi Ojiakor
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Rachel N. Gibbs
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Zhe Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China,School of Life Sciences, Shandong University, Qingdao, China
| | - Casey C. Fowler
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada,*Correspondence: Casey C. Fowler,
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2
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Eiamsam-ang T, Tadee P, Pascoe B, Patchanee P. Genome-based analysis of infrequent Salmonella serotypes through the Thai pork production chain. Front Microbiol 2022; 13:968695. [PMID: 36090074 PMCID: PMC9453559 DOI: 10.3389/fmicb.2022.968695] [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: 06/14/2022] [Accepted: 08/05/2022] [Indexed: 12/05/2022] Open
Abstract
Salmonella is a prevalent zoonotic foodborne pathogen. Swine and pork are implicated as important sources of salmonellosis in humans. In Chiang Mai and Lamphun Provinces in northern Thailand, there has been a high prevalence of Salmonella persistence for over a decade. Infection is usually with dominant S. enterica serotypes, including serotypes Rissen and 1,4,[5],12:i:-. However, other serotypes also contribute to disease but are less well characterized. The whole genome sequencing data of 43 S. enterica serotypes isolated from pork production chain through 2011-2014, were used to evaluate genetic diversity and ascertain the possible source of Salmonella contamination based on Core Genome Multilocus Sequence Typing (cgMLST) approach. The Salmonella serotypes recovered from farms and slaughterhouses were re-circulating by swine environmental contamination. Conversely, the Salmonella contamination in the retail market represents cross-contamination from multiple sources, including contaminated foodstuffs. Salmonella contamination in the pork production chain has the competency for host cell adhesion, host cell invasion, and intracellular survival, which is enough for the pathogenicity of salmonellosis. In addition, all of these isolates were multi-drug resistant Salmonella, which contained at least 10 antimicrobial resistance genes. This result indicated that these S. enterica serotypes also pose a significant public health risk. Our findings support the need for appropriate surveillance of food-animal products going to market to reduce public exposure to highly pathogenic, multi-drug resistant Salmonella. Acquiring information would motivate all stakeholders to reinforce sanitation standards throughout the pork production chain in order to eradicate Salmonella contamination and reduce the risk of salmonellosis in humans.
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Affiliation(s)
- Thanaporn Eiamsam-ang
- Graduate Program in Veterinary Science, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pakpoom Tadee
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Ben Pascoe
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
- The Milner Center for Evolution, University of Bath, Bath, United Kingdom
| | - Prapas Patchanee
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
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3
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Parada J, Galas M, Faccone D, Tamiozzo P, Carranza A. Antibiotic resistance and associated resistance determinants in different Salmonella enterica serovars isolated from pigs in Argentina. Vet World 2022; 15:1215-1220. [PMID: 35765497 PMCID: PMC9210835 DOI: 10.14202/vetworld.2022.1215-1220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/16/2022] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Salmonellosis is one of the most common foodborne diseases in the world, and the increasing antibiotic resistance in Salmonella enterica subsp. enterica recovered from food animals constitutes an important risk from a One Health approach. This study aimed to characterize antibiotic resistance and some of its associated resistance determinants in different S. enterica serovars isolated from pigs in Argentina. Materials and Methods: A retrospective study was conducted on Salmonella strains isolated between 2011 and 2015 from pigs in the Pampean region of Argentina. The antimicrobial susceptibility patterns to 21 antimicrobials and some antibiotic resistance determinants were characterized in 55 Salmonella isolates, representing 58 farms. Results: We identified 56% (n=30) of the strains as multidrug-resistant, where resistance to tetracycline (62%, n=34), ampicillin (53%, n=29), nalidixic acid (53%, n=29), chloramphenicol (33%, n=18), and trimethoprim-sulfamethoxazole (31%, n=17) was most common. The wide range of resistance to ampicillin correlates with the presence of TEM type β-lactamases in the strains. However, high susceptibility was found in the new generation of β-lactams. Fluoroquinolone resistance is a major concern. Most strains with decreased susceptibility to ciprofloxacin showed gyrA mutations and plasmid-mediated quinolone resistance gene qnrB. Conclusion: Here, we identified broad resistance to some antibiotics frequently used in human therapeutics and several easily transferable resistance mechanisms that could endanger public health.
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Affiliation(s)
- Julián Parada
- Department of Animal Pathology, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Marcelo Galas
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. C. Malbran," Buenos Aires, Argentina; Antimicrobial Resistance Special Program, Communicable Diseases and Environmental Determinants of Health, Pan American Health Organization, Washington, DC, United States of America
| | - Diego Faccone
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. C. Malbran," Buenos Aires, Argentina
| | - Pablo Tamiozzo
- Department of Animal Pathology, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Alicia Carranza
- Department of Animal Pathology, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
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Pulford CV, Perez-Sepulveda BM, Canals R, Bevington JA, Bengtsson RJ, Wenner N, Rodwell EV, Kumwenda B, Zhu X, Bennett RJ, Stenhouse GE, Malaka De Silva P, Webster HJ, Bengoechea JA, Dumigan A, Tran-Dien A, Prakash R, Banda HC, Alufandika L, Mautanga MP, Bowers-Barnard A, Beliavskaia AY, Predeus AV, Rowe WPM, Darby AC, Hall N, Weill FX, Gordon MA, Feasey NA, Baker KS, Hinton JCD. Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. Nat Microbiol 2021; 6:327-338. [PMID: 33349664 PMCID: PMC8018540 DOI: 10.1038/s41564-020-00836-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/20/2020] [Indexed: 02/07/2023]
Abstract
Bloodstream infections caused by nontyphoidal Salmonella are a major public health concern in Africa, causing ~49,600 deaths every year. The most common Salmonella enterica pathovariant associated with invasive nontyphoidal Salmonella disease is Salmonella Typhimurium sequence type (ST)313. It has been proposed that antimicrobial resistance and genome degradation has contributed to the success of ST313 lineages in Africa, but the evolutionary trajectory of such changes was unclear. Here, to define the evolutionary dynamics of ST313, we sub-sampled from two comprehensive collections of Salmonella isolates from African patients with bloodstream infections, spanning 1966 to 2018. The resulting 680 genome sequences led to the discovery of a pan-susceptible ST313 lineage (ST313 L3), which emerged in Malawi in 2016 and is closely related to ST313 variants that cause gastrointestinal disease in the United Kingdom and Brazil. Genomic analysis revealed degradation events in important virulence genes in ST313 L3, which had not occurred in other ST313 lineages. Despite arising only recently in the clinic, ST313 L3 is a phylogenetic intermediate between ST313 L1 and L2, with a characteristic accessory genome. Our in-depth genotypic and phenotypic characterization identifies the crucial loss-of-function genetic events that occurred during the stepwise evolution of invasive S. Typhimurium across Africa.
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Affiliation(s)
- Caisey V Pulford
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Blanca M Perez-Sepulveda
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Rocío Canals
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jessica A Bevington
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Rebecca J Bengtsson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Nicolas Wenner
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Ella V Rodwell
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | | | - Xiaojun Zhu
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Rebecca J Bennett
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - George E Stenhouse
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - P Malaka De Silva
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Hermione J Webster
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jose A Bengoechea
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Amy Dumigan
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Alicia Tran-Dien
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France
| | - Reenesh Prakash
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Happy C Banda
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Lovemore Alufandika
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Mike P Mautanga
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Arthur Bowers-Barnard
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Alexandra Y Beliavskaia
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Alexander V Predeus
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Will P M Rowe
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Alistair C Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Melita A Gordon
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Nicholas A Feasey
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Kate S Baker
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jay C D Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
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5
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Xu X, Chen Y, Pan H, Pang Z, Li F, Peng X, Ed-dra A, Li Y, Yue M. Genomic characterization of Salmonella Uzaramo for human invasive infection. Microb Genom 2020; 6:mgen000401. [PMID: 32589568 PMCID: PMC7478631 DOI: 10.1099/mgen.0.000401] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/05/2020] [Indexed: 12/11/2022] Open
Abstract
Salmonella is composed of a wide variety of serovars, causing human self-limited gastrointestinal illnesses or invasive infections. Invasive non-typhoidal Salmonella (iNTS) is well documented, with high mortality for children and immunocompromised adults in sub-Saharan Africa and has recently been reported in Southeast Asia. However, iNTS in China remains unknown. In May 2019, a case of invasive infection caused by Salmonella enterica serovar Uzaramo (S. Uzaramo) was reported for the first time in China. Phylogenomic analysis was performed by genomic sequencing the available contextualized isolates, which separated the two Chinese strains into different sublineages. Both phenotypic and genomic characterization demonstrated that the S. Uzaramo isolates showed in general low antimicrobial resistance potential, except one isolated from lake-water in China. Additional comparative genomic analysis and Caenorhabditis elegans killing assays suggested a unique combination of virulence factors, including typhoid toxin and tcf fimbrial adhesin, which might play a role in the invasive infection. This study highlights that the transparency of global surveillance genomic data could accelerate understanding of virulence and antimicrobial resistance makeup of a previously unknown threat.
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Affiliation(s)
- Xuebin Xu
- Department of Microbiology Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, PR China
| | - Yan Chen
- Panzhihua Center for Disease Control and Prevention, Panzhihua 617000, PR China
| | - Hang Pan
- Institute of Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, PR China
| | - Zaiyuan Pang
- Panzhihua Municipal Central Hospital, Panzhihua 617000, PR China
| | - Fang Li
- Institute of Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, PR China
| | - Xianqi Peng
- Institute of Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, PR China
| | - Abdelaziz Ed-dra
- Institute of Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, PR China
| | - Yan Li
- Institute of Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, PR China
- Zhejiang Provincial Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, PR China
| | - Min Yue
- Institute of Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, PR China
- Zhejiang Provincial Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, PR China
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6
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Busch A, Hotzel H, Methner U. Complete genome and plasmid sequences of a multidrug-resistant Salmonella enterica subsp. enterica serovar Panama isolate from a German cattle farm. J Genomics 2020; 8:71-75. [PMID: 32817763 PMCID: PMC7425046 DOI: 10.7150/jgen.48656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 06/16/2020] [Indexed: 12/28/2022] Open
Abstract
We describe a rare isolate of Salmonella enterica subsp. enterica serovar Panama with an extended-spectrum β-lactamase (ESBL) profile from a German cattle-fattening farm. Applying two next-generation sequencing methods we generated sequences of the genome as well as the plasmids; assembled the draft genome sequence of Salmonella enterica subsp. enterica serovar Panama isolate 18PM0209. Antimicrobial resistance genes, virulence-associated genes and plasmids were analyzed using bioinformatics. Occurrence of multidrug-resistant Salmonella serovars at cattle-fattening farms indicate the need of enhanced surveillance to prevent further spread of these organisms.
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Affiliation(s)
- Anne Busch
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany.,University Hospital Jena, Department of Anaesthesiology and Intensive Care Medicine, Am Klinikum 1, 07747 Jena, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany
| | - Ulrich Methner
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany
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