1
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Schadron T, van den Beld M, Mughini-Gras L, Franz E. Use of whole genome sequencing for surveillance and control of foodborne diseases: status quo and quo vadis. Front Microbiol 2024; 15:1460335. [PMID: 39345263 PMCID: PMC11427404 DOI: 10.3389/fmicb.2024.1460335] [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: 07/05/2024] [Accepted: 08/27/2024] [Indexed: 10/01/2024] Open
Abstract
Improvements in sequencing quality, availability, speed and costs results in an increased presence of genomics in infectious disease applications. Nevertheless, there are still hurdles in regard to the optimal use of WGS for public health purposes. Here, we discuss the current state ("status quo") and future directions ("quo vadis") based on literature regarding the use of genomics in surveillance, hazard characterization and source attribution of foodborne pathogens. The future directions include the application of new techniques, such as machine learning and network approaches that may overcome the current shortcomings. These include the use of fixed genomic distances in cluster delineation, disentangling similarity or lack thereof in source attribution, and difficulties ascertaining function in hazard characterization. Although, the aforementioned methods can relatively easily be applied technically, an overarching challenge is the inference and biological/epidemiological interpretation of these large amounts of high-resolution data. Understanding the context in terms of bacterial isolate and host diversity allows to assess the level of representativeness in regard to sources and isolates in the dataset, which in turn defines the level of certainty associated with defining clusters, sources and risks. This also marks the importance of metadata (clinical, epidemiological, and biological) when using genomics for public health purposes.
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Affiliation(s)
- Tristan Schadron
- 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
| | - Lapo Mughini-Gras
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
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2
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Rizzo NN, Núncio ASP, Levandowski R, Nascimento CAD, Borges KA, Furian TQ, Ruschel Dos Santos L, Pilotto F, Rodrigues LB, Nascimento VP. Whole genome analysis of Salmonella Gallinarum strains isolated from a fowl typhoid outbreak in southern Brazil. Br Poult Sci 2024:1-6. [PMID: 39257343 DOI: 10.1080/00071668.2024.2394973] [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: 04/23/2024] [Accepted: 07/11/2024] [Indexed: 09/12/2024]
Abstract
1. Salmonella Gallinarum strains isolated from a southern Brazil fowl typhoid outbreak were subjected to phenotypic and genotypic analyses to identify genetic elements that could improve prevention and control strategies.2. Whole-genome sequencing revealed the presence of the aac(6')-Iaa gene, conferring aminoglycoside resistance, along with novel chromosomal point mutations, including the first detection of parE p.S451F in Salmonella Gallinarum.3. Additionally, IncFII(S) plasmid replicons, Salmonella pathogenicity islands and 105 virulence genes associated with cell adhesion, invasion and antimicrobial peptide resistance were identified.4. These findings shed light on the molecular mechanisms of fowl typhoid and provide crucial insights into emerging antimicrobial resistance and virulence factors.
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Affiliation(s)
- N N Rizzo
- Graduate Program in Veterinary Science, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - A S P Núncio
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - R Levandowski
- School of Agricultural Sciences, Innovation and Business, University of Passo Fundo, Passo Fundo, Brazil
| | - C A D Nascimento
- School of Agricultural Sciences, Innovation and Business, University of Passo Fundo, Passo Fundo, Brazil
| | - K A Borges
- Faculty of Veterinary Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - T Q Furian
- Faculty of Veterinary Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - L Ruschel Dos Santos
- School of Agricultural Sciences, Innovation and Business, University of Passo Fundo, Passo Fundo, Brazil
| | - F Pilotto
- School of Agricultural Sciences, Innovation and Business, University of Passo Fundo, Passo Fundo, Brazil
| | - L B Rodrigues
- School of Agricultural Sciences, Innovation and Business, University of Passo Fundo, Passo Fundo, Brazil
| | - V P Nascimento
- Faculty of Veterinary Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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3
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Szmolka A, Lancz ZS, Rapcsák F, Egyed L. Emergence and Comparative Genome Analysis of Salmonella Ohio Strains from Brown Rats, Poultry, and Swine in Hungary. Int J Mol Sci 2024; 25:8820. [PMID: 39201506 PMCID: PMC11354295 DOI: 10.3390/ijms25168820] [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: 06/13/2024] [Revised: 08/06/2024] [Accepted: 08/08/2024] [Indexed: 09/02/2024] Open
Abstract
Rats are particularly important from an epidemiological point of view, because they are regarded as reservoirs for diverse zoonotic pathogens including enteric bacteria. This study is the first to report the emergence of Salmonella serovar Ohio in brown rats (Rattus norvegicus) and food-producing animals in Hungary. We first reveal the genomic diversity of the strains and their phylogenomic relationships in the context of the international collection of S. Ohio genomes. This pathogen was detected in 4.3% (4/92) of rats, captured from multiple sites in Hungary. A whole-genome-based genotype comparison of S. Ohio, Infantis, Enteritidis, and Typhimurium strains showed that 76.4% (117/153) of the virulence and antimicrobial resistance genes were conserved among these serovars, and none of the genes were specific to S. Ohio. All S. Ohio strains lacked virulence and resistance plasmids. The cgMLST phylogenomic comparison highlighted a close genetic relationship between rat and poultry strains of S. Ohio from Hungary. These strains clustered together with the international S. Ohio genomes from aquatic environments. Overall, this study contributes to our understanding of the epidemiology of Salmonella spp. in brown rats and highlights the importance of monitoring to minimize the public health risk of rodent populations. However, further research is needed to understand the route of infection and evolution of this serovar.
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Affiliation(s)
- Ama Szmolka
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary (L.E.)
| | | | - Fanni Rapcsák
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary (L.E.)
| | - László Egyed
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary (L.E.)
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4
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Krishnakant Kushwaha S, Wu Y, Leonardo Avila H, Anand A, Sicheritz-Pontén T, Millard A, Amol Marathe S, Nobrega FL. Comprehensive blueprint of Salmonella genomic plasticity identifies hotspots for pathogenicity genes. PLoS Biol 2024; 22:e3002746. [PMID: 39110680 PMCID: PMC11305592 DOI: 10.1371/journal.pbio.3002746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024] Open
Abstract
Understanding the dynamic evolution of Salmonella is vital for effective bacterial infection management. This study explores the role of the flexible genome, organised in regions of genomic plasticity (RGP), in shaping the pathogenicity of Salmonella lineages. Through comprehensive genomic analysis of 12,244 Salmonella spp. genomes covering 2 species, 6 subspecies, and 46 serovars, we uncover distinct integration patterns of pathogenicity-related gene clusters into RGP, challenging traditional views of gene distribution. These RGP exhibit distinct preferences for specific genomic spots, and the presence or absence of such spots across Salmonella lineages profoundly shapes strain pathogenicity. RGP preferences are guided by conserved flanking genes surrounding integration spots, implicating their involvement in regulatory networks and functional synergies with integrated gene clusters. Additionally, we emphasise the multifaceted contributions of plasmids and prophages to the pathogenicity of diverse Salmonella lineages. Overall, this study provides a comprehensive blueprint of the pathogenicity potential of Salmonella. This unique insight identifies genomic spots in nonpathogenic lineages that hold the potential for harbouring pathogenicity genes, providing a foundation for predicting future adaptations and developing targeted strategies against emerging human pathogenic strains.
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Affiliation(s)
- Simran Krishnakant Kushwaha
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, India
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Yi Wu
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Hugo Leonardo Avila
- Laboratory for Applied Science and Technology in Health, Instituto Carlos Chagas, FIOCRUZ Paraná, Brazil
| | - Abhirath Anand
- Department of Computer Sciences and Information Systems, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, India
| | - Thomas Sicheritz-Pontén
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Bedong, Kedah, Malaysia
| | - Andrew Millard
- Centre for Phage Research, Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Sandhya Amol Marathe
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, India
| | - Franklin L. Nobrega
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
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5
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Bansal G, Ghanem M, Sears KT, Galen JE, Tennant SM. Genetic engineering of Salmonella spp. for novel vaccine strategies and therapeutics. EcoSal Plus 2024:eesp00042023. [PMID: 39023252 DOI: 10.1128/ecosalplus.esp-0004-2023] [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: 02/16/2024] [Accepted: 06/24/2024] [Indexed: 07/20/2024]
Abstract
Salmonella enterica is a diverse species that infects both humans and animals. S. enterica subspecies enterica consists of more than 1,500 serovars. Unlike typhoidal Salmonella serovars which are human host-restricted, non-typhoidal Salmonella (NTS) serovars are associated with foodborne illnesses worldwide and are transmitted via the food chain. Additionally, NTS serovars can cause disease in livestock animals causing significant economic losses. Salmonella is a well-studied model organism that is easy to manipulate and evaluate in animal models of infection. Advances in genetic engineering approaches in recent years have led to the development of Salmonella vaccines for both humans and animals. In this review, we focus on current progress of recombinant live-attenuated Salmonella vaccines, their use as a source of antigens for parenteral vaccines, their use as live-vector vaccines to deliver foreign antigens, and their use as therapeutic cancer vaccines in humans. We also describe development of live-attenuated Salmonella vaccines and live-vector vaccines for use in animals.
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Affiliation(s)
- Garima Bansal
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Mostafa Ghanem
- Department of Veterinary Medicine, Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Khandra T Sears
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - James E Galen
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sharon M Tennant
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
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6
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Lê-Bury P, Echenique-Rivera H, Pizarro-Cerdá J, Dussurget O. Determinants of bacterial survival and proliferation in blood. FEMS Microbiol Rev 2024; 48:fuae013. [PMID: 38734892 PMCID: PMC11163986 DOI: 10.1093/femsre/fuae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/29/2024] [Accepted: 05/10/2024] [Indexed: 05/13/2024] Open
Abstract
Bloodstream infection is a major public health concern associated with high mortality and high healthcare costs worldwide. Bacteremia can trigger fatal sepsis whose prevention, diagnosis, and management have been recognized as a global health priority by the World Health Organization. Additionally, infection control is increasingly threatened by antimicrobial resistance, which is the focus of global action plans in the framework of a One Health response. In-depth knowledge of the infection process is needed to develop efficient preventive and therapeutic measures. The pathogenesis of bloodstream infection is a dynamic process resulting from the invasion of the vascular system by bacteria, which finely regulate their metabolic pathways and virulence factors to overcome the blood immune defenses and proliferate. In this review, we highlight our current understanding of determinants of bacterial survival and proliferation in the bloodstream and discuss their interactions with the molecular and cellular components of blood.
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Affiliation(s)
- Pierre Lê-Bury
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Autoimmune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), 18 route du Panorama, 92260 Fontenay-aux-Roses, France
| | - Hebert Echenique-Rivera
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
| | - Javier Pizarro-Cerdá
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Yersinia National Reference Laboratory, WHO Collaborating Research & Reference Centre for Plague FRA-146, 28 rue du Dr Roux, 75015 Paris, France
| | - Olivier Dussurget
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
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7
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Zeng J, Fu R, Ji J, Xing T, Hou D, Li Z, Zhao Z, Li S, Zhang H. Stress responses and Physiological Changes of Salmonella enterica Serovar Enteritidis on Short-Term and Long-Term Benzalkonium Bromide Adaptation. Foodborne Pathog Dis 2024. [PMID: 38635964 DOI: 10.1089/fpd.2023.0145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Salmonella enterica is a common foodborne pathogen that poses significant safety risks across the world. And benzalkonium bromide (BK) is widely used as a disinfectant to sterilize the food processing equipment. It has been reported that sub-lethal concentration of disinfectants induced not only the homologous resistance but also cross-resistances. This work analyzed the induced resistances of Salmonella Enteritidis by short-term adaptation (STA) and long-term adaptation (LTA) to BK. We have demonstrated that inefficient sterilization exposes Salmonella Enteritidis to sub-lethal concentrations of BK, and adapts bacteria to a higher minimum inhibitory concentration and minimum bactericidal concentration. In addition, STA, but not LTA, to BK induced heterogeneous resistance to sodium hypochlorite, and cross-resistance to freezing, desiccation, and heating, which may be caused by the membrane composition change of Salmonella Enteritidis. This work could be useful to the optimization of cleaning protocol.
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Affiliation(s)
- Ji Zeng
- Department of Bioengineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Rong Fu
- Department of Bioengineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Jiahao Ji
- Department of Bioengineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Tong Xing
- Department of Bioengineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Dongping Hou
- Department of Bioengineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Zefeng Li
- Department of Bioengineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Zepeng Zhao
- Department of Bioengineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Shaoting Li
- Department of Bioengineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Hongmei Zhang
- Department of Bioengineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
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8
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Vázquez X, Fernández J, Heinisch JJ, Rodicio R, Rodicio MR. Insights into the Evolution of IncR Plasmids Found in the Southern European Clone of the Monophasic Variant of Salmonella enterica Serovar Typhimurium. Antibiotics (Basel) 2024; 13:314. [PMID: 38666990 PMCID: PMC11047700 DOI: 10.3390/antibiotics13040314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/29/2024] Open
Abstract
Salmonella enterica subspecies enterica serovar 4,[5],12:i:- is a monophasic variant of S. Typhimurium which has emerged as a world-wide distributed pathogen in the last decades. Several clones have been identified within this variant, the European clone, the Spanish clone, the Southern European clone and the U.S./American clone. The present study focused on isolates of the Southern European clone that were obtained from clinical samples at Spanish hospitals. The selected isolates were multidrug resistant, with most resistance genes residing on IncR plasmids that also carried virulence genes. These plasmids had a mosaic structure, comprising a highly reduced IncR backbone, which has acquired a large amount of exogenous DNA mostly derived from pSLT and IncI1-I(alfa) plasmids. Although composed of approximately the same elements, the investigated plasmids displayed a high diversity, consistent with active evolution driven by a wealth of mobile genetic elements. They comprise multiple intact or truncated insertion sequences, transposons, pseudo-compound transposons and integrons. Particularly relevant was the role of IS26 (with six to nine copies per plasmid) in generating insertions, deletions and inversions, with many of the rearrangements uncovered by tracking the patterns of eight bp target site duplications. Most of the resistance genes detected in the analyzed isolates have been previously associated with the Southern European clone. However, erm(B), lnu(G) and blaTEM-1B are novel, with the last two carried by a second resistance plasmid found in one of the IncR-positive isolates. Thus, evolution of resistance in the Southern European clone is not only mediated by diversification of the IncR plasmids, but also through acquisition of additional plasmids. All isolates investigated in the present study have the large deletion affecting the fljBA region previously found to justify the monophasic phenotype in the Southern European and U.S./American clones. An SNP-based phylogenetic analysis revealed the close relationship amongst our isolates, and support that those sharing the large fljBA deletion could be more heterogeneous than previously anticipated.
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Affiliation(s)
- Xenia Vázquez
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo (UO), 33006 Oviedo, Spain; (X.V.); (J.F.)
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
| | - Javier Fernández
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo (UO), 33006 Oviedo, Spain; (X.V.); (J.F.)
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain
- Centro de Investigación Biomédica en Red-Enfermedades Respiratorias, 30627 Madrid, Spain
- Research & Innovation, Artificial Intelligence and Statistical Department, Pragmatech AI Solutions, 33001 Oviedo, Spain
| | - Jürgen J. Heinisch
- Department of Genetics, Faculty of Biology and Chemistry, University of Osnabrück, Barbarastrasse 11, D-49076 Osnabrück, Germany;
| | - Rosaura Rodicio
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo (UO), 33006 Oviedo, Spain
| | - M. Rosario Rodicio
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo (UO), 33006 Oviedo, Spain; (X.V.); (J.F.)
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
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9
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Kang L, You J, Li Y, Huang R, Wu S. Effects and mechanisms of Salmonella plasmid virulence gene spv on host-regulated cell death. Curr Microbiol 2024; 81:86. [PMID: 38305917 DOI: 10.1007/s00284-024-03612-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/04/2024] [Indexed: 02/03/2024]
Abstract
Salmonella is responsible for the majority of food poisoning outbreaks around the world. Pathogenic Salmonella mostly carries a virulence plasmid that contains the Salmonella plasmid virulence gene (spv), a highly conserved sequence encoding effector proteins that can manipulate host cells. Intestinal epithelial cells are crucial components of the innate immune system, acting as the first barrier of defense against infection. When the barrier is breached, Salmonella encounters the underlying macrophages in lamina propria, triggering inflammation and engaging in combat with immune cells recruited by inflammatory factors. Host regulated cell death (RCD) provides a variety of means to fight against or favour Salmonella infection. However, Salmonella releases effector proteins to regulate RCD, evading host immune killing and neutralizing host antimicrobial effects. This review provides an overview of pathogen-host interactions in terms of (1) pathogenicity of Salmonella spv on intestinal epithelial cells and macrophages, (2) mechanisms of host RCD to limit or promote pathogenic Salmonella expansion, and (3) effects and mechanisms of Salmonella spv gene on host RCD.
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Affiliation(s)
- Li Kang
- Department of Medical Microbiology, School of Biology & Basic Medical Science, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-Infective Medicine, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Jiayi You
- Department of Medical Microbiology, School of Biology & Basic Medical Science, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-Infective Medicine, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Yuanyuan Li
- Experimental Center, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-Infective Medicine, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Rui Huang
- Department of Medical Microbiology, School of Biology & Basic Medical Science, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-Infective Medicine, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Shuyan Wu
- Department of Medical Microbiology, School of Biology & Basic Medical Science, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China.
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-Infective Medicine, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China.
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10
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Gudeta DD, Foley SL. Versatile allelic replacement and self-excising integrative vectors for plasmid genome mutation and complementation. Microbiol Spectr 2024; 12:e0338723. [PMID: 37991378 PMCID: PMC10782977 DOI: 10.1128/spectrum.03387-23] [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: 10/04/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE In spite of the dissemination of multidrug-resistant plasmids among Gram-negative pathogens, including those carrying virulence genes, vector tools for studying plasmid-born genes are lacking. The allelic replacement vectors can be used to generate plasmid or chromosomal mutations including markless point mutations. This is the first report describing a self-excising integrative vector that can be used as a stable single-copy complementing tool to study medically important pathogens including in vivo studies without the need for antibiotic selection. Overall, our newly developed vectors can be applied for the assessment of the function of plasmid-encoded genes by specifically creating mutations, moving large operons between plasmids and to/from the chromosome, and complementing phenotypes associated with gene mutation. Furthermore, the vectors express chromophores for the detection of target gene modification or colony isolation, avoiding time-consuming screening procedures.
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Affiliation(s)
- Dereje D. Gudeta
- Division of Microbiology, National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Steven L. Foley
- Division of Microbiology, National Center for Toxicological Research, Jefferson, Arkansas, USA
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11
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Gaviria-Cantin T, Fernández-Coll L, Vargas AF, Jiménez CJ, Madrid C, Balsalobre C. Expression of accessory genes in Salmonella requires the presence of the Gre factors. Genomics 2024; 116:110777. [PMID: 38163572 DOI: 10.1016/j.ygeno.2023.110777] [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: 08/03/2023] [Revised: 12/13/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Genomic studies with Salmonella enterica serovar Typhimurium reveal a crucial role of horizontal gene transfer (HGT) in the acquisition of accessory cellular functions involved in host-interaction. Many virulence genes are located in genomic islands, plasmids and prophages. GreA and GreB proteins, Gre factors, interact transiently with the RNA polymerase alleviating backtracked complexes during transcription elongation. The overall effect of Gre factors depletion in Salmonella expression profile was studied. Both proteins are functionally redundant since only when both Gre factors were depleted a major effect in gene expression was detected. Remarkably, the accessory gene pool is particularly sensitive to the lack of Gre factors, with 18.6% of accessory genes stimulated by the Gre factors versus 4.4% of core genome genes. Gre factors involvement is particularly relevant for the expression of genes located in genomic islands. Our data reveal that Gre factors are required for the expression of accessory genes.
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Affiliation(s)
- Tania Gaviria-Cantin
- Department of Genetics, Microbiology and Statistics, School of Biology, Universitat de Barcelona, Avda. Diagonal 643, Barcelona 08028, Spain
| | - Llorenç Fernández-Coll
- Department of Genetics, Microbiology and Statistics, School of Biology, Universitat de Barcelona, Avda. Diagonal 643, Barcelona 08028, Spain
| | - Andrés Felipe Vargas
- Department of Genetics, Microbiology and Statistics, School of Biology, Universitat de Barcelona, Avda. Diagonal 643, Barcelona 08028, Spain
| | - Carlos Jonay Jiménez
- Department of Genetics, Microbiology and Statistics, School of Biology, Universitat de Barcelona, Avda. Diagonal 643, Barcelona 08028, Spain
| | - Cristina Madrid
- Department of Genetics, Microbiology and Statistics, School of Biology, Universitat de Barcelona, Avda. Diagonal 643, Barcelona 08028, Spain
| | - Carlos Balsalobre
- Department of Genetics, Microbiology and Statistics, School of Biology, Universitat de Barcelona, Avda. Diagonal 643, Barcelona 08028, Spain.
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12
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Scheik LK, Jaskulski IB, de Lima AS, Haubert L, Kroning IS, Lopes GV, da Silva WP. Occurrence, genetic diversity and resistance profiles of Salmonella enterica from Brazilian sausages collected at production facilities. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2024; 61:53-61. [PMID: 38192700 PMCID: PMC10771404 DOI: 10.1007/s13197-023-05809-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 06/15/2023] [Accepted: 07/18/2023] [Indexed: 01/10/2024]
Abstract
This study aimed to investigate the occurrence and the genetic diversity of Salmonella enterica subsp. enterica in sausages from Southern Brazil, evaluate virulence genes and determine the phenotypic and genotypic basis of antimicrobial and sanitizer resistance. Salmonella was detected in sausage samples with an overall prevalence of 5.5%. The prevalent serovars were S. Infantis and S. Rissen. Pulsed-field gel electrophoresis (PFGE) analysis yielded nine distinct PFGE profiles, and some of them were recurrently recovered in the same establishment on different dates. Among tested isolates, 28.5% showed resistance to at least one antimicrobial agent and a multidrug-resistance (MDR) profile was observed in 21.4%. Resistance occurred most frequently to ampicillin, sulfonamide, trimethoprim/sulfamethoxazole, and trimethoprim. Regarding the genotypic antimicrobial resistance profile, S. Schwarzengrund carried tet(B), strA, strB, and sul2 genes. Benzalkonium chloride and chlorhexidine were more effective than peracetic acid and sodium hypochlorite, showing lower minimum inhibitory concentration values. Six Salmonella serovars were found, demonstrating a potential risk of salmonellosis associated with consuming this food. Salmonella carrying virulence genes, MDR profile, and tolerance to sanitizers is a public health concern and a challenge for the food industry, suggesting that new strategies should be developed to control this pathogen. Supplementary Information The online version contains supplementary material available at 10.1007/s13197-023-05809-w.
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Affiliation(s)
- Letícia Klein Scheik
- Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas (UFPel), Campus Capão do Leão s/nº, Caixa Postal 354, Capão do Leão, Pelotas, RS 96160-000 Brazil
| | - Itiane Barcellos Jaskulski
- Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas (UFPel), Campus Capão do Leão s/nº, Caixa Postal 354, Capão do Leão, Pelotas, RS 96160-000 Brazil
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas (UFPel), Pelotas, RS Brazil
| | - Andreia Saldanha de Lima
- Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas (UFPel), Campus Capão do Leão s/nº, Caixa Postal 354, Capão do Leão, Pelotas, RS 96160-000 Brazil
| | - Louise Haubert
- Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas (UFPel), Campus Capão do Leão s/nº, Caixa Postal 354, Capão do Leão, Pelotas, RS 96160-000 Brazil
| | - Isabela Schneid Kroning
- Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas (UFPel), Campus Capão do Leão s/nº, Caixa Postal 354, Capão do Leão, Pelotas, RS 96160-000 Brazil
| | - Graciela Volz Lopes
- Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas (UFPel), Campus Capão do Leão s/nº, Caixa Postal 354, Capão do Leão, Pelotas, RS 96160-000 Brazil
| | - Wladimir Padilha da Silva
- Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas (UFPel), Campus Capão do Leão s/nº, Caixa Postal 354, Capão do Leão, Pelotas, RS 96160-000 Brazil
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas (UFPel), Pelotas, RS Brazil
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Liu S, Wang W, Jia T, Xin L, Xu TT, Wang C, Xie G, Luo K, Li J, Kong J, Zhang Q. Vibrio parahaemolyticus becomes lethal to post-larvae shrimp via acquiring novel virulence factors. Microbiol Spectr 2023; 11:e0049223. [PMID: 37850796 PMCID: PMC10714935 DOI: 10.1128/spectrum.00492-23] [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: 02/03/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023] Open
Abstract
IMPORTANCE As a severe emerging shrimp disease, TPD has heavily impacted the shrimp aquaculture industry and resulted in serious economic losses in China since spring 2020. This study aimed to identify the key virulent factors and related genes of the Vp TPD, for a better understanding of its pathogenicity of the novel highly lethal infectious pathogen, as well as its molecular epidemiological characteristics in China. The present study revealed that a novel protein, Vibrio high virulent protein-2 (MW >100 kDa), is responsible to the lethal virulence of V. parahaemolyticus to shrimp post-larvae. The results are essential for effectively diagnosing and monitoring novel pathogenic bacteria, like Vp TPD, in aquaculture shrimps and would be beneficial to the fisheries department in early warning of Vp TPD emergence and developing prevention strategies to reduce economic losses due to severe outbreaks of TPD. Elucidation of the key virulence genes and genomics of Vp TPD could also provide valuable information on the evolution and ecology of this emerging pathogen in aquaculture environments.
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Affiliation(s)
- Shuang Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, China
- Key Laboratory of Marine Aquaculture Disease Control, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
| | - Wei Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, China
| | - Tianchang Jia
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, China
| | - Lusheng Xin
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, China
- Key Laboratory of Marine Aquaculture Disease Control, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
| | - Ting-ting Xu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, China
- Key Laboratory of Marine Aquaculture Disease Control, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
| | - Chong Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, China
| | - Guosi Xie
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, China
- Key Laboratory of Marine Aquaculture Disease Control, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
| | - Kun Luo
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, China
| | - Jun Li
- School of Sciences and Medicine, Lake Superior State University, Sault Ste. Marie, Michigan, USA
| | - Jie Kong
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, China
- Key Laboratory of Marine Aquaculture Disease Control, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
| | - Qingli Zhang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, China
- Key Laboratory of Marine Aquaculture Disease Control, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
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Yuan Y, Wang X, Jin J, Tang Z, Xian W, Zhang X, Fu J, He K, Liu X. The Salmonella Typhimurium Effector SpvB Subverts Host Membrane Trafficking by Targeting Clathrin and AP-1. Mol Cell Proteomics 2023; 22:100674. [PMID: 37924977 PMCID: PMC10696399 DOI: 10.1016/j.mcpro.2023.100674] [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: 07/28/2023] [Revised: 10/21/2023] [Accepted: 11/01/2023] [Indexed: 11/06/2023] Open
Abstract
Salmonella enterica, the etiological agent of gastrointestinal and systemic diseases, translocates a plethora of virulence factors through its type III secretion systems to host cells during infection. Among them, SpvB has been reported to harbor an ADP-ribosyltransferase domain in its C terminus, which destabilizes host cytoskeleton by modifying actin. However, whether this effector targets other host factors as well as the function of its N terminus still remains to be determined. Here, we found that SpvB targets clathrin and its adaptor AP-1 (adaptor protein 1) via interactions with its N-terminal domain. Notably, our data suggest that SpvB-clathrin/AP-1 associations disrupt clathrin-mediated endocytosis and protein secretion pathway as well. In addition, knocking down of AP-1 promotes Salmonella intracellular survival and proliferation in host cells.
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Affiliation(s)
- Yi Yuan
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Xinghao Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jie Jin
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Zhiheng Tang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Wei Xian
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Xinyi Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jiaqi Fu
- Department of Respiratory Medicine, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Zoonotic Diseases, The First Hospital of Jilin University, Changchun, China.
| | - Kangmin He
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China.
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Ju Z, Cui L, Lei C, Song M, Chen X, Liao Z, Zhang T, Wang H. Whole-Genome Sequencing Analysis of Non-Typhoidal Salmonella Isolated from Breeder Poultry Farm Sources in China, 2020-2021. Antibiotics (Basel) 2023; 12:1642. [PMID: 37998844 PMCID: PMC10669045 DOI: 10.3390/antibiotics12111642] [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: 10/19/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023] Open
Abstract
Non-typhoidal salmonellosis is a dangerous foodborne disease that causes enormous economic loss and threatens public health worldwide. The consumption of food, especially poultry or poultry products, contaminated with non-typhoidal Salmonella (NTS) is the main cause of human salmonellosis. To date, no research has identified the molecular epidemiological characteristics of NTS strains isolated from breeder chicken farms in different provinces of China. In our study, we investigated the antimicrobial resistance, phylogenetic relationships, presence of antimicrobial resistance and virulence genes, and plasmids of NTS isolates recovered from breeder chicken farms in five provinces of China between 2020 and 2021 by using a whole-genome sequencing (WGS) approach and phenotypic methods. All sequenced isolates belonged to six serovars with seven sequence types. Nearly half of the isolates (44.87%) showed phenotypic resistance to at least three classes of antimicrobials. Salmonella enterica serotype Kentucky harbored more antimicrobial resistance genes than the others, which was highly consistent with phenotypic resistance. Furthermore, the carried rate of 104 out of 135 detected virulence genes was 100%. Overall, our WGS results highlight the need for the continuous monitoring of, and additional studies on, the antimicrobial resistance of NTS.
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Affiliation(s)
- Zijing Ju
- Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China; (Z.J.); (C.L.); (X.C.); (Z.L.); (T.Z.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Lulu Cui
- Shandong Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China; (L.C.); (M.S.)
| | - Changwei Lei
- Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China; (Z.J.); (C.L.); (X.C.); (Z.L.); (T.Z.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Mengze Song
- Shandong Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China; (L.C.); (M.S.)
| | - Xuan Chen
- Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China; (Z.J.); (C.L.); (X.C.); (Z.L.); (T.Z.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Ziwei Liao
- Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China; (Z.J.); (C.L.); (X.C.); (Z.L.); (T.Z.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Tiejun Zhang
- Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China; (Z.J.); (C.L.); (X.C.); (Z.L.); (T.Z.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Hongning Wang
- Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China; (Z.J.); (C.L.); (X.C.); (Z.L.); (T.Z.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
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Bhandari M, Poelstra JW, Kauffman M, Varghese B, Helmy YA, Scaria J, Rajashekara G. Genomic Diversity, Antimicrobial Resistance, Plasmidome, and Virulence Profiles of Salmonella Isolated from Small Specialty Crop Farms Revealed by Whole-Genome Sequencing. Antibiotics (Basel) 2023; 12:1637. [PMID: 37998839 PMCID: PMC10668983 DOI: 10.3390/antibiotics12111637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023] Open
Abstract
Salmonella is the leading cause of death associated with foodborne illnesses in the USA. Difficulty in treating human salmonellosis is attributed to the development of antimicrobial resistance and the pathogenicity of Salmonella strains. Therefore, it is important to study the genetic landscape of Salmonella, such as the diversity, plasmids, and presence antimicrobial resistance genes (AMRs) and virulence genes. To this end, we isolated Salmonella from environmental samples from small specialty crop farms (SSCFs) in Northeast Ohio from 2016 to 2021; 80 Salmonella isolates from 29 Salmonella-positive samples were subjected to whole-genome sequencing (WGS). In silico serotyping revealed the presence of 15 serotypes. AMR genes were detected in 15% of the samples, with 75% exhibiting phenotypic and genotypic multidrug resistance (MDR). Plasmid analysis demonstrated the presence of nine different types of plasmids, and 75% of AMR genes were located on plasmids. Interestingly, five Salmonella Newport isolates and one Salmonella Dublin isolate carried the ACSSuT gene cassette on a plasmid, which confers resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide, and tetracycline. Overall, our results show that SSCFs are a potential reservoir of Salmonella with MDR genes. Thus, regular monitoring is needed to prevent the transmission of MDR Salmonella from SSCFs to humans.
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Affiliation(s)
- Menuka Bhandari
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (M.B.); (M.K.)
| | - Jelmer W. Poelstra
- Molecular and Cellular Imaging Center, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA;
| | - Michael Kauffman
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (M.B.); (M.K.)
| | - Binta Varghese
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74074, USA; (B.V.); (J.S.)
| | - Yosra A. Helmy
- Department of Veterinary Science, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546, USA;
| | - Joy Scaria
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74074, USA; (B.V.); (J.S.)
| | - Gireesh Rajashekara
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (M.B.); (M.K.)
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Khoo E, Roslee R, Zakaria Z, Ahmad NI. Virulence gene profiles and antimicrobial susceptibility of Salmonella Brancaster from chicken. J Vet Sci 2023; 24:e82. [PMID: 38031519 PMCID: PMC10694367 DOI: 10.4142/jvs.23053] [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: 03/07/2023] [Revised: 08/17/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND The current conventional serotyping based on antigen-antisera agglutination could not provide a better understanding of the potential pathogenicity of Salmonella enterica subsp. enterica serovar Brancaster. Surveillance data from Malaysian poultry farms indicated an increase in its presence over the years. OBJECTIVE This study aims to investigate the virulence determinants and antimicrobial resistance in S. Brancaster isolated from chickens in Malaysia. METHODS One hundred strains of archived S. Brancaster isolated from chicken cloacal swabs and raw chicken meat from 2017 to 2022 were studied. Two sets of multiplex polymerase chain reaction (PCR) were conducted to identify eight virulence genes associated with pathogenicity in Salmonella (invasion protein gene [invA], Salmonella invasion protein gene [sipB], Salmonella-induced filament gene [sifA], cytolethal-distending toxin B gene [cdtB], Salmonella iron transporter gene [sitC], Salmonella pathogenicity islands gene [spiA], Salmonella plasmid virulence gene [spvB], and inositol phosphate phosphatase gene [sopB]). Antimicrobial susceptibility assessment was conducted by disc diffusion method on nine selected antibiotics for the S. Brancaster isolates. S. Brancaster, with the phenotypic ACSSuT-resistance pattern (ampicillin, chloramphenicol, streptomycin, sulphonamides, and tetracycline), was subjected to PCR to detect the corresponding resistance gene(s). RESULTS Virulence genes detected in S. Brancaster in this study were invA, sitC, spiA, sipB, sopB, sifA, cdtB, and spvB. A total of 36 antibiogram patterns of S. Brancaster with a high level of multidrug resistance were observed, with ampicillin exhibiting the highest resistance. Over a third of the isolates displayed ACSSuT-resistance, and seven resistance genes (β-lactamase temoneira [blaTEM], florfenicol/chloramphenicol resistance gene [floR], streptomycin resistance gene [strA], aminoglycoside nucleotidyltransferase gene [ant(3″)-Ia], sulfonamides resistance gene [sul-1, sul-2], and tetracycline resistance gene [tetA]) were detected. CONCLUSION Multidrug-resistant S. Brancaster from chickens harbored an array of virulence-associated genes similar to other clinically significant and invasive non-typhoidal Salmonella serovars, placing it as another significant foodborne zoonosis.
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Affiliation(s)
- Evie Khoo
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
- Bacteriology Section, Veterinary Research Institute, 31400 Ipoh, Perak, Malaysia
| | - Roseliza Roslee
- Bacteriology Section, Veterinary Research Institute, 31400 Ipoh, Perak, Malaysia
| | - Zunita Zakaria
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Nur Indah Ahmad
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
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Petano-Duque JM, Rueda-García V, Rondón-Barragán IS. Virulence genes identification in Salmonella enterica isolates from humans, crocodiles, and poultry farms from two regions in Colombia. Vet World 2023; 16:2096-2103. [PMID: 38023281 PMCID: PMC10668553 DOI: 10.14202/vetworld.2023.2096-2103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/11/2023] [Indexed: 12/01/2023] Open
Abstract
Background and Aim Salmonella spp. is frequently found in the digestive tract of birds and reptiles and transmitted to humans through food. Salmonellosis is a public health problem because of pathogenicity variability in strains for virulence factors. This study aimed to identify the virulence genes in Salmonella isolates from humans, crocodiles, broiler cloacas, and broiler carcasses from two departments of Colombia. Materials and Methods This study was conducted on 31 Salmonella enterica strains from humans with gastroenteritis (seven), crocodiles (seven), broiler cloacas (six), and broiler carcasses (12) from Tolima and Santander departments of Colombia, belonging to 21 serotypes. All samples were tested for Salmonella spp. using culture method on selective and non-selective mediums. Extraction of genomic DNA was performed from fresh colonies, DNA quality was verified by spectrophotometry and confirmed by amplification of InvA gene using conventional polymerase chain reaction (PCR). bapA, fimA, icmF, IroB, marT, mgtC, nlpI, oafA, pagN, siiD, spvC, spvR, spvB, Stn, and vexA genes were amplified by PCR. Results The most prevalent gene was bapA (100%), followed by marT (96.77%), mgtC (93.55%), and fimA (83.87%). Likewise, IroB (70.97%), Stn (67.74%), spvR (61.29%), pagN (54.84%), icmF (54.8%), and SiiD (45.16%) were positive for more than 50% of the strains. Furthermore, none of the isolates tested positive for the vexA gene. Salmonella isolates presented 26 virulence profiles. Conclusion This study reported 14 virulence genes in Salmonella spp. isolates from humans with gastroenteritis, crocodiles, and broiler cloacas and carcasses. The distribution of virulence genes differed among sources. This study could help in decision-making by health and sanitary authorities.
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Affiliation(s)
- Julieth Michel Petano-Duque
- Poultry Research Group, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué, Tolima, Colombia
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué, Tolima, Colombia
| | - Valentina Rueda-García
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué, Tolima, Colombia
| | - Iang Schroniltgen Rondón-Barragán
- Poultry Research Group, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué, Tolima, Colombia
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué, Tolima, Colombia
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Moyne AL, Lawal OU, Gauthier J, Kukavica-Ibrulj I, Potvin M, Goodridge L, Levesque RC, Harris LJ. Genetic diversity of Salmonella enterica isolated over 13 years from raw California almonds and from an almond orchard. PLoS One 2023; 18:e0291109. [PMID: 37676871 PMCID: PMC10484465 DOI: 10.1371/journal.pone.0291109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023] Open
Abstract
A comparative genomic analysis was conducted for 171 Salmonella isolates recovered from raw inshell almonds and raw almond kernels between 2001 and 2013 and for 30 Salmonella Enteritidis phage type (PT) 30 isolates recovered between 2001 and 2006 from a 2001 salmonellosis outbreak-associated almond orchard. Whole genome sequencing was used to measure the genetic distance among isolates by single nucleotide polymorphism (SNP) analyses and to predict the presence of plasmid DNA and of antimicrobial resistance (AMR) and virulence genes. Isolates were classified by serovars with Parsnp, a fast core-genome multi aligner, before being analyzed with the CFSAN SNP Pipeline (U.S. Food and Drug Administration Center for Food Safety and Applied Nutrition). Genetically similar (≤18 SNPs) Salmonella isolates were identified among several serovars isolated years apart. Almond isolates of Salmonella Montevideo (2001 to 2013) and Salmonella Newport (2003 to 2010) differed by ≤9 SNPs. Salmonella Enteritidis PT 30 isolated between 2001 and 2013 from survey, orchard, outbreak, and clinical samples differed by ≤18 SNPs. One to seven plasmids were found in 106 (62%) of the Salmonella isolates. Of the 27 plasmid families that were identified, IncFII and IncFIB plasmids were the most predominant. AMR genes were identified in 16 (9%) of the survey isolates and were plasmid encoded in 11 of 16 cases; 12 isolates (7%) had putative resistance to at least one antibiotic in three or more drug classes. A total of 303 virulence genes were detected among the assembled genomes; a plasmid that harbored a combination of pef, rck, and spv virulence genes was identified in 23% of the isolates. These data provide evidence of long-term survival (years) of Salmonella in agricultural environments.
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Affiliation(s)
- Anne-laure Moyne
- Department of Food Science and Technology, University of California, Davis, California, United States of America
- Western Center for Food Safety, University of California, Davis, California, United States of America
| | - Opeyemi U. Lawal
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Jeff Gauthier
- Institut de biologie intégrative et des systèmes (IBIS), Faculté de médecine, Université Laval, Québec, Québec, Canada
| | - Irena Kukavica-Ibrulj
- Institut de biologie intégrative et des systèmes (IBIS), Faculté de médecine, Université Laval, Québec, Québec, Canada
| | - Marianne Potvin
- Institut de biologie intégrative et des systèmes (IBIS), Faculté de médecine, Université Laval, Québec, Québec, Canada
| | - Lawrence Goodridge
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, Ontario, Canada
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Sainte Anne de Bellevue, Quebec, Canada
| | - Roger C. Levesque
- Institut de biologie intégrative et des systèmes (IBIS), Faculté de médecine, Université Laval, Québec, Québec, Canada
| | - Linda J. Harris
- Department of Food Science and Technology, University of California, Davis, California, United States of America
- Western Center for Food Safety, University of California, Davis, California, United States of America
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20
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Carroll LM, Piacenza N, Cheng RA, Wiedmann M, Guldimann C. A multidrug-resistant Salmonella enterica Typhimurium DT104 complex lineage circulating among humans and cattle in the USA lost the ability to produce pertussis-like toxin ArtAB. Microb Genom 2023; 9:mgen001050. [PMID: 37402177 PMCID: PMC10438809 DOI: 10.1099/mgen.0.001050] [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: 07/27/2022] [Accepted: 05/23/2023] [Indexed: 07/06/2023] Open
Abstract
Salmonella enterica subsp. enterica serotype Typhimurium definitive type 104 (DT104) can infect both humans and animals and is often multidrug-resistant (MDR). Previous studies have indicated that, unlike most S . Typhimurium, the overwhelming majority of DT104 strains produce pertussis-like toxin ArtAB via prophage-encoded genes artAB . However, DT104 that lack artAB have been described on occasion. Here, we identify an MDR DT104 complex lineage circulating among humans and cattle in the USA, which lacks artAB (i.e. the ‘U.S. artAB -negative major clade’; n =42 genomes). Unlike most other bovine- and human-associated DT104 complex strains from the USA (n =230 total genomes), which harbour artAB on prophage Gifsy-1 (n =177), members of the U.S. artAB -negative major clade lack Gifsy-1, as well as anti-inflammatory effector gogB . The U.S. artAB -negative major clade encompasses human- and cattle-associated strains isolated from ≥11 USA states over a 20-year period. The clade was predicted to have lost artAB , Gifsy-1 and gogB circa 1985–1987 (95 % highest posterior density interval 1979.0–1992.1). When compared to DT104 genomes from other regions of the world (n =752 total genomes), several additional, sporadic artAB , Gifsy-1 and/or gogB loss events among clades encompassing five or fewer genomes were observed. Using phenotypic assays that simulate conditions encountered during human and/or bovine digestion, members of the U.S. artAB -negative major clade did not differ from closely related Gifsy-1/artAB /gogB -harbouring U.S. DT104 complex strains (ANOVA raw P >0.05); thus, future research is needed to elucidate the roles that artAB , gogB and Gifsy-1 play in DT104 virulence in humans and animals.
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Affiliation(s)
- Laura M. Carroll
- Department of Clinical Microbiology, SciLifeLab, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
- Integrated Science Lab, Umeå University, Umeå, Sweden
| | - Nicolo Piacenza
- Chair for Food Safety and Analytics, Ludwig-Maximillians-University Munich, Munich, Germany
| | - Rachel A. Cheng
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, USA
| | - Claudia Guldimann
- Chair for Food Safety and Analytics, Ludwig-Maximillians-University Munich, Munich, Germany
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21
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Uzairue LI, Shittu OB, Ojo OE, Obuotor TM, Olanipekun G, Ajose T, Arogbonlo R, Medugu N, Ebruke B, Obaro SK. Antimicrobial resistance and virulence genes of invasive Salmonella enterica from children with bacteremia in north-central Nigeria. SAGE Open Med 2023; 11:20503121231175322. [PMID: 37223673 PMCID: PMC10201152 DOI: 10.1177/20503121231175322] [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: 12/27/2022] [Accepted: 04/25/2023] [Indexed: 05/25/2023] Open
Abstract
Objectives Bacteremia due to invasive Salmonella enterica has been reported earlier in children in Nigeria. This study aimed to detect the virulence and antibiotic resistance genes of invasive Salmonella enterica from children with bacteremia in north-central Nigeria. Method From June 2015 to June 2018, 4163 blood cultures yielded 83 Salmonella isolates. This is a secondary cross-sectional analysis of the Salmonella isolates. The Salmonella enterica were isolated and identified using standard bacteriology protocol. Biochemical identifications of the Salmonella enterica were made by Phoenix MD 50 identification system. Further identification and confirmation were done with polyvalent antisera O and invA gene. Antimicrobial susceptibility testing was done following clinical and laboratory standard institute guidelines. Resistant genes and virulence genes were determined using a real-time polymerase chain reaction. Result Salmonella typhi 51 (61.4%) was the most prevalent serovar, followed by Salmonella species 13 (15.7%), choleraesuis 8 (9.6%), enteritidis 6 (7.2%), and typhimurium 5 (6.1%). Fifty-one (61.4%) of 83 Salmonella enterica were typhoidal, while 32 (38.6%) were not. Sixty-five (78.3%) of the 83 Salmonella enterica isolates were resistant to ampicillin and trimethoprim-sulfamethoxazole, followed by chloramphenicol 39 (46.7%), tetracycline 41 (41.4%), piperacillin 33 (33.9%), amoxicillin-clavulanate, and streptomycin 21 (25.3%), while cephalothin was 19 (22.9%). Thirty-nine (46.9%) of the 83 Salmonella enterica isolates were multi-drug resistant, and none were extensive drug resistant or pan-drug resistant. A blaTEM 42 (50.6%), floR 32 (38.6%), qnrA 24 (28.9%), tetB 20 (20.1%), tetA 10 (10.0%), and tetG 5 (6.0%) were the antibiotic resistance genes detected. There were perfect agreement between phenotypic and genotypic detection of antimicrobial resistance in tetracycline, ciprofloxacin, and chloramphenicol, while beta-lactam showed κ = 0.60 agreement. All of the Salmonella enterica isolates had the virulence genes invA, sopB, mgtC, and sip4D, while 33 (39.8%), 45 (51.8%), and 2 (2.4%) had ssaQ, spvC, and ljsGI-1, respectively. Conclusion Our findings showed multi-drug resistant Salmonella enterica in children with bacteremia in northern Nigeria. In addition, significant virulence and antimicrobial resistance genes were found in invasive Salmonella enterica in northern Nigeria. Thus, our study emphasizes the need to monitor antimicrobial resistance in Salmonella enterica from invasive sources in Nigeria and supports antibiotic prudence.
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Affiliation(s)
- Leonard I Uzairue
- Department of Microbiology, Federal
University of Agriculture, Abeokuta, Ogun State, Nigeria
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
- Department of Medical Laboratory
Sciences, Federal University Oye Ekiti, Ekiti State, Nigeria
| | - Olufunke B Shittu
- Department of Microbiology, Federal
University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Olufemi E Ojo
- Department of Veterinary Microbiology
and Parasitology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Tolulope M Obuotor
- Department of Microbiology, Federal
University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Grace Olanipekun
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Theresa Ajose
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Ronke Arogbonlo
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Nubwa Medugu
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
- Department of Microbiology and
Parasitology, National Hospital, Abuja, FCT, Nigeria
| | - Bernard Ebruke
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Stephen K Obaro
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
- Pediatric Infectious Division, the
University of Nebraska Medical Center, Omaha, NE, USA
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22
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Teklemariam AD, Al-Hindi RR, Albiheyri RS, Alharbi MG, Alghamdi MA, Filimban AAR, Al Mutiri AS, Al-Alyani AM, Alseghayer MS, Almaneea AM, Albar AH, Khormi MA, Bhunia AK. Human Salmonellosis: A Continuous Global Threat in the Farm-to-Fork Food Safety Continuum. Foods 2023; 12:foods12091756. [PMID: 37174295 PMCID: PMC10178548 DOI: 10.3390/foods12091756] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Salmonella is one of the most common zoonotic foodborne pathogens and a worldwide public health threat. Salmonella enterica is the most pathogenic among Salmonella species, comprising over 2500 serovars. It causes typhoid fever and gastroenteritis, and the serovars responsible for the later disease are known as non-typhoidal Salmonella (NTS). Salmonella transmission to humans happens along the farm-to-fork continuum via contaminated animal- and plant-derived foods, including poultry, eggs, fish, pork, beef, vegetables, fruits, nuts, and flour. Several virulence factors have been recognized to play a vital role in attaching, invading, and evading the host defense system. These factors include capsule, adhesion proteins, flagella, plasmids, and type III secretion systems that are encoded on the Salmonella pathogenicity islands. The increased global prevalence of NTS serovars in recent years indicates that the control approaches centered on alleviating the food animals' contamination along the food chain have been unsuccessful. Moreover, the emergence of antibiotic-resistant Salmonella variants suggests a potential food safety crisis. This review summarizes the current state of the knowledge on the nomenclature, microbiological features, virulence factors, and the mechanism of antimicrobial resistance of Salmonella. Furthermore, it provides insights into the pathogenesis and epidemiology of Salmonella infections. The recent outbreaks of salmonellosis reported in different clinical settings and geographical regions, including Africa, the Middle East and North Africa, Latin America, Europe, and the USA in the farm-to-fork continuum, are also highlighted.
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Affiliation(s)
- Addisu D Teklemariam
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rashad R Al-Hindi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Raed S Albiheyri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mona G Alharbi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mashail A Alghamdi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Amani A R Filimban
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Abdullah S Al Mutiri
- Laboratory Department, Saudi Food and Drug Authority, Riyadh 12843, Saudi Arabia
| | - Abdullah M Al-Alyani
- Laboratory Department, Saudi Food and Drug Authority, Jeddah 22311, Saudi Arabia
| | - Mazen S Alseghayer
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Monitoring and Risk Assessment Department, Saudi Food and Drug Authority, Riyadh 13513, Saudi Arabia
| | - Abdulaziz M Almaneea
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Monitoring and Risk Assessment Department, Saudi Food and Drug Authority, Riyadh 13513, Saudi Arabia
| | - Abdulgader H Albar
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Microbiology and Medical Parasitology, Faculty of Medicine, Jeddah University, Jeddah 23218, Saudi Arabia
| | - Mohsen A Khormi
- Department of Biological Sciences, Faculty of Sciences, Jazan University, Jazan 82817, Saudi Arabia
| | - Arun K Bhunia
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
- Purdue University Interdisciplinary Life Science Program (PULSe), West Lafayette, IN 47907, USA
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
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23
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Comparison of Phenotype and Genotype Virulence and Antimicrobial Factors of Salmonella Typhimurium Isolated from Human Milk. Int J Mol Sci 2023; 24:ijms24065135. [PMID: 36982209 PMCID: PMC10048834 DOI: 10.3390/ijms24065135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023] Open
Abstract
Salmonella is a common foodborne infection. Many serovars belonging to Salmonella enterica subsp. enterica are present in the gut of various animal species. They can cause infection in human infants via breast milk or cross-contamination with powdered milk. In the present study, Salmonella BO was isolated from human milk in accordance with ISO 6579-1:2017 standards and sequenced using whole-genome sequencing (WGS), followed by serosequencing and genotyping. The results also allowed its pathogenicity to be predicted. The WGS results were compared with the bacterial phenotype. The isolated strain was found to be Salmonella enterica subsp. enterica serovar Typhimurium 4:i:1,2_69M (S. Typhimurium 69M); it showed a very close similarity to S. enterica subsp. enterica serovar Typhimurium LT2. Bioinformatics sequence analysis detected eleven SPIs (SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-9, SPI-12, SPI-13, SPI-14, C63PI, CS54_island). Significant changes in gene sequences were noted, causing frameshift mutations in yeiG, rfbP, fumA, yeaL, ybeU (insertion) and lpfD, avrA, ratB, yacH (deletion). The sequences of several proteins were significantly different from those coded in the reference genome; their three-dimensional structure was predicted and compared with reference proteins. Our findings indicate the presence of a number of antimicrobial resistance genes that do not directly imply an antibiotic resistance phenotype.
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24
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Casaux ML, Neto WS, Schild CO, Costa RA, Macías-Rioseco M, Caffarena RD, Silveira CS, Aráoz V, Díaz BD, Giannitti F, Fraga M. Epidemiological and clinicopathological findings in 15 fatal outbreaks of salmonellosis in dairy calves and virulence genes in the causative Salmonella enterica Typhimurium and Dublin strains. Braz J Microbiol 2023; 54:475-490. [PMID: 36602750 PMCID: PMC9943839 DOI: 10.1007/s42770-022-00898-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Salmonella enterica is a major food-borne pathogen that affects cattle-rearing systems worldwide. Little information is available on the epidemiology and pathology of salmonellosis and the virulence genes (VGs) carried by Salmonella in spontaneous outbreaks in cattle. We describe epidemiological findings in 15 fatal outbreaks of salmonellosis in Uruguayan dairy farms and the age, clinical signs, and pathology in 20 affected calves. We also describe the serotypes and frequencies of 17 VGs in the causative Salmonella strains and explore their associations with epidemiological, clinical, and pathological findings. Salmonella Typhimurium and Dublin were identified in 11/15 and 4/15 outbreaks, respectively. The most frequent reason for consultation was digestive disease (8 outbreaks caused by S. Typhimurium), followed by sudden death (4 outbreaks, 3 caused by S. Dublin). Morbidity, mortality, and lethality ranged 4.8-100%, 3.8-78.9%, and 10-100%, without significant differences between serotypes. Diarrhea, the most common clinical sign (14 cases), was associated with the Typhimurium serotype (OR = 26.95), especially in ≤ 30-day-old calves with fibrinous enteritis as the main autopsy finding. The Dublin serotype affected ≥ 50-day-old calves and was associated with fibrinosuppurative splenitis (p = 0.01) and tubulointerstitial nephritis (OR = 48.95). The chances of the Dublin serotype increased significantly with age. There was low variability of VG across serotypes. The pefA gene was associated with the Typhimurium serotype (OR = 21.95), macroscopic enteritis (p = 0.03), and microscopic fibrinosuppurative splenitis (p = 0.04). Understanding the epidemiology, pathology, and virulence of S. enterica at the farm level is key to delineating prevention and control strategies to mitigate its impact on animal and human health.
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Affiliation(s)
- M L Casaux
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, Ruta 50, Km 11, El Semillero, Uruguay
| | - W Santiago Neto
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, Ruta 50, Km 11, El Semillero, Uruguay
| | - C O Schild
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, Ruta 50, Km 11, El Semillero, Uruguay
| | - R A Costa
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, Ruta 50, Km 11, El Semillero, Uruguay
| | - M Macías-Rioseco
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, Ruta 50, Km 11, El Semillero, Uruguay
- California Animal Health and Food Safety (CAHFS) Laboratory, Tulare Branch, University of California at Davis, Tulare, CA, USA
| | - R D Caffarena
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, Ruta 50, Km 11, El Semillero, Uruguay
- Unidad Académica Salud de los Rumiantes, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - C S Silveira
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, Ruta 50, Km 11, El Semillero, Uruguay
| | - V Aráoz
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, Ruta 50, Km 11, El Semillero, Uruguay
| | - B Doncel Díaz
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, Ruta 50, Km 11, El Semillero, Uruguay
- Laboratorio de Patología Veterinaria Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Bogotá, Colombia
| | - F Giannitti
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, Ruta 50, Km 11, El Semillero, Uruguay
| | - M Fraga
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, Ruta 50, Km 11, El Semillero, Uruguay.
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25
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Wales A, Lawes J. JMM Profile: Salmonella enterica serovar Gallinarum, biovars Pullorum and Gallinarum. J Med Microbiol 2023; 72. [PMID: 36753431 DOI: 10.1099/jmm.0.001653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Salmonella
serovar Gallinarum has two distinct biovars, Pullorum and Gallinarum. They are host-adapted avian pathogens that infect a number of wild and domesticated species but they pose a particular threat to farmed and backyard chickens and turkeys. Both biovars cause invasive and septicaemic disease, often resulting in high mortality. Pullorum is transmitted in eggs and typically affects birds soon after hatch. Gallinarum may cause disease in any age of bird, which often progresses through mature flocks. The establishment of clean breeding stock has resulted in freedom from the pathogens in many countries although even in these territories sporadic incursions still occur.
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Affiliation(s)
- Andrew Wales
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, UK
| | - Joanna Lawes
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
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26
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The LysR-Type Transcription Regulator YhjC Promotes the Systemic Infection of Salmonella Typhimurium in Mice. Int J Mol Sci 2023; 24:ijms24021302. [PMID: 36674819 PMCID: PMC9867438 DOI: 10.3390/ijms24021302] [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: 12/12/2022] [Revised: 01/07/2023] [Accepted: 01/08/2023] [Indexed: 01/11/2023] Open
Abstract
Salmonella Typhimurium is a Gram-negative intestinal pathogen that can infect humans and a variety of animals, causing gastroenteritis or serious systemic infection. Replication within host macrophages is essential for S. Typhimurium to cause systemic infection. By analyzing transcriptome data, the expression of yhjC gene, which encodes a putative regulator in S. Typhimurium, was found to be significantly up-regulated after the internalization of Salmonella by macrophages. Whether yhjC gene is involved in S. Typhimurium systemic infection and the related mechanisms were investigated in this study. The deletion of yhjC reduced the replication ability of S. Typhimurium in macrophages and decreased the colonization of S. Typhimurium in mouse systemic organs (liver and spleen), while increasing the survival rate of the infected mice, suggesting that YhjC protein promotes systemic infection by S. Typhimurium. Furthermore, by using transcriptome sequencing and RT-qPCR assay, the transcription of several virulence genes, including spvD, iroCDE and zraP, was found to be down-regulated after the deletion of yhjC. Electrophoretic mobility shift assay showed that YhjC protein can directly bind to the promoter region of spvD and zraP to promote their transcription. These findings suggest that YhjC contributes to the systemic virulence of S. Typhimurium via the regulation of multiple virulence genes and YhjC could represent a promising target to control S. Typhimurium infection.
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27
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Molecular Detection of Virulence Factors in Salmonella serovars Isolated from Poultry and Human Samples. Vet Med Int 2023; 2023:1875253. [PMID: 36910894 PMCID: PMC9998162 DOI: 10.1155/2023/1875253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023] Open
Abstract
Salmonellosis is a common infectious disease in humans caused by Salmonella spp., which in recent years has shown an increase in its incidence, with products of avian origin being a common source of transmission. To present a successful infective cycle, there are molecular mechanisms such as virulence factors that provide characteristics that facilitate survival, colonization, and damage to the host. According to this, the study aims to characterize the virulence factors of Salmonella spp. strains isolated from broilers (n = 39) and humans (n = 10). The presence of 24 virulence genes was evaluated using end-point PCR. All the strains of Salmonella spp. isolated from broiler chickens revealed presence of 7/24 (29, 16%) virulence genes (lpfA, csgA, sitC, sipB, sopB, sopE, and sivH). Regarding the strains isolated from cases of gastroenteritis in humans, all strains contained (14/24, 58, 33%) virulence genes (lpfA, csgA, pagC, msgA, spiA, sitC, iroN, sipB, orgA, hilA, sopB, sifA, avrA, and sivH). In summary, the presence of virulence genes in different strains of Salmonella isolated from broilers and humans could be described as bacteria with potential pathogenicity due to the type and number of virulence genes detected. These findings are beneficial for the pathogenic monitoring of Salmonella in Colombia.
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28
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Pavon RDN, Mendoza PDG, Flores CAR, Calayag AMB, Rivera WL. Genotypic virulence profiles and associations in Salmonella isolated from meat samples in wet markets and abattoirs of Metro Manila, Philippines. BMC Microbiol 2022; 22:292. [PMID: 36474155 PMCID: PMC9724337 DOI: 10.1186/s12866-022-02697-6] [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: 08/09/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Salmonella are pathogenic foodborne bacteria with complex pathogenicity from numerous virulence genes housed in Salmonella pathogenicity islands (SPIs), plasmids, and other gene cassettes. However, Salmonella virulence gene distributions and mechanisms remain unestablished. In the Philippines, studies mainly report Salmonella incidences and antimicrobial resistance, but little to none on virulence profiles, their associations to animal sources, collection sites and Salmonella serogroups. Hence, a total of 799 Salmonella isolates, previously obtained from pig, cow, and chicken meat samples in wet markets and abattoirs (wet markets: 124 chicken, 151 cow, and 352 pig meat isolates; abattoirs: 172 pig tonsil and jejunum isolates) in Metro Manila, Philippines, were revived and confirmed as Salmonella through invA gene polymerase chain reaction (PCR). Isolates were then screened for eight virulence genes, namely avrA, hilA, sseC, mgtC, spi4R, pipB, spvC and spvR, by optimized multiplex PCR and significant pair associations between virulence genes were determined through Fisher's exact test. Gene frequency patterns were also determined. Salmonella serogroups in addition to animal sources and location types were also used to predict virulence genes prevalence using binary logistic regression. RESULTS High frequencies (64 to 98%) of SPI virulence genes were detected among 799 Salmonella isolates namely mgtC, pipB, avrA, hilA, spi4R and sseC, from most to least. However, only one isolate was positive for plasmid-borne virulence genes, spvC and spvR. Diversity in virulence genes across Salmonella serogroups for 587 Salmonella isolates (O:3 = 250, O:4 = 133, O:6,7 = 99, O:8 = 93, O:9 = 12) was also demonstrated through statistical predictions, particularly for avrA, hilA, sseC, and mgtC. mgtC, the most frequent virulence gene, was predicted by serogroup O:9, while sseC, the least frequent, was predicted by serogroup O:4 and chicken animal source. The highest virulence gene pattern involved SPIs 1-5 genes which suggests the wide distribution and high pathogenic potential of Salmonella. Statistical analyses showed five virulence gene pair associations, namely avrA and hilA, avrA and spi4R, hilA and spi4R, sseC and spi4R, and mgtC and pipB. The animal sources predicted the presence of virulence genes, sseC and pipB, whereas location type for hilA and spi4R, suggesting that these factors may contribute to the type and pathogenicity of Salmonella present. CONCLUSION The high prevalence of virulence genes among Salmonella in the study suggests the high pathogenic potential of Salmonella from abattoirs and wet markets of Metro Manila, Philippines which poses food safety and public health concerns and threatens the Philippine food animal industry. Statistical associations between virulence genes and prediction analyses across Salmonella serogroups and external factors such as animal source and location type and presence of virulence genes suggest the diversity of Salmonella virulence and illustrate determining factors to Salmonella pathogenicity. This study recommends relevant agencies in the Philippines to improve standards in food animal industries and increase efforts in monitoring of foodborne pathogens.
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Affiliation(s)
- Rance Derrick N. Pavon
- grid.11134.360000 0004 0636 6193Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, 1101 Philippines
| | - Paolo D. G. Mendoza
- grid.11134.360000 0004 0636 6193Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, 1101 Philippines
| | - Camille Andrea R. Flores
- grid.11134.360000 0004 0636 6193Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, 1101 Philippines
| | - Alyzza Marie B. Calayag
- grid.11134.360000 0004 0636 6193Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, 1101 Philippines
| | - Windell L. Rivera
- grid.11134.360000 0004 0636 6193Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, 1101 Philippines
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Hassena AB, Belmabrouk S, Amor MGB, Zormati S, Guermazi-Toumi S, Siala-Trigui M, Gdoura R. Study of Virulence Genes, Antimicrobial Resistance, and Genetic Relatedness of Foodborne Salmonella Isolates from Tunisia. J Food Prot 2022; 85:1779-1789. [PMID: 36135724 DOI: 10.4315/jfp-22-167] [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: 06/08/2022] [Accepted: 09/17/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT Nontyphoidal Salmonella strains are among the major foodborne pathogens with emerging multidrug-resistant phenotypes. In this study, antimicrobial susceptibility testing of a collection of Salmonella isolates (n = 54) recovered from poultry and bivalve molluscs was performed. The study also investigated profiling of virulence and resistance genes as well as phylogenetic relationships through pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting. Results revealed the presence of multiple virulence genes among Salmonella isolates. Salmonella intestinal infection A (siiA), Salmonella outer protein (sopB and sopE), putative 4-hydroxybutyrate coenzyme A transferase (cat2), Salmonella atypical fimbria C (safC), and Salmonella Enteritidis fimbria B (sefB) were present in most (83.32 to 100%) of the isolates, whereas the remaining tested genes (Salmonella plasmid virulence [spvC and spvB]), and the sopE gene, were exclusively detected within the serotype Enteritidis. The highest resistance rates were observed for oxacillin (94.4%), ampicillin (37%), and nalidixic acid (27.7%), followed by cefotaxime and amoxicillin-clavulanic acid (14.8%), trimethoprim-sulfamethoxazole (9.3%), and ciprofloxacin (5.5%). The results indicate that the Salmonella Enteritidis serotype possessed the widest range of virulence determinants and increasing levels of resistance. Such high-risk clones should be particularly controlled in Tunisia. Overall, increased resistance and virulence confer a selective advantage for the evolution of these bacteria and represent an alarming problem for global public health. The genetic study via PFGE and ERIC-PCR showed the high diversity of the clonal origins of these bacteria and the sources of contamination and revealed the great capacity of Salmonella to diversify within food-producing animals. HIGHLIGHTS
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Affiliation(s)
- Amal Ben Hassena
- Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences of Sfax, Tunisia
| | - Sabrine Belmabrouk
- Molecular and Cellular Screening Process Laboratory, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Maroua Gdoura-Ben Amor
- Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences of Sfax, Tunisia
| | - Sonia Zormati
- Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences of Sfax, Tunisia.,Regional Center of Veterinary Research of Sfax, Sfax, Tunisia
| | - Sonda Guermazi-Toumi
- Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences of Sfax, Tunisia.,Department of Biotechnology and Health, Higher Institute of Biotechnology of Sfax, Sfax, Tunisia
| | - Mariam Siala-Trigui
- Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences of Sfax, Tunisia.,Department of Biology, Preparatory Institute for Engineering Studies of Sfax, University of Sfax, Sfax, Tunisia
| | - Radhouane Gdoura
- Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences of Sfax, Tunisia
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Lactobacilli, a Weapon to Counteract Pathogens through the Inhibition of Their Virulence Factors. J Bacteriol 2022; 204:e0027222. [PMID: 36286515 PMCID: PMC9664955 DOI: 10.1128/jb.00272-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To date, several studies have reported an alarming increase in pathogen resistance to current antibiotic therapies and treatments. Therefore, the search for effective alternatives to counter their spread and the onset of infections is becoming increasingly important.
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Khan M, Shamim S. Understanding the Mechanism of Antimicrobial Resistance and Pathogenesis of Salmonella enterica Serovar Typhi. Microorganisms 2022; 10:2006. [PMID: 36296282 PMCID: PMC9606911 DOI: 10.3390/microorganisms10102006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Salmonella enterica serovar Typhi (S. Typhi) is a Gram-negative pathogen that causes typhoid fever in humans. Though many serotypes of Salmonella spp. are capable of causing disease in both humans and animals alike, S. Typhi and S. Paratyphi are common in human hosts only. The global burden of typhoid fever is attributable to more than 27 million cases each year and approximately 200,000 deaths worldwide, with many regions such as Africa, South and Southeast Asia being the most affected in the world. The pathogen is able to cause disease in hosts by evading defense systems, adhesion to epithelial cells, and survival in host cells in the presence of several virulence factors, mediated by virulence plasmids and genes clustered in distinct regions known as Salmonella pathogenicity islands (SPIs). These factors, coupled with plasmid-mediated antimicrobial resistance genes, enable the bacterium to become resistant to various broad-spectrum antibiotics used in the treatment of typhoid fever and other infections caused by Salmonella spp. The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains in many countries of the world has raised great concern over the rise of antibiotic resistance in pathogens such as S. Typhi. In order to identify the key virulence factors involved in S. Typhi pathogenesis and infection, this review delves into various mechanisms of virulence, pathogenicity, and antimicrobial resistance to reinforce efficacious disease management.
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Affiliation(s)
| | - Saba Shamim
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Defence Road Campus, Lahore 54000, Pakistan
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32
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Khajanchi BK, Foley SL. Antimicrobial Resistance and Increased Virulence of Salmonella. Microorganisms 2022; 10:microorganisms10091829. [PMID: 36144431 PMCID: PMC9504589 DOI: 10.3390/microorganisms10091829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 11/25/2022] Open
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Chen J, Ed-Dra A, Zhou H, Wu B, Zhang Y, Yue M. Antimicrobial resistance and genomic investigation of non-typhoidal Salmonella isolated from outpatients in Shaoxing city, China. Front Public Health 2022; 10:988317. [PMID: 36176509 PMCID: PMC9513250 DOI: 10.3389/fpubh.2022.988317] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/17/2022] [Indexed: 01/26/2023] Open
Abstract
Human non-typhoidal salmonellosis is among the leading cause of morbidity and mortality worldwide, resulting in huge economic losses and threatening the public health systems. To date, epidemiological characteristics of non-typhoidal Salmonella (NTS) implicated in human salmonellosis in China are still obscure. Herein, we investigate the antimicrobial resistance and genomic features of NTS isolated from outpatients in Shaoxing city in 2020. Eighty-seven Salmonella isolates were recovered and tested against 28 different antimicrobial agents, representing 12 categories. The results showed high resistance to cefazolin (86.21%), streptomycin (81.61%), ampicillin (77.01%), ampicillin-sulbactam (74.71%), doxycycline (72.41%), tetracycline (71.26%), and levofloxacin (70.11%). Moreover, 83.91% of isolates were resistant to ≥3 categories, which were considered multi-drug resistant (MDR). Whole-genome sequencing (WGS) combined with bioinformatic analysis was used to predict serovars, MLST types, plasmid replicons, antimicrobial resistance genes, and virulence genes, in addition to the construction of phylogenomic to determine the epidemiological relatedness between isolates. Fifteen serovars and 16 STs were identified, with the dominance of S. I 4, [5], 12:i:- ST34 (25.29%), S. Enteritidis ST11 (22.99%), and S. Typhimurium ST19. Additionally, 50 resistance genes representing ten categories were detected with a high prevalence of aac(6')-Iaa (100%), bla TEM-1B (65.52%), and tet(A) (52.87%), encoding resistance to aminoglycosides, β-lactams, and tetracyclines, respectively; in addition to chromosomic mutations affecting gyrA gene. Moreover, we showed the detection of 18 different plasmids with the dominance of IncFIB(S) and IncFII(S) (39.08%). Interestingly, all isolates harbor the typical virulence genes implicated in the virulence mechanisms of Salmonella, while one isolate of S. Jangwani contains the cdtB gene encoding typhoid toxin production. Furthermore, the phylogenomic analysis showed that all isolates of the same serovar are very close to each other and clustered together in the same clade. Together, we showed a high incidence of MDR among the studied isolates which is alarming for public health services and is a major threat to the currently available treatments to deal with human salmonellosis; hence, efforts should be gathered to further introduce WGS in routinely monitoring of AMR Salmonella in the medical field in order to enhance the effectiveness of surveillance systems and to limit the spread of MDR clones.
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Affiliation(s)
- Jiancai Chen
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | | | - Haiyang Zhou
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Beibei Wu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yunyi Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China,*Correspondence: Yunyi Zhang
| | - Min Yue
- Hainan Institute of Zhejiang University, Sanya, China,Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China,Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China,Min Yue
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34
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Calarga AP, Gontijo MTP, de Almeida LGP, de Vasconcelos ATR, Nascimento LC, de Moraes Barbosa TMC, de Carvalho Perri TM, Dos Santos SR, Tiba-Casas MR, Marques EGL, Ferreira CM, Brocchi M. Antimicrobial resistance and genetic background of non-typhoidal Salmonella enterica strains isolated from human infections in São Paulo, Brazil (2000-2019). Braz J Microbiol 2022; 53:1249-1262. [PMID: 35446010 PMCID: PMC9433476 DOI: 10.1007/s42770-022-00748-8] [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: 12/11/2021] [Accepted: 03/30/2022] [Indexed: 11/02/2022] Open
Abstract
Salmonella enterica causes Salmonellosis, an important infection in humans and other animals. The number of multidrug-resistant (MDR) phenotypes associated with Salmonella spp. isolates is increasing worldwide, causing public health concern. Here, we aim to characterize the antimicrobial-resistant phenotype of 789 non-typhoidal S. enterica strains isolated from human infections in the state of São Paulo, Brazil, along 20 years (2000-2019). Among the non-susceptible isolates, 31.55, 14.06, and 13.18% were resistant to aminoglycosides, tetracycline, and β-lactams, respectively. Moreover, 68 and 11 isolates were considered MDR and Extended Spectrum β-Lactamase (ESBL) producers, respectively, whereas one isolate was colistin-resistant. We selected four strains to obtain a draft of the Genome Sequence; one S. Infantis (ST32), one S. Enteritidis (ST11), one S. I 4,[5],12:i:- (ST19), and one S. Typhimurium (ST313). Among them, three presented at least one of the following antimicrobial resistance genes (AMR) linked to mobile DNA: blaTEM-1B, dfrA1, tetA, sul1, floR, aac(6')-laa, and qnrE1. This is the first description of the plasmid-mediated quinolone resistance (PMQR) gene qnrE1 in a clinical isolate of S. I 4,[5],12:i:-. The S. Typhimurium is a colistin-resistant isolate, but did not harbor mcr genes, but it presented mutations within the mgrB, pmrB, and pmrC regions that might be linked to the colistin-resistant phenotype. The virulence pattern of the four isolates resembled the virulence pattern of the highly pathogenic S. Typhimurium UK-1 reference strain in assays involving the in vivo Galleria mellonella model. In conclusion, most isolates studied here are susceptible, but a small percentage present an MDR or ESBL-producer and pathogenic phenotype. Sequence analyses revealed plasmid-encoded AMR genes, such as β-lactam and fluoroquinolone resistance genes, indicating that these characteristics can be potentially disseminated among other bacterial strains.
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Affiliation(s)
- Aline Parolin Calarga
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), 255 Monteiro Lobato St, Campinas, São Paulo, 13083-650, Brazil.
| | - Marco Tulio Pardini Gontijo
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), 255 Monteiro Lobato St, Campinas, São Paulo, 13083-650, Brazil
| | | | | | - Leandro Costa Nascimento
- Central Laboratory for High Performance Technologies (LaCTAD), University of Campinas (UNICAMP), Campinas, São Paulo, 13083-886, Brazil
| | | | | | - Silvia Regina Dos Santos
- Division of Clinical Laboratory of the University Hospital of São Paulo, University of São Paulo (USP), São Paulo, São Paulo, 05508-000, Brazil
| | | | | | - Cleide Marques Ferreira
- Adolfo Lutz Institute, Regional Laboratory Center Campinas III, Campinas, São Paulo, 13035-420, Brazil
| | - Marcelo Brocchi
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), 255 Monteiro Lobato St, Campinas, São Paulo, 13083-650, Brazil.
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Identification and Characterisation of pST1023 A Mosaic, Multidrug-Resistant and Mobilisable IncR Plasmid. Microorganisms 2022; 10:microorganisms10081592. [PMID: 36014010 PMCID: PMC9412624 DOI: 10.3390/microorganisms10081592] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/01/2022] [Accepted: 08/04/2022] [Indexed: 11/22/2022] Open
Abstract
We report the identification and characterisation of a mosaic, multidrug-resistant and mobilisable IncR plasmid (pST1023) detected in Salmonella ST1023, a monophasic variant 4,[5],12:i: strain of widespread pandemic lineage, reported as a Southern European clone. pST1023 contains exogenous DNA regions, principally gained from pSLT-derivatives and IncI1 plasmids. Acquisition from IncI1 included oriT and nikAB and these conferred the ability to be mobilisable in the presence of a helper plasmid, as we demonstrated with the conjugative plasmids pST1007-1D (IncFII) or pVC1035 (IncC). A sul3-associated class 1 integron, conferring resistance to aminoglycosides, chloramphenicol and trimethoprim-sulphonamides, was also embedded in the acquired IncI1 DNA segment. pST1023 also harboured an additional site-specific recombination system (rfsF/rsdB) and IS elements of the IS1, IS5 (IS903 group) and IS6 families. Four of the six IS26 elements present constituted two pseudo-compound-transposons, named PCT-sil and PCT-Tn10 (identified here for the first time). The study further highlighted the mosaic genetic architecture and the clinical importance of IncR plasmids. Moreover, it provides the first experimental data on the ability of IncR plasmids to be mobilised and their potential role in the horizontal spread of antimicrobial-resistant genes.
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Role of RpoS in Regulating Stationary Phase Salmonella Typhimurium Pathogenesis-Related Stress Responses under Physiological Low Fluid Shear Force Conditions. mSphere 2022; 7:e0021022. [PMID: 35913142 PMCID: PMC9429890 DOI: 10.1128/msphere.00210-22] [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] [Indexed: 11/24/2022] Open
Abstract
The discovery that biomechanical forces regulate microbial virulence was established with the finding that physiological low fluid shear (LFS) forces altered gene expression, stress responses, and virulence of the enteric pathogen Salmonella enterica serovar Typhimurium during the log phase. These log phase LFS-induced phenotypes were independent of the master stress response regulator, RpoS (σS). Given the central importance of RpoS in regulating stationary-phase stress responses of S. Typhimurium cultured under conventional shake flask and static conditions, we examined its role in stationary-phase cultures grown under physiological LFS. We constructed an isogenic rpoS mutant derivative of wild-type S. Typhimurium and compared the ability of these strains to survive in vitro pathogenesis-related stresses that mimic those encountered in the infected host and environment. We also compared the ability of these strains to colonize (adhere, invade, and survive within) human intestinal epithelial cell cultures. Unexpectedly, LFS-induced resistance of stationary-phase S. Typhimurium cultures to acid and bile salts stresses did not rely on RpoS. Likewise, RpoS was dispensable for stationary-phase LFS cultures to adhere to and survive within intestinal epithelial cells. In contrast, the resistance of these cultures to challenges of oxidative and thermal stresses, and their invasion into intestinal epithelial cells was influenced by RpoS. These findings expand our mechanistic understanding of how physiological fluid shear forces modulate stationary-phase S. Typhimurium physiology in unexpected ways and provide clues into microbial mechanobiology and nuances of Salmonella responses to microenvironmental niches in the infected host. IMPORTANCE Bacterial pathogens respond dynamically to a variety of stresses in the infected host, including physical forces of fluid flow (fluid shear) across their surfaces. While pathogens experience wide fluctuations in fluid shear during infection, little is known about how these forces regulate microbial pathogenesis. This is especially important for stationary-phase bacterial growth, which is a critical period to understand microbial resistance, survival, and infection potential, and is regulated in many bacteria by the general stationary-phase stress response protein RpoS. Here, we showed that, unlike conventional culture conditions, several stationary-phase Salmonella pathogenic stress responses were not impacted by RpoS when bacteria were cultured under fluid shear conditions relevant to those encountered in the intestine of the infected host. These findings offer new insight into how physiological fluid shear forces encountered by Salmonella during infection might impact pathogenic responses in unexpected ways that are relevant to their disease-causing ability.
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Dawan J, Ahn J. Bacterial Stress Responses as Potential Targets in Overcoming Antibiotic Resistance. Microorganisms 2022; 10:microorganisms10071385. [PMID: 35889104 PMCID: PMC9322497 DOI: 10.3390/microorganisms10071385] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/03/2022] [Accepted: 07/08/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteria can be adapted to adverse and detrimental conditions that induce general and specific responses to DNA damage as well as acid, heat, cold, starvation, oxidative, envelope, and osmotic stresses. The stress-triggered regulatory systems are involved in bacterial survival processes, such as adaptation, physiological changes, virulence potential, and antibiotic resistance. Antibiotic susceptibility to several antibiotics is reduced due to the activation of stress responses in cellular physiology by the stimulation of resistance mechanisms, the promotion of a resistant lifestyle (biofilm or persistence), and/or the induction of resistance mutations. Hence, the activation of bacterial stress responses poses a serious threat to the efficacy and clinical success of antibiotic therapy. Bacterial stress responses can be potential targets for therapeutic alternatives to antibiotics. An understanding of the regulation of stress response in association with antibiotic resistance provides useful information for the discovery of novel antimicrobial adjuvants and the development of effective therapeutic strategies to control antibiotic resistance in bacteria. Therefore, this review discusses bacterial stress responses linked to antibiotic resistance in Gram-negative bacteria and also provides information on novel therapies targeting bacterial stress responses that have been identified as potential candidates for the effective control of Gram-negative antibiotic-resistant bacteria.
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Affiliation(s)
- Jirapat Dawan
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Korea;
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Korea;
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Gangwon, Korea
- Correspondence: ; Tel.: +82-33-250-6564
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Cheng RA, Orsi RH, Wiedmann M. The Number and Type of Chaperone-Usher Fimbriae Reflect Phylogenetic Clade Rather than Host Range in Salmonella. mSystems 2022; 7:e0011522. [PMID: 35467401 PMCID: PMC9238391 DOI: 10.1128/msystems.00115-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/03/2022] [Indexed: 01/21/2023] Open
Abstract
Salmonella is one of the most successful foodborne pathogens worldwide, owing in part to its ability to colonize or infect a wide range of hosts. Salmonella serovars are known to encode a variety of different fimbriae (hairlike organelles that facilitate binding to surfaces); however, the distribution, number, and sequence diversity of fimbriae encoded across different lineages of Salmonella were unknown. We queried whole-genome sequence (WGS) data for 242 Salmonella enterica subsp. enterica (subspecies enterica) isolates from the top 217 serovars associated with isolation from humans and agricultural animals; this effort identified 2,894 chaperone-usher (CU)-type fimbrial usher sequences, representing the most conserved component of CU fimbriae. On average, isolates encoded 12 different CU fimbrial ushers (6 to 18 per genome), although the distribution varied significantly (P = 1.328E-08) by phylogenetic clade, with isolates in section Typhi having significantly fewer fimbrial ushers than isolates in clade A2 (medians = 10 and 12 ushers, respectively). Characterization of fimbriae in additional non-enterica subspecies genomes suggested that 8 fimbrial ushers were classified as being unique to subspecies enterica isolates, suggesting that the majority of fimbriae were most likely acquired prior to the divergence of subspecies enterica. Characterization of mobile elements suggested that plasmids represent an important vehicle facilitating the acquisition of a wide range of fimbrial ushers, particularly for the acquisition of fimbriae from other Gram-negative genera. Overall, our results suggest that differences in the number and type of fimbriae encoded most likely reflect differences in phylogenetic clade rather than differences in host range. IMPORTANCE Fimbriae of the CU assembly pathway represent important organelles that mediate Salmonella's interactions with host tissues and abiotic surfaces. Our analyses provide a comprehensive overview of the diversity of CU fimbriae in Salmonella spp., highlighting that the majority of CU fimbriae are distributed broadly across multiple subspecies and suggesting that acquisition most likely occurred prior to the divergence of subspecies enterica. Our data also suggest that plasmids represent the primary vehicles facilitating the horizontal transfer of diverse CU fimbriae in Salmonella. Finally, the observed high sequence similarity between some ushers suggests that different names may have been assigned to closely related fimbrial ushers that likely should be represented by a single designation. This highlights the need to establish standard criteria for fimbria classification and nomenclature, which will also facilitate future studies seeking to associate virulence factors with adaptation to or differences in the likelihood of causing disease in a given host.
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Affiliation(s)
- Rachel A. Cheng
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Renato H. Orsi
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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Weng R, Gu Y, Zhang W, Hou X, Wang H, Tao J, Deng M, Zhou M, Zhao Y. Whole-Genome Sequencing Provides Insight Into Antimicrobial Resistance and Molecular Characteristics of Salmonella From Livestock Meat and Diarrhea Patient in Hanzhong, China. Front Microbiol 2022; 13:899024. [PMID: 35756010 PMCID: PMC9219581 DOI: 10.3389/fmicb.2022.899024] [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: 03/18/2022] [Accepted: 04/15/2022] [Indexed: 11/13/2022] Open
Abstract
Salmonella is a major zoonotic pathogen, which usually contaminates food resulting in salmonellosis in humans. Exploring the characteristics and origins of Salmonella is essential in formulating prevention and control measures for Salmonella infection. We used slide agglutination, antimicrobial susceptibility testing, and whole-genome sequencing to analyze and compare Salmonella’s phenotype, genotyping diversity, and genetic relatedness from livestock meat and diarrhea patients in Hanzhong, China, from 2018 to 2020. Totally 216 Salmonella enterica isolates were screened from frozen whole chicken carcasses (44.3%, 70/158), frozen raw ground pork (36.2%, 59/163), and diarrhea patients (4.4%, 87/1964). Salmonella Typhimurium was the dominant serotype. Notably, compared with other sources, isolates obtained from frozen whole chicken carcasses showed significant resistance to third-generation cephalosporin and fluoroquinolones (p < 0.05). All strains were assigned into 36 sequence types (STs) and two novel STs, and an excellent consistency was observed between ST and serotype. Genomic data revealed that extended-spectrum β-lactamase genes were responsible for third-generation cephalosporin resistance in 52 Salmonella strains, and the most predominant resistance determinant was blaCTX–M. Furthermore, of the 60 ciprofloxacin-resistant isolates, five single-base mutations in quinolone resistance-determining regions were identified in gyrA or parC, and the plasmid-mediated quinolone resistance gene aac(6’)Ib-cr was most often detected. The cgMLST clusters show that five clusters among four serotypes (including S. Typhimurium, S. London, S. Derby, and S. Agona) cover samples from diarrhea patients and livestock meat pathway isolate, indicating a possibility of cross-host transmission. In conclusion, the livestock meat isolates have a higher level of resistance than diarrhea patients’ isolates and could be an essential source of human Salmonella infection.
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Affiliation(s)
- Rui Weng
- Department of Microbiology, School of Medicine, Xi'an Jiaotong University, Hanzhong, China.,Department of Medical Technology, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Yihai Gu
- Department of Microbiology, School of Medicine, Xi'an Jiaotong University, Hanzhong, China
| | - Wei Zhang
- Department of Microbiology, School of Medicine, Xi'an Jiaotong University, Hanzhong, China
| | - Xuan Hou
- Department of Microbiology, School of Medicine, Xi'an Jiaotong University, Hanzhong, China
| | - Hui Wang
- Department of Microbiology, School of Medicine, Xi'an Jiaotong University, Hanzhong, China
| | - Junqi Tao
- Department of Microbiology, School of Medicine, Xi'an Jiaotong University, Hanzhong, China
| | - Minghui Deng
- Department of Microbiology, School of Medicine, Xi'an Jiaotong University, Hanzhong, China
| | - Mengrong Zhou
- Department of Microbiology, School of Medicine, Xi'an Jiaotong University, Hanzhong, China
| | - Yifei Zhao
- The Second Clinical Medical College of Nanchang University, Nanchang, China
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Basit A, Tahir H, Haider Z, Tariq H, Ullah A, Rehman SU. CRISPR/Cas9-Based Deletion of SpvB Gene From Salmonella gallinarum Leads to Loss of Virulence in Chicken. Front Bioeng Biotechnol 2022; 10:885227. [PMID: 35769104 PMCID: PMC9234527 DOI: 10.3389/fbioe.2022.885227] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/25/2022] [Indexed: 12/03/2022] Open
Abstract
Salmonella Gallinarum causes fowl typhoid in poultry leading to a huge economic loss to the poultry industry. The large virulence plasmid of S. gallinarum has been associated with various systemic infections in poultry. A five-gene spanning region (spvRABCD) of 7.8 kb on the large plasmid mainly confers virulence to the bacteria. However, the exact role of these genes in virulence has not been elucidated yet. SpvB exhibits delayed cell death by preventing actin polymerization followed by apoptosis during intracellular infection. The specific role of SpvB in causing the disease is not known yet. In the current study, the SpvB gene was deleted through CRISPR/Cas9 method from a large virulent plasmid of locally isolated S. gallinarum strain (SG18). The homology-directed repair method was used for complete deletion of SpvB gene using the modified pCas9 plasmid. The SpvB-deleted S. gallinarum strain (ΔSpvB_SG18), when tested for its virulence in broiler chicken showed no diseases signs and mortality. In addition, the avirulent strain does not affect the bird’s weight and was rapidly cleared from the liver after infection. However, it cleared from the intestine only after 4–5 days, which suggests that the ΔSpvB_SG18 strain is unable to invade from the intestine to the liver. This is the first study to report a complete gene deletion from the S. gallinarum virulent plasmid and its effect. This method will be useful for the deletion of virulent genes from S. gallinarum, to study their role in pathogenesis, and to prepare an effective vaccine strain for controlling fowl typhoid in poultry.
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Affiliation(s)
- Abdul Basit
- *Correspondence: Abdul Basit, ; Shafiq Ur Rehman ,
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Bacillus-Based Direct-Fed Microbial Reduces the Pathogenic Synergy of a Coinfection with Salmonella enterica Serovar Choleraesuis and Porcine Reproductive and Respiratory Syndrome Virus. Infect Immun 2022; 90:e0057421. [PMID: 35254092 PMCID: PMC9022502 DOI: 10.1128/iai.00574-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Viral respiratory infections predispose lungs to bacterial coinfections causing a worse outcome than either infection alone. Porcine reproductive and respiratory syndrome virus (PRRSV) causes pneumonia in pigs and is often associated with bacterial coinfections. We examined the impact of providing weanling pigs a Bacillus-based direct-fed microbial (DFM) on the syndrome resulting from infection with either Salmonella enterica serotype Choleraesuis alone, or in combination with PRRSV. Nine days after the bacterial challenge, Salmonella was isolated from ileocecal lymph nodes of all challenged pigs regardless of DFM treatment. Compared to the single bacterial challenge, the dual challenge with Salmonella and PRRSV resulted in a pathogenic synergy exhibited by a higher rate of Salmonella colonization in the lung and a more extensive and severe interstitial pneumonia. Provision of DFM to dually challenged pigs reduced the rate of lung colonization by Salmonella, eliminated or reduced the presence of PRRSV in the lung, and reduced the extent and severity of gross lung pathology. Dually challenged pigs that received DFM had increased concentrations of interleukin 1 (IL-1) and IL-8 in lung lavage fluids, accompanied by increased expression in their blood cells of nucleotide-binding oligomerization domain receptor 2 (NOD2) and triggering receptor expressed in myeloid cells 1 (TREM-1) molecules. These changes in pulmonary inflammatory cytokine production and increased expression of NOD2 and TREM-1 suggest that the DFM exerted a systemic modulating effect on innate immunity. These observations are consistent with the notion that tonic stimulation by gut-derived microbial products can poise innate immunity to fight infections in the respiratory tract.
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Salmonella pSLT-encoded effector SpvB promotes RIPK3-dependent necroptosis in intestinal epithelial cells. Cell Death Dis 2022; 8:44. [PMID: 35110556 PMCID: PMC8810775 DOI: 10.1038/s41420-022-00841-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/04/2022] [Accepted: 01/20/2022] [Indexed: 12/30/2022]
Abstract
Salmonella is one of the most important worldwide zoonotic pathogens. After invading a host orally, the bacteria break through the intestinal epithelial barrier for further invasion. Intestinal epithelial cells (IECs) play a crucial role in maintaining the integrity of the intestinal epithelial barrier. Necroptosis is considered one of the virulence strategies utilized by invasive Salmonella. Our previous work has shown that SpvB, an effector encoded by S. Typhimurium virulence plasmid (pSLT), promotes bacterial translocation via the paracellular route. However, it is still unknown whether SpvB could promote bacterial invasion through disrupting the integrity of IECs. Here, we demonstrated that SpvB promoted necroptosis of IECs and contributed to the destruction of the intestinal barrier during Salmonella infection. We found that SpvB enhanced the protein level of receptor-interacting protein kinase 3 (RIPK3) through inhibiting K48-linked poly-ubiquitylation of RIPK3 and the degradation of the protein in an autophagy-dependent manner. The abundant accumulation of RIPK3 upregulated the phosphorylation of MLKL, which contributed to necroptosis. The damage to IECs ultimately led to the disruption of the intestinal barrier and aggravated infection. In vivo, SpvB promoted the pathogenesis of Salmonella, favoring intestinal injury and colonic necroptosis. Our findings reveal a novel function of Salmonella effector SpvB, which could facilitate salmonellosis by promoting necroptosis, and broaden our understanding of the molecular mechanisms of bacterial invasion.
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Medina-Santana JL, Ortega-Paredes D, de Janon S, Burnett E, Ishida M, Sauders B, Stevens M, Vinueza-Burgos C. Investigating the dynamics of Salmonella contamination in integrated poultry companies using a whole genome sequencing approach. Poult Sci 2022; 101:101611. [PMID: 34953378 PMCID: PMC8715213 DOI: 10.1016/j.psj.2021.101611] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/22/2022] Open
Abstract
The study of non-typhoid Salmonella in broiler integrations has been limited by the resolution of typing techniques. Although serotyping of Salmonella isolates is used as a traditional approach, it is not of enough resolution to clearly understand the dynamics of this pathogen within poultry companies. The aim of this research was to investigate the epidemiology and population dynamics of Salmonella serotypes in 2 poultry integrations using a whole genome sequencing approach. Two hundred and forty-three Salmonella isolates recovered from the broiler production chain of 2 integrated poultry companies were whole genome sequenced and analyzed with dedicated databases and bioinformatic software. The analyses of sequences revealed that S. Infantis was the most frequent serotype (82.3%). Most isolates showed a potential for resistance against medically important antibiotics and disinfectants. Furthermore, 97.5% of isolates harbored the pESI-like mega plasmid, that plays an important role in the global dissemination of AMR. SNP tree analysis showed that there were clones that are niche-specific while other ones were distributed throughout the broiler production chains. In this study, we demonstrated the potential of whole genome sequencing analysis for a comprehensive understanding of Salmonella distribution in integrated poultry companies. Data obtained with these techniques allow determination of the presence of genetic factors that play an important role in the environmental fitness and pathogenicity of Salmonella.
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Affiliation(s)
- José L Medina-Santana
- Unidad de investigación de Enfermedades Transmitidas por Alimentos y Resistencia a los Antimicrobianos (UNIETAR), Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Quito 170103, Ecuador
| | - David Ortega-Paredes
- Unidad de investigación de Enfermedades Transmitidas por Alimentos y Resistencia a los Antimicrobianos (UNIETAR), Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Quito 170103, Ecuador
| | - Sofia de Janon
- Unidad de investigación de Enfermedades Transmitidas por Alimentos y Resistencia a los Antimicrobianos (UNIETAR), Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Quito 170103, Ecuador
| | - Elton Burnett
- Institute of Parasitology, McGill University, Montreal, QC H9X3V9, Canada
| | - Maria Ishida
- Division of Food Laboratory, New York State Department of Agriculture and Markets, Albany, NY 12206, USA
| | - Brian Sauders
- Division of Food Laboratory, New York State Department of Agriculture and Markets, Albany, NY 12206, USA
| | | | - Christian Vinueza-Burgos
- Unidad de investigación de Enfermedades Transmitidas por Alimentos y Resistencia a los Antimicrobianos (UNIETAR), Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Quito 170103, Ecuador.
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Deng Q, Yang S, Sun L, Dong K, Li Y, Wu S, Huang R. Salmonella effector SpvB aggravates dysregulation of systemic iron metabolism via modulating the hepcidin-ferroportin axis. Gut Microbes 2022; 13:1-18. [PMID: 33475464 PMCID: PMC7833757 DOI: 10.1080/19490976.2020.1849996] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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
Iron withholding, an essential component of nutritional immunity, plays a fundamental role in host resistance to Salmonella infection. Our previous study showed that SpvB, an important pSLT-encoded cytotoxic effector, facilitated Salmonella pathogenesis within macrophages via perturbing cellular iron metabolism. However, the underlying mechanisms of SpvB in Salmonella-relevant disorders of systemic iron metabolism have not yet been identified. Here, we demonstrated that SpvB facilitated Salmonella to scavenge iron from the host by modulating the hepcidin-ferroportin axis, a key regulator of systemic iron metabolism. We observed that SpvB enhanced hepatic hepcidin synthesis in a STAT3-dependent manner, but not the BMP/SMAD pathway. This subsequently resulted in a reduction of the unique cellular iron exporter ferroportin, which facilitated hypoferremia and hepatic iron accumulation and ultimately countered the limitation of iron availability, thereby improving the chances of Salmonella survival and replication. Moreover, SpvB promoted the production of proinflammatory molecules associated with the infiltration of inflammatory cells via highly upregulating TREM-1 signaling. Our data supported a role of TREM-1 in SpvB-related dysregulation of host iron metabolism and suggested that targeting TREM-1 might provide a potential therapeutic strategy to prevent or alleviate Salmonella pathogenesis.
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Affiliation(s)
- Qifeng Deng
- Department of Medical Microbiology, School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou, Jiangsu, PR China,CONTACT Shuyan Wu Department of Medical Microbiology, School of Biology & Basic Medical Sciences, Medical College of Soochow University, No. 199, Ren Ai Road, Suzhou, Jiangsu 215123, PR China
| | - Sidi Yang
- Department of Medical Microbiology, School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou, Jiangsu, PR China,Rui Huang Department of Medical Microbiology, School of Biology & Basic Medical Sciences, Medical College of Soochow University, No. 199, Ren Ai Road, Suzhou, Jiangsu 215123, PR China
| | - Lanqing Sun
- Department of Medical Microbiology, School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou, Jiangsu, PR China
| | - Kedi Dong
- Department of Medical Microbiology, School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou, Jiangsu, PR China
| | - Yuanyuan Li
- Department of Medical Microbiology, School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou, Jiangsu, PR China
| | - Shuyan Wu
- Department of Medical Microbiology, School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou, Jiangsu, PR China,CONTACT Shuyan Wu Department of Medical Microbiology, School of Biology & Basic Medical Sciences, Medical College of Soochow University, No. 199, Ren Ai Road, Suzhou, Jiangsu 215123, PR China
| | - Rui Huang
- Department of Medical Microbiology, School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou, Jiangsu, PR China,Rui Huang Department of Medical Microbiology, School of Biology & Basic Medical Sciences, Medical College of Soochow University, No. 199, Ren Ai Road, Suzhou, Jiangsu 215123, PR China
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AB 5 Enterotoxin-Mediated Pathogenesis: Perspectives Gleaned from Shiga Toxins. Toxins (Basel) 2022; 14:toxins14010062. [PMID: 35051039 PMCID: PMC8779504 DOI: 10.3390/toxins14010062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Foodborne diseases affect an estimated 600 million people worldwide annually, with the majority of these illnesses caused by Norovirus, Vibrio, Listeria, Campylobacter, Salmonella, and Escherichia coli. To elicit infections in humans, bacterial pathogens express a combination of virulence factors and toxins. AB5 toxins are an example of such toxins that can cause various clinical manifestations, including dehydration, diarrhea, kidney damage, hemorrhagic colitis, and hemolytic uremic syndrome (HUS). Treatment of most bacterial foodborne illnesses consists of fluid replacement and antibiotics. However, antibiotics are not recommended for infections caused by Shiga toxin-producing E. coli (STEC) because of the increased risk of HUS development, although there are conflicting views and results in this regard. Lack of effective treatment strategies for STEC infections pose a public health threat during outbreaks; therefore, the debate on antibiotic use for STEC infections could be further explored, along with investigations into antibiotic alternatives. The overall goal of this review is to provide a succinct summary on the mechanisms of action and the pathogenesis of AB5 and related toxins, as expressed by bacterial foodborne pathogens, with a primary focus on Shiga toxins (Stx). The role of Stx in human STEC disease, detection methodologies, and available treatment options are also briefly discussed.
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Nikiema MEM, Kakou-Ngazoa S, Ky/Ba A, Sylla A, Bako E, Addablah AYA, Ouoba JB, Sampo E, Gnada K, Zongo O, Traoré KA, Sanou A, Bonkoungou IJO, Ouédraogo R, Barro N, Sangaré L. Characterization of virulence factors of Salmonella isolated from human stools and street food in urban areas of Burkina Faso. BMC Microbiol 2021; 21:338. [PMID: 34895140 PMCID: PMC8665542 DOI: 10.1186/s12866-021-02398-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 11/24/2021] [Indexed: 01/19/2023] Open
Abstract
Background This study was undertaken to identify and functionally characterize virulence genes from Salmonella isolates in street food and stool cultures. From February 2017 to May 2018, clinical and food Salmonella strains were isolated in three regions in Burkina Faso. Salmonella was serotyped according to the White-Kauffmann-Le Minor method, and polymerase chain reaction (PCR) was used to detec invA, spvR, spvC, fimA and stn virulence genes commonly associated with salmonellosis in Sub-Saharan Africa. Results A total of 106 Salmonella isolates (77 human stools; 14 sandwiches) was analyzed using a serological identification with an O-group test reagent. The presence of Salmonella was confirmed in 86% (91/106) of the samples were reactive (OMA-positive/OMB-positive). Salmonella serogroup O:4,5 was the most common serogroup detected (40%; 36/91). Salmonella Enteritidis and Typhimurium represented 5.5% (5/91) and 3.3% (3/91), respectively and were identified only from clinical isolates. Furthermore, 14 serotypes of Salmonella (12/91 human strains and 2/15 sandwich strains) were evocative of Kentucky/Bargny serotype. For the genetic profile, 66% (70/106) of the Salmonella had invA and stn genes; 77.4% (82/106) had the fimA gene. The spvR gene was found in 36.8% (39/106) of the isolates while 48.1% (51/106) had the spvC gene. Among the identified Salmonella Enteritidis and Salmonella Typhimurium isolated from stools, the virulence genes detected were invA (3/5) versus (2/3), fimA (4/5) versus (3/3), stn (3/5) versus (2/3), spvR (4/5) versus (2/3) and spvC (3/5) versus (2/3), respectively. Conclusion This study reports the prevalence of Salmonella serotypes and virulence genes in clinical isolates and in street foods. It shows that food could be a significant source of Salmonella transmission to humans. Our results could help decision-making by the Burkina Faso health authority in the fight against street food-related diseases, in particular by training restaurateurs in food hygiene.
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Affiliation(s)
- Marguerite E M Nikiema
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA). Ecole Doctorale Sciences et Technologies, Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso. .,Plateforme de Biologie Moléculaire, Institut Pasteur de Côte d'Ivoire, Abidjan, Côte d'Ivoire. .,Service de Bactériologie-Virologie, CHU-Yalgado OUEDRAOGO, 03 BP 7022, Ouagadougou, Burkina Faso.
| | - Solange Kakou-Ngazoa
- Plateforme de Biologie Moléculaire, Institut Pasteur de Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Absatou Ky/Ba
- Laboratoire de Bactériologie-Virologie, CHU-Bogodogo, Ouagadougou, Burkina Faso
| | - Aboubacar Sylla
- Plateforme de Biologie Moléculaire, Institut Pasteur de Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Evariste Bako
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA). Ecole Doctorale Sciences et Technologies, Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso
| | | | - Jean Bienvenue Ouoba
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA). Ecole Doctorale Sciences et Technologies, Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso
| | - Emmanuel Sampo
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA). Ecole Doctorale Sciences et Technologies, Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso.,Hôpital Protestant Schiphra, 07 BP 5246, Ouagadougou, 07, Burkina Faso
| | - Kobo Gnada
- Centre MURAZ, Bobo-Dioulasso, Burkina Faso
| | - Oumarou Zongo
- Laboratoire de Biochimie et Immunologie Appliquées (LABIA), Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso
| | - Kuan Abdoulaye Traoré
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA). Ecole Doctorale Sciences et Technologies, Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso
| | - Adama Sanou
- Centre MURAZ, Bobo-Dioulasso, Burkina Faso.,Université Nazi Boni, 01 BP 1091, Bobo-Dioulasso, 01, Burkina Faso
| | - Isidore Juste Ouindgueta Bonkoungou
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA). Ecole Doctorale Sciences et Technologies, Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso
| | - Rasmata Ouédraogo
- Laboratoire de Bactériologie-Virologie, CHU-Pédiatrie Charles De Gaulle, 01 BP 1198 BP, Ouagadougou, 01, Burkina Faso
| | - Nicolas Barro
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA). Ecole Doctorale Sciences et Technologies, Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso
| | - Lassana Sangaré
- Service de Bactériologie-Virologie, CHU-Yalgado OUEDRAOGO, 03 BP 7022, Ouagadougou, Burkina Faso
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Chen D, Burford WB, Pham G, Zhang L, Alto LT, Ertelt JM, Winter MG, Winter SE, Way SS, Alto NM. Systematic reconstruction of an effector-gene network reveals determinants of Salmonella cellular and tissue tropism. Cell Host Microbe 2021; 29:1531-1544.e9. [PMID: 34536347 DOI: 10.1016/j.chom.2021.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/24/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022]
Abstract
The minimal genetic requirements for microbes to survive within multiorganism communities, including host-pathogen interactions, remain poorly understood. Here, we combined targeted gene mutagenesis with phenotype-guided genetic reassembly to identify a cooperative network of SPI-2 T3SS effector genes that are sufficient for Salmonella Typhimurium (STm) to cause disease in a natural host organism. Five SPI-2 effector genes support pathogen survival within the host cell cytoplasm by coordinating bacterial replication with Salmonella-containing vacuole (SCV) division. Unexpectedly, this minimal genetic repertoire does not support STm systemic infection of mice. In vivo screening revealed a second effector-gene network, encoded by the spv operon, that expands the life cycle of STm from growth in cells to deep-tissue colonization in a murine model of typhoid fever. Comparison between Salmonella infection models suggests how cooperation between effector genes drives tissue tropism in a pathogen group.
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Affiliation(s)
- Didi Chen
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wesley B Burford
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Giang Pham
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Lishu Zhang
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Laura T Alto
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - James M Ertelt
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Maria G Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sing Sing Way
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Neal M Alto
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Luo L, Payne M, Kaur S, Hu D, Cheney L, Octavia S, Wang Q, Tanaka MM, Sintchenko V, Lan R. Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing. Microb Genom 2021; 7. [PMID: 34292145 PMCID: PMC8477392 DOI: 10.1099/mgen.0.000605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica serovar Enteritidis is a major cause of foodborne Salmonella infections and outbreaks in humans. Effective surveillance and timely outbreak detection are essential for public health control. Multilevel genome typing (MGT) with multiple levels of resolution has been previously demonstrated as a promising tool for this purpose. In this study, we developed MGT with nine levels for S. Enteritidis and characterised the genomic epidemiology of S. Enteritidis in detail. We examined 26 670 publicly available S. Enteritidis genome sequences from isolates spanning 101 years from 86 countries to reveal their spatial and temporal distributions. Using the lower resolution MGT levels, globally prevalent and regionally restricted sequence types (STs) were identified; avian associated MGT4-STs were found that were common in human cases in the USA; temporal trends were observed in the UK with MGT5-STs from 2014 to 2018 revealing both long lived endemic STs and the rapid expansion of new STs. Using MGT3 to MGT6, we identified multidrug resistance (MDR) associated STs at various MGT levels, which improves precision of detection and global tracking of MDR clones. We also found that the majority of the global S. Enteritidis population fell within two predominant lineages, which had significantly different propensity of causing large scale outbreaks. An online open MGT database has been established for unified international surveillance of S. Enteritidis. We demonstrated that MGT provides a flexible and high-resolution genome typing tool for S. Enteritidis surveillance and outbreak detection.
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Affiliation(s)
- Lijuan Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Dalong Hu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Liam Cheney
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Westmead Hospital, New South Wales, Australia
| | - Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Westmead Hospital, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
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Wójcicki M, Świder O, Daniluk KJ, Średnicka P, Akimowicz M, Roszko MŁ, Sokołowska B, Juszczuk-Kubiak E. Transcriptional Regulation of the Multiple Resistance Mechanisms in Salmonella-A Review. Pathogens 2021; 10:pathogens10070801. [PMID: 34202800 PMCID: PMC8308502 DOI: 10.3390/pathogens10070801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 02/07/2023] Open
Abstract
The widespread use of antibiotics, especially those with a broad spectrum of activity, has resulted in the development of multidrug resistance in many strains of bacteria, including Salmonella. Salmonella is among the most prevalent causes of intoxication due to the consumption of contaminated food and water. Salmonellosis caused by this pathogen is pharmacologically treated using antibiotics such as fluoroquinolones, ceftriaxone, and azithromycin. This foodborne pathogen developed several molecular mechanisms of resistance both on the level of global and local transcription modulators. The increasing rate of antibiotic resistance in Salmonella poses a significant global concern, and an improved understanding of the multidrug resistance mechanisms in Salmonella is essential for choosing the suitable antibiotic for the treatment of infections. In this review, we summarized the current knowledge of molecular mechanisms that control gene expression related to antibiotic resistance of Salmonella strains. We characterized regulators acting as transcription activators and repressors, as well as two-component signal transduction systems. We also discuss the background of the molecular mechanisms of the resistance to metals, regulators of multidrug resistance to antibiotics, global regulators of the LysR family, as well as regulators of histone-like proteins.
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Affiliation(s)
- Michał Wójcicki
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.A.)
| | - Olga Świder
- Department of Food Safety and Chemical Analysis, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (O.Ś.); (M.Ł.R.)
| | - Kamila J. Daniluk
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (K.J.D.); (B.S.)
| | - Paulina Średnicka
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.A.)
| | - Monika Akimowicz
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.A.)
| | - Marek Ł. Roszko
- Department of Food Safety and Chemical Analysis, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (O.Ś.); (M.Ł.R.)
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (K.J.D.); (B.S.)
| | - Edyta Juszczuk-Kubiak
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.A.)
- Correspondence: ; Tel.: +48-22-6063605
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50
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Vázquez X, García P, García V, de Toro M, Ladero V, Heinisch JJ, Fernández J, Rodicio R, Rodicio MR. Genomic analysis and phylogenetic position of the complex IncC plasmid found in the Spanish monophasic clone of Salmonella enterica serovar Typhimurium. Sci Rep 2021; 11:11482. [PMID: 34075064 PMCID: PMC8169936 DOI: 10.1038/s41598-021-90299-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 05/07/2021] [Indexed: 11/12/2022] Open
Abstract
pUO-STmRV1 is an IncC plasmid discovered in the Spanish clone of the emergent monophasic variant of Salmonella enterica serovar Typhimurium, which has probably contributed to its epidemiological success. The sequence of the entire plasmid determined herein revealed a largely degenerated backbone with accessory DNA incorporated at four different locations. The acquired DNA constitutes more than two-thirds of the pUO-STmRV1 genome and originates from plasmids of different incompatibility groups, including IncF (such as R100 and pSLT, the virulence plasmid specific of S. Typhimurium), IncN and IncI, from the integrative element GIsul2, or from yet unknown sources. In addition to pSLT virulence genes, the plasmid carries genes conferring resistance to widely-used antibiotics and heavy metals, together with a wealth of genetic elements involved in DNA mobility. The latter comprise class 1 integrons, transposons, pseudo-transposons, and insertion sequences, strikingly with 14 copies of IS26, which could have played a crucial role in the assembly of the complex plasmid. Typing of pUO-STmRV1 revealed backbone features characteristically associated with type 1 and type 2 IncC plasmids and could therefore be regarded as a hybrid plasmid. However, a rooted phylogenetic tree based on core genes indicates that it rather belongs to an ancient lineage which diverged at an early stage from the branch leading to most extant IncC plasmids detected so far. pUO-STmRV1 may have evolved at a time when uncontrolled use of antibiotics and biocides favored the accumulation of multiple resistance genes within an IncC backbone. The resulting plasmid thus allowed the Spanish clone to withstand a wide variety of adverse conditions, while simultaneously promoting its own propagation through vertical transmission.
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Affiliation(s)
- Xenia Vázquez
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006, Oviedo, Spain.,Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011, Oviedo, Spain
| | - Patricia García
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006, Oviedo, Spain.,Department of Microbiology, University Hospital A Coruña (CHUAC)-Biomedical Research Institute A Coruña (INIBIC), 15006, A Coruña, Spain
| | - Vanesa García
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006, Oviedo, Spain.,Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Universidade de Santiago de Compostela (USC), 27002, Lug, Spain
| | - María de Toro
- Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006, Logroño, Spain
| | - Víctor Ladero
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300, Villaviciosa, Spain.,Grupo de Microbiología Molecular, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011, Oviedo, Spain
| | - Jürgen J Heinisch
- Department of Genetics, Faculty of Biology and Chemistry, University of Osnabrück, Barbarastrasse 11, 49076, Osnabrück, Germany
| | - Javier Fernández
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011, Oviedo, Spain.,Servicio de Microbiología, Hospital Universitario Central de Asturias, 33011, Oviedo, Spain
| | - Rosaura Rodicio
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011, Oviedo, Spain.,Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006, Oviedo, Spain
| | - M Rosario Rodicio
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006, Oviedo, Spain. .,Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011, Oviedo, Spain.
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