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Che M, Fresno AH, Calvo-Fernandez C, Hasman H, Kurittu PE, Heikinheimo A, Hansen LT. Comparison of IncK- blaCMY-2 Plasmids in Extended-Spectrum Cephalosporin-Resistant Escherichia coli Isolated from Poultry and Humans in Denmark, Finland, and Germany. Antibiotics (Basel) 2024; 13:349. [PMID: 38667025 PMCID: PMC11047599 DOI: 10.3390/antibiotics13040349] [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: 03/05/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/29/2024] Open
Abstract
Escherichia coli carrying IncK-blaCMY-2 plasmids mediating resistance to extended-spectrum cephalosporins (ESC) has been frequently described in food-producing animals and in humans. This study aimed to characterize IncK-blaCMY-2-positive ESC-resistant E. coli isolates from poultry production systems in Denmark, Finland, and Germany, as well as from Danish human blood infections, and further compare their plasmids. Whole-genome sequencing (Illumina) of all isolates (n = 46) confirmed the presence of the blaCMY-2 gene. Minimum inhibitory concentration (MIC) testing revealed a resistant phenotype to cefotaxime as well as resistance to ≥3 antibiotic classes. Conjugative transfer of the blaCMY-2 gene confirmed the resistance being on mobile plasmids. Pangenome analysis showed only one-third of the genes being in the core with the remainder being in the large accessory gene pool. Single nucleotide polymorphism (SNP) analysis on sequence type (ST) 429 and 1286 isolates showed between 0-60 and 13-90 SNP differences, respectively, indicating vertical transmission of closely related clones in the poultry production, including among Danish, Finnish, and German ST429 isolates. A comparison of 22 ST429 isolates from this study with 80 ST429 isolates in Enterobase revealed the widespread geographical occurrence of related isolates associated with poultry production. Long-read sequencing of a representative subset of isolates (n = 28) allowed further characterization and comparison of the IncK-blaCMY-2 plasmids with publicly available plasmid sequences. This analysis revealed the presence of highly similar plasmids in ESC-resistant E. coli from Denmark, Finland, and Germany pointing to the existence of common sources. Moreover, the analysis presented evidence of global plasmid transmission and evolution. Lastly, our results indicate that IncK-blaCMY-2 plasmids and their carriers had been circulating in the Danish production chain with an associated risk of spreading to humans, as exemplified by the similarity of the clinical ST429 isolate to poultry isolates. Its persistence may be driven by co-selection since most IncK-blaCMY-2 plasmids harbor resistance factors to drugs used in veterinary medicine.
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Affiliation(s)
- Meiyao Che
- National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark; (M.C.); (C.C.-F.)
| | - Ana Herrero Fresno
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, Campus Terra, Universidade da Santiago de Compostela (USC), 27002 Lugo, Spain;
| | - Cristina Calvo-Fernandez
- National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark; (M.C.); (C.C.-F.)
| | - Henrik Hasman
- Reference Laboratory for Antibiotic Resistance, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark;
| | - Paula E. Kurittu
- Department of Food Health and Environmental Hygiene, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland; (P.E.K.); (A.H.)
| | - Annamari Heikinheimo
- Department of Food Health and Environmental Hygiene, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland; (P.E.K.); (A.H.)
- Microbiology Unit, Finnish Food Authority, Mustialankatu 3, 00790 Helsinki, Finland
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Garrido-Palazuelos LI, Aguirre-Sánchez JR, Castro-Del Campo N, López-Cuevas O, González-Torres B, Chaidez C, Medrano-Félix JA. Genomic characteristics of Salmonella Montevideo and Pomona: impact of isolation source on antibiotic resistance, virulence and metabolic capacity. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-16. [PMID: 38576268 DOI: 10.1080/09603123.2024.2336597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Salmonella enterica is known for its disease-causing serotypes, including Montevideo and Pomona. These serotypes have been found in various environments, including river water, sediments, food, and animals. However, the global spread of these serotypes has increased, leading to many reported infections and outbreaks. The goal of this study was the genomic analysis of 48 strains of S. Montevideo and S. Pomona isolated from different sources, including clinical. Results showed that environmental strains carried more antibiotic resistance genes than the clinical strains, such as genes for resistance to aminoglycosides, chloramphenicol, and sulfonamides. Additionally, the type 4 secretion system, was only found in environmental strains. .Also many phosphotransferase transport systems were identified and the presence of genes for the alternative pathway Entner-Doudoroff. The origin of isolation may have a significant impact on the ability of Salmonella isolates to adapt and survive in different environments, leading to genomic flexibility and a selection advantage.
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Affiliation(s)
- Lennin Isaac Garrido-Palazuelos
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - José Roberto Aguirre-Sánchez
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Nohelia Castro-Del Campo
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Osvaldo López-Cuevas
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Berenice González-Torres
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Cristóbal Chaidez
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - José Andrés Medrano-Félix
- Investigadoras e investigadores por México Centro de Investigación En Alimentación y Desarrollo A.C. Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán, México
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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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Li C, Tate H, Huang X, Hsu CH, Harrison LB, Zhao S, Fortenberry GZ, Dessai U, McDermott PF, Strain EA. The spread of pESI-mediated extended-spectrum cephalosporin resistance in Salmonella serovars-Infantis, Senftenberg, and Alachua isolated from food animal sources in the United States. PLoS One 2024; 19:e0299354. [PMID: 38483966 PMCID: PMC10939224 DOI: 10.1371/journal.pone.0299354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024] Open
Abstract
The goal of this study is to investigate the origin, prevalence, and evolution of the pESI megaplasmid in Salmonella isolated from animals, foods, and humans. We queried 510,097 Salmonella genomes under the National Center for Biotechnology Information (NCBI) Pathogen Detection (PD) database for the presence of potential sequences containing the pESI plasmid in animal, food, and environmental sources. The presence of the pESI megaplasmid was confirmed by using seven plasmid-specific markers (rdA, pilL, SogS, TrbA, ipf, ipr2 and IncFIB(pN55391)). The plasmid and chromosome phylogeny of these isolates was inferred from single nucleotide polymorphisms (SNPs). Our search resolved six Salmonella clusters carrying the pESI plasmid. Four were emergent Salmonella Infantis clusters, and one each belonged to serovar Senftenberg and Alachua. The Infantis cluster with a pESI plasmid carrying blaCTX-M-65 gene was the biggest of the four emergent Infantis clusters, with over 10,000 isolates. This cluster was first detected in South America and has since spread widely in United States. Over time the composition of pESI in United States has changed with the average number of resistance genes showing a decrease from 9 in 2014 to 5 in 2022, resulting from changes in gene content in two integrons present in the plasmid. A recent and emerging cluster of Senftenberg, which carries the blaCTX-M-65 gene and is primarily associated with turkey sources, was the second largest in the United States. SNP analysis showed that this cluster likely originated in North Carolina with the recent acquisition of the pESI plasmid. A single Alachua isolate from turkey was also found to carry the pESI plasmid containing blaCTX-M-65 gene. The study of the pESI plasmid, its evolution and mechanism of spread can help us in developing appropriate strategies for the prevention and further spread of this multi-drug resistant plasmid in Salmonella in poultry and humans.
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Affiliation(s)
- Cong Li
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
| | - Heather Tate
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
| | - Xinyang Huang
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, United States of America
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety Security Systems, University of Maryland,College Park, Maryland, United States of America
| | - Chih-Hao Hsu
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
| | - Lucas B. Harrison
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
| | - Shaohua Zhao
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
| | - Gamola Z. Fortenberry
- Food Safety and Inspection Service, U.S. Department of Agriculture, Athens, Georgia, United States of America
| | - Uday Dessai
- Food Safety and Inspection Service, U.S. Department of Agriculture, Athens, Georgia, United States of America
| | - Patrick F. McDermott
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
| | - Errol A. Strain
- Center for Food Safety and Applied Nutrition, College Park, Maryland, United States of America
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Iduu NV, Raiford D, Conley A, Scaria J, Nelson J, Ruesch L, Price S, Yue M, Gong J, Wei L, Wang C. A Retrospective Analysis of Salmonella Isolates across 11 Animal Species (1982-1999) Led to the First Identification of Chromosomally Encoded blaSCO-1 in the USA. Microorganisms 2024; 12:528. [PMID: 38543579 PMCID: PMC10974302 DOI: 10.3390/microorganisms12030528] [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: 02/08/2024] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 04/01/2024] Open
Abstract
Antimicrobial resistance (AMR) in non-typhoidal Salmonella is a pressing public health concern in the United States, necessitating continuous surveillance. We conducted a retrospective analysis of 251 Salmonella isolates from 11 animal species recovered between 1982 and 1999, utilizing serotyping, antimicrobial susceptibility testing, and whole-genome sequencing (WGS). Phenotypic resistance was observed in 101 isolates, with S. Typhimurium, S. Dublin, S. Agona, and S. Muenster prevailing among 36 identified serovars. Notably, resistance to 12 of 17 antibiotics was detected, with ampicillin being most prevalent (79/251). We identified 38 resistance genes, primarily mediating aminoglycoside (n = 13) and β-lactamase (n = 6) resistance. Plasmid analysis unveiled nine distinct plasmids associated with AMR genes in these isolates. Chromosomally encoded blaSCO-1 was present in three S. Typhimurium and two S. Muenster isolates from equine samples, conferring resistance to amoxicillin/clavulanic acid. Phylogenetic analysis revealed three distinct clusters for these five isolates, indicating evolutionary divergence. This study represents the first report of blaSCO-1 in the USA, and our recovered isolates harboring this gene as early as 1989 precede those of all other reports. The enigmatic nature of blaSCO-1 prompts further research into its function. Our findings highlight the urgency of addressing antimicrobial resistance in Salmonella for effective public health interventions.
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Affiliation(s)
- Nneka Vivian Iduu
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (N.V.I.); (D.R.); (S.P.)
| | - Donna Raiford
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (N.V.I.); (D.R.); (S.P.)
| | - Austin Conley
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (N.V.I.); (D.R.); (S.P.)
| | - Joy Scaria
- Department of Veterinary Pathobiology, Stillwater, Oklahoma State University, Stillwater, OK 74078, USA;
| | - Julie Nelson
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; (J.N.); (L.R.)
| | - Laura Ruesch
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; (J.N.); (L.R.)
| | - Stuart Price
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (N.V.I.); (D.R.); (S.P.)
| | - Min Yue
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310027, China
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China;
| | - Lanjing Wei
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA;
| | - Chengming Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (N.V.I.); (D.R.); (S.P.)
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Ge B, Mukherjee S, Li C, Harrison LB, Hsu CH, Tran TT, Whichard JM, Dessai U, Singh R, Gilbert JM, Strain EA, McDermott PF, Zhao S. Genomic analysis of azithromycin-resistant Salmonella from food animals at slaughter and processing, and retail meats, 2011-2021, United States. Microbiol Spectr 2024; 12:e0348523. [PMID: 37991374 PMCID: PMC10783062 DOI: 10.1128/spectrum.03485-23] [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: 09/26/2023] [Accepted: 10/18/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE Macrolides of different ring sizes are critically important antimicrobials for human medicine and veterinary medicine, though the widely used 15-membered ring azithromycin in humans is not approved for use in veterinary medicine. We document here the emergence of azithromycin-resistant Salmonella among the NARMS culture collections between 2011 and 2021 in food animals and retail meats, some with co-resistance to ceftriaxone or decreased susceptibility to ciprofloxacin. We also provide insights into the underlying genetic mechanisms and genomic contexts, including the first report of a novel combination of azithromycin resistance determinants and the characterization of multidrug-resistant plasmids. Further, we highlight the emergence of a multidrug-resistant Salmonella Newport clone in food animals (mainly cattle) with both azithromycin resistance and decreased susceptibility to ciprofloxacin. These findings contribute to a better understating of azithromycin resistance mechanisms in Salmonella and warrant further investigations on the drivers behind the emergence of resistant clones.
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Affiliation(s)
- Beilei Ge
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Sampa Mukherjee
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Cong Li
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Lucas B. Harrison
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Chih-Hao Hsu
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Thu-Thuy Tran
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Jean M. Whichard
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Uday Dessai
- Food Safety and Inspection Service, U.S. Department of Agriculture, Washington, DC, USA
| | - Ruby Singh
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Rockville, Maryland, USA
| | - Jeffrey M. Gilbert
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Rockville, Maryland, USA
| | - Errol A. Strain
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Patrick F. McDermott
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Shaohua Zhao
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
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Jia C, Wang Z, Huang C, Teng L, Zhou H, An H, Liao S, Liu Y, Huang L, Tang B, Yue M. Mobilome-driven partitions of the resistome in Salmonella. mSystems 2023; 8:e0088323. [PMID: 37855620 PMCID: PMC10734508 DOI: 10.1128/msystems.00883-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Antimicrobial resistance (AMR) has become a significant global challenge, with an estimated 10 million deaths annually by 2050. The emergence of AMR is mainly attributed to mobile genetic elements (MGEs or mobilomes), which accelerate wide dissemination among pathogens. The interaction between mobilomes and AMR genes (or resistomes) in Salmonella, a primary cause of diarrheal diseases that results in over 90 million cases annually, remains poorly understood. The available fragmented or incomplete genomes remain a significant limitation in investigating the relationship between AMR and MGEs. Here, we collected the most extensive closed Salmonella genomes (n = 1,817) from various sources across 58 countries. Notably, our results demonstrate that resistome transmission between Salmonella lineages follows a specific pattern of MGEs and is influenced by external drivers, including certain socioeconomic factors. Therefore, targeted interventions are urgently needed to mitigate the catastrophic consequences of Salmonella AMR.
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Affiliation(s)
- Chenghao Jia
- 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
| | - Zining Wang
- 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
- Hainan Institute of Zhejiang University, Sanya, China
| | - Chenghu Huang
- 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
- Hainan Institute of Zhejiang University, Sanya, China
| | - Lin Teng
- 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
| | - Haiyang Zhou
- 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
- Hainan Institute of Zhejiang University, Sanya, China
| | - Hongli An
- 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
- Hainan Institute of Zhejiang University, Sanya, China
| | - Sihao Liao
- 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
| | - Yuhao Liu
- 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
- Hainan Institute of Zhejiang University, Sanya, China
| | - Linlin Huang
- 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
| | - Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Min Yue
- 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
- Hainan Institute of Zhejiang University, Sanya, 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
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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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9
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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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10
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Uhland FC, Li XZ, Mulvey MR, Reid-Smith R, Sherk LM, Ziraldo H, Jin G, Young KM, Reist M, Carson CA. Extended Spectrum β-Lactamase-Producing Enterobacterales of Shrimp and Salmon Available for Purchase by Consumers in Canada-A Risk Profile Using the Codex Framework. Antibiotics (Basel) 2023; 12:1412. [PMID: 37760708 PMCID: PMC10525137 DOI: 10.3390/antibiotics12091412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/24/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
The extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-EB) encompass several important human pathogens and are found on the World Health Organization (WHO) priority pathogens list of antibiotic-resistant bacteria. They are a group of organisms which demonstrate resistance to third-generation cephalosporins (3GC) and their presence has been documented worldwide, including in aquaculture and the aquatic environment. This risk profile was developed following the Codex Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance with the objectives of describing the current state of knowledge of ESBL-EB in relation to retail shrimp and salmon available to consumers in Canada, the primary aquacultured species consumed in Canada. The risk profile found that Enterobacterales and ESBL-EB have been found in multiple aquatic environments, as well as multiple host species and production levels. Although the information available did not permit the conclusion as to whether there is a human health risk related to ESBLs in Enterobacterales in salmon and shrimp available for consumption by Canadians, ESBL-EB in imported seafood available at the retail level in Canada have been found. Surveillance activities to detect ESBL-EB in seafood are needed; salmon and shrimp could be used in initial surveillance activities, representing domestic and imported products.
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Affiliation(s)
- F. Carl Uhland
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Xian-Zhi Li
- Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Richard Reid-Smith
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Lauren M. Sherk
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Hilary Ziraldo
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Grace Jin
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Kaitlin M. Young
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Mark Reist
- Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Carolee A. Carson
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
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11
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Vázquez X, García-Fierro R, Fernández J, Bances M, Herrero-Fresno A, Olsen JE, Rodicio R, Ladero V, García V, Rodicio MR. Incidence and Genomic Background of Antibiotic Resistance in Food-Borne and Clinical Isolates of Salmonella enterica Serovar Derby from Spain. Antibiotics (Basel) 2023; 12:1204. [PMID: 37508300 PMCID: PMC10376468 DOI: 10.3390/antibiotics12071204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Salmonella enterica serovar Derby (S. Derby) ranks fifth among nontyphoidal Salmonella serovars causing human infections in the European Union. S. Derby isolates (36) collected between 2006 and 2018 in a Spanish region (Asturias) from human clinical samples (20) as well as from pig carcasses, pork- or pork and beef-derived products, or wild boar (16) were phenotypically characterized with regard to resistance, and 22 (12 derived from humans and 10 from food-related samples) were also subjected to whole genome sequence analysis. The sequenced isolates belonged to ST40, a common S. Derby sequence type, and were positive for SPI-23, a Salmonella pathogenicity island involved in adherence and invasion of the porcine jejune enterocytes. Isolates were either susceptible (30.6%), or resistant to one or more of the 19 antibiotics tested for (69.4%). Resistances to tetracycline [tet(A), tet(B) and tet(C)], streptomycin (aadA2), sulfonamides (sul1), nalidixic acid [gyrA (Asp87 to Asn)] and ampicillin (blaTEM-1-like) were detected, with frequencies ranging from 8.3% to 66.7%, and were higher in clinical than in food-borne isolates. The fosA7.3 gene was present in all sequenced isolates. The most common phenotype was that conferred by the tet(A), aadA2 and sul1 genes, located within identical or closely related variants of Salmonella Genomic Island 1 (SGI1), where mercury resistance genes were also present. Diverse IncI1-I(α) plasmids belonging to distinct STs provided antibiotic [blaTEM-1, tet(A) and/or tet(B)] and heavy metal resistance genes (copper and silver), while small pSC101-like plasmids carried tet(C). Regardless of their location, most resistance genes were associated with genetic elements involved in DNA mobility, including a class one integron, multiple insertion sequences and several intact or truncated transposons. By phylogenetic analysis, the isolates were distributed into two distinct clades, both including food-borne and clinical isolates. One of these clades included all SGI1-like positive isolates, which were found in both kinds of samples throughout the entire period of study. Although the frequency of S. Derby in Asturias was very low (0.5% and 3.1% of the total clinical and food isolates of S. enterica recovered along the period of study), it still represents a burden to human health linked to transmission across the food chain. The information generated in the present study can support further epidemiological surveillance aimed to control this zoonotic pathogen.
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Affiliation(s)
- Xenia Vázquez
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo (UO), 33006 Oviedo, Spain
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), 33300 Villaviciosa, Spain
| | - Raquel García-Fierro
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo (UO), 33006 Oviedo, Spain
| | - 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 (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
| | - Margarita Bances
- Laboratorio de Salud Pública, Dirección General de Salud Pública, Consejería de Salud del Principado de Asturias, 33011 Oviedo, Spain
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - 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
| | - Víctor Ladero
- Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), 33300 Villaviciosa, Spain
- Grupo de Microbiología Molecular, Instituto de Investigación Sanitaria del Principado de Asturias (IAPA), 33011 Oviedo, Spain
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - M Rosario Rodicio
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo (UO), 33006 Oviedo, Spain
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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12
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Cao G, Zhao S, Kuang D, Hsu CH, Yin L, Luo Y, Chen Z, Xu X, Strain E, McDermott P, Allard M, Brown E, Meng J, Zheng J. Geography shapes the genomics and antimicrobial resistance of Salmonella enterica Serovar Enteritidis isolated from humans. Sci Rep 2023; 13:1331. [PMID: 36693882 PMCID: PMC9873609 DOI: 10.1038/s41598-022-24150-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/10/2022] [Indexed: 01/25/2023] Open
Abstract
Multidrug-resistant (MDR) Salmonella has been a long-standing challenge in public health and food safety. The prevalence of MDR S. Enteritidis, especially isolated from humans, in China is significantly higher than those from the U.S. and other countries. A dataset of 197 S. Enteritidis genomes, including 16 sequenced clinical isolates from China and 181 downloaded genomes of human isolates from the U.S., Europe, and Africa, was analyzed for genomic diversity, virulence potential, and antimicrobial resistance (AMR). Phylogenomic analyses identified four major well-supported clades (I-IV). While AMR genotype in the majority of isolates in clades I and IV displayed as pan-susceptible, 81.8% (9/11) and 22.4% (13/58) of isolates in clades III and II were MDR, respectively. It is noted that 77% (10/13) of MDR isolates in clade II were from China. The most common antimicrobial resistance genes (ARGs) carried by the Chinese isolates were aph(3')-IIa, blaCTX-M-55, and blaTEM-1B, whereas blaTEM-1B, sul1, sul2, drfA7, aph(3")-Ib/strA, and aph(6)-Id/strB were most often identified in those from Africa (clade III). Among the 14 plasmid types identified, IncX1 and IncFII(pHN7A8) were found exclusively in the Chinese MDR isolates, while IncQ1 was highly associated with the African MDR isolates. The spvRABCD virulence operon was present in 94.9% (187/197) of isolates tested and was highly associated with both the IncF (IncFII and IncFIB) plasmids. In addition, phylogenetic differences in distribution of Salmonella pathogenicity islands (SPIs), prophages and other accessory genes were also noted. Taken together, these findings provide new insights into the molecular mechanisms underpinning diversification of MDR S. Enteritidis.
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Affiliation(s)
- Guojie Cao
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, 20740, USA.
| | - Shaohua Zhao
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, 20708, USA
| | - Dai Kuang
- Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chih-Hao Hsu
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, 20708, USA
| | - Lanlan Yin
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, 20740, USA
| | - Yan Luo
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, 20740, USA
| | - Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety & Security Systems, Department of Nutrition and Food Science, University of Maryland, College Park, MD, USA
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Errol Strain
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, 20708, USA
| | - Patrick McDermott
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, 20708, USA
| | - Marc Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, 20740, USA
| | - Eric Brown
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, 20740, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety & Security Systems, Department of Nutrition and Food Science, University of Maryland, College Park, MD, USA
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, 20740, USA.
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13
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Khan AS, Pierneef RE, Gonzalez-Escalona N, Maguire M, Georges K, Abebe W, Adesiyun AA. Phylogenetic analyses of Salmonella detected along the broiler production chain in Trinidad and Tobago. Poult Sci 2022; 102:102322. [PMID: 36473385 PMCID: PMC9720344 DOI: 10.1016/j.psj.2022.102322] [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: 06/10/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/12/2022] Open
Abstract
This study was conducted to determine the phylogenies of Salmonella strains isolated from cross-sectional studies conducted at hatcheries, broiler farms, processing plants, and retail outlets (broiler production chain) in Trinidad and Tobago over 4 yr (2016-2019). Whole-genome sequencing (WGS) was used to characterize Salmonella isolates. Core genome phylogenies of 8 serovars of public health significance were analyzed for similarities in origin and relatedness. In addition, Salmonella strains isolated from human salmonellosis cases in Trinidad were analyzed for their relatedness to the isolates detected along the broiler production chain. The common source of these isolates of diverse serovars within farms, within processing plants, between processing plants and retail outlets, and among farm-processing plant-retail outlet continuum was well-supported (bootstrap value >70%) by the core genome phylogenies for the respective serovars. Also, genome analyses revealed clustering of Salmonella serovars of regional (intra-Caribbean) and international (extra-Caribbean) origin. Similarly, strains of S. Enteritidis and S. Infantis isolated from human clinical salmonellosis in 2019 from Trinidad and Tobago clustered with our processing plant isolates recovered in 2018. This study is the first phylogenetic analysis of Salmonella isolates using WGS from the broiler industry in the Caribbean region. The use of WGS confirmed the genetic relatedness and transmission of Salmonella serovars contaminating chickens in broiler processing, and retailing in the country, with zoonotic and food safety implications for humans.
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Affiliation(s)
- Anisa S. Khan
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Rian E. Pierneef
- Agricultural Research Council-Biotechnology Platform, Pretoria 0110, South Africa
| | - Narjol Gonzalez-Escalona
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Meghan Maguire
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Karla Georges
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Woubit Abebe
- Department of Pathobiology, Center for Food Animal Health, Food Safety and Food Defense, Tuskegee University, College of Veterinary Medicine, Tuskegee, AL 36088, USA
| | - Abiodun A. Adesiyun
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago,Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa,Corresponding author:
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14
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Young SR, Domesle KJ, McDonald RC, Lozinak KA, Laksanalamai P, Harrell E, Thakur S, Kabera C, Strain EA, McDermott PF, Ge B. Toward the Adoption of Loop-Mediated Isothermal Amplification for Salmonella Screening at the National Antimicrobial Resistance Monitoring System's Retail Meat Sites. Foodborne Pathog Dis 2022; 19:758-766. [PMID: 36367550 PMCID: PMC9700350 DOI: 10.1089/fpd.2022.0047] [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: 11/13/2022] Open
Abstract
The National Antimicrobial Resistance Monitoring System (NARMS) is a One Health program in the United States that collects data on antimicrobial resistance in enteric bacteria from humans, animals, and the environment. Salmonella is a major pathogen tracked by the NARMS retail meat arm but currently lacks a uniform screening method. We evaluated a loop-mediated isothermal amplification (LAMP) assay for the rapid screening of Salmonella from 69 NARMS retail meat and poultry samples. All samples were processed side by side for culture isolation using two protocols, one from NARMS and the other one described in the U.S. Food and Drug Administration's Bacteriological Analytical Manual (BAM). Overall, 10 (14.5%) samples screened positive by the Salmonella LAMP assay. Of those, six were culture-confirmed by the NARMS protocol and six by the BAM method with overlap on four samples. No Salmonella isolates were recovered from samples that screened negative with LAMP. These results suggested 100% sensitivity for LAMP in reference to culture. Antimicrobial susceptibility testing and whole-genome sequencing analysis confirmed identities of these isolates. Using the BAM protocol, all Salmonella isolates were recovered from samples undergoing Rappaport-Vassiliadis medium selective enrichment and presumptive colonies (n = 130) were dominated by Hafnia alvei (44.6%), Proteus mirabilis (22.3%), and Morganella morganii (9.9%) based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. This method comparison study clearly demonstrated the benefit of a rapid, robust, and highly sensitive molecular screening method in streamlining the laboratory workflow. Fourteen NARMS retail meat sites further verified the performance of this assay using a portion of their routine samples, reporting an overall specificity of 98.8% and sensitivity of 90%. As of July 2022, the vast majority of NARMS retail meat sites have adopted the Salmonella LAMP assay for rapid screening of Salmonella in all samples.
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Affiliation(s)
- Shenia R. Young
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Kelly J. Domesle
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Ryan C. McDonald
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | | | | | - Erin Harrell
- College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Siddhartha Thakur
- College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Claudine Kabera
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Errol A. Strain
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Patrick F. McDermott
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Beilei Ge
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA.,Address correspondence to: Beilei Ge, PhD, Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD 20708, USA
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15
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Five Complete
Salmonella enterica
Serotype Reading Genomes Recovered from Patients in the United States. Microbiol Resour Announc 2022; 11:e0038822. [PMID: 35727013 PMCID: PMC9302092 DOI: 10.1128/mra.00388-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Between 2018 and 2019,
Salmonella enterica
serotype Reading caused a large, multistate outbreak linked to contact with raw turkey products in the United States. Here, we provide five
Salmonella
Reading reference genomes collected from US patients between 2016 and 2018.
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16
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Genomic Analysis of Two MDR Isolates of Salmonella enterica Serovar Infantis from a Spanish Hospital Bearing the blaCTX-M-65 Gene with or without fosA3 in pESI-like Plasmids. Antibiotics (Basel) 2022; 11:antibiotics11060786. [PMID: 35740192 PMCID: PMC9219668 DOI: 10.3390/antibiotics11060786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/02/2022] [Accepted: 06/05/2022] [Indexed: 02/04/2023] Open
Abstract
Salmonella enterica serovar Infantis (S. Infantis) is a broiler-associated pathogen which ranks in the fourth position as a cause of human salmonellosis in the European Union. Here, we report a comparative genomic analysis of two clinical S. Infantis isolates recovered in Spain from children who just returned from Peru. The isolates were selected on the basis of resistance to cefotaxime, one of the antibiotics of choice for treatment of S. enterica infections. Antimicrobial susceptibility testing demonstrated that they were resistant to eight classes of antimicrobial agents: penicillins, cephalosporins, phenicols, aminoglycosides, tetracyclines, inhibitors of folate synthesis, (fluoro)quinolones and nitrofurans, and one of them was also resistant to fosfomycin. As shown by whole-genome sequence analysis, each isolate carried a pESI-like megaplasmid of ca. 300 kb harboring multiple resistance genes [blaCTX-M-65, aph(4)-Ia, aac(3)-IVa, aph(3′)-Ia, floR, dfrA14, sul1, tet(A), aadA1 ± fosA3], as well as genes for resistance to heavy metals and disinfectants (mer, ars and qacEΔ1). These genes were distributed in two complex regions, separated by DNA belonging to the plasmid backbone, and associated with a wealth of transposable elements. The two isolates had a D87Y amino acid substitution in the GyrA protein, and truncated variants of the nitroreductase genes nfsA and nsfB, accounting for chromosomally encoded resistances to nalidixic acid and nitrofurantoin, respectively. The two S. Infantis isolates were assigned to sequence type ST32 by in silico multilocus sequence typing (MLST). Phylogenetic analysis revealed that they were closely related, differing only by 12 SNPs, although they were recovered from different children two years apart. They were also genetically similar to blaCTX-M-65-positive ± fosA3 isolates obtained from humans and along the poultry production chain in the USA, South America, as well as from humans in several European countries, usually associated with a travel history to America. However, this is the first time that the S. Infantis blaCTX-M-65 ± fosA3 MDR clone has been reported in Spain.
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Sun H, Mu X, Zhang K, Lang H, Su Q, Li X, Zhou X, Zhang X, Zheng H. Geographical resistome profiling in the honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids. MICROBIOME 2022; 10:69. [PMID: 35501925 PMCID: PMC9063374 DOI: 10.1186/s40168-022-01268-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/04/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND The spread of antibiotic resistance genes (ARGs) has been of global concern as one of the greatest environmental threats. The gut microbiome of animals has been found to be a large reservoir of ARGs, which is also an indicator of the environmental antibiotic spectrum. The conserved microbiota makes the honeybee a tractable and confined ecosystem for studying the maintenance and transfer of ARGs across gut bacteria. Although it has been found that honeybee gut bacteria harbor diverse sets of ARGs, the influences of environmental variables and the mechanism driving their distribution remain unclear. RESULTS We characterized the gut resistome of two closely related honeybee species, Apis cerana and Apis mellifera, domesticated in 14 geographic locations across China. The composition of the ARGs was more associated with host species rather than with geographical distribution, and A. mellifera had a higher content of ARGs in the gut. There was a moderate geographic pattern of resistome distribution, and several core ARG groups were found to be prevalent among A. cerana samples. These shared genes were mainly carried by the honeybee-specific gut members Gilliamella and Snodgrassella. Transferrable ARGs were frequently detected in honeybee guts, and the load was much higher in A. mellifera samples. Genomic loci of the bee gut symbionts containing a streptomycin resistance gene cluster were nearly identical to those of the broad-host-range IncQ plasmid, a proficient DNA delivery system in the environment. By in vitro conjugation experiments, we confirmed that the mobilizable plasmids could be transferred between honeybee gut symbionts by conjugation. Moreover, "satellite plasmids" with fragmented genes were identified in the integrated regions of different symbionts from multiple areas. CONCLUSIONS Our study illustrates that the gut microbiota of different honeybee hosts varied in their antibiotic resistance structure, highlighting the role of the bee microbiome as a potential bioindicator and disseminator of antibiotic resistance. The difference in domestication history is highly influential in the structuring of the bee gut resistome. Notably, the evolution of plasmid-mediated antibiotic resistance is likely to promote the probability of its persistence and dissemination. Video Abstract.
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Affiliation(s)
- Huihui Sun
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xiaohuan Mu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Kexun Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Haoyu Lang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Qinzhi Su
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xingan Li
- Key Laboratory for Bee Genetics and Breeding, Jilin Provincial Institute of Apicultural Sciences, Jilin, 132000, China
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100083, China
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100083, China.
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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