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Gruzdev N, Katz C, Yadid I. Curing of a field strain of Salmonella enterica serovar Infantis isolated from poultry from its highly stable pESI like plasmid. J Microbiol Methods 2024; 222:106959. [PMID: 38782300 DOI: 10.1016/j.mimet.2024.106959] [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: 02/15/2024] [Revised: 05/05/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Salmonella enterica serovar Infantis (S. infantis) is an important emerging pathogen, associated with poultry and poultry products and related to an increasing number of human infections in many countries. A concerning trend among S. infantis isolates is the presence of plasmid-mediated multidrug resistance. In many instances, the genes responsible for this resistance are carried on a megaplasmid known as the plasmid of emerging S. infantis (pESI) or pESI like plasmids. Plasmids can be remarkably stable due to the presence of multiple replicons and post-segregational killing systems (PSKs), which contribute to their maintenance within bacterial populations. To enhance our understanding of S. infantis and its multidrug resistance determinants toward the development of new vaccination strategies, we have devised a new method for targeted plasmid curing. This approach effectively overcomes plasmid addiction by leveraging the temporal overproduction of specific antitoxins coupled with the deletion of the partition region. By employing this strategy, we successfully generated a plasmid-free strain from a field isolate derived from S. infantis 119,944. This method provides valuable tools for studying S. infantis and its plasmid-borne multidrug resistance mechanisms and can be easily adopted for plasmid curing from other related bacteria.
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Affiliation(s)
- Nadya Gruzdev
- Migal-Galilee Research Institute, Kiryat-Shmona 1101602, Israel
| | - Chen Katz
- Migal-Galilee Research Institute, Kiryat-Shmona 1101602, Israel
| | - Itamar Yadid
- Migal-Galilee Research Institute, Kiryat-Shmona 1101602, Israel; Tel-Hai College, Upper Galilee 1220800, Israel.
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2
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Zhang Z, Kuang D, Xu X, Zhan Z, Ren H, Shi C. Dissemination of IncC plasmids in Salmonella enterica serovar Thompson recovered from seafood and human diarrheic patients in China. Int J Food Microbiol 2024; 417:110708. [PMID: 38653121 DOI: 10.1016/j.ijfoodmicro.2024.110708] [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: 12/18/2023] [Revised: 03/26/2024] [Accepted: 04/13/2024] [Indexed: 04/25/2024]
Abstract
Salmonella Thompson is a prevalent foodborne pathogen and a major threat to food safety and public health. This study aims to reveal the dissemination mechanism of S. Thompson with co-resistance to ceftriaxone and ciprofloxacin. In this study, 181 S. Thompson isolates were obtained from a retrospective screening on 2118 serotyped Salmonella isolates from foods and patients, which were disseminated in 12 of 16 districts in Shanghai, China. A total of 10 (5.5 %) S. Thompson isolates exhibited resistance to ceftriaxone (MIC ranging from 8 to 32 μg/mL) and ciprofloxacin (MIC ranging from 2 to 8 μg/mL). The AmpC β-lactamase gene blaCMY-2 and plasmid-mediated quinolone resistance (PMQR) genes of qnrS and qepA were identified in the 9 isolates. Conjugation results showed that the co-transfer of blaCMY-2, qnrS, and qepA occurred on the IncC plasmids with sizes of ∼150 (n = 8) or ∼138 (n = 1) kbp. Three typical modules of ISEcp1-blaCMY-2-blc-sugE, IS26-IS15DIV-qnrS-ISKpn19, and ISCR3-qepA-intl1 were identified in an ST3 IncC plasmid pSH11G0791. Phylogenetic analysis indicated that IncC plasmids evolved into Lineages 1, 2, and 3. IncC plasmids from China including pSH11G0791 in this study fell into Lineage 1 with those from the USA, suggesting their close genotype relationship. In conclusion, to our knowledge, it is the first report of the co-existence of blaCMY-2, qnrS, and qepA in IncC plasmids, and the conjugational transfer contributed to their dissemination in S. Thompson. These findings underline further challenges for the prevention and treatment of Enterobacteriaceae infections posed by IncC plasmids bearing blaCMY-2, qnrS, and qepA.
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Affiliation(s)
- Zengfeng Zhang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dai Kuang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China; National Health Commission (NHC) Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, China
| | - Xuebin Xu
- Laboratory of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200050, China
| | - Zeqiang Zhan
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Ren
- Xianyang Center for Food and Drug Control, Shaanxi, China
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China.
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Garrido V, Arrieta-Gisasola A, Migura-García L, Laorden L, Grilló MJ. Multidrug resistance in Salmonella isolates of swine origin: mobile genetic elements and plasmids associated with cephalosporin resistance with potential transmission to humans. Appl Environ Microbiol 2024; 90:e0026424. [PMID: 38695519 PMCID: PMC11107176 DOI: 10.1128/aem.00264-24] [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: 02/13/2024] [Accepted: 04/03/2024] [Indexed: 05/22/2024] Open
Abstract
The emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context requiring continuous surveillance. Resistance to ciprofloxacin and cephalosporins is of particular concern. Since pigs are a relevant source of foodborne Salmonella for human beings, we studied transmissible AMR genes and MGE in a collection of 83 strains showing 9 different serovars and 15 patterns of multidrug resistant (MDR) previously isolated from pigs raised in the conventional breeding system of Northern Spain. All isolates were susceptible to ciprofloxacin and three isolates carried blaCMY-2 or blaCTX-M-9 genes responsible for cefotaxime resistance. Filter mating experiments showed that the two plasmids carrying blaCTX-M-9 were conjugative while that carrying blaCMY-2 was self-transmissible by transformation. Whole-genome sequencing and comparative analyses were performed on the isolates and plasmids. The IncC plasmid pSB109, carrying blaCMY-2, was similar to one found in S. Reading from cattle, indicating potential horizontal transfer between serovars and animal sources. The IncHI2 plasmids pSH102 in S. Heidelberg and pSTM45 in S. Typhimurium ST34, carrying blaCTX-M-9, shared similar backbones and two novel "complex class 1 integrons" containing different AMR and heavy metal genes. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.IMPORTANCEThe emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context. Since pigs are a relevant source of foodborne Salmonella for humans, in this study, we investigate different aspects of AMR in a collection of 83 Salmonella showing nine different serovars and 15 patterns of multidrug resistant (MDR) isolated from pigs raised in the conventional breeding system. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.
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Affiliation(s)
- V. Garrido
- Instituto de Agrobiotecnología (IdAB; CSIC-Gobierno de Navarra), Mutilva, Navarra, Spain
| | - A. Arrieta-Gisasola
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, MikroIker Research Group, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - L. Migura-García
- Joint Research Unit IRTA-UAB in Animal Health, Animal Health Research Centre (CReSA), Autonomous University of Barcelona (UAB), Catalonia, Spain
- Institute of Agrifood Research and Technology (IRTA), Animal Health Program (CReSA), WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
| | - L. Laorden
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, MikroIker Research Group, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - M. J. Grilló
- Instituto de Agrobiotecnología (IdAB; CSIC-Gobierno de Navarra), Mutilva, Navarra, Spain
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Algarni S, Foley SL, Tang H, Zhao S, Gudeta DD, Khajanchi BK, Ricke SC, Han J. Development of an antimicrobial resistance plasmid transfer gene database for enteric bacteria. FRONTIERS IN BIOINFORMATICS 2023; 3:1279359. [PMID: 38033626 PMCID: PMC10682676 DOI: 10.3389/fbinf.2023.1279359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction: Type IV secretion systems (T4SSs) are integral parts of the conjugation process in enteric bacteria. These secretion systems are encoded within the transfer (tra) regions of plasmids, including those that harbor antimicrobial resistance (AMR) genes. The conjugal transfer of resistance plasmids can lead to the dissemination of AMR among bacterial populations. Methods: To facilitate the analyses of the conjugation-associated genes, transfer related genes associated with key groups of AMR plasmids were identified, extracted from GenBank and used to generate a plasmid transfer gene dataset that is part of the Virulence and Plasmid Transfer Factor Database at FDA, serving as the foundation for computational tools for the comparison of the conjugal transfer genes. To assess the genetic feature of the transfer gene database, genes/proteins of the same name (e.g., traI/TraI) or predicted function (VirD4 ATPase homologs) were compared across the different plasmid types to assess sequence diversity. Two analyses tools, the Plasmid Transfer Factor Profile Assessment and Plasmid Transfer Factor Comparison tools, were developed to evaluate the transfer genes located on plasmids and to facilitate the comparison of plasmids from multiple sequence files. To assess the database and associated tools, plasmid, and whole genome sequencing (WGS) data were extracted from GenBank and previous WGS experiments in our lab and assessed using the analysis tools. Results: Overall, the plasmid transfer database and associated tools proved to be very useful for evaluating the different plasmid types, their association with T4SSs, and increased our understanding how conjugative plasmids contribute to the dissemination of AMR genes.
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Affiliation(s)
- Suad Algarni
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Steven L. Foley
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
| | - Hailin Tang
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
| | - Shaohua Zhao
- Office of Applied Science, Center for Veterinary Medicine, Food and Drug Administration, Laurel, MD, United States
| | - Dereje D. Gudeta
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
| | - Bijay K. Khajanchi
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
| | - Steven C. Ricke
- Meat Science and Animal Biologics Discovery Program, Animal and Dairy Sciences Department, University of Wisconsin, Madison, WI, United States
| | - Jing Han
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
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Chung The H, Pham P, Ha Thanh T, Phuong LVK, Yen NP, Le SNH, Vu Thuy D, Chau TTH, Le Phuc H, Ngoc NM, Vi LL, Mather AE, Thwaites GE, Thomson NR, Baker S, Pham DT. Multidrug resistance plasmids underlie clonal expansions and international spread of Salmonella enterica serotype 1,4,[5],12:i:- ST34 in Southeast Asia. Commun Biol 2023; 6:1007. [PMID: 37789208 PMCID: PMC10547704 DOI: 10.1038/s42003-023-05365-1] [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: 02/14/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023] Open
Abstract
Salmonella enterica serotype 1,4,[5],12:i:- (Typhimurium monophasic variant) of sequence type (ST) 34 has emerged as the predominant pandemic genotype in recent decades. Despite increasing reports of resistance to antimicrobials in Southeast Asia, Salmonella ST34 population structure and evolution remained understudied in the region. Here we performed detailed genomic investigations on 454 ST34 genomes collected from Vietnam and diverse geographical sources to elucidate the pathogen's epidemiology, evolution and antimicrobial resistance. We showed that ST34 has been introduced into Vietnam in at least nine occasions since 2000, forming five co-circulating major clones responsible for paediatric diarrhoea and bloodstream infection. Most expansion events were associated with acquisitions of large multidrug resistance plasmids of IncHI2 or IncA/C2. Particularly, the self-conjugative IncA/C2 pST34VN2 (co-transferring blaCTX-M-55, mcr-3.1, and qnrS1) underlies local expansion and intercontinental spread in two separate ST34 clones. At the global scale, Southeast Asia was identified as a potential hub for the emergence and dissemination of multidrug resistant Salmonella ST34, and mutation analysis suggests of selection in antimicrobial responses and key virulence factors.
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Affiliation(s)
- Hao Chung The
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
| | - Phuong Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Son-Nam H Le
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Duong Vu Thuy
- Children's Hospital No. 1, Ho Chi Minh City, Vietnam
| | | | - Hoang Le Phuc
- Children's Hospital No. 1, Ho Chi Minh City, Vietnam
| | | | - Lu Lan Vi
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Nicholas R Thomson
- London School of Hygiene and Tropical Medicine, London, UK
- The Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Stephen Baker
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Diseases (CITIID), University of Cambridge, Cambridge, UK
| | - Duy Thanh Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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Yee R, Simner PJ. Next-Generation Sequencing Approaches to Predicting Antimicrobial Susceptibility Testing Results. Clin Lab Med 2022; 42:557-572. [PMID: 36368782 DOI: 10.1016/j.cll.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rebecca Yee
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B1-193, 600 North Wolfe Street, Baltimore, MD 21287-7093, USA
| | - Patricia J Simner
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B1-193, 600 North Wolfe Street, Baltimore, MD 21287-7093, USA.
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Zhang F, Ye X, Yin Z, Hu M, Wang B, Liu W, Li B, Ren H, Jin Y, Yue J. Comparative genomics reveals new insights into the evolution of the IncA and IncC family of plasmids. Front Microbiol 2022; 13:1045314. [PMID: 36466664 PMCID: PMC9709138 DOI: 10.3389/fmicb.2022.1045314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/24/2022] [Indexed: 06/13/2024] Open
Abstract
Incompatibility groups IncA and IncC plasmids are of great concern due to their ability to disseminate antibiotic resistance in bacteria via conjugative transfer. A deep understanding of their genomic structures and evolutionary characteristics is of great significance for improving our knowledge about its multidrug-resistance evolution and dissemination. However, current knowledge of their backbone structure, features of core functional modules and the characteristics of variable regions is based on a few plasmids, which highlights the need for a comprehensive systematic study. The present study thoroughly compared and analysed 678 IncA and IncC plasmid genomes. We found that their core functional genes were occasionally deficient and sometimes existed as multiple functional copies/multiple families, which resulted in much diversity. The phylogeny of 13 core functional genes corresponded well to the plasmid subtypes. The conjugative transfer system gained diverse complexity and exhibited many previously unnoticed types with multiple combinations. The insertion of mobile genetic elements (MGEs) in plasmids varied between types and was present in 4 insertion spots in different types of plasmids with certain types of transposons, integrons and insertion sequences. The impact of gene duplication, deletion, the insertion of MGEs, genome rearrangement and recombination resulted in the complex dynamic variable backbone of IncA and IncC plasmids. And IncA and IncC plasmids were more complex than their closest relative SXT/R391 integrative conjugative elements (ICEs), which included nearly all of the diversity of SXT/R391 in key systems. Our work demonstrated a global and systematic view of the IncA and IncC plasmids and provides many new insights into their genome evolution.
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Affiliation(s)
- Fengwei Zhang
- Medical College of Guizhou University, Guiyang, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Xianwei Ye
- Medical College of Guizhou University, Guiyang, China
- Guizhou Provincial People’s Hospital, Guiyang, China
| | - Zhiqiu Yin
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai’an, China
| | - Mingda Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Boqian Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Wenting Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Beiping Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Hongguang Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Yuan Jin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Junjie Yue
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
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Khan MAS, Rahman SR. Use of Phages to Treat Antimicrobial-Resistant Salmonella Infections in Poultry. Vet Sci 2022; 9:438. [PMID: 36006353 PMCID: PMC9416511 DOI: 10.3390/vetsci9080438] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 01/18/2023] Open
Abstract
Salmonellosis is one of the most common bacterial infections that impacts both human health and poultry production. Although antibiotics are usually recommended for treating Salmonella infections, their misuse results in the evolution and spread of multidrug-resistant (MDR) bacteria. To minimize the health and economic burdens associated with antimicrobial resistance, a novel antibacterial strategy that can obliterate pathogens without any adverse effects on humans and animals is urgently required. Therefore, therapeutic supplementation of phages has gained renewed attention because of their unique ability to lyse specific hosts, cost-effective production, environmentally-friendly properties, and other potential advantages over antibiotics. In addition, the safety and efficacy of phage therapy for controlling poultry-associated Salmonella have already been proven through experimental studies. Phages can be applied at every stage of poultry production, processing, and distribution through different modes of application. Despite having a few limitations, the optimized and regulated use of phage cocktails may prove to be an effective option to combat infections caused by MDR pathogens in the post-antibiotic era. This article mainly focuses on the occurrence of salmonellosis in poultry and its reduction with the aid of bacteriophages. We particularly discuss the prevalence of Salmonella infections in poultry and poultry products; review the trends in antibiotic resistance; and summarize the application, challenges, and prospects of phage therapy in the poultry industry.
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Strantzali D, Kostoglou D, Perikleous A, Zestas M, Ornithopoulou S, Dubois-Brissonnet F, Giaouris E. Comparative assessment of the disinfection effectiveness of thymol and benzalkonium chloride against adapted and non-adapted to thymol biofilm cells of a Salmonella Typhimurium epidemic phage type DT193 strain. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH, Hoffmann M, Pettengill JB, Prasad AB, Tillman GE, Tyson GH, Klimke W. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep 2021; 11:12728. [PMID: 34135355 PMCID: PMC8208984 DOI: 10.1038/s41598-021-91456-0] [Citation(s) in RCA: 394] [Impact Index Per Article: 131.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/19/2021] [Indexed: 12/26/2022] Open
Abstract
Antimicrobial resistance (AMR) is a significant public health threat. With the rise of affordable whole genome sequencing, in silico approaches to assessing AMR gene content can be used to detect known resistance mechanisms and potentially identify novel mechanisms. To enable accurate assessment of AMR gene content, as part of a multi-agency collaboration, NCBI developed a comprehensive AMR gene database, the Bacterial Antimicrobial Resistance Reference Gene Database and the AMR gene detection tool AMRFinder. Here, we describe the expansion of the Reference Gene Database, now called the Reference Gene Catalog, to include putative acid, biocide, metal, stress resistance genes, in addition to virulence genes and species-specific point mutations. Genes and point mutations are classified by broad functions, as well as more detailed functions. As we have expanded both the functional repertoire of identified genes and functionality, NCBI released a new version of AMRFinder, known as AMRFinderPlus. This new tool allows users the option to utilize only the core set of AMR elements, or include stress response and virulence genes, too. AMRFinderPlus can detect acquired genes and point mutations in both protein and nucleotide sequence. In addition, the evidence used to identify the gene has been expanded to include whether nucleotide or protein sequence was used, its location in the contig, and presence of an internal stop codon. These database improvements and functional expansions will enable increased precision in identifying AMR genes, linking AMR genotypes and phenotypes, and determining possible relationships between AMR, virulence, and stress response.
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Affiliation(s)
- Michael Feldgarden
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
| | - Vyacheslav Brover
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Narjol Gonzalez-Escalona
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, USA
| | - Julie Haendiges
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Daniel H Haft
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - James B Pettengill
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Arjun B Prasad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Glenn E Tillman
- Food Safety and Inspection Service, U.S. Department of Agriculture, Athens, GA, USA
| | - Gregory H Tyson
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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11
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Campylobacter and Salmonella in Scavenging Indigenous Chickens in Rural Central Tanzania: Prevalence, Antimicrobial Resistance, and Genomic Features. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12020030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Introduction: Salmonella and Campylobacter spp. are commonly reported bacterial foodborne pathogens causing morbidity and mortality worldwide. In rural areas, where there is a high occurrence rate of human–animal interactions and poor hygiene practices, shedding animals present a high risk to humans in acquiring animal-associated infections. Materials and methods: Seasonal prevalence of Campylobacter jejuni, Campylobacter coli, and Salmonella spp. in scavenging indigenous chicken faeces was determined by polymerase chain reaction (PCR). Antimicrobial resistance was studied in Salmonella isolates by disc diffusion method, and whole-genome sequenced isolates were used to determine Salmonella serovars, antimicrobial resistance genes, virulence genes, and plasmid profile. Results: The overall prevalence of Campylobacter in chickens was 7.2% in the dry season and 8.0% in the rainy season (p = 0.39), and that of Salmonella was 11.1% in the dry season and 16.2% in the rainy season (p = 0.29). Salmonella serovars detected were II 35:g,m,s,t:-, Ball, Typhimurium, Haardt/Blockley, Braenderup, and Enteritidis/Gallinarum. One S. II 35:g,m,s,t:- isolate was resistant to ampicillin and the rest were either intermediate resistant or pansusceptible to the tested antimicrobials. The resistance genes observed were CatA, tetJ, and fosA7, most common in Ball than in other serovars. Seven plasmids were identified, more common in serovar Ball and less common in II 35:g,m,s,t:-. Serovar II 35:g,m,s,t:- isolates were missing some of the virulence genes important for Salmonella pathogenicity found in other serovars isolated. Conclusion: PCR detection of Campylobacter spp. and Salmonella spp. in chickens necessitate the improvement of hygiene at the household level and reducing human–chicken interaction as a strategy of preventing humans from acquiring chicken-associated bacteria, which would enter the human food chain. Infrequent use of antimicrobials in this type of poultry is most likely the reason for the low rates of antimicrobial resistance observed in this study.
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12
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Yao K, González-Escalona N, Hoffmann M. Multiple Displacement Amplification as a Solution for Low Copy Number Plasmid Sequencing. Front Microbiol 2021; 12:617487. [PMID: 33643244 PMCID: PMC7904871 DOI: 10.3389/fmicb.2021.617487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/13/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmids play a major role in bacterial adaptation to environmental stress and often contribute to antibiotic resistance and disease virulence. Although the complete sequence of each plasmid is essential for studying plasmid biology, most antibiotic resistance and virulence plasmids in Salmonella are present only in a low copy number, making extraction and sequencing difficult. Long read sequencing technologies require higher concentrations of DNA to provide optimal results. To resolve this problem, we assessed the sufficiency of multiple displacement amplification (MDA) for replicating Salmonella plasmid DNA to a satisfactory concentration for accurate sequencing and multiplexing. Nine Salmonella enterica isolates, representing nine different serovars carrying plasmids for which sequence data are already available at NCBI, were cultured and their plasmids isolated using an alkaline lysis extraction protocol. We then used the Phi29 polymerase to perform MDA, thereby obtaining enough plasmid DNA for long read sequencing. These amplified plasmids were multiplexed and sequenced on one single molecule, real-time (SMRT) cell with the Pacific Biosciences (Pacbio) Sequel sequencer. We were able to close all Salmonella plasmids (sizes ranged from 38 to 166 Kb) with sequencing coverage from 24 to 2,582X. This protocol, consisting of plasmid isolation, MDA, and multiplex sequencing, is an effective and fast method for closing high-molecular weight and low-copy-number plasmids. This high throughput protocol reduces the time and cost of plasmid closure.
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Affiliation(s)
- Kuan Yao
- Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Narjol González-Escalona
- Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Maria Hoffmann
- Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
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Characterization of a novel class 1 integron InSW39 and a novel transposon Tn5393k identified in an imipenem-nonsusceptible Salmonella Typhimurium strain in Sichuan, China. Diagn Microbiol Infect Dis 2020; 99:115263. [PMID: 33248418 DOI: 10.1016/j.diagmicrobio.2020.115263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 08/30/2020] [Accepted: 11/08/2020] [Indexed: 11/22/2022]
Abstract
This study aimed to characterize molecular mechanism of 3 Salmonella enterica strains and novel mobile genetic elements identified in them. The strains, designated SW1, SW39, and SW109084, were obtained from diarrhea patients. The results of susceptibility testing showed SW39 was nonsusceptible to imipenem and cefotaxime. Whole genome sequencing was performed on Illumina HiSeq platform. Multilocus-sequence typing revealed SW1 belonged to ST2529 which was first confirmed in S. enterica, SW109084 was ST34 which was first reported in Enteritidis and SW39 was ST19. Resistome analysis showed SW1, SW109084, and SW39 carried 14, 19, and 17 antibiotic resistance genes. Seven transposons and 4 integrons were confirmed in these strains. Notably, a novel In6- and In7-like class 1 integron designated InSW39 and a novel transposon Tn5393k were identified in plasmid pSW39. The study of genomics and resistance in S. enterica plays a significant role in prevention and treatment of Salmonella infections.
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14
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McMillan EA, Jackson CR, Frye JG. Transferable Plasmids of Salmonella enterica Associated With Antibiotic Resistance Genes. Front Microbiol 2020; 11:562181. [PMID: 33133037 PMCID: PMC7578388 DOI: 10.3389/fmicb.2020.562181] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
Salmonella enterica is a common foodborne illness in the United States and globally. An increasing number of Salmonella infections are resistant to antibiotics, and many of the genes responsible for those resistances are carried by plasmids. Plasmids are important mediators of horizontal gene exchange, which could potentially increase the spread of antibiotic resistance (AR) genes. Twenty-eight different incompatibility groups of plasmids have been described in Enterobacteriaceae. Incompatibility groups differ in their accessory gene content, replication mechanisms, and their associations with Salmonella serotypes and animal sources. Plasmids also differ in their ability to conjugate or be mobilized, essential genes, and conditions required for transfer. It is important to understand the differences in gene content and transfer mechanisms to accurately determine the impact of plasmids on the dissemination and persistence of antibiotic resistance genes. This review will cover the most common plasmid incompatibility groups present in S. enterica with a focus on the transfer mechanisms and associated antibiotic resistance genes.
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Affiliation(s)
- Elizabeth A McMillan
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, United States
| | - Charlene R Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, United States
| | - Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, United States
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15
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Berbers B, Ceyssens PJ, Bogaerts P, Vanneste K, Roosens NHC, Marchal K, De Keersmaecker SCJ. Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination. Antibiotics (Basel) 2020; 9:E503. [PMID: 32796589 PMCID: PMC7460218 DOI: 10.3390/antibiotics9080503] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the most prominent public health threats. AMR genes localized on plasmids can be easily transferred between bacterial isolates by horizontal gene transfer, thereby contributing to the spread of AMR. Next-generation sequencing (NGS) technologies are ideal for the detection of AMR genes; however, reliable reconstruction of plasmids is still a challenge due to large repetitive regions. This study proposes a workflow to reconstruct plasmids with NGS data in view of AMR gene localization, i.e., chromosomal or on a plasmid. Whole-genome and plasmid DNA extraction methods were compared, as were assemblies consisting of short reads (Illumina MiSeq), long reads (Oxford Nanopore Technologies) and a combination of both (hybrid). Furthermore, the added value of conjugation of a plasmid to a known host was evaluated. As a case study, an isolate harboring a large, low-copy mcr-1-carrying plasmid (>200 kb) was used. Hybrid assemblies of NGS data obtained from whole-genome DNA extractions of the original isolates resulted in the most complete reconstruction of plasmids. The optimal workflow was successfully applied to multidrug-resistant Salmonella Kentucky isolates, where the transfer of an ESBL-gene-containing fragment from a plasmid to the chromosome was detected. This study highlights a strategy including wet and dry lab parameters that allows accurate plasmid reconstruction, which will contribute to an improved monitoring of circulating plasmids and the assessment of their risk of transfer.
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Affiliation(s)
- Bas Berbers
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (B.B.); (K.V.); (N.H.C.R.)
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052 Ghent, Belgium;
| | | | - Pierre Bogaerts
- National Reference Center for Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, 5530 Yvoir, Belgium;
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (B.B.); (K.V.); (N.H.C.R.)
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (B.B.); (K.V.); (N.H.C.R.)
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052 Ghent, Belgium;
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria 0083, South Africa
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16
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Clark CG, Landgraff C, Robertson J, Pollari F, Parker S, Nadon C, Gannon VPJ, Johnson R, Nash J. Distribution of heavy metal resistance elements in Canadian Salmonella 4,[5],12:i:- populations and association with the monophasic genotypes and phenotype. PLoS One 2020; 15:e0236436. [PMID: 32716946 PMCID: PMC7384650 DOI: 10.1371/journal.pone.0236436] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/06/2020] [Indexed: 12/02/2022] Open
Abstract
Salmonella 4,[5],12:i:- are monophasic S. Typhimurium variants incapable of producing the second-phase flagellar antigen. They have emerged since the mid-1990s to become one of the most prevalent Salmonella serotypes causing human disease world-wide. Multiple genetic events associated with different genetic elements can result in the monophasic phenotype. Several jurisdictions have reported the emergence of a Salmonella 4,[5],12:i:- clone with SGI-4 and a genetic element (MREL) encoding a mercury resistance operon and antibiotic resistance loci that disrupts the second phase antigen region near the iroB locus in the Salmonella genome. We have sequenced 810 human and animal Canadian Salmonella 4,[5],12:i:- isolates and determined that isolates with SGI-4 and the mercury resistance element (MREL; also known as RR1&RR2) constitute several global clades containing various proportions of Canadian, US, and European isolates. Detailed analysis of the data provides a clearer picture of how these heavy metal elements interact with bacteria within the Salmonella population to produce the monophasic phenotype. Insertion of the MREL near iroB is associated with several deletions and rearrangements of the adjacent flaAB hin region, which may be useful for defining human case clusters that could represent outbreaks. Plasmids carrying genes encoding silver, copper, mercury, and antimicrobial resistance appear to be derived from IS26 mediated acquisition of these genes from genomes carrying SGI-4 and the MREL. Animal isolates with the mercury and As/Cu/Ag resistance elements are strongly associated with porcine sources in Canada as has been shown previously for other jurisdictions. The data acquired in these investigations, as well as from the extensive literature on the subject, may aid source attribution in outbreaks of the organism and interventions to decrease the prevalence of this clone and reduce its impact on human disease.
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Affiliation(s)
- Clifford G Clark
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Chrystal Landgraff
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - James Robertson
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Frank Pollari
- FoodNet Canada, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Stephen Parker
- FoodNet Canada, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Celine Nadon
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- PulseNet Canada, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Victor P J Gannon
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Canada
| | - Roger Johnson
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - John Nash
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
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17
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Douarre PE, Mallet L, Radomski N, Felten A, Mistou MY. Analysis of COMPASS, a New Comprehensive Plasmid Database Revealed Prevalence of Multireplicon and Extensive Diversity of IncF Plasmids. Front Microbiol 2020; 11:483. [PMID: 32265894 PMCID: PMC7105883 DOI: 10.3389/fmicb.2020.00483] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/05/2020] [Indexed: 12/20/2022] Open
Abstract
Plasmids are genetic elements that enable rapid adaptation and evolution by transferring genes conferring selective advantages to their hosts. Conjugative plasmids are predominantly responsible for the global dissemination of antimicrobial resistance, representing an important threat to global health. As the number of plasmid sequences grows exponentially, it becomes critical to depict the global diversity and decipher the distribution of circulating plasmids in the bacterial community. To this end, we created COMPASS, a novel and comprehensive database compiling 12,084 complete plasmids with associated metadata from 1571 distinct species isolated worldwide over more than 100 years. The curation of the database allowed us to identify identical plasmids across different bacteria revealing mainly intraspecies dissemination and rare cases of horizontal transmission. We outlined and analyzed all relevant features, plasmid properties, host range and characterized their replication and mobilization systems. After an exhaustive comparison of PlasmidFinder and MOB-typer, the MOB-typer-based analysis revealed that the current knowledge embedded in the current typing schemes fails to classify all the plasmid sequences collected in COMPASS. We were able to categorize 6828 and 5229 plasmids by replicon and MOB typing, respectively, mostly associated with Proteobacteria and Firmicutes. We then searched for the presence of multiple core genes involved in replication and propagation. Our results showed that 2403 plasmids carried multiple replicons that were distributed in 206 bacterial species. The co-integration of replicon types from different incompatibility (Inc) groups is an adaptive mechanism, which plays an important role in plasmid survival and dissemination by extending their host range. Our results highlight the crucial role of IncF alleles (present in 56% of all multireplicons) and revealed that IncH, IncR, and IncU replicons were also frequently carried in multireplicons. Here, we provided a comprehensive picture of the different IncF subtypes by identifying 20 different profiles in 849 IncF multireplicons, which were mostly associated with Enterobacteriaceae. These results could provide the basis for a novel IncF plasmid nomenclature based on different allelic profiles.
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Affiliation(s)
- Pierre-Emmanuel Douarre
- Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food Safety, Paris, France
| | - Ludovic Mallet
- Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food Safety, Paris, France
| | - Nicolas Radomski
- Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food Safety, Paris, France
| | - Arnaud Felten
- Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food Safety, Paris, France
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18
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Eyler AB, M'ikanatha NM, Xiaoli L, Dudley EG. Whole-genome sequencing reveals resistome of highly drug-resistant retail meat and human Salmonella Dublin. Zoonoses Public Health 2019; 67:251-262. [PMID: 31867871 DOI: 10.1111/zph.12680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 11/28/2022]
Abstract
Non-typhoidal Salmonella (NTS) are a significant source of foodborne illness worldwide, with disease symptoms most often presenting as self-limiting gastroenteritis; however, occasionally the infection spreads and becomes invasive, frequently requiring anti-microbial treatment. The cattle-adapted Dublin serovar of NTS has commonly been associated with invasive illness and anti-microbial resistance (AMR). Here, the enhanced resolution conferred by whole-genome sequencing was utilized to elucidate and compare the resistome and genetic relatedness of 14 multidrug-resistant (MDR) and one pan-susceptible S. Dublin, isolated primarily in Pennsylvania, from fresh retail meat (one isolate) and humans (14 isolates). Twelve different genetic AMR determinants, including both acquired and chromosomal, were identified. Furthermore, comparative plasmid analysis indicated that AMR was primarily conferred by a putative IncA/C2 plasmid. A single pan-susceptible S. Dublin isolate, collected from the same timeframe and geographical region as the MDR isolates, did not carry an IncA/C2 replicon sequence within its genome. Moreover, the pan-susceptible isolate was genetically distinct from its MDR counterparts, as it was separated by ≥267 single nucleotide polymorphisms (SNPs), whereas there was a ≤38 SNP distance between the MDR isolates. Collectively, this data set advances our understanding of the genetic basis of the highly drug-resistant nature of S. Dublin, a serovar with significant public health implications.
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Affiliation(s)
- Andrea B Eyler
- Department of Food Science, The Pennsylvania State University, University Park, PA, USA
| | | | - Lingzi Xiaoli
- E. coli Reference Center, The Pennsylvania State University, University Park, PA, USA
| | - Edward G Dudley
- Department of Food Science, The Pennsylvania State University, University Park, PA, USA.,E. coli Reference Center, The Pennsylvania State University, University Park, PA, USA
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19
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Gupta SK, Sharma P, McMillan EA, Jackson CR, Hiott LM, Woodley T, Humayoun SB, Barrett JB, Frye JG, McClelland M. Genomic comparison of diverse Salmonella serovars isolated from swine. PLoS One 2019; 14:e0224518. [PMID: 31675365 PMCID: PMC6824618 DOI: 10.1371/journal.pone.0224518] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/15/2019] [Indexed: 12/19/2022] Open
Abstract
Food animals act as a reservoir for many foodborne pathogens. Salmonella enterica is one of the leading pathogens that cause food borne illness in a broad host range including animals and humans. They can also be associated with a single host species or a subset of hosts, due to genetic factors associated with colonization and infection. Adult swine are often asymptomatic carriers of a broad range of Salmonella servoars and can act as an important reservoir of infections for humans. In order to understand the genetic variations among different Salmonella serovars, Whole Genome Sequences (WGS) of fourteen Salmonella serovars from swine products were analyzed. More than 75% of the genes were part of the core genome in each isolate and the higher fraction of gene assign to different functional categories in dispensable genes indicated that these genes acquired for better adaptability and diversity. High concordance (97%) was detected between phenotypically confirmed antibiotic resistances and identified antibiotic resistance genes from WGS. The resistance determinants were mainly located on mobile genetic elements (MGE) on plasmids or integrated into the chromosome. Most of known and putative virulence genes were part of the core genome, but a small fraction were detected on MGE. Predicted integrated phage were highly diverse and many harbored virulence, metal resistance, or antibiotic resistance genes. CRISPR (Clustered regularly interspaced short palindromic repeats) patterns revealed the common ancestry or infection history among Salmonella serovars. Overall genomic analysis revealed a great deal of diversity among Salmonella serovars due to acquired genes that enable them to thrive and survive during infection.
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Affiliation(s)
- Sushim K. Gupta
- Bacterial Epidemiology and Antimicrobial Resistance Unit, USDA-ARS, Athens, GA, United States of America
| | - Poonam Sharma
- Bacterial Epidemiology and Antimicrobial Resistance Unit, USDA-ARS, Athens, GA, United States of America
| | - Elizabeth A. McMillan
- Bacterial Epidemiology and Antimicrobial Resistance Unit, USDA-ARS, Athens, GA, United States of America
- Department of Microbiology, University of Georgia, Athens, GA, United States of America
| | - Charlene R. Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Unit, USDA-ARS, Athens, GA, United States of America
| | - Lari M. Hiott
- Bacterial Epidemiology and Antimicrobial Resistance Unit, USDA-ARS, Athens, GA, United States of America
| | - Tiffanie Woodley
- Bacterial Epidemiology and Antimicrobial Resistance Unit, USDA-ARS, Athens, GA, United States of America
| | - Shaheen B. Humayoun
- Bacterial Epidemiology and Antimicrobial Resistance Unit, USDA-ARS, Athens, GA, United States of America
| | - John B. Barrett
- Bacterial Epidemiology and Antimicrobial Resistance Unit, USDA-ARS, Athens, GA, United States of America
| | - Jonathan G. Frye
- Bacterial Epidemiology and Antimicrobial Resistance Unit, USDA-ARS, Athens, GA, United States of America
- * E-mail:
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, United States of America
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20
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Unknown Risk on the Farm: Does Agricultural Use of Ionophores Contribute to the Burden of Antimicrobial Resistance? mSphere 2019; 4:4/5/e00433-19. [PMID: 31554722 PMCID: PMC6763768 DOI: 10.1128/msphere.00433-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ionophores are the second most widely used class of antibiotic in agriculture, with over 4 million kilograms sold in the United States in 2016. Because ionophores are not used in humans, it is widely assumed that their agricultural use will not impact human health. Consequently, these drugs have not been subject to the same regulations as medically important antibiotics. Ionophores are the second most widely used class of antibiotic in agriculture, with over 4 million kilograms sold in the United States in 2016. Because ionophores are not used in humans, it is widely assumed that their agricultural use will not impact human health. Consequently, these drugs have not been subject to the same regulations as medically important antibiotics. Here, I argue that the current evidence base is insufficient to conclude that ionophores do not contribute to human relevant antimicrobial resistance. It is unclear whether ionophore resistance can result in cross-resistance to medically important antibiotics. Moreover, recent evidence suggests that ionophore use may coselect for resistance to vancomycin in some cases. Systematic investigation of the consequences of agricultural ionophore use for human health is therefore imperative.
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21
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McMillan EA, Gupta SK, Williams LE, Jové T, Hiott LM, Woodley TA, Barrett JB, Jackson CR, Wasilenko JL, Simmons M, Tillman GE, McClelland M, Frye JG. Antimicrobial Resistance Genes, Cassettes, and Plasmids Present in Salmonella enterica Associated With United States Food Animals. Front Microbiol 2019; 10:832. [PMID: 31057528 PMCID: PMC6479191 DOI: 10.3389/fmicb.2019.00832] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/01/2019] [Indexed: 11/13/2022] Open
Abstract
The ability of antimicrobial resistance (AR) to transfer, on mobile genetic elements (MGEs) between bacteria, can cause the rapid establishment of multidrug resistance (MDR) in bacteria from animals, thus creating a foodborne risk to human health. To investigate MDR and its association with plasmids in Salmonella enterica, whole genome sequence (WGS) analysis was performed on 193 S. enterica isolated from sources associated with United States food animals between 1998 and 2011; 119 were resistant to at least one antibiotic tested. Isolates represented 86 serotypes and variants, as well as diverse phenotypic resistance profiles. A total of 923 AR genes and 212 plasmids were identified among the 193 strains. Every isolate contained at least one AR gene. At least one plasmid was detected in 157 isolates. Genes were identified for resistance to aminoglycosides (n = 472), β-lactams (n = 84), tetracyclines (n = 171), sulfonamides (n = 91), phenicols (n = 42), trimethoprim (n = 8), macrolides (n = 5), fosfomycin (n = 48), and rifampicin (n = 2). Plasmid replicon types detected in the isolates were A/C (n = 32), ColE (n = 76), F (n = 43), HI1 (n = 4), HI2 (n = 20), I1 (n = 62), N (n = 4), Q (n = 7), and X (n = 35). Phenotypic resistance correlated with the AR genes identified in 95.4% of cases. Most AR genes were located on plasmids, with many plasmids harboring multiple AR genes. Six antibiotic resistance cassette structures (ARCs) and one pseudo-cassette were identified. ARCs contained between one and five resistance genes (ARC1: sul2, strAB, tetAR; ARC2: aac3-iid; ARC3: aph, sph; ARC4: cmy-2; ARC5: floR; ARC6: tetB; pseudo-ARC: aadA, aac3-VIa, sul1). These ARCs were present in multiple isolates and on plasmids of multiple replicon types. To determine the current distribution and frequency of these ARCs, the public NCBI database was analyzed, including WGS data on isolates collected by the USDA Food Safety and Inspection Service (FSIS) from 2014 to 2018. ARC1, ARC4, and ARC5 were significantly associated with cattle isolates, while ARC6 was significantly associated with chicken isolates. This study revealed that a diverse group of plasmids, carrying AR genes, are responsible for the phenotypic resistance seen in Salmonella isolated from United States food animals. It was also determined that many plasmids carry similar ARCs.
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Affiliation(s)
| | - Sushim K Gupta
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - Laura E Williams
- Department of Biology, Providence College, Providence, RI, United States
| | - Thomas Jové
- INSERM, CHU Limoges, RESINFIT, University of Limoges, Limoges, France
| | - Lari M Hiott
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - Tiffanie A Woodley
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - John B Barrett
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - Charlene R Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - Jamie L Wasilenko
- Eastern Lab, United States Department of Agriculture, Food Safety and Inspection Service, Athens, GA, United States
| | - Mustafa Simmons
- Eastern Lab, United States Department of Agriculture, Food Safety and Inspection Service, Athens, GA, United States
| | - Glenn E Tillman
- Eastern Lab, United States Department of Agriculture, Food Safety and Inspection Service, Athens, GA, United States
| | - Michael McClelland
- Department of Microbiology & Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
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22
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Ambrose SJ, Harmer CJ, Hall RM. Evolution and typing of IncC plasmids contributing to antibiotic resistance in Gram-negative bacteria. Plasmid 2018; 99:40-55. [PMID: 30081066 DOI: 10.1016/j.plasmid.2018.08.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/12/2018] [Accepted: 08/02/2018] [Indexed: 01/14/2023]
Abstract
The large, broad host range IncC plasmids are important contributors to the spread of key antibiotic resistance genes and over 200 complete sequences of IncC plasmids have been reported. To track the spread of these plasmids accurate typing to identify the closest relatives is needed. However, typing can be complicated by the high variability in resistance gene content and various typing methods that rely on features of the conserved backbone have been developed. Plasmids can be broadly typed into two groups, type 1 and type 2, using four features that differentiate the otherwise closely related backbones. These types are found in many different countries in bacteria from humans and animals. However, hybrids of type 1 and type 2 are also occasionally seen, and two further types, each represented by a single plasmid, were distinguished. Generally, the antibiotic resistance genes are located within a small number of resistance islands, only one of which, ARI-B, is found in both type 1 and type 2. The introduction of each resistance island generates a new lineage and, though they are continuously evolving via the loss of resistance genes or introduction of new ones, the island positions serve as valuable lineage-specific markers. A current type 2 lineage of plasmids is derived from an early type 2 plasmid but the sequences of early type 1 plasmids include features not seen in more recent type 1 plasmids, indicating a shared ancestor rather than a direct lineal relationship. Some features, including ones essential for maintenance or for conjugation, have been examined experimentally.
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Affiliation(s)
- Stephanie J Ambrose
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Christopher J Harmer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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23
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Cao G, Allard M, Hoffmann M, Muruvanda T, Luo Y, Payne J, Meng K, Zhao S, McDermott P, Brown E, Meng J. Sequence Analysis of IncA/C and IncI1 Plasmids Isolated from Multidrug-Resistant Salmonella Newport Using Single-Molecule Real-Time Sequencing. Foodborne Pathog Dis 2018; 15:361-371. [DOI: 10.1089/fpd.2017.2385] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Guojie Cao
- Department of Nutrition and Food Science, Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Marc Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Tim Muruvanda
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Yan Luo
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Justin Payne
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Kevin Meng
- Department of Microbiology and Immunology, Stanford School of Medicine, Stanford University, Palo Alto, California
| | - Shaohua Zhao
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland
| | - Patrick McDermott
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland
| | - Eric Brown
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Jianghong Meng
- Department of Nutrition and Food Science, Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland
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24
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Kudirkiene E, Andoh LA, Ahmed S, Herrero-Fresno A, Dalsgaard A, Obiri-Danso K, Olsen JE. The Use of a Combined Bioinformatics Approach to Locate Antibiotic Resistance Genes on Plasmids From Whole Genome Sequences of Salmonella enterica Serovars From Humans in Ghana. Front Microbiol 2018; 9:1010. [PMID: 29867897 PMCID: PMC5966558 DOI: 10.3389/fmicb.2018.01010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/30/2018] [Indexed: 11/20/2022] Open
Abstract
In the current study, we identified plasmids carrying antimicrobial resistance genes in draft whole genome sequences of 16 selected Salmonella enterica isolates representing six different serovars from humans in Ghana. The plasmids and the location of resistance genes in the genomes were predicted using a combination of PlasmidFinder, ResFinder, plasmidSPAdes and BLAST genomic analysis tools. Subsequently, S1-PFGE was employed for analysis of plasmid profiles. Whole genome sequencing confirmed the presence of antimicrobial resistance genes in Salmonella isolates showing multidrug resistance phenotypically. ESBL, either blaTEM52-B or blaCTX-M15 were present in two cephalosporin resistant isolates of S. Virchow and S. Poona, respectively. The systematic genome analysis revealed the presence of different plasmids in different serovars, with or without insertion of antimicrobial resistance genes. In S. Enteritidis, resistance genes were carried predominantly on plasmids of IncN type, in S. Typhimurium on plasmids of IncFII(S)/IncFIB(S)/IncQ1 type. In S. Virchow and in S. Poona, resistance genes were detected on plasmids of IncX1 and TrfA/IncHI2/IncHI2A type, respectively. The latter two plasmids were described for the first time in these serovars. The combination of genomic analytical tools allowed nearly full mapping of the resistance plasmids in all Salmonella strains analyzed. The results suggest that the improved analytical approach used in the current study may be used to identify plasmids that are specifically associated with resistance phenotypes in whole genome sequences. Such knowledge would allow the development of rapid multidrug resistance tracking tools in Salmonella populations using WGS.
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Affiliation(s)
- Egle Kudirkiene
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Linda A. Andoh
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Shahana Ahmed
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kwasi Obiri-Danso
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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25
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Zhao Y, Zhang XX, Zhao Z, Duan C, Chen H, Wang M, Ren H, Yin Y, Ye L. Metagenomic analysis revealed the prevalence of antibiotic resistance genes in the gut and living environment of freshwater shrimp. JOURNAL OF HAZARDOUS MATERIALS 2018; 350:10-18. [PMID: 29448209 DOI: 10.1016/j.jhazmat.2018.02.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/12/2018] [Accepted: 02/03/2018] [Indexed: 05/08/2023]
Abstract
Antibiotic resistance disseminating from animals and their environments is a public issue that poses significant threats to human health. In the present study, the diversity and abundance of antibiotic resistance genes (ARGs) in 15 samples from the guts and related aquaculture environments (water and sediment) of shrimp were investigated. In total, 60 ARGs, 102 ARGs and 67 ARGs primarily belonging to 13, 15 and 15 different types were detected in the shrimp gut, pond water and sediment samples, respectively. Efflux pump and target modification were the predominant resistance mechanisms in all samples. It was found that Aeromonas, Yersinia and Clostridium XlVb were significantly correlated with the distribution of the ARGs. Besides, the relative abundance of ARGs was positively correlated with the levels of mobile genetic elements (MGEs). Moreover, variation partitioning analysis showed that MGEs, contributing to 74.46% of the resistome variation, played an important role in the affecting of the antibiotic resistome than the bacterial communities and their joint effects. Collectively, this study provides comprehensive information to better understand the ARG dissemination in aquaculture environments and to improve the ecological management of aquatic ecosystems.
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Affiliation(s)
- Yanting Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Zhonghua Zhao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Cuilan Duan
- Fisheries Technology Extension Center of Jiangsu Province, Nanjing 210036, China
| | - Huangen Chen
- Fisheries Technology Extension Center of Jiangsu Province, Nanjing 210036, China
| | - Miaomiao Wang
- Fisheries Technology Extension Center of Jiangsu Province, Nanjing 210036, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Ying Yin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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