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Zhao QY, Cai RM, Cai P, Zhang L, Jiang HX, Zeng ZL. Characterization of Salmonella Phage P1-CTX and the Potential Mechanism Underlying the Acquisition of the blaCTX-M-27 Gene. Antibiotics (Basel) 2024; 13:446. [PMID: 38786174 PMCID: PMC11117986 DOI: 10.3390/antibiotics13050446] [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: 04/08/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The P1 phage has garnered attention as a carrier of antibiotic resistance genes (ARGs) in Enterobacteriaceae. However, the transferability of ARGs by P1-like phages carrying ARGs, in addition to the mechanism underlying ARG acquisition, remain largely unknown. In this study, we elucidated the biological characteristics, the induction and transmission abilities, and the acquisition mechanism of the blaCTX-M-27 gene in the P1 phage. The P1-CTX phage exhibited distinct lytic plaques and possessed a complete head and tail structure. Additionally, the P1-CTX phage was induced successfully under various conditions, including UV exposure, heat treatment at 42 °C, and subinhibitory concentrations (sub-MICs) of antibiotics. Moreover, the P1-CTX phage could mobilize the blaCTX-M-27 gene into three strains of Escherichia coli (E. coli) and the following seven different serotypes of Salmonella: Rissen, Derby, Kentucky, Typhimurium, Cerro, Senftenberg, and Muenster. The mechanism underlying ARG acquisition by the P1-CTX phage involved Tn1721 transposition-mediated movement of blaCTX-M-27 into the ref and mat genes within its genome. To our knowledge, this is the first report documenting the dynamic processes of ARG acquisition by a phage. Furthermore, this study enriches the research on the mechanism underlying the phage acquisition of drug resistance genes and provides a basis for determining the risk of drug resistance during phage transmission.
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Affiliation(s)
- Qiu-Yun Zhao
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou 311300, China
| | - Run-Mao Cai
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
| | - Ping Cai
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
| | - Lin Zhang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
| | - Hong-Xia Jiang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
| | - Zhen-Ling Zeng
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
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Chu Y, Wang D, Hao W, Sun R, Sun J, Liu Y, Liao X. Prevalence, antibiotic resistance, virulence genes and molecular characteristics of Salmonella isolated from ducks and wild geese in China. Food Microbiol 2024; 118:104423. [PMID: 38049277 DOI: 10.1016/j.fm.2023.104423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 12/06/2023]
Abstract
Salmonella is a major foodborne pathogen and the cause of significant morbidity and mortality via consumption of contaminated meat and meat-products. The prevalence of Salmonella in ducks and wild geese in China are poorly characterized and these sources represent a potential pool that could be transferred to farm-reared fowl. In this study, we isolated 335 (18.3%) Salmonella from 1830 samples and identified 24 serotypes and most prevalent were Salmonella Indiana, Salmonella Kentucky and Salmonella Typhimurium. Whole genome sequencing revealed the presence of the dominant sequence types ST17, ST198 and ST19 for these three serotypes, respectively. In addition, these isolates were most likely clonally spread across different regions while S. Kentucky also crossed the species barrier. The majority of the Salmonella isolates possessed β-lactam and fluoroquinolone resistance and these were consistent with antibiotic resistance gene profiles. We also identified 8 plasmid replicon types and all isolates possessed virulence genes and the numbers were greatest for S. Enteritidis and S. Typhimurium isolates. This study provides novel insights concerning the epidemiology of Salmonella in ducks and wild geese and provides basic data for public health screening and management.
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Affiliation(s)
- Ying Chu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Dong Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Weihua Hao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Ruanyang Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yahong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Xiaoping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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Gong J, Zeng X, Xu J, Zhang D, Dou X, Lin J, Wang C. Genomic Characterization of a Plasmid-Free and Highly Drug-Resistant Salmonella enterica Serovar Indiana Isolate in China. Vet Sci 2024; 11:46. [PMID: 38275928 PMCID: PMC10819017 DOI: 10.3390/vetsci11010046] [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: 11/27/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
The emergence of multi-drug resistant (MDR) Salmonella enterica serovar Indiana (S. Indiana) strains in China is commonly associated with the presence of one or more resistance plasmids harboring integrons pivotal in acquiring antimicrobial resistance (AMR). This study aims to elucidate the genetic makeup of this plasmid-free, highly drug-resistant S. Indiana S1467 strain. Genomic sequencing was performed using Illumina HiSeq 2500 sequencer and PacBio RS II System. Prodigal software predicted putative protein-coding sequences while BLASTP analysis was conducted. The S1467 genome comprises a circular 4,998,300 bp chromosome with an average GC content of 51.81%, encompassing 4709 open reading frames (ORFs). Fifty-four AMR genes were identified, conferring resistance across 16 AMR categories, aligning closely with the strain's antibiotic susceptibility profile. Genomic island prediction unveiled an approximately 51 kb genomic island housing a unique YeeVU toxin-antitoxin system (TAS), a rarity in Salmonella species. This suggests that the AMR gene cluster on the S1467 genomic island may stem from the integration of plasmids originating from other Enterobacteriaceae. This study contributes not only to the understanding of the genomic characteristics of a plasmid-free, highly drug-resistant S. Indiana strain but also sheds light on the intricate mechanisms underlying antimicrobial resistance. The implications of our findings extend to the broader context of horizontal gene transfer between bacterial species, emphasizing the need for continued surveillance and research to address the evolving challenges posed by drug-resistant pathogens.
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Affiliation(s)
- Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China; (J.G.); (D.Z.); (X.D.)
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou 225009, China
| | - Ximin Zeng
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA; (X.Z.); (J.L.)
| | - Jingxiao Xu
- School of Life Sciences, Fudan University, Shanghai 200438, China;
| | - Di Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China; (J.G.); (D.Z.); (X.D.)
| | - Xinhong Dou
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China; (J.G.); (D.Z.); (X.D.)
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou 225009, China
| | - Jun Lin
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA; (X.Z.); (J.L.)
| | - Chengming Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
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Qin X, Zhang Z. Emergence of a Hybrid IncI1-Iα Plasmid-Encoded blaCTX-M-101 Conferring Resistance to Cephalosporins in Salmonella enterica Serovar Enteritidis. Microorganisms 2023; 11:1275. [PMID: 37317249 DOI: 10.3390/microorganisms11051275] [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: 04/21/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 06/16/2023] Open
Abstract
The increasing resistance to cephalosporins in Salmonella poses a serious threat to public health. In our previous study, the blaCTX-M-101 gene, a new blaCTX-M variant, was first reported in Salmonella enterica serovar Enteritidis (S. Enteritidis). Here, we further analyzed the genome characterization, transferability, and resistance mechanism of one S. Enteritidis isolate (SJTUF14523) carrying blaCTX-M-101 from an outpatient in 2016 in Xinjiang, China. This strain was a multidrug resistance (MDR) isolate and exhibited resistance to ceftazidime (MIC = 64 μg/mL), cefotaxime (MIC = 256 μg/mL), and cefepime (MIC = 16 μg/mL). Phylogenetic analysis revealed that SJTUF14523 had a close relationship to another S. Enteritidis isolate from the United States. In the presence of plasmid p14523A, there were 8- and 2133-fold increases in the MICs of cephalosporins in Escherichia coli C600 in the conjugation. Gene cloning results indicated that blaCTX-M-101 was the decisive mechanism leading to ceftazidime and cefotaxime resistance that could make the MICs break through the resistance breakpoint. Plasmid sequencing revealed that the blaCTX-M-101 gene was located on an IncI1-Iα transferable plasmid (p14523A) that was 85,862 bp in length. Sequence comparison showed that p14523A was a novel hybrid plasmid that might have resulted from the interaction between a homologous region. Furthermore, we found a composite transposon unit composed of ISEcp1, blaCTX-M-101, and orf477 in p14523A. ISEcp1-mediated transposition was likely to play a key role in the horizontal transfer of blaCTX-M-101 among plasmids in S. Enteritidis. Collectively, these findings underline further challenges in the prevention and control of antibiotic resistance posed by new CTX-M-101-like variants in Salmonella.
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Affiliation(s)
- Xiaojie Qin
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Zengfeng Zhang
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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Hu Y, He Y, Nguyen SV, Liu C, Liu C, Gan X, Wang W, Dong Y, Xu J, Li F, Fanning S. Antimicrobial resistance of Salmonella Indiana from retail chickens in China and emergence of an mcr-1-harboring isolate with concurrent resistance to ciprofloxacin, cefotaxime, and colistin. Front Microbiol 2022; 13:955827. [PMID: 36160190 PMCID: PMC9493365 DOI: 10.3389/fmicb.2022.955827] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
Salmonella enterica serotype Indiana (S. Indiana) in Chinese poultry meat has aroused widespread concern because of its high prevalence and strong antimicrobial resistance. In consideration of the relationship in our previous study between S. Indiana and co-resistance to ciprofloxacin and cefotaxime (CIP-CTX), which were the first-line drug which were used in Salmonella infection in clinical, the antimicrobial resistance (AMR) of 224 CIP-CTX co-resistant S. Indiana isolated from retail chicken samples in China were investigated, with the aim of characterizing the AMR profiles and related resistance mechanisms to ciprofloxacin and cefotaxime among these CIP-CTX co-resistant S. Indiana isolates, all of which showed multi-drug-resistant (MDR) phenotypes. GyrA (S83F and D87N/G) with ParC (T57S and S80R) were the dominant amino acid substitution types, with oqxA, oqxB, and aac (6′)-Ib-cr identified as common plasmid-mediated quinolone resistance (PMQR)-encoding genes. Five blaCTX-M gene subtypes were identified with blaCTX-M-65 ranking at the top. Equally important, we obtained one isolate CFSA664 harboring the mcr-1 gene was ESBL producer with co-resistance to nine in ten classes of tested drugs inclduing colistin. A single circular chromosome and 3 circular plasmids were found in its genome. Among the 26 AMR genes identified, 24 were located on plasmid pCFSA664-1, including three ESBL genes, while plasmid pCFSA664-3 owning only the mcr-1 gene and sharing the same backbone structure with plasmids from Enterobacteriaceae. No insertion sequences were found near the mcr-1 gene but a relaxase-encoding gene in the flank, which could transfer into E. coli J53 at a relatively high frequency. S. Indiana in this study exhibited highly drug-resistant phenotypes, contributing to the acceleration of the dissemination and emergence of this pathogen among different sources. Surveillance and a One Health strategy are needed to limit the emergence of S. Indiana along the food chain.
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Affiliation(s)
- Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, 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, Belfield, Dublin, Ireland
| | - Yingying He
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Scott V. Nguyen
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland
- Public Health Laboratory, District of Columbia Department of Forensic Sciences, Washington, DC, United States
| | - Chang Liu
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chang Liu
- Food Science and Engineering College, Beijing University of Agriculture, Beijing, China
| | - Xin Gan
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, 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, Belfield, Dublin, Ireland
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
- *Correspondence: Fengqin Li,
| | - Séamus Fanning
- NHC Key Laboratory of Food Safety Risk Assessment, 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, Belfield, Dublin, Ireland
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
- Séamus Fanning,
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