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Verburg I, Hernández Leal L, Waar K, Rossen JWA, Schmitt H, García-Cobos S. Klebsiella pneumoniae species complex: From wastewater to the environment. One Health 2024; 19:100880. [PMID: 39263320 PMCID: PMC11387367 DOI: 10.1016/j.onehlt.2024.100880] [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: 05/08/2024] [Revised: 08/15/2024] [Accepted: 08/15/2024] [Indexed: 09/13/2024] Open
Abstract
Klebsiella pneumoniae plays a significant role in nosocomial infections and spreading antibiotic resistance, and therefore forms a major threat to public health. In this study, we investigated the role of the wastewater pathway in the spread of pathogenic bacteria and more specifically, in the spread of antibiotic resistant Klebsiella pneumoniae subspecies. Whole-genome sequencing was performed of 185 K. pneumoniae isolates collected from hospital, nursing home, and community wastewater, the receiving wastewater treatment plant (WWTP), and clinical isolates from the investigated hospital. K. pneumoniae isolates from different sources were not genetically related, except for WWTP influent (46.5%) and effluent (62.5%), revealing survival of bacteria from wastewater treatment. The content of antibiotic resistance (ARGs), virulence, and plasmid replicon genes differed between K. pneumoniae subspecies and their origin. While chromosomal bla genes were specific for each K. pneumoniae subspecies, bla genes predicted in plasmid contigs were found in several K. pneumoniae subspecies, implying possible gene transfer between subspecies. Transferable ARGs were most abundant in patients and hospital isolates (70%), but the average number of plasmid replicon genes per isolate was similar across all sources, showing plasmid content being more relevant than plasmid quantity. Most patient (90%) and hospital wastewater (34%) isolates were K. pneumoniae subsp. pneumoniae, and the yersiniabactin cluster genes ybt, fyuA, and irp12 were only found in this subspecies, as were the IncFII(pECLA), IncHI2A, and IncHI2 plasmid replicon genes, suggesting the clinical origin of these type of plasmids.
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Affiliation(s)
- Ilse Verburg
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900, CC, Leeuwarden, the Netherlands
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713, GZ, Groningen, the Netherlands
| | - Lucia Hernández Leal
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900, CC, Leeuwarden, the Netherlands
| | - Karola Waar
- Certe Medische Microbiologie Friesland, 8900, JA, Leeuwarden, the Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713, GZ, Groningen, the Netherlands
| | - Heike Schmitt
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900, CC, Leeuwarden, the Netherlands
- Institute for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721, MA, Bilthoven, the Netherlands
| | - Silvia García-Cobos
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713, GZ, Groningen, the Netherlands
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
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Ammar AM, Abd El-Aziz NK, Aggour MG, Ahmad AAM, Abdelkhalek A, Muselin F, Smuleac L, Pascalau R, Attia FA. A Newly Incompatibility F Replicon Allele (FIB81) in Extensively Drug-Resistant Escherichia coli Isolated from Diseased Broilers. Int J Mol Sci 2024; 25:8347. [PMID: 39125914 PMCID: PMC11312129 DOI: 10.3390/ijms25158347] [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: 06/21/2024] [Revised: 07/16/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
Multiple drug resistance (MDR) has gained pronounced attention among Enterobacterales. The transfer of multiple antimicrobial resistance genes, frequently carried on conjugative incompatibility F (IncF) plasmids and facilitating interspecies resistance transmission, has been linked to Salmonella spp. and E. coli in broilers. In Egypt, the growing resistance is exacerbated by the limited clinical efficacy of many antimicrobials. In this study, IncF groups were screened and characterized in drug-resistant Salmonella spp. and E. coli isolated from broilers. The antimicrobial resistance profile, PCR-based replicon typing of bacterial isolates pre- and post-plasmid curing, and IncF replicon allele sequence typing were investigated. Five isolates of E. coli (5/31; 16.13%) and Salmonella spp. (5/36; 13.89%) were pan-susceptible to the examined antimicrobial agents, and 85.07% of tested isolates were MDR and extensively drug-resistant (XDR). Twelve MDR and XDR E. coli and Salmonella spp. isolates were examined for the existence of IncF replicons (FII, FIA, and FIB). They shared resistance to ampicillin, ampicillin/sulbactam, amoxicillin/clavulanate, doxycycline, cefotaxime, and colistin. All isolates carried from one to two IncF replicons. The FII-FIA-FIB+ and FII-FIA+FIB- were the predominant replicon patterns. FIB was the most frequently detected replicon after plasmid curing. Three XDR E. coli isolates that were resistant to 12-14 antimicrobials carried a newly FIB replicon allele with four nucleotide substitutions: C99→A, G112→T, C113→T, and G114→A. These findings suggest that broilers are a significant reservoir of IncF replicons with highly divergent IncF-FIB plasmid incompatibility groups circulating among XDR Enterobacterales. Supporting these data with additional comprehensive epidemiological studies involving replicons other than the IncF can provide insights for implementing efficient policies to prevent the spreading of new replicons to humans.
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Affiliation(s)
- Ahmed M. Ammar
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt; (A.M.A.); (A.A.M.A.)
| | - Norhan K. Abd El-Aziz
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt; (A.M.A.); (A.A.M.A.)
| | | | - Adel A. M. Ahmad
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt; (A.M.A.); (A.A.M.A.)
| | - Adel Abdelkhalek
- Food Safety, Hygiene and Technology Department, Faculty of Veterinary Medicine, Badr University in Cairo (BUC), Badr 11829, Egypt;
| | - Florin Muselin
- Department of Toxicology, Faculty of Veterinary Medicine, University of Life Sciences “King Michael I” from Timisoara, 300645 Timisoara, Romania;
| | - Laura Smuleac
- Department of Sustainable Development and Environmental Engineering, Faculty of Agriculture, University of Life Sciences “King Mihai I” from Timisoara, 300645 Timisoara, Romania;
| | - Raul Pascalau
- Department of Agricultural Technologies, Faculty of Agriculture, University of Life Sciences “ King Mihai I” from Timisoara, 300645 Timisoara, Romania
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Sun RY, Fang LX, Dai JJ, Chen KC, Ke BX, Sun J, Ke CW, Wai Chi Chan E, Liu YH, Chen S, Liao XP. Antimicrobial resistance and population genomics of emerging multidrug-resistant Salmonella 4,[5],12:i:- in Guangdong, China. mSystems 2024; 9:e0116423. [PMID: 38747582 PMCID: PMC11237462 DOI: 10.1128/msystems.01164-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/09/2024] [Indexed: 06/19/2024] Open
Abstract
Salmonella 4,[5],12:i:-, a monophasic variant of Salmonella Typhimurium, has emerged as a global cause of multidrug-resistant salmonellosis and has become endemic in many developing and developed countries, especially in China. Here, we have sequenced 352 clinical isolates in Guangdong, China, during 2009-2019 and performed a large-scale collection of Salmonella 4,[5],12:i:- with whole genome sequencing (WGS) data across the globe, to better understand the population structure, antimicrobial resistance (AMR) genomic characterization, and transmission routes of Salmonella 4,[5],12:i:- across Guangdong. Salmonella 4,[5],12:i:- strains showed broad genetic diversity; Guangdong isolates were found to be widely distributed among the global lineages. Of note, we identified the formation of a novel Guangdong clade (Bayesian analysis of population structure lineage 1 [BAPS1]) genetically diversified from the global isolates and likely emerged around 1990s. BAPS1 exhibits unique genomic features, including large pan-genome, decreased ciprofloxacin susceptibility due to mutation in gyrA and carriage of plasmid-mediated quinolone resistance (PMQR) genes, and the multidrug-resistant IncHI2 plasmid. Furthermore, high genetic similarity was found between strains collected from Guangdong, Europe, and North America, indicating the association with multiple introductions from overseas. These results suggested that global dissemination and local clonal expansion simultaneously occurred in Guangdong, China, and horizontally acquired resistance to first-line and last-line antimicrobials at local level, underlying emergences of extensive drug and pan-drug resistance. Our findings have increased the knowledge of global and local epidemics of Salmonella 4,[5],12:i:- in Guangdong, China, and provided a comprehensive baseline data set essential for future molecular surveillance.IMPORTANCESalmonella 4,[5],12:i:- has been regarded as the predominant pandemic serotype causing diarrheal diseases globally, while multidrug resistance (MDR) constitutes great public health concerns. This study provided a detailed and comprehensive genome-scale analysis of this important Salmonella serovar in the past decade in Guangdong, China. Our results revealed the complexity of two distinct transmission modes, namely global transmission and local expansion, circulating in Guangdong over a decade. Using phylogeography models, the origin of Salmonella 4,[5],12:i:- was predicted from two aspects, year and country, that is, Salmonella 4,[5],12:i:- emerged in 1983, and was introduced from the UK, and subsequently differentiated into the local endemic lineage circa 1991. Additionally, based on the pan-genome analysis, it was found that the gene accumulation rate in local endemic BAPS 1 lineage was higher than in other lineages, and the horizontal transmission of MDR IncHI2 plasmid associated with high resistance played a major role, which showed the potential threat to public health.
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Affiliation(s)
- Ruan-Yang Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
| | - Liang-Xing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
| | - Jing-Jing Dai
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
| | - Kai-Chao Chen
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Bi-Xia Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
| | - Chang-Wen Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Edward Wai Chi Chan
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Sheng Chen
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
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Peng J, Feng J, Ji H, Kong X, Hong J, Zhu L, Qian H. Emergence of Rarely Reported Extensively Drug-Resistant Salmonella Enterica Serovar Paratyphi B among Patients in East China. Antibiotics (Basel) 2024; 13:519. [PMID: 38927185 PMCID: PMC11201502 DOI: 10.3390/antibiotics13060519] [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: 04/23/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND In recent years, global concern over increasing multidrug resistance (MDR) among various Salmonella serotypes has grown significantly. However, reports on MDR Salmonella Paratyphi B remain scarce, let alone the extensively drug-resistant (XDR) strains. METHODS In this retrospective study, we investigated the isolates of Salmonella Paratyphi B in Jiangsu Province over the past decade and carried out antimicrobial susceptibility tests, then the strains were sequenced and bioinformatics analyses were performed. RESULTS 27 Salmonella Paratyphi B strains were identified, of which the predominant STs were ST42 (11), ST86 (10), and ST2814 (5). Among these strains, we uncovered four concerning XDR Salmonella Paratyphi B ST2814 strains (4/5) which were previously unreported. These alarmingly resistant isolates showed resistance to all three major antibiotic classes for Salmonella treatment and even the last resort treatment tigecycline. Bioinformatics analysis revealed high similarity between the plasmids harbored by these XDR strains and diverse Salmonella serotypes and Escherichia coli from China and neighboring regions. Notably, these four plasmids carried the ramAp gene responsible for multiple antibiotic resistance by regulating the AcrAB-TolC pump, predominantly originating from China. Additionally, a distinct MDR ST42(1/11) strain with an ICE on chromosome was also identified. Furthermore, phylogenetic analysis of global ST42/ST2814 isolates highlighted the regional specificity of these strains, with Jiangsu isolates clustering together with domestic isolates and XDR ST2814 forming a distinct branch, suggesting adaptation to local antibiotic pressures. CONCLUSIONS This research underscores the pressing need for closely monitoring the MDR/XDR Salmonella Paratyphi B, particularly the emerging ST2814 strains in Jiangsu Province, to effectively curb its spread and protect public health. Moreover, surveillance should be strengthened across different ecological niches and genera to track resistance genes and horizontal gene transfer elements under the concept of "ONE HEALTH".
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Affiliation(s)
- Jiefu Peng
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China; (J.P.)
| | - Jingchao Feng
- School of Public Health, Xiamen University, Xiamen 361102, China
- Vanke School of Public Health, Tsinghua University, Beijing 100084, China
| | - Hong Ji
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China; (J.P.)
| | - Xiaoxiao Kong
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China; (J.P.)
| | - Jie Hong
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China; (J.P.)
| | - Liguo Zhu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China; (J.P.)
| | - Huimin Qian
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China; (J.P.)
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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, Gudeta DD, Han J, Nayak R, Foley SL. Genotypic analyses of IncHI2 plasmids from enteric bacteria. Sci Rep 2024; 14:9802. [PMID: 38684834 PMCID: PMC11058233 DOI: 10.1038/s41598-024-59870-2] [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: 11/22/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Incompatibility (Inc) HI2 plasmids are large (typically > 200 kb), transmissible plasmids that encode antimicrobial resistance (AMR), heavy metal resistance (HMR) and disinfectants/biocide resistance (DBR). To better understand the distribution and diversity of resistance-encoding genes among IncHI2 plasmids, computational approaches were used to evaluate resistance and transfer-associated genes among the plasmids. Complete IncHI2 plasmid (N = 667) sequences were extracted from GenBank and analyzed using AMRFinderPlus, IntegronFinder and Plasmid Transfer Factor database. The most common IncHI2-carrying genera included Enterobacter (N = 209), Escherichia (N = 208), and Salmonella (N = 204). Resistance genes distribution was diverse, with plasmids from Escherichia and Salmonella showing general similarity in comparison to Enterobacter and other taxa, which grouped together. Plasmids from Enterobacter and other taxa had a higher prevalence of multiple mercury resistance genes and arsenic resistance gene, arsC, compared to Escherichia and Salmonella. For sulfonamide resistance, sul1 was more common among Enterobacter and other taxa, compared to sul2 and sul3 for Escherichia and Salmonella. Similar gene diversity trends were also observed for tetracyclines, quinolones, β-lactams, and colistin. Over 99% of plasmids carried at least 25 IncHI2-associated conjugal transfer genes. These findings highlight the diversity and dissemination potential for resistance across different enteric bacteria and value of computational-based approaches for the resistance-gene assessment.
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Affiliation(s)
- Suad Algarni
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA.
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Dereje D Gudeta
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
| | - Jing Han
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
| | - Rajesh Nayak
- Office of Regulatory Compliance and Risk Management, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
| | - Steven L Foley
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA.
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA.
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Chen Y, Liu L, Guo Y, Chu J, Wang B, Sui Y, Wei H, Hao H, Huang L, Cheng G. Distribution and genetic characterization of fluoroquinolone resistance gene qnr among Salmonella strains from chicken in China. Microbiol Spectr 2024; 12:e0300023. [PMID: 38411972 PMCID: PMC10986518 DOI: 10.1128/spectrum.03000-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/06/2023] [Indexed: 02/28/2024] Open
Abstract
The prevalence and dissemination of the plasmid-mediated fluoroquinolone (FQ) resistance gene qnr in Salmonella are considered serious public health concerns worldwide. So far, no comprehensive large-scale studies have focused on the prevalence and genetic characteristics of the qnr gene in Salmonella isolated from chickens. Herein, this study aimed to investigate the prevalence, antimicrobial resistance (AMR) patterns, and molecular characteristics of chicken-originated qnr-positive Salmonella strains from chicken farms, slaughterhouses, and markets in 12 provinces of China in 2020-2021. The overall prevalence of the qnr gene was 21.13% (56/265), with the highest prevalence in markets (36.11%, 26/72), followed in farms (17.95%, 21/117), and slaughterhouses (10.53%, 9/76). Only the qnrS and qnrB genes were detected, and the prevalence rate of the qnrS gene (19.25%, 51/265) was higher than that of the qnrB gene (1.89%, 5/265). Whole genome sequencing identified 37 distinct AMR genes and 15 plasmid replicons, and the most frequent mutation in quinolone resistance determining regions was parC (T57S; 91.49%, 43/47). Meanwhile, four different qnrS and two qnrB genetic environments were discovered among 47 qnr-positive Salmonella strains. In total, 21.28% (10/47) of the strains were capable of conjugative transfer, and all were qnrS1-positive strains, with the majority of transferable plasmids being IncHI2 types (n = 4). Overall, the prevalence of qnr-positive Salmonella strains from chickens in China and their carriage of multiple resistance and virulence genes and transferable plasmids is a major concern, which calls for continuous surveillance of qnr-positive Salmonella and the development of measures to control its prevalence and transmission.IMPORTANCESalmonella is a common foodborne pathogen responsible for 155,000 deaths annually worldwide. Fluoroquinolones (FQs) are used as first-line drugs for the treatment of Salmonella infections in several countries and regions. However, the emergence and increasing prevalence of the FQ-resistant gene qnr in Salmonella isolated from chickens have been widely reported. Gaining insight into the genetic mechanisms of AMR genes in chicken could lead to the development of preventive measures to control and reduce the risk of drug resistance. In this study, we identified qnr-positive Salmonellae isolated from chickens in different regions of China and their AMR patterns and genome-wide characteristics, providing a theoretical basis for further control of their prevalence and transmission.
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Affiliation(s)
- Yang Chen
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lihui Liu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yali Guo
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinhua Chu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Bangjuan Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuxin Sui
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hanqi Wei
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Haihong Hao
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lingli Huang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Guyue Cheng
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
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Zhou L, Ye Q, Zhou Q, Wang J, Li G, Xiang J, Huang J, Zhao Y, Zheng T, Zuo H, Li S. Antimicrobial resistance and genomic investigation of Salmonella isolated from retail foods in Guizhou, China. Front Microbiol 2024; 15:1345045. [PMID: 38510999 PMCID: PMC10951074 DOI: 10.3389/fmicb.2024.1345045] [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: 11/27/2023] [Accepted: 02/19/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction Salmonella is a major foodborne pathogen worldwide that causes severe morbidity and mortality. It is mainly caused by consuming contaminated food, with retail food considered the primary source. Methods In Guizhou, China, 102 Salmonella strains isolated from 2016 to 2021 underwent phenotypic antimicrobial resistance testing and whole-genome sequencing (WGS) to understand Salmonella diversity, including serotypes, sequencing types (STs), antimicrobial genes, virulence genes, plasmid types, multi-locus sequence types (MLST), and core genome MLST (cgMLST). Results and discussion S.Typhimurium was the dominant serotype, and O:4(B) was the leading serogroup. The most prevalent genotype was ST40. Phenotypic antimicrobial resistance identified 66.7% of the sampled isolates as multi-drug resistant (MDR). S.Enteritidis (n = 7), S.Typhimurium (n = 1), S.Indiana (n = 1), S.Kentucky (n = 1), S.Uganda (n = 1), all of which were MDR, were resistant to Colistin. Resistance rates varied significantly across different strains and food types, particularly meat products exhibiting higher resistance. Notably, significant increases in resistance were observed from 2016 to 2021 for the following: ≥ 1 resistant (P = 0.001), MDR (P = 0.001), ampicillin (P = 0.001), tetracycline (P < 0.001), chloramphenicol (P = 0.030), and trimethoprim/sulfamethoxazole (P = 0.003). The marked escalation in drug resistance over the recent years, coupled with the varying resistance rates among food sources, underscores the growing public health concern. Our findings highlight the need for a coordinated approach to effectively monitor and respond to Salmonella infections in Guizhou, China.
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Affiliation(s)
- Li Zhou
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, China
| | - Qian Ye
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Qian Zhou
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, China
| | - Jian Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province, Chengdu, China
| | - Guanqiao Li
- Institute of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Jingshu Xiang
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, China
| | - Jingyu Huang
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, China
| | - Yuanyuan Zhao
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Tianli Zheng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Haojiang Zuo
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province, Chengdu, China
| | - Shijun Li
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, China
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Wu Y, Mao W, Shao J, He X, Bao D, Yue M, Wang J, Shen W, Qiang X, Jia H, He F, Ruan Z. Monitoring the long-term spatiotemporal transmission dynamics and ecological surveillance of multidrug-resistant Salmonella enterica serovar Goldcoast: A multicenter genomic epidemiology study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169116. [PMID: 38065491 DOI: 10.1016/j.scitotenv.2023.169116] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 12/02/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023]
Abstract
The emergence of multidrug-resistant Salmonella enterica serovar Goldcoast poses a significant threat to the effective treatment and control of salmonellosis within the ecological environment. Here, we conducted a genomic epidemiological study delineate the global dissemination scenarios of the multidrug-resistant S. Goldcoast originated from 11 countries for over 20 years. The population structure and evolutionary history of multidrug-resistant S. Goldcoast was investigated through phylogenomic and long-term spatiotemporal transmission dynamic analysis. ST358 and ST2529 are the predominant lineages of S. Goldcoast. Multidrug-resistant S. Goldcoast strains have mainly been identified in the ST358 lineage from human and the ST2529 lineage from livestock. ST358 S. Goldcoast was estimated to have emerged in the United Kingdom in 1969, and then spread to China, with both countries serve as centers for the global dissemination of the ST358 lineage. After its emergence and subsequent spread in Chinese clinical and environmental samples, occasional instances of this lineage have been reported in Canada, the United Kingdom, and Ireland. Clonal transmission of ST358 and ST2529 S. Goldcoast have occurred not only on an international and intercontinental scale but also among clinical, environmental and livestock samples. These data indicated that international circulation and local transmission of S. Goldcoast have occurred for over a decade. Continued surveillance of multidrug-resistant S. Goldcoast from a global "One Health" perspective is urgently needed to facilitate monitoring the spread of the antimicrobial resistant high-risk clones.
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Affiliation(s)
- Yuye Wu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Weifang Mao
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China; Department of Clinical Laboratory, Shaoxing University Affiliated Hospital, Shaoxing 312000, China
| | - Jiayu Shao
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China; Department of Clinical Laboratory, The Third People's Hospital of Xiaoshan District, Hangzhou 311251, China
| | - Xianhong He
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China; Department of Clinical Laboratory, The Third People's Hospital of Xiaoshan District, Hangzhou 311251, China
| | - Danni Bao
- Department of Clinical Laboratory, Sanmen People's Hospital, Taizhou 317199, China
| | - Meina Yue
- Department of Clinical Laboratory, Hangzhou Children's Hospital, Hangzhou 310005, China
| | - Jinyue Wang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Weiwei Shen
- Taizhou Center for Disease Control and Prevention, Taizhou 318000, China
| | - Xinhua Qiang
- Department of Clinical Laboratory, The First People's Hospital of Huzhou, Huzhou 313000, China
| | - Huiqiong Jia
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Fang He
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 314408, China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China; Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou 310016, China.
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10
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Chowdhury AR, Mukherjee D, Chatterjee R, Chakravortty D. Defying the odds: Determinants of the antimicrobial response of Salmonella Typhi and their interplay. Mol Microbiol 2024; 121:213-229. [PMID: 38071466 DOI: 10.1111/mmi.15209] [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: 07/31/2023] [Revised: 11/12/2023] [Accepted: 11/27/2023] [Indexed: 02/12/2024]
Abstract
Salmonella Typhi, the invasive serovar of S. enterica subspecies enterica, causes typhoid fever in healthy human hosts. The emergence of antibiotic-resistant strains has consistently challenged the successful treatment of typhoid fever with conventional antibiotics. Antimicrobial resistance (AMR) in Salmonella is acquired either by mutations in the genomic DNA or by acquiring extrachromosomal DNA via horizontal gene transfer. In addition, Salmonella can form a subpopulation of antibiotic persistent (AP) cells that can survive at high concentrations of antibiotics. These have reduced the effectiveness of the first and second lines of antibiotics used to treat Salmonella infection. The recurrent and chronic carriage of S. Typhi in human hosts further complicates the treatment process, as a remarkable shift in the immune response from pro-inflammatory Th1 to anti-inflammatory Th2 is observed. Recent studies have also highlighted the overlap between AP, persistent infection (PI) and AMR. These incidents have revealed several areas of research. In this review, we have put forward a timeline for the evolution of antibiotic resistance in Salmonella and discussed the different mechanisms of the same availed by the pathogen at the genotypic and phenotypic levels. Further, we have presented a detailed discussion on Salmonella antibiotic persistence (AP), PI, the host and bacterial virulence factors that can influence PI, and how both AP and PI can lead to AMR.
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Affiliation(s)
- Atish Roy Chowdhury
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Debapriya Mukherjee
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Ritika Chatterjee
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, India
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11
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Benevides VP, Saraiva MMS, Nascimento CF, Delgado-Suárez EJ, Oliveira CJB, Silva SR, Miranda VFO, Christensen H, Olsen JE, Berchieri Junior A. Genomic Features and Phylogenetic Analysis of Antimicrobial-Resistant Salmonella Mbandaka ST413 Strains. Microorganisms 2024; 12:312. [PMID: 38399716 PMCID: PMC10893270 DOI: 10.3390/microorganisms12020312] [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: 12/29/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
In recent years, Salmonella enterica subsp. enterica serovar Mbandaka (S. Mbandaka) has been increasingly isolated from laying hens and shell eggs around the world. Moreover, this serovar has been identified as the causative agent of several salmonellosis outbreaks in humans. Surprisingly, little is known about the characteristics of this emerging serovar, and therefore, we investigated antimicrobial resistance, virulence, and prophage genes of six selected Brazilian strains of Salmonella Mbandaka using Whole Genome Sequencing (WGS). Multi-locus sequence typing revealed that the tested strains belong to Sequence Type 413 (ST413), which has been linked to recent multi-country salmonellosis outbreaks in Europe. A total of nine resistance genes were detected, and the most frequent ones were aac(6')-Iaa, sul1, qacE, blaOXA-129, tet(B), and aadA1. A point mutation in ParC at the 57th position (threonine → serine) associated with quinolone resistance was present in all investigated genomes. A 112,960 bp IncHI2A plasmid was mapped in 4/6 strains. This plasmid harboured tetracycline (tetACDR) and mercury (mer) resistance genes, genes contributing to conjugative transfer, and genes involved in plasmid maintenance. Most strains (four/six) carried Salmonella genomic island 1 (SGI1). All S. Mbandaka genomes carried seven pathogenicity islands (SPIs) involved in intracellular survival and virulence: SPIs 1-5, 9, and C63PI. The virulence genes csgC, fimY, tcfA, sscA, (two/six), and ssaS (one/six) were absent in some of the genomes; conversely, fimA, prgH, and mgtC were present in all of them. Five Salmonella bacteriophage sequences (with homology to Escherichia phage phiV10, Enterobacteria phage Fels-2, Enterobacteria phage HK542, Enterobacteria phage ST64T, Salmonella phage SW9) were identified, with protein counts between 31 and 54, genome lengths of 24.7 bp and 47.7 bp, and average GC content of 51.25%. In the phylogenetic analysis, the genomes of strains isolated from poultry in Brazil clustered into well-supported clades with a heterogeneous distribution, primarily associated with strains isolated from humans and food. The phylogenetic relationship of Brazilian S. Mbandaka suggests the presence of strains with high epidemiological significance and the potential to be linked to foodborne outbreaks. Overall, our results show that isolated strains of S. Mbandaka are multidrug-resistant and encode a rather conserved virulence machinery, which is an epidemiological hallmark of Salmonella strains that have successfully disseminated both regionally and globally.
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Affiliation(s)
- Valdinete P Benevides
- Postgraduate Program in Agricultural Microbiology, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal 14884-900, Brazil
- Department of Pathology, Reproduction and One Health, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal 14884-900, Brazil
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Mauro M S Saraiva
- Department of Pathology, Reproduction and One Health, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal 14884-900, Brazil
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Camila F Nascimento
- Department of Pathology, Reproduction and One Health, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal 14884-900, Brazil
| | - Enrique J Delgado-Suárez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico
| | - Celso J B Oliveira
- Center for Agricultural Sciences, Department of Animal Science, Federal University of Paraiba (CCA/UFPB), Areia 58051-900, Brazil
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH 43210, USA
| | - Saura R Silva
- Laboratory of Plant Systematics, Department of Biology, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal 14884-900, Brazil
| | - Vitor F O Miranda
- Laboratory of Plant Systematics, Department of Biology, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal 14884-900, Brazil
| | - Henrik Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - John E Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Angelo Berchieri Junior
- Department of Pathology, Reproduction and One Health, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal 14884-900, Brazil
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12
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Gudeta DD, Foley SL. Versatile allelic replacement and self-excising integrative vectors for plasmid genome mutation and complementation. Microbiol Spectr 2024; 12:e0338723. [PMID: 37991378 PMCID: PMC10782977 DOI: 10.1128/spectrum.03387-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE In spite of the dissemination of multidrug-resistant plasmids among Gram-negative pathogens, including those carrying virulence genes, vector tools for studying plasmid-born genes are lacking. The allelic replacement vectors can be used to generate plasmid or chromosomal mutations including markless point mutations. This is the first report describing a self-excising integrative vector that can be used as a stable single-copy complementing tool to study medically important pathogens including in vivo studies without the need for antibiotic selection. Overall, our newly developed vectors can be applied for the assessment of the function of plasmid-encoded genes by specifically creating mutations, moving large operons between plasmids and to/from the chromosome, and complementing phenotypes associated with gene mutation. Furthermore, the vectors express chromophores for the detection of target gene modification or colony isolation, avoiding time-consuming screening procedures.
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Affiliation(s)
- Dereje D. Gudeta
- Division of Microbiology, National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Steven L. Foley
- Division of Microbiology, National Center for Toxicological Research, Jefferson, Arkansas, USA
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13
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Baker M, Zhang X, Maciel-Guerra A, Babaarslan K, Dong Y, Wang W, Hu Y, Renney D, Liu L, Li H, Hossain M, Heeb S, Tong Z, Pearcy N, Zhang M, Geng Y, Zhao L, Hao Z, Senin N, Chen J, Peng Z, Li F, Dottorini T. Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China. Nat Commun 2024; 15:206. [PMID: 38182559 PMCID: PMC10770378 DOI: 10.1038/s41467-023-44272-1] [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: 04/04/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024] Open
Abstract
Sharing of genetic elements among different pathogens and commensals inhabiting same hosts and environments has significant implications for antimicrobial resistance (AMR), especially in settings with high antimicrobial exposure. We analysed 661 Escherichia coli and Salmonella enterica isolates collected within and across hosts and environments, in 10 Chinese chicken farms over 2.5 years using data-mining methods. Most isolates within same hosts possessed the same clinically relevant AMR-carrying mobile genetic elements (plasmids: 70.6%, transposons: 78%), which also showed recent common evolution. Supervised machine learning classifiers revealed known and novel AMR-associated mutations and genes underlying resistance to 28 antimicrobials, primarily associated with resistance in E. coli and susceptibility in S. enterica. Many were essential and affected same metabolic processes in both species, albeit with varying degrees of phylogenetic penetration. Multi-modal strategies are crucial to investigate the interplay of mobilome, resistance and metabolism in cohabiting bacteria, especially in ecological settings where community-driven resistance selection occurs.
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Affiliation(s)
- Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Xibin Zhang
- Shandong New Hope Liuhe Group Co. Ltd. and Qingdao Key Laboratory of Animal Feed Safety, Qingdao, Shandong, 266000, P.R. China
| | - Alexandre Maciel-Guerra
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Kubra Babaarslan
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - David Renney
- Nimrod Veterinary Products Limited, 2, Wychwood Court, Cotswold Business Village, Moreton-in-Marsh, GL56 0JQ, London, UK
| | - Longhai Liu
- Shandong Kaijia Food Co. Ltd, Weifang, P. R. China
| | - Hui Li
- Luoyang Center for Disease Control and Prevention, No. 9, Zhenghe Road, Luolong District, Luoyang City, Henan Province, Luolong, 471000, P. R. China
| | - Maqsud Hossain
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Stephan Heeb
- School of Life Sciences, University of Nottingham, East Drive, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - Zhiqin Tong
- Luoyang Center for Disease Control and Prevention, No. 9, Zhenghe Road, Luolong District, Luoyang City, Henan Province, Luolong, 471000, P. R. China
| | - Nicole Pearcy
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
- School of Life Sciences, University of Nottingham, East Drive, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - Meimei Zhang
- Liaoning Provincial Center for Disease Control and Prevention, No. 168, Jinfeng Street, Hunnan District, Shenyang City, Liaoning Province, 110072, P. R. China
| | - Yingzhi Geng
- Liaoning Provincial Center for Disease Control and Prevention, No. 168, Jinfeng Street, Hunnan District, Shenyang City, Liaoning Province, 110072, P. R. China
| | - Li Zhao
- Agricultural Biopharmaceutical Laboratory, College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao City, Shandong Province, 266109, P. R. China
| | - Zhihui Hao
- Chinese Veterinary Medicine Innovation Center, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing City, 100193, P. R. China
| | - Nicola Senin
- Department of Engineering, University of Perugia, Perugia, I06125, Italy
| | - Junshi Chen
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China.
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China.
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK.
- Centre for Smart Food Research, Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, 315100, P. R. China.
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14
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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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15
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Sheng H, Suo J, Dai J, Wang S, Li M, Su L, Cao M, Cao Y, Chen J, Cui S, Yang B. Prevalence, antibiotic susceptibility and genomic analysis of Salmonella from retail meats in Shaanxi, China. Int J Food Microbiol 2023; 403:110305. [PMID: 37421839 DOI: 10.1016/j.ijfoodmicro.2023.110305] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/06/2023] [Accepted: 06/25/2023] [Indexed: 07/10/2023]
Abstract
Salmonella is a major foodborne pathogen that poses a substantial risk to food safety and public health. This study aimed to assess the prevalence, antibiotic susceptibility, and genomic features of Salmonella isolates recovered from 600 retail meat samples (300 pork, 150 chicken and 150 beef) from August 2018 to October 2019 in Shaanxi, China. Overall, 40 (6.67 %) of 600 samples were positive to Salmonella, with the highest prevalence in chicken (21.33 %, 32/150), followed in pork (2.67 %, 8/300), while no Salmonella was detected in beef. A total of 10 serotypes and 11 sequence types (STs) were detected in 40 Salmonella isolates, with the most common being ST198 S. Kentucky (n = 15), ST13 S. Agona (n = 6), and ST17 S. Indiana (n = 5). Resistance was most commonly found to tetracycline (82.50 %), followed by to ampicillin (77.50 %), nalidixic acid (70.00 %), kanamycin (57.50 %), ceftriaxone (55.00 %), cefotaxime (52.50 %), cefoperazone (52.50 %), chloramphenicol (50.00 %), levofloxacin (57.50 %), cefotaxime (52.50 %), kanamycin (52.50 %), chloramphenicol (50.00 %), ciprofloxacin (50.00 %), and levofloxacin (50.00 %). All ST198 S. Kentucky isolates showed multi-drug resistance (MDR; ≥3 antimicrobial categories) pattern. Genomic analysis showed 56 distinct antibiotic resistance genes (ARGs) and 6 target gene mutations of quinolone resistance determining regions (QRDRs) in 40 Salmonella isolates, among which, the most prevalent ARG types were related to aminoglycosides and β-lactams resistance, and the most frequent mutation in QRDRs was GyrA (S83F) (47.5 %). The number of ARGs in Salmonella isolates showed a significant positive correlation with the numbers of insert sequences (ISs) and plasmid replicons. Taken together, our findings indicated retail chickens were seriously contaminated, while pork and beef are rarely contaminated by Salmonella. Antibiotic resistance determinants and genetic relationships of the isolates provide crucial data for food safety and public health safeguarding.
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Affiliation(s)
- Huanjing Sheng
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jia Suo
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jinghan Dai
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Siyue Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mei Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Su
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengyuan Cao
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanwei Cao
- Hebei Quality Inspection and Testing Center of Forest, Grass and Flower, Shijiazhuang 050081, China
| | - Jia Chen
- College of Chemical Technology, Shijiazhuang University, Shijiazhuang 050035, China.
| | - Shenghui Cui
- National Institutes for Food and Drug Control, Beijing 100050, China.
| | - Baowei Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Engineering Research Centre of Dairy Products Quality, Safety and Health, Yangling, Shaanxi 712100, China.
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16
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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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17
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Adedokun FL, Ajayi A, Essiet UU, Oduyebo O, Adeleye AI, Smith SI. Antibiotic Resistance and Plasmid Replicon Types of Non-Typhoidal Salmonella Serovars Isolated From Food Animals and Humans in Lagos, Nigeria. Microbiol Insights 2023; 16:11786361231181909. [PMID: 37377945 PMCID: PMC10291401 DOI: 10.1177/11786361231181909] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Multidrug resistance and invasiveness of non-typhoidal Salmonella (NTS) serovars have in recent times brought to the fore the public health risk associated with salmonellosis. This study was aimed at profiling NTS serovars isolated from food animals and humans for their susceptibility to antibiotics and plasmid replicon types. Forty seven NTS serovars were profiled for their susceptibility to antibiotics using the disk diffusion method. Polymerase chain reaction based replicon typing assay was used for profiling plasmid replicon types detected in Salmonella isolates. High rate of resistance were found for amoxicillin/clavulanic acid (40/47; 85.1%), cefuroxime (38/47; 80.9%) and ceftazidime (30/47; 63.8%). Thirty one (65.9%) and 33 (70.2%) showed intermediate resistance to ofloxacin and ciprofloxacin respectively. Plasmids of sizes ranging from 14.3 to 16.7 kb were detected in 24 (51.1%) of Salmonella isolates with some serovars harbouring multiple plasmids. FIA, FIB, Frep and W plasmid replicon types were detected in 11, 4, 2 and 1 of the Salmonella isolates respectively. Three of the isolates harboured both FIA and FIB replicon types. The high rate of resistance to β-lactams observed in Salmonella serovars harbouring different plasmid replicon types in this study highlight potential public health threat and the need for prudent use of antibiotics in human and veterinary medicine.
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Affiliation(s)
| | - Abraham Ajayi
- Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Utibeima Udo Essiet
- Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Oyin Oduyebo
- Department of Medical Microbiology, College Medicine University of Lagos, Idi-Araba, Lagos, Nigeria
| | | | - Stella Ifeanyi Smith
- Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Department of Biological Sciences, Mountain Top University, Ogun State, Nigeria
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18
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Grudlewska-Buda K, Bauza-Kaszewska J, Wiktorczyk-Kapischke N, Budzyńska A, Gospodarek-Komkowska E, Skowron K. Antibiotic Resistance in Selected Emerging Bacterial Foodborne Pathogens-An Issue of Concern? Antibiotics (Basel) 2023; 12:antibiotics12050880. [PMID: 37237783 DOI: 10.3390/antibiotics12050880] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/30/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Antibiotic resistance (AR) and multidrug resistance (MDR) have been confirmed for all major foodborne pathogens: Campylobacter spp., Salmonella spp., Escherichia coli and Listeria monocytogenes. Of great concern to scientists and physicians are also reports of antibiotic-resistant emerging food pathogens-microorganisms that have not previously been linked to food contamination or were considered epidemiologically insignificant. Since the properties of foodborne pathogens are not always sufficiently recognized, the consequences of the infections are often not easily predictable, and the control of their activity is difficult. The bacteria most commonly identified as emerging foodborne pathogens include Aliarcobacter spp., Aeromonas spp., Cronobacter spp., Vibrio spp., Clostridioides difficile, Escherichia coli, Mycobacterium paratuberculosis, Salmonella enterica, Streptocccus suis, Campylobacter jejuni, Helicobacter pylori, Listeria monocytogenes and Yersinia enterocolitica. The results of our analysis confirm antibiotic resistance and multidrug resistance among the mentioned species. Among the antibiotics whose effectiveness is steadily declining due to expanding resistance among bacteria isolated from food are β-lactams, sulfonamides, tetracyclines and fluoroquinolones. Continuous and thorough monitoring of strains isolated from food is necessary to characterize the existing mechanisms of resistance. In our opinion, this review shows the scale of the problem of microbes related to health, which should not be underestimated.
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Affiliation(s)
- Katarzyna Grudlewska-Buda
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Justyna Bauza-Kaszewska
- Department of Microbiology and Food Technology, Bydgoszcz University of Science and Technology, 85-029 Bydgoszcz, Poland
| | - Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Anna Budzyńska
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
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19
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Sun Y, Han Y, Qian C, Zhang Q, Yao Z, Zeng W, Zhou T, Wang Z. A novel transposon Tn7540 carrying bla NDM-9 and fosA3 in chromosome of a pathogenic multidrug-resistant Salmonella enterica serovar Indiana isolated from human faeces. J Glob Antimicrob Resist 2023; 33:72-77. [PMID: 36854357 DOI: 10.1016/j.jgar.2023.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 03/01/2023] Open
Abstract
OBJECTIVES Emergence of multidrug-resistant (MDR) Salmonella enterica serovar Indiana has raised global concern. Mobile genetic elements (MGEs) play vital roles in accelerating the dissemination of resistance genes in bacteria communities. The study aims to improve our understanding of the underlying resistance mechanisms and characterize the MGEs in a MDR S. Indiana isolate. METHODS Here, we report the characteristics of a MDR pathogenic S. Indiana isolate. The antimicrobial susceptibility pattern of S. Indiana QT6365 was determined. The genomic structure of the chromosome and the plasmid, serotype, and multi-locus sequence type were analysed by whole genome sequencing. The circular form derived from IS26-flanked transposon was confirmed by reverse polymerase chain reaction and sequencing. RESULTS S. Indiana QT6365 exhibited resistance to all tested antimicrobials except for aztreonam, amikacin, polymyxin, and tigecycline, was defined as MDR, and belonged to ST17. S. Indiana QT6365 was closely related with food resource S. Indiana C629 with similar resistance gene profiles. Multiple resistance genes are mainly carried by a novel transposon Tn7540 located on the chromosome and an IncHI2/HI2A/N plasmid. Sequence analysis and the formed circular intermediate suggested Tn7540 might be generated through homologous recombination by IS26-bounded translocatable units (IS26-fosA-IS26-intI1-dfrA12-aadA2-sul1-ISCR1-blaNDM-9-IS26). CONCLUSIONS To the best of our knowledge, this is the first report of the novel chromosomal transposon possessing blaNDM-9 and fosA3 in S. Indiana isolated from human specimen, which might facilitate the dissemination of resistance genes and should arouse serious awareness.
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Affiliation(s)
- Yao Sun
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University; Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, China
| | - Yijia Han
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Changrui Qian
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qi Zhang
- Department of Clinical Laboratory, Yongjia Hospital of Traditional Chinese Medicine, Wenzhou, China
| | - Zhuocheng Yao
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Weiliang Zeng
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University; Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, China
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University; Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, China.
| | - Zhongyong Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University; Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, China.
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20
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Plasmid Composition, Antimicrobial Resistance and Virulence Genes Profiles of Ciprofloxacin- and Third-Generation Cephalosporin-Resistant Foodborne Salmonella enterica Isolates from Russia. Microorganisms 2023; 11:microorganisms11020347. [PMID: 36838312 PMCID: PMC9961839 DOI: 10.3390/microorganisms11020347] [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: 01/14/2023] [Revised: 01/25/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
Salmonella enterica is an important foodborne pathogen worldwide. Ciprofloxacin and extended-spectrum cephalosporins are the common first-line antimicrobial drugs for the treatment of salmonellosis, antimicrobial resistance genes for which are mostly transferred via plasmids. The goal of this work was to perform genomic analysis of plasmids from foodborne S. enterica isolates obtained in Russia based on whole-genome sequencing. In the current study, 11 multidrug-resistant samples isolated in 2021 from 8 regions of Russia were selected based on their resistance to ciprofloxacin and third-generation cephalosporins (CIP-3rd). Whole-genome short-read sequencing (WGS) was performed for all isolates; the samples belonged to five different sequence types (ST32, ST469, ST11, ST142, and ST548) which had different profiles of antimicrobial resistance (AMR) and virulence genes. We have performed additional long-read sequencing of four representative S. enterica isolates, which showed that they carried pESI-like megaplasmids of 202-280 kb length harboring extended-spectrum β-lactamase genes, fluoroquinolone, tetracycline, and aminoglycosides resistance genes, as well as several virulence determinants. We believe that the WGS data obtained will greatly facilitate further studies of foodborne S. enterica isolates epidemiology in terms of their self-transmissible plasmid composition that mediated antimicrobial resistance and virulence determinants conferring selective advantages of this important bacterial pathogen.
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21
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Whole Genome Sequencing Reveals Presence of High-Risk Global Clones of Klebsiella pneumoniae Harboring Multiple Antibiotic Resistance Genes in Multiple Plasmids in Mwanza, Tanzania. Microorganisms 2022; 10:microorganisms10122396. [PMID: 36557648 PMCID: PMC9785957 DOI: 10.3390/microorganisms10122396] [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: 10/25/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Klebsiella pneumoniae is an important multidrug-resistant (MDR) pathogen, causing both community- and healthcare-associated infections. The resistance is due to the continuous accumulation of multiple antibiotic-resistance-genes (ARGs) through spontaneous genomic mutations and the acquisition of conjugative plasmids. This study presents antibiotics resistance genes, plasmids replicons, and virulence genes of K. pneumoniae isolates from clinical specimens in a tertiary hospital, Mwanza, Tanzania. METHODS Whole genome sequencing (WGS) of 34 K. pneumoniae was performed, using an Illumina NextSeq 500, followed by in silco analysis. RESULTS A total of 34 extended-spectrum beta-lactamase-producing K. pneumoniae, isolated from blood samples from neonatal units were whole-genome sequenced. Of these, 28 (82.4%) had an identified sequence type (ST), with ST14 (39.3%, n = 11) being frequently identified. Moreover, 18 (52.9%) of the bacteria harbored at least one plasmid, from which a total of 25 plasmid replicons were identified with a predominance of IncFIB(K) 48.0% (n = 12). Out of 34 sequenced K. pneumoniae, 32 (94.1%) were harboring acquired antibiotic/biocides-resistance-genes (ARGs) with a predominance of blaCTX-M-15 (90.6%), followed by oqxB (87.5%), oqxA (84.4%), blaTEM-1B (84.4%) and sul2 (84.4%). Interestingly, we observed the ColRNAI plasmid-replicon (n = 1) and qacE gene (n = 4) for the first time in this setting. CONCLUSION Global high-risk clones of K. pneumoniae isolates carry multiple ARGs in multiple plasmid-replicons. Findings from this study warrant genomic-based surveillance to monitor high-risk global clones, epidemic plasmids and ARGs in low- and middle-income countries.
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22
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Tang B, Elbediwi M, Nambiar RB, Yang H, Lin J, Yue M. Genomic Characterization of Antimicrobial-Resistant Salmonella enterica in Duck, Chicken, and Pig Farms and Retail Markets in Eastern China. Microbiol Spectr 2022; 10:e0125722. [PMID: 36047803 PMCID: PMC9603869 DOI: 10.1128/spectrum.01257-22] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/17/2022] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial-resistant Salmonella enterica poses a significant public health concern worldwide. However, the dissemination of Salmonella enterica among food animals in eastern China has not been fully addressed. Here, we demonstrated the antimicrobial resistance (AMR) patterns and the whole-genome characterization of 105 S. enterica isolates from 1,480 fecal samples and anal swabs collected from 22 different farms (chickens, ducks, and pigs) and two live animal markets located in Zhejiang and Fujian Provinces in eastern China in 2019. The prevalence of isolates in duck farms (19.17%, 23/120) was statistically significantly higher (P < 0.001) than that in chicken farms (6.61%, 37/523) and pig farms (3.50%, 7/200). Among these isolates, 75.26% (79/105) were multidrug resistant, with the highest rates of resistance to tetracycline (76.20%) and ampicillin (67.62%) and the lowest resistance rate to meropenem (0.00%). The serotypes were consistent with sequence types and were closely related to the sampling animal species and sites. S. enterica serotype Kentucky (20.95%, 22/105) was the most frequent serotype and harbored more AMR patterns and genes than others. Furthermore, IncFII(S) and IncHI2 were the most prevalent replicons. A total of 44 acquired AMR genes were found. Among those genes, aac(6')-Iaa, blaTEM-1B, floR, dfrA14, fosA7, mph(A), qnrS1, sul1, tet(A), and ARR-3 were the dominant AMR genes mediating the AMR toward aminoglycosides, β-lactams, phenicol, trimethoprim, fosfomycin, macrolide, quinolone, sulfonamides, tetracycline, and rifampin, respectively. The consistency of acquired AMR genes with AMR phenotypes for ampicillin, ceftiofur, ceftazidime, meropenem, sulfamethoxazole-trimethoprim, and tetracycline was >90%. Together, our study highlights the application of whole-genome sequencing to assess veterinary public health threats. IMPORTANCE Public health is a significant concern in China, and the foodborne pathogen Salmonella, which is spread via the animal-borne food chain, plays an important role in the overall disease burden in China annually. The development of advanced sequencing technologies has introduced a new way of understanding emerging pathogens. However, the routine surveillance application of this method in China remains in its infancy. Here, we applied a pool of all isolates from the prevalence data in Zhejiang and Fujian for whole-genome sequencing and combined these data with the cutting-edge bioinformatic analysis pipeline for one-step determination of the complete genetic makeup for all 105 genomes. The illustrated method could provide a cost-effective approach, without labor-intensive laboratory characterization, for predicting serotypes, genotypes, plasmid types, antimicrobial resistance genes, and virulence genes, and thus would provide essential knowledge for emerging pathogens. Our findings and perspectives are essential for delivering updated knowledge on foodborne pathogens in an understudied region in China.
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Affiliation(s)
- 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
| | - Mohammed Elbediwi
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
| | - Reshma B. Nambiar
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
| | - Hua Yang
- 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
| | - Jiahui Lin
- 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, Zhejiang, 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
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
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23
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Souza SSR, Turcotte MR, Li J, Zhang X, Wolfe KL, Gao F, Benton CS, Andam CP. Population analysis of heavy metal and biocide resistance genes in Salmonella enterica from human clinical cases in New Hampshire, United States. Front Microbiol 2022; 13:983083. [PMID: 36338064 PMCID: PMC9626534 DOI: 10.3389/fmicb.2022.983083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022] Open
Abstract
Microbes frequently encounter heavy metals and other toxic compounds generated from natural biogeochemical processes and anthropogenic activities. Here, we analyzed the prevalence and association of genes conferring resistance to heavy metals, biocides, and antimicrobial compounds in 394 genome sequences of clinical human-derived S. enterica from New Hampshire, USA. The most prevalent was the gold operon (gesABC-golTSB), which was present in 99.2% of the genomes. In contrast, the other five heavy metal operons (arsenic, copper, mercury, silver, tellurite) were present in 0.76% (3/394)-5.58% (22/394) of the total population. The heavy metal operons and three biocide resistance genes were differentially distributed across 15 sequence types (STs) and 16 serotypes. The number of heavy metal operons and biocide resistance genes per genome was significantly associated with high number of antimicrobial resistance (AMR) genes per genome. Notable is the mercury operon which exhibited significant association with genes conferring resistance to aminoglycosides, cephalosporins, diaminopyrimidine, sulfonamide, and fosfomycin. The mercury operon was co-located with the AMR genes aac(3)-IV, ant(3")-IIa, aph(3')-Ia, and aph(4)-Ia, CTX-M-65, dfrA14, sul1, and fosA3 genes within the same plasmid types. Lastly, we found evidence for negative selection of individual genes of each heavy metal operon and the biocide resistance genes (dN/dS < 1). Our study highlights the need for continued surveillance of S. enterica serotypes that carry those genes that confer resistance to heavy metals and biocides that are often associated with mobile AMR genes. The selective pressures imposed by heavy metals and biocides on S. enterica may contribute to the co-selection and spread of AMR in human infections.
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Affiliation(s)
- Stephanie S. R. Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
| | - Madison R. Turcotte
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
| | - Jinfeng Li
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Xinglu Zhang
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Kristin L. Wolfe
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Fengxiang Gao
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | | | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
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WGS-Based Lineage and Antimicrobial Resistance Pattern of Salmonella Typhimurium Isolated during 2000-2017 in Peru. Antibiotics (Basel) 2022; 11:antibiotics11091170. [PMID: 36139949 PMCID: PMC9495214 DOI: 10.3390/antibiotics11091170] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Salmonella Typhimurium is associated with foodborne diseases worldwide, including in Peru, and its emerging antibiotic resistance (AMR) is now a global public health problem. Therefore, country-specific monitoring of the AMR emergence is vital to control this pathogen, and in these aspects, whole genome sequence (WGS)—based approaches are better than gene-based analyses. Here, we performed the antimicrobial susceptibility test for ten widely used antibiotics and WGS-based various analyses of 90 S. Typhimurium isolates (human, animal, and environment) from 14 cities of Peru isolated from 2000 to 2017 to understand the lineage and antimicrobial resistance pattern of this pathogen in Peru. Our results suggest that the Peruvian isolates are of Typhimurium serovar and predominantly belong to sequence type ST19. Genomic diversity analyses indicate an open pan-genome, and at least ten lineages are circulating in Peru. A total of 48.8% and 31.0% of isolates are phenotypically and genotypically resistant to at least one antibiotic, while 12.0% are multi-drug resistant (MDR). Genotype−phenotype correlations for ten tested drugs show >80% accuracy, and >90% specificity. Sensitivity above 90% was only achieved for ciprofloxacin and ceftazidime. Two lineages exhibit the majority of the MDR isolates. A total of 63 different AMR genes are detected, of which 30 are found in 17 different plasmids. Transmissible plasmids such as lncI-gamma/k, IncI1-I(Alpha), Col(pHAD28), IncFIB, IncHI2, and lncI2 that carry AMR genes associated with third-generation antibiotics are also identified. Finally, three new non-synonymous single nucleotide variations (SNVs) for nalidixic acid and eight new SNVs for nitrofurantoin resistance are predicted using genome-wide association studies, comparative genomics, and functional annotation. Our analysis provides for the first time the WGS-based details of the circulating S. Typhimurium lineages and their antimicrobial resistance pattern in Peru.
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Dynamics of Antimicrobial Resistance and Genomic Epidemiology of Multidrug-Resistant Salmonella enterica Serovar Indiana ST17 from 2006 to 2017 in China. mSystems 2022; 7:e0025322. [PMID: 35861536 PMCID: PMC9426611 DOI: 10.1128/msystems.00253-22] [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] [Indexed: 12/02/2022] Open
Abstract
The genetic features of foodborne Salmonella have changed in recent years as multidrug-resistant (MDR) strains have become prevalent among various serovars. The recent expansion of MDR Salmonella enterica serovar Indiana sequence type 17 (ST17) poses an increasing threat to global public health, as 24.3% (61/251) of S. Indiana isolates in this study exhibited resistance to three clinically important antimicrobial agents: fluoroquinolones (ciprofloxacin), extended-spectrum β-lactams (cephalosporin), and macrolides (azithromycin). Both the evolutionary histories and antimicrobial resistance (AMR) profiles of this serovar remain to be described. Bioinformatic analysis revealed multiple lineages have coexisted and spread throughout China. Specifically, emergence of a predominant lineage appears to be associated with accumulated various substitutions in the chromosomal quinolone resistance-determining regions (GyrA S83F D87N and ParC T57S S80R) (141 [56.2%]), as well as acquisition of an extended-spectrum β-lactamase (ESBL)-producing IncHI2 plasmid that has subsequently undergone extensive rearrangement and an IncX1 plasmid that contains mph(A), conferring resistance to azithromycin. Several other evolutionary events influencing the trajectory of this drug-resistant serovar were also identified, including sporadic acquisitions of blaCTX-M-carrying plasmids, along with chromosomal integration of blaCTX-M within subclusters. Most human isolates reside in clusters containing isolates from animals, mainly from chickens, indicating the close relationship of human isolates with those from food animals. These data demonstrate that MDR S. Indiana ST17 is already widespread and capable of acquiring resistance traits against the clinical important antimicrobial agents, suggesting it should be considered a high-risk global MDR pathogen. The complexity of its evolutionary history has implications for AMR surveillance, epidemiological analysis, and control of emerging clinical lineages. IMPORTANCE The emergence and worldwide spread of AMR Salmonella constitute great public health concerns. S. enterica serovar Indiana is a typical MDR serovar characterized by sporadic reports. However, comprehensive population genomics studies have not been performed on this serovar. This study provides a detailed and comprehensive insight into the rapid evolution of AMR in this important Salmonella serovar in the past 15 years in eight provinces of China. We documented diverse contributory genetic processes, including stable chromosomal integrations of resistance genes, the persistence and evolution of mobile resistance elements within sublineages, and sporadic acquisition of different resistance determinants that occur at all genetic levels (genes, genetic contexts, plasmids, and host strains). There are different mechanisms of antimicrobial resistance in S. enterica serovar Indiana from those of other serovars. This study sheds light on the formation of MDR S. enterica serovar Indiana with chickens as its potential reservoirs and paves the way to curb its further expansion among food animals.
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Zeng S, Zhuo Z, Huang Y, Luo J, Feng Y, Gong B, Huang X, Wu A, Zhuo C, Li X. Prevalence of Chromosomally Located blaCTX-M-55 in Salmonella Typhimurium ST34 Isolates Recovered from a Tertiary Hospital in Guangzhou, China. Microbiol Spectr 2022; 10:e0277121. [PMID: 35616373 PMCID: PMC9241639 DOI: 10.1128/spectrum.02771-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/01/2022] [Indexed: 12/31/2022] Open
Abstract
Nontyphoidal Salmonella (NTS) is one of the most prevalent bacterial causes of gastrointestinal infections worldwide. Meanwhile, the detection rate of CTX-M-55 ESBL-positive has increased gradually in China. To identify the molecular epidemiological and genomic characteristics of blaCTX-M-55-carrying nontyphoidal Salmonella (NTS) clinical isolates, a total of 105 NTS isolates were collected from a Chinese tertiary hospital. Antimicrobial susceptibility testing was performed to determine the resistance phenotype. Whole-genome sequencing and bioinformatics analysis were used to determine the antimicrobial resistance genes, serotypes, phylogenetic relationships, and the genetic environment of the blaCTX-M-55 gene. The results showed that among the 22 ceftriaxone resistant isolates, the blaCTX-M-55 was the most common β-Lactamase gene carried by 14 isolates, including serotypes S. Typhimurium (10/14), S. Muenster (2/14), S. Rissen (1/14), and S. Saintpaul (1/14). Phylogenetic analysis shows that 10 blaCTX-M-55-positive S. Typhimurium ST34 isolates were divided into two clusters. The genetic relationship of isolates in each cluster was very close (≤10 cgMLST loci). The blaCTX-M-55 gene was located on the chromosome in 10 isolates, on IncI1 plasmid in three isolates, and IncHI2 plasmid in one isolate. In conclusion, the blaCTX-M-55 gene, mainly located on the chromosome of S. Typhimurium ST34 isolates, was the main driving force associated with the resistance of NTS to cephalosporins. Therefore, close attention to the clonal dissemination of blaCTX-M-55-carrying S. Typhimurium ST34 in clinical settings must be monitored carefully. IMPORTANCE ESCs are the first choice for treating NTS infections. However, ESBLs and AmpC β-lactamases are the most typical cause for ESCs resistance. The CTX-M-55 ESBL-positive rate has gradually increased in the clinic in recent years. At present, the research about blaCTX-M-55-positive Salmonella mainly focuses on the foodborne animals or the environment while less on clinical patients. Thus, this study was carried out for identifying molecular epidemiological and genomic characteristics of blaCTX-M-55-carrying NTS clinical isolates. The results showed that the blaCTX-M-55 gene, mainly located on the chromosome of S. Typhimurium ST34 isolates from Conghua District, was the main driving force associated with the resistance of NTS to cephalosporins. Therefore, our work highlights the importance of monitoring the clonal dissemination of blaCTX-M-55-carrying S. Typhimurium ST34 in clinical settings.
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Affiliation(s)
- Shihan Zeng
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Zhenxu Zhuo
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Yulan Huang
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Jiajun Luo
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Yulian Feng
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Baiyan Gong
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Xiyi Huang
- Department of Clinical Laboratory, The Affiliated Shunde Hospital of Guangzhou Medical University (Lecong Hospital of Shunde District), Foshan, China
| | - Aiwu Wu
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Chao Zhuo
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaoyan Li
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
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Chang MX, Zhang J, Zhang JF, Ding XM, Lu Y, Zhang J, Li R, Jiang HX. Formation, Transmission, and Dynamic Evolution of a Multidrug-Resistant Chromosomally Integrated Plasmid in Salmonella Spp. Front Microbiol 2022; 13:846954. [PMID: 35464949 PMCID: PMC9019673 DOI: 10.3389/fmicb.2022.846954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/17/2022] [Indexed: 11/24/2022] Open
Abstract
IncHI2 plasmids, possessing high flexibility and genetic plasticity, play a vital role in the acquisition and transmission of resistance determinants. Polymorphic mobile genetic elements (MGEs) generated by a chromosomally integrated IncHI2 plasmid in an individual Salmonella isolate have not yet been detected, and the mechanisms of the formation, excision, and dynamic evolution of a multidrug-resistant chromosomally integrated plasmid (MRCP) have remained obscure. Herein, we identified a 260-kb blaCTX–M–55-qnrS1-bearing IncHI2 plasmid within a Salmonella Muenster strain. Plenty of heterogeneous MGEs (new Escherichia coli chromosomally integrated plasmid or circular plasmids with different profiles) were yielded when this MRCP was conjugated into E. coli J53 with a transfer frequency of 10–4–10–5 transconjugants per donor. A bioinformatic analysis indicated that replicative transposition and homologous recombination of IS26 elements were particularly active, and the truncated Tn1721 also played a vital role in the formation of MRCP offspring. More importantly, when released from the chromosome, MRCP could capture and co-transfer adjacent chromosomal segments to form larger plasmid progeny than itself. Stability and growth kinetics assays showed that the biological characteristics of MRCP progeny were differentiated. This study provides an insight into a flexible existence of MRCP. The conversion between vertical and horizontal transmission endowed MRCP with genetic stability as a chromosomal coding structure and transferability as extra-chromosomal elements. This alternation may accelerate the acquisition and persistence of antibiotic resistance of clinical pathogens and enhance their ability to respond to adverse environments, which poses a great challenge to the traditional antibiotic treatment.
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Affiliation(s)
- Man-Xia Chang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jing Zhang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jin-Fei Zhang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao-Min Ding
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yang Lu
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jie Zhang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Hong-Xia Jiang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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28
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Detection of Antimicrobial Resistance, Pathogenicity, and Virulence Potentials of Non-Typhoidal Salmonella Isolates at the Yaounde Abattoir Using Whole-Genome Sequencing Technique. Pathogens 2022; 11:pathogens11050502. [PMID: 35631023 PMCID: PMC9148033 DOI: 10.3390/pathogens11050502] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
One of the crucial public health problems today is the emerging and re-emerging of multidrug-resistant (MDR) bacteria coupled with a decline in the development of new antimicrobials. Non-typhoidal Salmonella (NTS) is classified among the MDR pathogens of international concern. To predict their MDR potentials, 23 assembled genomes of NTS from live cattle (n = 1), beef carcass (n = 19), butchers’ hands (n = 1) and beef processing environments (n = 2) isolated from 830 wet swabs at the Yaounde abattoir between December 2014 and November 2015 were explored using whole-genome sequencing. Phenotypically, while 22% (n = 5) of Salmonella isolates were streptomycin-resistant, 13% (n = 3) were MDR. Genotypically, all the Salmonella isolates possessed high MDR potentials against several classes of antibiotics including critically important drugs (carbapenems, third-generation cephalosporin and fluoroquinolone). Moreover, >31% of NTS exhibited resistance potentials to polymyxin, considered as the last resort drug. Additionally, ≤80% of isolates harbored “silent resistant genes” as a potential reservoir of drug resistance. Our isolates showed a high degree of pathogenicity and possessed key virulence factors to establish infection even in humans. Whole-genome sequencing unveiled both broader antimicrobial resistance (AMR) profiles and inference of pathogen characteristics. This study calls for the prudent use of antibiotics and constant monitoring of AMR of NTS.
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Fu Y, M'ikanatha NM, Whitehouse CA, Tate H, Ottesen A, Lorch JM, Blehert DS, Berlowski-Zier B, Dudley EG. Low occurrence of multi-antimicrobial and heavy metal resistance in Salmonella enterica from wild birds in the United States. Environ Microbiol 2021; 24:1380-1394. [PMID: 34897945 DOI: 10.1111/1462-2920.15865] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/12/2023]
Abstract
Wild birds are common reservoirs of Salmonella enterica. Wild birds carrying resistant S. enterica may pose a risk to public health as they can spread the resistant bacteria across large spatial scales within a short time. Here, we whole-genome sequenced 375 S. enterica strains from wild birds collected in 41 U.S. states during 1978-2019 to examine bacterial resistance to antibiotics and heavy metals. We found that Typhimurium was the dominant S. enterica serovar, accounting for 68.3% (256/375) of the bird isolates. Furthermore, the proportions of the isolates identified as multi-antimicrobial resistant (multi-AMR: resistant to at least three antimicrobial classes) or multi-heavy metal resistant (multi-HMR: resistant to at least three heavy metals) were both 1.87% (7/375). Interestingly, all the multi-resistant S. enterica (n = 12) were isolated from water birds or raptors; none of them was isolated from songbirds. Plasmid profiling demonstrated that 75% (9/12) of the multi-resistant strains carried resistance plasmids. Our study indicates that wild birds do not serve as important reservoirs of multi-resistant S. enterica strains. Nonetheless, continuous surveillance for bacterial resistance in wild birds is necessary because the multi-resistant isolates identified in this study also showed close genetic relatedness with those from humans and domestic animals.
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Affiliation(s)
- Yezhi Fu
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Chris A Whitehouse
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, 20708, USA
| | - Heather Tate
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, 20708, USA
| | - Andrea Ottesen
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, 20708, USA
| | - Jeffrey M Lorch
- U.S. Geological Survey - National Wildlife Health Center, Madison, WI, 53711, USA
| | - David S Blehert
- U.S. Geological Survey - National Wildlife Health Center, Madison, WI, 53711, USA
| | | | - Edward G Dudley
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA.,E. coli Reference Center, The Pennsylvania State University, University Park, PA, 16802, USA
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Characterisation of Early Positive mcr-1 Resistance Gene and Plasmidome in Escherichia coli Pathogenic Strains Associated with Variable Phylogroups under Colistin Selection. Antibiotics (Basel) 2021; 10:antibiotics10091041. [PMID: 34572623 PMCID: PMC8466100 DOI: 10.3390/antibiotics10091041] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 01/08/2023] Open
Abstract
An antibiotic susceptibility monitoring programme was conducted from 2004 to 2010, resulting in a collection of 143 Escherichia coli cultured from bovine faecal samples (diarrhoea) and milk-aliquots (mastitis). The isolates were subjected to whole-genome sequencing and were distributed in phylogroups A, B1, B2, C, D, E, and G with no correlation for particular genotypes with pathotypes. In fact, the population structure showed that the strains belonging to the different phylogroups matched broadly to ST complexes; however, the isolates are randomly associated with the diseases, highlighting the necessity to investigate the virulence factors more accurately in order to identify the mechanisms by which they cause disease. The antimicrobial resistance was assessed phenotypically, confirming the genomic prediction on three isolates that were resistant to colistin, although one isolate was positive for the presence of the gene mcr-1 but susceptible to colistin. To further characterise the genomic context, the four strains were sequenced by using a single-molecule long read approach. Genetic analyses indicated that these four isolates harboured complex and diverse plasmids encoding not only antibiotic resistant genes (including mcr-1 and bla) but also virulence genes (siderophore, ColV, T4SS). A detailed description of the plasmids of these four E. coli strains, which are linked to bovine mastitis and diarrhoea, is presented for the first time along with the characterisation of the predicted antibiotic resistance genes. The study highlighted the diversity of incompatibility types encoding complex antibiotic resistance elements such as Tn6330, ISEcp1, Tn6029, and IS5075. The mcr-1 resistance determinant was identified in IncHI2 plasmids pCFS3273-1 and pCFS3292-1, thus providing some of the earliest examples of mcr-1 reported in Europe, and these sequences may be a representative of the early mcr-1 plasmidome characterisation in the EU/EEA.
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31
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Elbediwi M, Tang Y, Shi D, Ramadan H, Xu Y, Xu S, Li Y, Yue M. Genomic Investigation of Antimicrobial-Resistant Salmonella enterica Isolates From Dead Chick Embryos in China. Front Microbiol 2021; 12:684400. [PMID: 34497590 PMCID: PMC8419455 DOI: 10.3389/fmicb.2021.684400] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022] Open
Abstract
Salmonella spp. is recognized as an important zoonotic pathogen. The emergence of antimicrobial resistance in Salmonella enterica poses a great public health concern worldwide. While the knowledge on the incidence and the characterization of different S. enterica serovars causing chick embryo death remains obscure in China. In this study, we obtained 45 S. enterica isolates from 2,139 dead chick embryo samples collected from 28 breeding chicken hatcheries in Henan province. The antimicrobial susceptibility assay was performed by the broth microdilution method and the results showed that 31/45 (68.8%) isolates were multidrug-resistant (≥3 antimicrobial classes). Besides the highest resistance rate was observed in the aminoglycoside class, all the isolates were susceptible to chloramphenicol, azithromycin, and imipenem. Furthermore, genomic characterization revealed that S. Enteritidis (33.33%; 15/45) was a frequent serovar that harbored a higher number of virulence factors compared to other serovars. Importantly, genes encoding β-lactamases were identified in three serovars (Thompson, Enteritidis, and Kottbus), whereas plasmid-mediated quinolone resistance genes (qnrB4) were detected in certain isolates of S. Thompson and the two S. Kottbus isolates. All the examined isolates harbored the typical virulence factors from Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2). Additionally, a correlation analysis between the antimicrobial resistance genes, phenotype, and plasmids was conducted among Salmonella isolates. It showed strong positive correlations (r < 0.6) between the different antimicrobial-resistant genes belonging to certain antimicrobial classes. Besides, IncF plasmid showed a strong negative correlation (r > −0.6) with IncHI2 and IncHI2A plasmids. Together, our study demonstrated antimicrobial-resistant S. enterica circulating in breeding chicken hatcheries in Henan province, highlighting the advanced approach, by using genomic characterization and statistical analysis, in conducting the routine monitoring of the emerging antimicrobial-resistant pathogens. Our findings also proposed that the day-old breeder chicks trading could be one of the potential pathways for the dissemination of multidrug-resistant S. enterica serovars.
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Affiliation(s)
- Mohammed Elbediwi
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Yanting Tang
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Dawei Shi
- National Institutes for Food and Drug Control, Beijing, China
| | - Hazem Ramadan
- Hygiene and Zoonoses Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt.,Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States National Poultry Research Center, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Athens, GA, United States
| | - Yaohui Xu
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Sihong Xu
- National Institutes for Food and Drug Control, Beijing, China
| | - Yan Li
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China.,Hainan Institute of Zhejiang University, Sanya, China.,Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
| | - Min Yue
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China.,Hainan Institute of Zhejiang University, Sanya, China.,Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Robertson J, Bessonov K, Schonfeld J, Nash JHE. Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance. Microb Genom 2021; 6. [PMID: 32969786 PMCID: PMC7660255 DOI: 10.1099/mgen.0.000435] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bacterial plasmids play a large role in allowing bacteria to adapt to changing environments and can pose a significant risk to human health if they confer virulence and antimicrobial resistance (AMR). Plasmids differ significantly in the taxonomic breadth of host bacteria in which they can successfully replicate, this is commonly referred to as 'host range' and is usually described in qualitative terms of 'narrow' or 'broad'. Understanding the host range potential of plasmids is of great interest due to their ability to disseminate traits such as AMR through bacterial populations and into human pathogens. We developed the MOB-suite to facilitate characterization of plasmids and introduced a whole-sequence-based classification system based on clustering complete plasmid sequences using Mash distances (https://github.com/phac-nml/mob-suite). We updated the MOB-suite database from 12 091 to 23 671 complete sequences, representing 17 779 unique plasmids. With advances in new algorithms for rapidly calculating average nucleotide identity (ANI), we compared clustering characteristics using two different distance measures - Mash and ANI - and three clustering algorithms on the unique set of plasmids. The plasmid nomenclature is designed to group highly similar plasmids together that are unlikely to have multiple representatives within a single cell. Based on our results, we determined that clusters generated using Mash and complete-linkage clustering at a Mash distance of 0.06 resulted in highly homogeneous clusters while maintaining cluster size. The taxonomic distribution of plasmid biomarker sequences for replication and relaxase typing, in combination with MOB-suite whole-sequence-based clusters have been examined in detail for all high-quality publicly available plasmid sequences. We have incorporated prediction of plasmid replication host range into the MOB-suite based on observed distributions of these sequence features in combination with known plasmid hosts from the literature. Host range is reported as the highest taxonomic rank that covers all of the plasmids which share replicon or relaxase biomarkers or belong to the same MOB-suite cluster code. Reporting host range based on these criteria allows for comparisons of host range between studies and provides information for plasmid surveillance.
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Affiliation(s)
- James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Kyrylo Bessonov
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Justin Schonfeld
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - John H E Nash
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
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Adel WA, Ahmed AM, Hegazy Y, Torky HA, Shimamoto T. High Prevalence of ESBL and Plasmid-Mediated Quinolone Resistance Genes in Salmonella enterica Isolated from Retail Meats and Slaughterhouses in Egypt. Antibiotics (Basel) 2021; 10:antibiotics10070881. [PMID: 34356803 PMCID: PMC8300843 DOI: 10.3390/antibiotics10070881] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 11/30/2022] Open
Abstract
The emergence and spread of multidrug-resistant Salmonella enterica (S. enterica) to humans through food of animal origin are considered a major global public health concern. Currently, little is known about the prevalence of important antimicrobial resistance genes in S. enterica from retail food in Africa. Therefore, the screening and characterization of the extended-spectrum β-lactamase (ESBL) and plasmid-mediated quinolone resistance (PMQR) genes in S. enterica isolated from retail meats and slaughterhouses in Egypt were done by using PCR and DNA sequencing techniques. Twenty-eight out of thirty-four (82.4%) non-duplicate S. enterica isolates showed multidrug-resistance phenotypes to at least three classes of antimicrobials, and fourteen (41.2%) exhibited an ESBL-resistance phenotype and harbored at least one ESBL-encoding gene. The identified β-lactamase-encoding genes included blaCTX-M-1, blaCTX-M-3, blaCTX-M-13, blaCTX-M-14, blaCTX-M-15, and blaSHV-12 (ESBL types); blaCMY-2 (AmpC type); and blaTEM-1 and blaOXA-1 (narrow-spectrum types). PMQR genes (included qnrA, qnrB, qnrS, and aac(6′)-Ib-cr) were identified in 23 (67.6%) isolates. The presence of ESBL- and PMQR-producing S. enterica with a high prevalence rate in retail meats and slaughterhouses is considered a major threat to public health as these strains with resistance genes could be transmitted to humans through the food chain.
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Affiliation(s)
- Wesam A. Adel
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt;
| | - Ashraf M. Ahmed
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt;
- Correspondence: (A.M.A.); (T.S.); Tel.: +20-111-811-1488 (A.M.A.); +81-(82)-424-7897 (T.S.)
| | - Yamen Hegazy
- Department of Animal Medicine, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt;
| | - Helmy A. Torky
- Department of Microbiology, Faculty of Veterinary Medicine, Alexandria University, Alexandria 22758, Egypt;
| | - Tadashi Shimamoto
- Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8528, Japan
- Correspondence: (A.M.A.); (T.S.); Tel.: +20-111-811-1488 (A.M.A.); +81-(82)-424-7897 (T.S.)
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Hu Y, Nguyen SV, Wang W, Gan X, Dong Y, Liu C, Cui X, Xu J, Li F, Fanning S. Antimicrobial Resistance and Genomic Characterization of Two mcr-1-Harboring Foodborne Salmonella Isolates Recovered in China, 2016. Front Microbiol 2021; 12:636284. [PMID: 34211439 PMCID: PMC8239406 DOI: 10.3389/fmicb.2021.636284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/06/2021] [Indexed: 12/16/2022] Open
Abstract
The mcr-1 gene mediating mobile colistin resistance in Escherichia coli was first reported in China in 2016 followed by reports among different species worldwide, especially in E. coli and Klebsiella. However, data on its transmission in Salmonella are still lacking. This study analyzed the antimicrobial resistance (AMR) profiles and the mcr-1 gene presence in 755 foodborne Salmonella from 26 provinces of mainland, China in 2016. Genomic features of two mcr-1-carrying isolates, genome sequencing, serotypes and further resistance profiles were studied. Among the 755 Salmonella tested, 72.6% were found to be resistant to at least one antimicrobial agent and 10% were defined as multi-drug resistant (MDR). Salmonella Derby CFSA231 and Salmonella Typhimurium CFSA629 were mcr-1-harboring isolates. Both expressed an MDR phenotype and included a single circular chromosome and one plasmid. Among the 22 AMR genes identified in S. Derby CFSA231, only the mcr-1 gene was localized on the IncX4 type plasmid pCFSA231 while 20 chromosomal AMR genes, including four plasmid-mediated quinolone resistance (PMQR) genes, were mapped within a 64 kb Salmonella genomic island (SGI) like region. S. Typhimurium CFSA629 possessed 11 resistance genes including an mcr-1.19 variant and two ESBL genes. Two IS26-flanked composite-like transposons were identified. Additionally, 153 and 152 virulence factors were separately identified in these two isolates with secretion system and fimbrial adherence determinants as the dominant virulence classes. Our study extends our concern on mcr-1-carrying Salmonella in regards to antimicrobial resistance and virulence factors, and highlight the importance of surveillance to mitigate dissemination of mcr-encoding genes among foodborne Salmonella.
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Affiliation(s)
- Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Dublin, Ireland
| | - Scott V Nguyen
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Dublin, Ireland.,Public Health Laboratory, District of Columbia Department of Forensic Sciences, Washington, DC, United States
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Xin Gan
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Dublin, Ireland
| | - Chang Liu
- Food Science and Engineering College, Beijing University of Agriculture, Beijing, China
| | - Xinnan Cui
- Food Science and Engineering College, Beijing University of Agriculture, Beijing, China.,China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries, Beijing, China
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Séamus Fanning
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Dublin, Ireland.,Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
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Xu M, Zhao J, Xu L, Yang Q, Xu H, Kong H, Zhou J, Fu Y. Emergence of transferable ceftazidime-avibactam resistance in KPC-producing Klebsiella pneumoniae due to a novel CMY AmpC β-lactamase in China. Clin Microbiol Infect 2021; 28:136.e1-136.e6. [PMID: 34044150 DOI: 10.1016/j.cmi.2021.05.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/26/2022]
Abstract
OBJECTIVES To evaluate the molecular mechanisms of ceftazidime/avibactam (CAZ/AVI) resistance in six Klebsiella pneumoniae strains that co-produce K. pneumoniae carbapenemase (KPC)-2 and a novel variant of CMY cephalosporinase in a Chinese hospital. METHODS Antimicrobial susceptibility was determined by broth microdilution. Whole-genome sequencing (WGS) was performed to investigate potential resistance determinants. Plasmid conjugation, electroporation, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) hybridization and cloning experiment were carried out to investigate the resistance plasmids and genes. RESULTS A high level of CAZ/AVI resistance was observed in six KPC-Kp strains (MIC 128 mg/L). Five strains were isolated in 2015 and one in 2016, before the approval of CAZ/AVI in China. Sequence analysis indicated that all the strains belonged to sequence type (ST) 11 and uniformly carried a novel CMY AmpC β-lactamase gene, designated blaCMY-172. When compared with CMY-2, CMY-172 has a deletion of three consecutive amino acids (K290, V291 and A292) in the R2-loop region and a non-synonymous amino acid substitution at position 346 (N346I). The blaCMY-172-bearing plasmid, pKPCZA02_4, was 93.3 Kb, IncI1-I type, and conjugative; blaCMY-172 was located in an IS1294-mediated transposon. Plasmid conjugation and DNA fragment cloning proved that blaCMY-172 was responsible for CAZ/AVI resistance. CONCLUSIONS Our study identified conjugative plasmid-mediated blaCMY-172 as a new mechanism for CAZ/AVI resistance in clinical KPC-Kp strains. Careful monitoring of CAZ/AVI susceptibility is imperative for preventing the spread of the resistance gene.
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Affiliation(s)
- Min Xu
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Zhao
- Department of Respiratory Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Li Xu
- Department of Clinical Laboratory, Yangzhou Centre for Disease Control and Prevention, Yangzhou, China
| | - Qing Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haishen Kong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianying Zhou
- Department of Respiratory Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Yiqi Fu
- Department of Respiratory Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Meneguzzi M, Pissetti C, Rebelatto R, Trachsel J, Kuchiishi SS, Reis AT, Guedes RMC, Leão JA, Reichen C, Kich JD. Re-Emergence of Salmonellosis in Hog Farms: Outbreak and Bacteriological Characterization. Microorganisms 2021; 9:947. [PMID: 33925758 PMCID: PMC8146755 DOI: 10.3390/microorganisms9050947] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 11/17/2022] Open
Abstract
Clinical salmonellosis has been increasing significantly in Brazil in recent years. A total of 130 outbreaks distributed among 10 swine-producing states were investigated. One representative Salmonella isolate from each outbreak was characterized through serotyping, antimicrobial resistance profiles, PFGE, and WGS. From 130 outbreaks: 50 were enteric, 48 were septicemic, 17 cases were characterized as hepato-biliary invasive, 13 as nodal and two were not classified. The most prevalent serovars were a monophasic variant of S. typhimurium (55/130), Choleraesuis (46/130), and Typhimurium (14/130). Most of the strains (86.92%) demonstrated a high rate of multi-drug resistance. The identification of a major Choleraesuis clonal group in several Brazilian states sharing the same resistance genes suggested that these strains were closely related. Six strains from this clonal group were sequenced, revealing the same ST-145 and 11 to 47 different SNPs. The detected plasmid type showed multiple marker genes as RepA_1_pKPC-CAV1321, the first to be reported in Salmonella. All AMR genes detected in the genomes were likely present on plasmids, and their phenotype was related to genotypic resistance genes. These findings reveal that salmonellosis is endemic in the most important pig-producing states in Brazil, emphasizing the need to make data available to aid in reducing its occurrence.
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Affiliation(s)
- Mariana Meneguzzi
- Curso de Medicina Veterinária, Instituto Federal Catarinense, Concórdia 89703-720, SC, Brazil; (M.M.); (C.R.)
| | - Caroline Pissetti
- Departamento de Medicina Veterinária Preventiva, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre 91540-000, RS, Brazil;
| | - Raquel Rebelatto
- Embrapa Suínos e Aves, Empresa Brasileira de Pesquisa Agropecuária, Concórdia 89715-899, SC, Brazil;
| | - Julian Trachsel
- National Animal Disease Center, Food Safety and Enteric Pathogens, Ames, IA 50010, USA;
| | | | - Adrienny Trindade Reis
- Centro de Diagnóstico e Monitoramento Animal, CDMA, Belo Horizonte 30411-191, MG, Brazil;
| | - Roberto Maurício Carvalho Guedes
- Departamento de Clínica e Cirurgia Veterinária, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | | | - Caroline Reichen
- Curso de Medicina Veterinária, Instituto Federal Catarinense, Concórdia 89703-720, SC, Brazil; (M.M.); (C.R.)
| | - Jalusa Deon Kich
- Embrapa Suínos e Aves, Empresa Brasileira de Pesquisa Agropecuária, Concórdia 89715-899, SC, Brazil;
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Pightling AW, Pettengill J, Luo Y, Strain E, Rand H. Genomic diversity of Salmonella enterica isolated from papaya samples collected during multiple outbreaks in 2017. MICROBIOLOGY-SGM 2021; 166:453-459. [PMID: 32100709 DOI: 10.1099/mic.0.000895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In 2017, the US Food and Drug Administration investigated the sources of multiple outbreaks of salmonellosis. Epidemiologic and traceback investigations identified Maradol papayas as the suspect vehicles. During the investigations, the genomes of 55 Salmonella enterica that were isolated from papaya samples were sequenced. Serovar assignments and phylogenetic analysis placed the 55 isolates into ten distinct groups, each representing a different serovar. Within-serovar SNP differences are generally between 0 and 20 SNPs, while the median between-serovar distance is 51 812 SNPs. We observed two groups with SNP distances between 21 and 100 SNPs. These relatively large within-serovar SNP distances may indicate that the isolates represent either diverse populations or multiple, genetically distinct subpopulations. Further inspection of these cases with traceback evidence allowed us to identify an 11th population. We observed that high levels of genomic diversity from individual firms is possible, with one firm yielding five of the ten serovars. Also, high levels of diversity are possible within small geographic regions, as five of the serovars were isolated from papayas that originated from farms located in Armería and Tecomán, Colima. In addition, we identified AMR genes that are present in three of the serovars studied here (aph(3')-lb, aph(6)-ld, tet(C), fosA7, and qnrB19) and we detected the presence of the plasmid IncHI2A among S. Urbana isolates.
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Affiliation(s)
| | | | - Yan Luo
- US Food and Drug Administration, Maryland, USA
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Shang D, Zhao H, Xu X, Arunachalam K, Chang J, Bai L, Shi C. Conjugative IncHI2 plasmid harboring novel class 1 integron mediated dissemination of multidrug resistance genes in Salmonella Typhimurium. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Shin H, Kim Y, Han D, Hur HG. Emergence of High Level Carbapenem and Extensively Drug Resistant Escherichia coli ST746 Producing NDM-5 in Influent of Wastewater Treatment Plant, Seoul, South Korea. Front Microbiol 2021; 12:645411. [PMID: 33833746 PMCID: PMC8021692 DOI: 10.3389/fmicb.2021.645411] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/04/2021] [Indexed: 12/26/2022] Open
Abstract
High level carbapenem and extensively drug resistant (XDR) Escherichia coli strain N7, which produces a variant of New Delhi metallo-β-lactamase (NDM-5), was isolated from the influent of the Jungnang wastewater treatment plant located on Han River, Seoul, South Korea. Phenotypic and genotypic resistances to carbapenem were tested using agar and broth dilution methods, and polymerase chain reaction. Whole-genome sequencing was performed to characterize the genetic structure of strain N7. E. coli strain N7, which harbors the bla NDM-5 gene, showed high level of carbapenem resistance at concentrations of doripenem (512 mg/L) and meropenem (256 mg/L), and XDR to 15 antibiotics. Based on the genomic sequence analysis, two plasmids, a hybrid IncHI2/N-type and an IncX3 type, were present. The former contains a cluster (bla NDM-5-ble MBL -trpF-dsbD) bracketed by multi-insertional sequences, IS3000, ISAba125, IS5, and IS26. The latter carries the following resistance genes: bla CTX-14, aac(3)-IV, aadA1, aadA2, aph(3')-Ia, aph(4)-Ia, sul1, sul2, sul3, dfrA12, fosA3, oqxA, oqxB, mph(A), and floR, and cmlA1. The chromosome, contig3, and contig5 also carry bla CTX-64 and mdf(A), tet(A), and erm(B), tet(M) and aadA22, respectively. Strain N7 also harbors virulence factors such as fimH, flu, ecpABCDE, sfmA, hlyE, and gadA. This study demonstrates the emergence of high level carbapenem resistant XDR E. coli strain N7 containing bla NDM-5 in aquatic environment, Seoul, South Korea. Due to the presence of mobile genetic elements, this strain could horizontally transfer resistance genes, including bla NDM-5 to environmental bacteria. Thus, it is necessary to conduct continuous surveillance for carbapenem resistance in various aquatic environments.
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Affiliation(s)
- Hanseob Shin
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Yeonghyeon Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Dukki Han
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, South Korea
- Department of Marine Molecular Bioscience, Gangneung-Wonju National University, Gangneung, South Korea
| | - Hor-Gil Hur
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, South Korea
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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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Pan Y, Fang Y, Song X, Lyu N, Chen L, Feng Y, Xu X, Zhu B, Hu Y. Co-occurrence of mcr-9, extended spectrum β-lactamase (ESBL) and AmpC genes in a conjugative IncHI2A plasmid from a multidrug-resistant clinical isolate of Salmonella diarizonae. J Infect 2020; 82:84-123. [PMID: 33188799 DOI: 10.1016/j.jinf.2020.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 11/26/2022]
Affiliation(s)
- Yuanlong Pan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Yuan Fang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofeng Song
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Na Lyu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Luping Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Yuqing Feng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xuebin Xu
- Department of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China; Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China.
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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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Antony L, Fenske G, Kaushik RS, Nagaraja TG, Thomas M, Scaria J. Population structure of Salmonella enterica serotype Mbandaka reveals similar virulence potential irrespective of source and phylogenomic stratification. F1000Res 2020; 9:1142. [PMID: 33214877 PMCID: PMC7653644 DOI: 10.12688/f1000research.25540.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/08/2020] [Indexed: 11/22/2022] Open
Abstract
Background: Salmonella enterica serotype Mbandaka ( Salmonella ser. Mbandaka) is a multi-host adapted Non-typhoidal Salmonella (NTS) that can cause foodborne illnesses in human. Outbreaks of Salmonella ser. Mbandaka contributed to the economic stress caused by NTS due to hospitalizations. Whole genome sequencing (WGS)-based phylogenomic analysis facilitates better understanding of the genomic features that may expedite the foodborne spread of Salmonella ser. Mbandaka. Methods: In the present study, we define the population structure, antimicrobial resistance (AMR), and virulence profile of Salmonella ser. Mbandaka using WGS data of more than 400 isolates collected from different parts of the world. We validated the genotypic prediction of AMR and virulence phenotypically using an available set of representative isolates. Results: Phylogenetic analysis of Salmonella ser. Mbandaka using Bayesian approaches revealed clustering of the population into two major groups; however, clustering of these groups and their subgroups showed no pattern based on the host or geographical origin. Instead, we found a uniform virulence gene repertoire in all isolates. Phenotypic analysis on a representative set of isolates showed a similar trend in cell invasion behavior and adaptation to a low pH environment. Both genotypic and phenotypic analysis revealed the carriage of multidrug resistance (MDR) genes in Salmonella ser. Mbandaka. Conclusions: Overall, our results show that the presence of multidrug resistance along with adaptation to broad range of hosts and uniformity in the virulence potential, isolates of Salmonella ser. Mbandaka from any source could have the potential to cause foodborne outbreaks as well as AMR dissemination.
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Affiliation(s)
- Linto Antony
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
- South Dakota Center for Biologics Research and Commercialization, Brookings, SD, USA
| | - Gavin Fenske
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
- South Dakota Center for Biologics Research and Commercialization, Brookings, SD, USA
| | - Radhey S Kaushik
- Department of Biology & Microbiology, South Dakota State University, Brookings, SD, 57007, USA
| | - Tiruvoor G Nagaraja
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Milton Thomas
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
| | - Joy Scaria
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
- South Dakota Center for Biologics Research and Commercialization, Brookings, SD, USA
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Chiu CH, Lee JJ, Wang MH, Chu C. Genetic analysis and plasmid-mediated bla CMY-2 in Salmonella and Shigella and the Ceftriaxone Susceptibility regulated by the ISEcp-1 tnpA-bla CMY-2-blc-sugE. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2020; 54:649-657. [PMID: 32169530 DOI: 10.1016/j.jmii.2020.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/18/2020] [Accepted: 01/21/2020] [Indexed: 12/01/2022]
Abstract
BACKGROUND Nontyphoid Salmonella and Shigella can cause gastroenteritis in humans. Ceftriaxone (CRO) has been used to treat their infection, however, development of CRO resistance are often associated with plasmid-mediated blaCMY. Here, we investigated the presence of plasmid-mediated ISEcp-1 tnpA-blaCMY-2-blc-sugE and the role of these genes in regulation of CRO susceptibility in different hosts. METHODS 194 strains of Salmonella serovars and Shigella were tested for CRO susceptibility. Non-susceptibility strains were examined for plasmid-mediated ISEcp-1 tnpA-blaCMY-2-blc-sugE by PCR amplification, Southern blot, and DNA sequencing. The plasmid profiles were determined by HindIII-digested restriction fragment length polymorphism (RFLP). Four recombinant plasmids with different genes from ISEcp-1 tnpA-blaCMY-2-blc-sugE were constructed and then were transferred into Escherichia coli and different Salmonella serovars to evaluate the CRO susceptibility. RESULTS Among 20 CRO-nonsusceptible isolates of Salmonella Choleraesuis (5), S. Typhimurium (4), S. Mons (1), S. Stanley (2) and Shigella sonnei (8) with plasmid-mediated blaCMY-2, 19 isolates carried the ISEcp-1 tnpA-blaCMY-2-blc-sugE and only one isolate with tnpA-blaCMY-2. Transformation of these plasmids into E. coli pir116 produced multidrug resistance. Furthermore, PCR-RFLP analysis determined 5 different plasmid profiles and identical RFLP pattern between S. Typhimurium and S. sonnei. Transformation of the recombinant plasmids into E. coli and different Salmonella serovars resulted in phenotypes ranging from susceptible to resistant (especially inducible resistance) to CRO that were dependent on the genes, and host. CONCLUSION The CRO susceptibility associated with the ISEcp-1 tnpA-blaCMY-2-blc-sugE element is regulated positively by ISEcp-1 tnpA and SugE and negatively regulated by Blc and unknown species-dependent host factor(s).
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Affiliation(s)
- Cheng-Hsun Chiu
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC; Division of Pediatric Infectious Diseases, Chang Gung Children's Hospital, Taoyuan, Taiwan, ROC
| | - Jen-Jain Lee
- Medical Laboratory Division, Chiayi Branch, Taichung Veterans General Hospital, No.600, Sec. 2, Shixian Rd., Chiayi City, 60090, Taiwan, ROC
| | - Mei-Hui Wang
- Department of Microbiology, Immunology, and Biopharmaceuticals, College of Life Sciences, National Chiayi University, Chiayi, Taiwan, ROC
| | - Chishih Chu
- Department of Microbiology, Immunology, and Biopharmaceuticals, College of Life Sciences, National Chiayi University, Chiayi, Taiwan, ROC.
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Zhou X, Li M, Xu L, Shi C, Shi X. Characterization of Antibiotic Resistance Genes, Plasmids, Biofilm Formation, andIn VitroInvasion Capacity ofSalmonellaEnteritidis Isolates from Children with Gastroenteritis. Microb Drug Resist 2019; 25:1191-1198. [DOI: 10.1089/mdr.2018.0421] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Xiujuan Zhou
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Meiya Li
- Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Li Xu
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xianming Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
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Hüttener M, Prieto A, Aznar S, Bernabeu M, Glaría E, Valledor AF, Paytubi S, Merino S, Tomás J, Juárez A. Expression of a novel class of bacterial Ig-like proteins is required for IncHI plasmid conjugation. PLoS Genet 2019; 15:e1008399. [PMID: 31527905 PMCID: PMC6764697 DOI: 10.1371/journal.pgen.1008399] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/27/2019] [Accepted: 09/04/2019] [Indexed: 01/10/2023] Open
Abstract
Antimicrobial resistance (AMR) is currently one of the most important challenges to the treatment of bacterial infections. A critical issue to combat AMR is to restrict its spread. In several instances, bacterial plasmids are involved in the global spread of AMR. Plasmids belonging to the incompatibility group (Inc)HI are widespread in Enterobacteriaceae and most of them express multiple antibiotic resistance determinants. They play a relevant role in the recent spread of colistin resistance. We present in this report novel findings regarding IncHI plasmid conjugation. Conjugative transfer in liquid medium of an IncHI plasmid requires expression of a plasmid-encoded, large-molecular-mass protein that contains an Ig-like domain. The protein, termed RSP, is encoded by a gene (ORF R0009) that maps in the Tra2 region of the IncHI1 R27 plasmid. The RSP protein is exported outside the cell by using the plasmid-encoded type IV secretion system that is also used for its transmission to new cells. Expression of the protein reduces cell motility and enables plasmid conjugation. Flagella are one of the cellular targets of the RSP protein. The RSP protein is required for a high rate of plasmid transfer in both flagellated and nonflagellated Salmonella cells. This effect suggests that RSP interacts with other cellular structures as well as with flagella. These unidentified interactions must facilitate mating pair formation and, hence, facilitate IncHI plasmid conjugation. Due to its location on the outer surfaces of the bacterial cell, targeting the RSP protein could be a means of controlling IncHI plasmid conjugation in natural environments or of combatting infections caused by AMR enterobacteria that harbor IncHI plasmids. Dissemination of antimicrobial resistance (AMR) among different bacterial populations occurs due to mainly the presence of plasmids that encode AMR determinants. IncHI plasmids are one of the groups of bacterial plasmids that confer AMR to several enterobacteria. Recently, resistance to one of the last-resort antibiotics (colistin) for some multidrug-resistant infections has spread very rapidly. IncHI plasmids represent 20% of all plasmids transmitting colistin resistance worldwide and 40% in Europe. When analyzing the interactions of the IncHI1 plasmid R27 with Salmonella, we identified a large-molecular-mass protein that is encoded by this plasmid and is exported to the external medium. The R27 plasmid gene coding for that protein (R0009) is widespread among IncHI plasmids. In this report, we characterize the protein, termed RSP. The presented data show that RSP plays a relevant role in IncHI plasmid conjugation and suggest that the protein is retained on the outer surface of the bacterial cells and facilitates cell-to-cell contact before plasmid DNA transfer. Considering that IncHI plasmids significantly contribute to AMR dissemination within enterobacteria, the findings reported in this paper suggest that the identified protein can be a target to control both IncHI-mediated AMR dissemination and infections caused by AMR enterobacteria that harbor these plasmids.
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Affiliation(s)
- Mário Hüttener
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Alejandro Prieto
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Sonia Aznar
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Manuel Bernabeu
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Estibaliz Glaría
- Department of Cell Biology, Physiology and Immunology, University of Barcelona, Barcelona, Spain
| | - Annabel F. Valledor
- Department of Cell Biology, Physiology and Immunology, University of Barcelona, Barcelona, Spain
| | - Sonia Paytubi
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Susana Merino
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Joan Tomás
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Antonio Juárez
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, Barcelona, Spain
- * E-mail:
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Draft Genome Sequences of Four Antibiotic-Resistant Salmonella Strains Isolated from Australian Red Meat Animal Species. Microbiol Resour Announc 2019; 8:8/35/e00925-19. [PMID: 31467110 PMCID: PMC6715880 DOI: 10.1128/mra.00925-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome sequences of four antibiotic-resistant Salmonella strains isolated from red meat animals in Australia are presented. Multidrug-resistant Salmonella enterica serovar Heidelberg 329 and Salmonella enterica serovar Typhimurium 2470 harbored an IncHI2 plasmid similar to the multidrug-resistant S. Heidelberg strain N13-01290 plasmid pN13-01290_23 previously isolated in Canada.
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Mutai WC, Waiyaki PG, Kariuki S, Muigai AWT. Plasmid profiling and incompatibility grouping of multidrug resistant Salmonella enterica serovar Typhi isolates in Nairobi, Kenya. BMC Res Notes 2019; 12:422. [PMID: 31311578 PMCID: PMC6636098 DOI: 10.1186/s13104-019-4468-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/11/2019] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Plasmids harbour antibiotic resistance genes which contribute to the emergence of multidrug resistant pathogens. We detected the presence of plasmids in multidrug resistant Salmonella enterica serovar Typhi (S. Typhi) isolates from our previous study and consequently determined their incompatibility groups and possibility of conjugation transmission. Plasmids were extracted from 98 multidrug resistant S. Typhi isolates based on alkaline lysis technique. Plasmid incompatibility grouping was established by PCR replicon typing using 18 pairs of primers to amplify FIA, FIB, FIC, HI1, HI2, I1-Iγ, L/M, N, P, W, T, A/C, K, B/O, X, Y, F and FIIA replicons. Antibiotic resistance phenotypes were conjugally transferred from S. Typhi isolates with plasmids to Escherichia coli K12F strain devoid of plasmids. RESULTS Approximately 79.6% of the MDR S. Typhi isolates were related to the existence of plasmids. We detected 93.6% of plasmids belonging to incompatibility (Inc) group HI1. The other incompatibility groups identified included IncFIC (16.7%), IncP (1.3%), and IncI1 (1.3%) which appeared together with Inc HI1. MDR S. Typhi isolated carried a homologous plasmid of incompatibility group HI1 most of which transferred the resistance phenotypes of ampicillin, tetracycline and chloramphenicol to the transconjugants.
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Affiliation(s)
- Winnie C Mutai
- Department of Medical Microbiology, School of Medicine, University of Nairobi, Nairobi, Kenya.
| | - Peter G Waiyaki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Anne W T Muigai
- School of Biological Sciences, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
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Trujillo-Soto T, Machuca J, Arca-Suárez J, Rodríguez-Iglesias M, Galán-Sánchez F. Co-Occurrence of mcr-1 and qnrS1 on an IncHI2 Plasmid in Clinical Isolates of Salmonella Typhimurium in Spain. Vector Borne Zoonotic Dis 2019; 19:662-665. [PMID: 31145042 DOI: 10.1089/vbz.2018.2398] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Salmonella enterica is a well-adapted zoonotic bacterium associated to cases of gastroenteritis and bacteremia with increased morbidity and mortality. In this study, three isolates of Salmonella Typhimurium obtained from human clinical samples, showing colistin resistance and low-level resistance to quinolones, have been genetically characterized. We detected the co-occurrence of mcr-1 and qnrS1 on a single IncHI2 plasmid in isolates of Salmonella Typhimurium obtained from Spanish children without a travel history. The multiresistant region contained numerous resistance genes. Isolates were clonally related, which suggests the presence of these clones in the community and the potential to cause outbreaks affecting the most susceptible population. It is necessary to monitor the presence of these plasmid-mediated resistance genes in human European strains of Salmonella spp. because of the risk of producing outbreaks of community-acquired infections.
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Affiliation(s)
| | - Jesús Machuca
- Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain
| | - Jorge Arca-Suárez
- UGC Microbiología, Hospital Universitario Puerta del Mar, Cadiz, Spain
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Sun YW, Liu YY, Wu H, Wang LF, Liu JH, Yuan L, Pan YS, He DD, Hu GZ. IS26-Flanked Composite Transposon Tn6539 Carrying the tet(M) Gene in IncHI2-Type Conjugative Plasmids From Escherichia coli Isolated From Ducks in China. Front Microbiol 2019; 9:3168. [PMID: 30697195 PMCID: PMC6340991 DOI: 10.3389/fmicb.2018.03168] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/07/2018] [Indexed: 12/27/2022] Open
Abstract
Tet(M)-type proteins confer resistance to tetracycline and related antibiotics by interacting with the ribosome. Genes encoding Tet(M) have been found in a range of bacteria, including Escherichia coli. In the current study, conjugation experiments were performed between seven different tetracycline-resistant, azide-susceptible E. coli strains isolated from ducks and tetracycline-sensitive, azide-resistant E.coli J53. Transconjugants were obtained from two of the strains at a frequency of 1.2 × 10-8. PCR, southern blotting and sequencing demonstrated that tet(M) in the transconjugants was located on a ~50 kb IncHI2-type plasmid and was part of a composite transposon, designated Tn6539. This transposon is flanked by two IS26 elements in opposite orientation and contains the Tn3ΔtnpA+Δorf13-lp-tet(M)+gamma delta+tnpX+ΔtnpR sequences. The Δorf13-lp-tet(M) sequence was a highly conserved genetic fragment in E. coli harboring tet(M) and mainly located in the composite transposons flanked by IS6-family elements. In summary, Tn6539 is a new composite transposon capable of horizontal transfer of tet(M) among E. coli isolates.
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Affiliation(s)
- Ya-Wei Sun
- Department of Pharmacology and Toxicology, College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China.,Department of Animal Science, Henan Institute of Science and Technology, Xinxiang, China
| | - Ying-Ying Liu
- Department of Pharmacology and Toxicology, College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Hua Wu
- Department of Pharmacology and Toxicology, College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Ling-Fei Wang
- Department of Pharmacology and Toxicology, College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Jian-Hua Liu
- Department of Pharmacology and Toxicology, College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Li Yuan
- Department of Pharmacology and Toxicology, College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Yu-Shan Pan
- Department of Pharmacology and Toxicology, College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Dan-Dan He
- Department of Pharmacology and Toxicology, College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Gong-Zheng Hu
- Department of Pharmacology and Toxicology, College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
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