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Wang Q, Han YY, Zhang TJ, Chen X, Lin H, Wang HN, Lei CW. Whole-genome sequencing of Escherichia coli from retail meat in China reveals the dissemination of clinically important antimicrobial resistance genes. Int J Food Microbiol 2024; 415:110634. [PMID: 38401379 DOI: 10.1016/j.ijfoodmicro.2024.110634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/08/2024] [Accepted: 02/18/2024] [Indexed: 02/26/2024]
Abstract
Escherichia coli is one of the important reservoirs of antimicrobial resistance genes (ARG), which often causes food-borne diseases and clinical infections. Contamination with E. coli carrying clinically important antimicrobial resistance genes in retail meat products can be transmitted to humans through the food chain, posing a serious threat to public health. In this study, a total of 330 E. coli strains were isolated from 464 fresh meat samples from 17 food markets in China, two of which were identified as enterotoxigenic and enteropathogenic E. coli. Whole genome sequencing revealed the presence of 146 different sequence types (STs) including 20 new STs, and 315 different clones based on the phylogenetic analysis, indicating the high genetic diversity of E. coli from retail meat products. Antimicrobial resistance profiles showed that 82.42 % E. coli were multidrug-resistant strains. A total of 89 antimicrobial resistance genes were detected and 12 E. coli strains carried clinically important antimicrobial resistance genes blaNDM-1, blaNDM-5, mcr-1, mcr-10 and tet(X4), respectively. Nanopore sequencing revealed that these resistance genes are located on different plasmids with the ability of horizontal transfer, and their genetic structure and environment are closely related to plasmids isolated from humans. Importantly, we reported for the first time the presence of plasmid-mediated mcr-10 in E. coli from retail meat. This study revealed the high genetic diversity of food-borne E. coli in retail meat and emphasized their risk of spreading clinically important antimicrobial resistance genes.
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Affiliation(s)
- Qin Wang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Ying-Yue Han
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Tie-Jun Zhang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Xuan Chen
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Heng Lin
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Hong-Ning Wang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China.
| | - Chang-Wei Lei
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China.
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Kyung SM, Lee JH, Lee ES, Xiang XR, Yoo HS. Emergence and genomic chion of Proteus mirabilis harboring bla NDM-1 in Korean companion dogs. Vet Res 2024; 55:50. [PMID: 38594755 PMCID: PMC11005143 DOI: 10.1186/s13567-024-01306-w] [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: 01/16/2024] [Accepted: 02/26/2024] [Indexed: 04/11/2024] Open
Abstract
Proteus mirabilis is a commensal bacterium dwelling in the gastrointestinal (GI) tract of humans and animals. Although New Delhi metallo-β-lactamase 1 (NDM-1) producing P. mirabilis is emerging as a threat, its epidemiology in our society remains largely unknown. LHPm1, the first P. mirabilis isolate harboring NDM-1, was detected from a companion dog that resides with a human owner. The whole-genome study revealed 20 different antimicrobial resistance (AMR) genes against various classes of antimicrobial agents, which corresponded to the MIC results. Genomic regions, including MDR genes, were identified with multiple variations and visualized in a comparative manner. In the whole-genome epidemiological analysis, multiple phylogroups were identified, revealing the genetic relationship of LHPm1 with other P. mirabilis strains carrying various AMR genes. These genetic findings offer comprehensive insights into NDM-1-producing P. mirabilis, underscoring the need for urgent control measures and surveillance programs using a "one health approach".
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Affiliation(s)
- Su Min Kyung
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jun Ho Lee
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Eun-Seo Lee
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Xi-Rui Xiang
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Han Sang Yoo
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.
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Ofosu-Appiah F, Acquah EE, Mohammed J, Sakyi Addo C, Agbodzi B, Ofosu DAS, Myers CJ, Mohktar Q, Ampomah OW, Ablordey A, Amissah NA. Klebsiella pneumoniae ST147 harboring blaNDM-1, multidrug resistance and hypervirulence plasmids. Microbiol Spectr 2024; 12:e0301723. [PMID: 38315028 PMCID: PMC10913492 DOI: 10.1128/spectrum.03017-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/17/2023] [Indexed: 02/07/2024] Open
Abstract
The spread of hypervirulent (hv) and carbapenem-/multidrug-resistant Klebsiella pneumoniae is an emerging problem in healthcare settings. The New Delhi metallo-β-lactamase-1 (blaNDM-1) is found in Enterobacteriaceae including K. pneumoniae. The blaNDM-1 is capable of hydrolyzing β-lactam antibiotics which are used for treatment of severe infections caused by multidrug-resistant Gram-negative bacteria. This is associated with the unacceptably high mortality rate in immunocompromised burn injury patients. This study reports on the characterization of blaNDM-1 gene and virulence factors in hv carbapenem-/multidrug-resistant K. pneumoniae ST147 in the burns unit of a tertiary teaching hospital during routine surveillance. Two K. pneumoniae strains were obtained from wounds of burn-infected patients from May 2020 to July 2021. The hypervirulence genes and genetic context of the blaNDM-1 gene and mobile genetic elements potentially involved in the transposition of the gene were analyzed. We identified a conserved genetic background and an IS26 and open reading frame flanking the blaNDM-1 gene that could suggest its involvement in the mobilization of the gene. The plasmid harbored additional antibiotic resistance predicted regions that were responsible for resistance to almost all the routinely used antibiotics. To ensure the identification of potential outbreak strains during routine surveillance, investigations on resistance genes and their environment in relation to evolution are necessary for molecular epidemiology.IMPORTANCEData obtained from this study will aid in the prompt identification of disease outbreaks including evolving resistance and virulence of the outbreak bacteria. This will help establish and implement antimicrobial stewardship programs and infection prevention protocols in fragile health systems in countries with limited resources. Integration of molecular surveillance and translation of whole-genome sequencing in routine diagnosis will provide valuable data for control of infection. This study reports for the first time a high-risk clone K. pneumoniae ST147 with hypervirulence and multidrug-resistance features in Ghana.
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Affiliation(s)
- Frederick Ofosu-Appiah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Ezra E. Acquah
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Jibril Mohammed
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Comfort Sakyi Addo
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Bright Agbodzi
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dorcas A. S. Ofosu
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Charles J. Myers
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Quaneeta Mohktar
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Opoku-Ware Ampomah
- The Burns Unit, Reconstructive Plastic Surgery and Burns Unit, Korle Bu Teaching Hospital, Accra, Ghana
| | - Anthony Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Nana Ama Amissah
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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Rezzoug I, Emeraud C, Rodriguez C, Pawlotsky JM, Bonnin RA, Dortet L. Regional dissemination of NDM-1 producing Enterobacter hormaechei ST1740, with a subset of strains co-producing VIM-4 or IMP-13, France, 2019 to 2022. Euro Surveill 2024; 29:2300521. [PMID: 38487887 PMCID: PMC10941310 DOI: 10.2807/1560-7917.es.2024.29.11.2300521] [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: 09/28/2023] [Accepted: 02/02/2024] [Indexed: 03/17/2024] Open
Abstract
BackgroundFrom 2019 to 2022, the French National Reference Centre for Antibiotic Resistance (NRC) received a total of 25 isolates of Enterobacter hormaechei subsp. hoffmannii sequence type (ST)1740. All produced metallo-β-lactamase(s) and were from the Lyon area.AimTo understand these strains' spread and evolution, more extended microbiological and molecular analyses were conducted.MethodsPatients' demographics and specimen type related to isolates were retrieved. All strains underwent short-read whole genome sequencing, and for 15, long-read sequencing to understand carbapenemase-gene acquisition. Clonal relationships were inferred from core-genome single nt polymorphisms (SNPs). Plasmids and the close genetic environment of each carbapenemase-encoding gene were analysed.ResultsPatients (10 female/15 male) were on average 56.6 years old. Seven isolates were recovered from infections and 18 through screening. With ≤ 27 SNPs difference between each other's genome sequences, the 25 strains represented a clone dissemination. All possessed a chromosome-encoded bla NDM-1 gene inside a composite transposon flanked by two IS3000. While spreading, the clone independently acquired a bla VIM-4-carrying plasmid of IncHI2 type (n = 12 isolates), or a bla IMP-13-carrying plasmid of IncP-1 type (n = 1 isolate). Of the 12 isolates co-producing NDM-1 and VIM-4, seven harboured the colistin resistance gene mcr9.2; the remaining five likely lost this gene through excision.ConclusionThis long-term outbreak was caused by a chromosome-encoded NDM-1-producing ST1740 E. hormaechei subsp. hoffmannii clone, which, during its dissemination, acquired plasmids encoding VIM-4 or IMP-13 metallo-β-lactamases. To our knowledge, IMP-13 has not prior been reported in Enterobacterales in France. Epidemiological and environmental investigations should be considered alongside microbiological and molecular ones.
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Affiliation(s)
- Inès Rezzoug
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacterales, Le Kremlin-Bicêtre, France
| | - Cécile Emeraud
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacterales, Le Kremlin-Bicêtre, France
| | - Christophe Rodriguez
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
- INSERM U955, Team « Viruses, Hepatology, Cancer », Créteil, France
| | - Jean-Michel Pawlotsky
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
- INSERM U955, Team « Viruses, Hepatology, Cancer », Créteil, France
| | - Rémy A Bonnin
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacterales, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacterales, Le Kremlin-Bicêtre, France
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Ding L, Yang Z, Sun B. Understanding blaNDM-1 gene regulation in CRKP infections: toward novel antimicrobial strategies for hospital-acquired pneumonia. Mol Med 2024; 30:29. [PMID: 38395744 PMCID: PMC10893750 DOI: 10.1186/s10020-024-00794-y] [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: 11/24/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND The escalating challenge of Carbapenem-resistant Klebsiella pneumoniae (CRKP) in hospital-acquired pneumonia (HAP) is closely linked to the blaNDM-1 gene. This study explores the regulatory mechanisms of blaNDM-1 expression and aims to enhance antibacterial tactics to counteract the spread and infection of resistant bacteria. METHODS KP and CRKP strains were isolated from HAP patients' blood samples. Transcriptomic sequencing (RNA-seq) identified significant upregulation of blaNDM-1 gene expression in CRKP strains. Bioinformatics analysis revealed blaNDM-1 gene involvement in beta-lactam resistance pathways. CRISPR-Cas9 was used to delete the blaNDM-1 gene, restoring sensitivity. In vitro and in vivo experiments demonstrated enhanced efficacy with Imipenem and Thanatin or Subatan combination therapy. RESULTS KP and CRKP strains were isolated with significant upregulation of blaNDM-1 in CRKP strains identified by RNA-seq. The Beta-lactam resistance pathway was implicated in bioinformatics analysis. Knockout of blaNDM-1 reinstated sensitivity in CRKP strains. Further, co-treatment with Imipenem, Thanatin, or Subactam markedly improved antimicrobial effectiveness. CONCLUSION Silencing blaNDM-1 in CRKP strains from HAP patients weakens their Carbapenem resistance and optimizes antibacterial strategies. These results provide new theoretical insights and practical methods for treating resistant bacterial infections.
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Affiliation(s)
- Liang Ding
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Chongchuan District, Nantong, 226001, Jiangsu Province, China
| | - Zheng Yang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Chongchuan District, Nantong, 226001, Jiangsu Province, China
| | - Baier Sun
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Chongchuan District, Nantong, 226001, Jiangsu Province, China.
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Han Y, Gao YF, Xu HT, Li JP, Li C, Song CL, Lei CW, Chen X, Wang Q, Ma BH, Wang HN. Characterization and risk assessment of novel SXT/R391 integrative and conjugative elements with multidrug resistance in Proteus mirabilis isolated from China, 2018-2020. Microbiol Spectr 2024; 12:e0120923. [PMID: 38197656 PMCID: PMC10871549 DOI: 10.1128/spectrum.01209-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 11/09/2023] [Indexed: 01/11/2024] Open
Abstract
Proteus mirabilis can transfer transposons, insertion sequences, and gene cassettes to the chromosomes of other hosts through SXT/R391 integrative and conjugative elements (ICEs), significantly increasing the possibility of antibiotic resistance gene (ARG) evolution and expanding the risk of ARGs transmission among bacteria. A total of 103 strains of P. mirabilis were isolated from 25 farms in China from 2018 to 2020. The positive detection rate of SXT/R391 ICEs was 25.2% (26/103). All SXT/R391 ICEs positive P. mirabilis exhibited a high level of overall drug resistance. Conjugation experiments showed that all 26 SXT/R391 ICEs could efficiently transfer to Escherichia coli EC600 with a frequency of 2.0 × 10-7 to 6.0 × 10-5. The acquired ARGs, genetic structures, homology relationships, and conservation sequences of 26 (19 different subtypes) SXT/R391 ICEs were investigated by high-throughput sequencing, whole-genome typing, and phylogenetic tree construction. ICEPmiChnHBRJC2 carries erm (42), which have never been found within an SXT/R391 ICE in P. mirabilis, and ICEPmiChnSC1111 carries 19 ARGs, including clinically important cfr, blaCTX-M-65, and aac(6')-Ib-cr, making it the ICE with the most ARGs reported to date. Through genetic stability, growth curve, and competition experiments, it was found that the transconjugant of ICEPmiChnSCNNC12 did not have a significant fitness cost on the recipient bacterium EC600 and may have a higher risk of transmission and dissemination. Although the transconjugant of ICEPmiChnSCSZC20 had a relatively obvious fitness cost on EC600, long-term resistance selection pressure may improve bacterial fitness through compensatory adaptation, providing scientific evidence for risk assessment of horizontal transfer and dissemination of SXT/R391 ICEs in P. mirabilis.IMPORTANCEThe spread of antibiotic resistance genes (ARGs) is a major public health concern. The study investigated the prevalence and genetic diversity of integrative and conjugative elements (ICEs) in Proteus mirabilis, which can transfer ARGs to other hosts. The study found that all of the P. mirabilis strains carrying ICEs exhibited a high level of drug resistance and a higher risk of transmission and dissemination of ARGs. The analysis of novel multidrug-resistant ICEs highlighted the potential for the evolution and spread of novel resistance mechanisms. These findings emphasize the importance of monitoring the spread of ICEs carrying ARGs and the urgent need for effective strategies to combat antibiotic resistance. Understanding the genetic diversity and potential for transmission of ARGs among bacteria is crucial for developing targeted interventions to mitigate the threat of antibiotic resistance.
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Affiliation(s)
- Yun Han
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yu-Feng Gao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - He-ting Xu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jin-Peng Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Cai-Liang Song
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Chang-Wei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xuan Chen
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Qin Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Bo-Heng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Hong-Ning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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Ryan MP, Carraro N, Slattery S, Pembroke JT. Integrative Conjugative Elements (ICEs) of the SXT/R391 family drive adaptation and evolution in γ-Proteobacteria. Crit Rev Microbiol 2024; 50:105-126. [PMID: 36634159 DOI: 10.1080/1040841x.2022.2161870] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023]
Abstract
Integrative Conjugative Elements (ICEs) are mosaics containing functional modules allowing maintenance by site-specific integration and excision into and from the host genome and conjugative transfer to a specific host range. Many ICEs encode a range of adaptive functions that aid bacterial survival and evolution in a range of niches. ICEs from the SXT/R391 family are found in γ-Proteobacteria. Over 100 members have undergone epidemiological and molecular characterization allowing insight into their diversity and function. Comparative analysis of SXT/R391 elements from a wide geographic distribution has revealed conservation of key functions, and the accumulation and evolution of adaptive genes. This evolution is associated with gene acquisition in conserved hotspots and variable regions within the SXT/R391 ICEs catalysed via element-encoded recombinases. The elements can carry IS elements and transposons, and a mutagenic DNA polymerase, PolV, which are associated with their evolution. SXT/R391 ICEs isolated from different niches appear to have retained adaptive functions related to that specific niche; phage resistance determinants in ICEs carried by wastewater bacteria, antibiotic resistance determinants in clinical isolates and metal resistance determinants in bacteria recovered from polluted environments/ocean sediments. Many genes found in the element hotspots are undetermined and have few homologs in the nucleotide databases.
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Affiliation(s)
- Michael P Ryan
- Department of Applied Sciences, Technological University of the Shannon, Limerick, Ireland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Shannon Slattery
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
| | - J Tony Pembroke
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
- Bernal Institute, University of Limerick, Ireland
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Peng K, Li Y, Wang Q, Yang P, Wang Z, Li R. Integrative conjugative elements mediate the high prevalence of tmexCD3-toprJ1b in Proteus spp. of animal source. mSystems 2023; 8:e0042923. [PMID: 37707055 PMCID: PMC10654056 DOI: 10.1128/msystems.00429-23] [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: 04/29/2023] [Accepted: 07/23/2023] [Indexed: 09/15/2023] Open
Abstract
IMPORTANCE The emergence and spread of tmexCD-toprJ have greatly weakened the function of tigecycline. Although studies have demonstrated the significance of Proteus as carriers for tmexCD-toprJ, the epidemic mechanism and characteristics of tmexCD-toprJ in Proteus remain unclear. Herein, we deciphered that the umuC gene in VRIII of SXT/R391 ICEs was a hotspot for the integration of tmexCD3-toprJ1b-bearing mobile genetic elements by genomic analysis. The mobilization and dissemination of tmexCD3-toprJ1b in Proteus were mediated by highly prevalent ICEs. Furthermore, the co-occurrence of tmexCD3-toprJ1b-bearing ICEs with other chromosomally encoded multidrug resistance gene islands warned that the chromosomes of Proteus are significant reservoirs of ARGs. Overall, our results provide significant insights for the prevention and control of tmexCD3-toprJ1b in Proteus.
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Affiliation(s)
- Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yangfan Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Qiaojun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Pengbin Yang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 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, Jiangsu, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China
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Wen R, Wei H, Zhang T, Ma P, Wang Q, Li C, Li Z, Lei C, Wang H. Epidemiological Characterisation of blaNDM-Positive Enterobacterales from Food-Producing Animal Farms in Southwest China. Microorganisms 2023; 11:2304. [PMID: 37764148 PMCID: PMC10536151 DOI: 10.3390/microorganisms11092304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Carbapenems are atypical β-lactam antibiotics with a broade antibacterial spectrum and strong antibacterial activity; however, the emergence and spread of carbapenemases have led to a decline in their effectiveness. New Delhi metallo-β-lactamase (NDM) is an important carbapenemase that has attracted widespread attention and poses a major threat to public health. To investigate the epidemiological characteristics of blaNDM in swine and chicken farms in southwestern China, we isolated 102 blaNDM-positive Enterobacterales strains from 18 farms in Sichuan and Yunnan provinces in 2021, with Escherichia coli and Klebsiella spp. being the main reservoirs of blaNDM, variant blaNDM-5 being the most prevalent, and all strains being multi-drug resistant. Whole-genome sequencing analysis of 102 blaNDM-positive Enterobacterales strains revealed that blaNDM had spread primarily through its carriers on the same farm and among the 18 farms in this study. A high degree of genetic similarity between animal-derived blaNDM-positive Escherichia coli strains and human-derived strains was also identified, suggesting a potential mutual transmission between them. Nanopore sequencing results indicated that blaNDM is predominantly present on the IncX3 plasmid, that an insertion sequence might be important for recombination in the blaNDM genetic environment, and that most of the plasmids carrying blaNDM are transferable. Collectively, our results enrich the current epidemiological information regarding blaNDM in pig and chicken farms in Southwest China, revealing its transmission pattern, as well as the potential risk of transmission to humans, which could help to better understand and control the spread of blaNDM.
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Affiliation(s)
- Renqiao Wen
- Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Hongcheng Wei
- Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China
- 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
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Peng Ma
- Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Qin Wang
- Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Chao Li
- Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Zhonghan Li
- Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Changwei Lei
- Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China
- 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
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
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Li Y, Yin M, Fang C, Fu Y, Dai X, Zeng W, Zhang L. Genetic analysis of resistance and virulence characteristics of clinical multidrug-resistant Proteus mirabilis isolates. Front Cell Infect Microbiol 2023; 13:1229194. [PMID: 37637463 PMCID: PMC10457174 DOI: 10.3389/fcimb.2023.1229194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Objective Proteus mirabilis is the one of most important pathogens of catheter-associated urinary tract infections. The emergence of multidrug-resistant (MDR) P. mirabilis severely limits antibiotic treatments, which poses a public health risk. This study aims to investigate the resistance characteristics and virulence potential for a collection of P. mirabilis clinical isolates. Methods and results Antibiotic susceptibility testing revealed fourteen MDR strains, which showed high resistance to most β-lactams and trimethoprim/sulfamethoxazole, and a lesser extent to quinolones. All the MDR strains were sensitive to carbapenems (except imipenem), ceftazidime, and amikacin, and most of them were also sensitive to aminoglycosides. The obtained MDR isolates were sequenced using an Illumina HiSeq. The core genome-based phylogenetic tree reveals the high genetic diversity of these MDR P. mirabilis isolates and highlights the possibility of clonal spread of them across China. Mobile genetic elements SXT/R391 ICEs were commonly (10/14) detected in these MDR P. mirabilis strains, whereas the presence of resistance island PmGRI1 and plasmid was sporadic. All ICEs except for ICEPmiChn31006 carried abundant antimicrobial resistance genes (ARGs) in the HS4 region, including the extended-spectrum β-lactamase (ESBL) gene blaCTX-M-65. ICEPmiChn31006 contained the sole ARG blaCMY-2 and was nearly identical to the global epidemic ICEPmiJpn1. The findings highlight the important roles of ICEs in mediating the spread of ARGs in P. mirabilis strains. Additionally, these MDR P. mirabilis strains have great virulence potential as they exhibited significant virulence-related phenotypes including strong crystalline biofilm, hemolysis, urease production, and robust swarming motility, and harbored abundant virulence genes. Conclusion In conclusion, the prevalence of MDR P. mirabilis with high virulence potential poses an urgent threat to public health. Intensive monitoring is needed to reduce the incidence of infections by MDR P. mirabilis.
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Affiliation(s)
- Ying Li
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Ming Yin
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Chengju Fang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Yu Fu
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Xiaoyi Dai
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Wei Zeng
- Department of Clinical Laboratory, The Hejiang People’s hospital, Luzhou, Sichuan, China
| | - Luhua Zhang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
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11
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Ma S, Shen J, Xu Y, Ding P, Gao X, Pan Y, Wu H, Hu G, He D. Epidemic characteristics of the SXT/R391 integrated conjugative elements in multidrug-resistant Proteus mirabilis isolated from chicken farm. Poult Sci 2023; 102:102640. [PMID: 37068352 PMCID: PMC10130350 DOI: 10.1016/j.psj.2023.102640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/14/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
This study was designed to depict prevalence and antimicrobial resistance characteristics of Proteus mirabilis (P. mirabilis) strains in 4 chicken farms and to probe the transfer mechanism of resistance genes. A total of 187 P. mirabilis isolates were isolated from 4 chicken farms. The susceptibility testing of these isolates to 14 antimicrobials showed that the multidrug resistance (MDR) rate was as high as 100%. The β-lactamase resistance genes blaOXA-1, blaCTX-M-1G, blaCTX-M-9G and colistin resistance gene mcr-1 were highly carried in the P. mirabilis isolates. An MDR strain W47 was selected for whole genome sequencing (WGS) and conjugation experiment. The results showed that W47 carried 23 resistance genes and 64 virulence genes, and an SXT/R391 integrated conjugative elements (ICEs) named ICEPmiChn5 carrying 17 genes was identified in chromosome. ICEPmiChn5 was able to be excised from the chromosome of W47 forming a circular intermediate, but repeated conjugation experiments were unsuccessful. Among 187 P. mirabilis isolates, 144 (77.01%, 144/187) isolates carried ICEPmiChn5-like ICEs, suggesting that ICEs may be the major vector for the transmission of resistance genes among MDR chicken P. mirabilis strains in this study. The findings were conducive to insight into the resistance mechanism of chicken P. mirabilis strains and provide a theoretical basis for the use of antibiotics for the treatment of MDR P. mirabilis infections in veterinary clinic.
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Affiliation(s)
- Shengnan Ma
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiaxing Shen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Yakun Xu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Pengyun Ding
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiao Gao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Yushan Pan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Hua Wu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Gongzheng Hu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Dandan He
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
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12
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Brenciani A, Morroni G, Schwarz S, Giovanetti E. Oxazolidinones: mechanisms of resistance and mobile genetic elements involved. J Antimicrob Chemother 2022; 77:2596-2621. [PMID: 35989417 DOI: 10.1093/jac/dkac263] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The oxazolidinones (linezolid and tedizolid) are last-resort antimicrobial agents used for the treatment of severe infections in humans caused by MDR Gram-positive bacteria. They bind to the peptidyl transferase centre of the bacterial ribosome inhibiting protein synthesis. Even if the majority of Gram-positive bacteria remain susceptible to oxazolidinones, resistant isolates have been reported worldwide. Apart from mutations, affecting mostly the 23S rDNA genes and selected ribosomal proteins, acquisition of resistance genes (cfr and cfr-like, optrA and poxtA), often associated with mobile genetic elements [such as non-conjugative and conjugative plasmids, transposons, integrative and conjugative elements (ICEs), prophages and translocatable units], plays a critical role in oxazolidinone resistance. In this review, we briefly summarize the current knowledge on oxazolidinone resistance mechanisms and provide an overview on the diversity of the mobile genetic elements carrying oxazolidinone resistance genes in Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Gianluca Morroni
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.,Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China.,Veterinary Centre for Resistance Research (TZR), Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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13
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Song Z, Lei CW, Zuo L, Li C, Wang YL, Tian YM, Wang HN. Whole genome sequence of Proteus mirabilis ChSC1905 strain harbouring a new SXT/R391-family ICE. J Glob Antimicrob Resist 2022; 30:279-281. [PMID: 35817261 DOI: 10.1016/j.jgar.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 11/06/2020] [Accepted: 07/01/2022] [Indexed: 12/01/2022] Open
Abstract
OBJECTIVES The aim of this study was to characterise the whole genome sequence of a multidrug-resistant (MDR) Proteus mirabilis strain ChSC1905 isolated from a swine farm in China. METHODS The genome was sequenced by Illumina NovaSeq and Oxford Nanopore platforms, and it was assembled via Canu v.1.5. The acquired antimicrobial resistance genes (ARGs) were identified by ResFinder. A conjugation experiment was carried out to determine the mobilisation of integrative and conjugative element. RESULTS Strain ChSC1905 exhibited a MDR phenotype. The genome of strain ChSC1905 was 4 038 038 bp in length with a GC content of 39.1%, which contained 3645 coding sequences and 110 RNA genes. A total of 23 acquired ARGs were identified, among which 21 ARGs including the clinically important resistance genes blaCTX-M-65, cfr, fosA3, and aac(6')-Ib-cr were located on a SXT/R391 integrative and conjugative element (ICE). BLAST analysis showed that this new SXT/R391-family ICE (ICEPmiChnChSC1905 of 143 689 bp) was involved in sequence inversion mediated by ISVsa3 and genetic rearrangement mediated by IS26, and it could be transferred to E. coli EC600. CONCLUSION In this study, we report the genome sequence of MDR P. mirabilis strain ChSC1905 that harboured a novel SXT/R391-family ICE (ICEPmiChnChSC1905) involved in genetic rearrangement in China, which promotes the diversity of ICE and should receive more attention.
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Affiliation(s)
- Zhou Song
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Chang-Wei Lei
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Lei Zuo
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Cui Li
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Yu-Long Wang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Yi-Ming Tian
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Hong-Ning Wang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China.
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Luo X, Mu K, Zhao Y, Zhang J, Qu Y, Hu D, Jia Y, Dai P, Weng J, Wang D, Yu L. Emergence of blaNDM– 1-Carrying Aeromonas caviae K433 Isolated From Patient With Community-Acquired Pneumonia. Front Microbiol 2022; 13:825389. [PMID: 35663877 PMCID: PMC9161076 DOI: 10.3389/fmicb.2022.825389] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/16/2022] [Indexed: 11/24/2022] Open
Abstract
To demonstrate the detailed genetic characteristics of a blaNDM–1-carrying multidrug-resistant Aeromonas caviae strain, the complete genome of the A. caviae strain K433 was sequenced by Illumina HiSeq and Oxford nanopore platforms, and mobile genetic elements associated with antibiotic resistance genes were analyzed by a series of bioinformatics methods. A. caviae K433 which was determined to produce class B carbapenemase, was resistant to most antibiotics tested except amikacin. The genome of K433 consisted of a chromosome cK433 (6,482-kb length) and two plasmids: pK433-qnrS (7.212-kb length) and pK433-NDM (200.855-kb length), the last being the first investigated blaNDM-carrying plasmid from Aeromonas spp. By comparison of the backbone and MDR regions from the plasmids studied, they involved a highly homologous sequence structure. This study provides in-depth genetic insights into the plasmids integrated with blaNDM-carrying genetic elements from Aeromonas spp.
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Affiliation(s)
- Xinhua Luo
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated With Taizhou University, Taizhou, China
| | - Kai Mu
- Beijing Institute of Radiation Medicine, Beijing, China
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, China
| | - Yujie Zhao
- Department of Clinical Laboratory Medicine, Ningbo Medical Center Li Huili Hospital, Ningbo, China
| | - Jin Zhang
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated With Taizhou University, Taizhou, China
| | - Ying Qu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated With Taizhou University, Taizhou, China
| | - Dakang Hu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated With Taizhou University, Taizhou, China
| | - Yifan Jia
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated With Taizhou University, Taizhou, China
| | - Piaopiao Dai
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated With Taizhou University, Taizhou, China
| | - Jian Weng
- Taizhou Center for Disease Control and Prevention, Taizhou, China
| | - Dongguo Wang
- Department of Central Laboratory, Taizhou Municipal Hospital Affiliated With Taizhou University, Taizhou, China
- Dongguo Wang,
| | - Lianhua Yu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated With Taizhou University, Taizhou, China
- *Correspondence: Lianhua Yu,
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15
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Li X, Wang W, Jin X, Zhang X, Zou X, Ma Q, Hu Q, Huang H, Tu Y. Emergence of Plasmids Co-Harboring Carbapenem Resistance Genes and tmexCD2-toprJ2 in Sequence Type 11 Carbapenem Resistant Klebsiella pneumoniae Strains. Front Cell Infect Microbiol 2022; 12:902774. [PMID: 35646740 PMCID: PMC9134201 DOI: 10.3389/fcimb.2022.902774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectivesTo characterize two plasmids co-harboring carbapenem resistance genes and tmexCD2-toprJ2 in carbapenem-resistant Klebsiella pneumoniae (CRKP) strains.MethodsTwo clinical CRKP strains were isolated and characterized by antimicrobial susceptibility testing, conjugation assays, whole-genome sequencing, and bioinformatics analysis.ResultsThe two CRKP strains NB4 and NB5 were both resistant to imipenem, meropenem and tigecycline. Whole-genome sequencing revealed that two CRKP strains belonged to the ST11 type and carried multiple resistance genes. The tmexCD2-toprJ2 clusters in both strains were located on the IncFIB(Mar)-like/HI1B-like group of hybrid plasmids, which co-harbored the metallo-β-lactamase gene blaNDM-1. In addition, the co-existence of blaNDM-1 and blaKPC-2 and the presence of tmexCD2-toprJ2 in CRKP strain NB5 was observed.ConclusionsIn this study, tmexCD2-toprJ2 gene clusters were identified in two NDM-1-producing CRKP ST11 strains. These gene clusters will likely spread into clinical high-risk CRKP clones and exacerbate the antimicrobial resistance crisis. In addition, we detected the co-occurrence of blaNDM-1, blaKPC-2 and tmexCD2-toprJ2 in a single strain, which will undoubtedly accelerate the formation of a “superdrug resistant” bacteria. Hence, effective control measures should be implemented to prevent the further dissemination of such organisms in clinical settings.
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Affiliation(s)
- Xi Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Weizhong Wang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Xi Jin
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Xiaofan Zhang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Xuehan Zou
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Qiang Ma
- Department of Respiratory Medicine, Yuhang Second People’s Hospital, Hangzhou, China
| | - Qingfeng Hu
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Qingfeng Hu, ; Haijun Huang, ; Yuexing Tu,
| | - Haijun Huang
- Department of Infectious Diseases, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou, China
- *Correspondence: Qingfeng Hu, ; Haijun Huang, ; Yuexing Tu,
| | - Yuexing Tu
- Department of Critical Care Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, China
- *Correspondence: Qingfeng Hu, ; Haijun Huang, ; Yuexing Tu,
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Genomic Characterization of a Proteus sp. Strain of Animal Origin Co-Carrying blaNDM-1 and lnu(G). Antibiotics (Basel) 2021; 10:antibiotics10111411. [PMID: 34827349 PMCID: PMC8615141 DOI: 10.3390/antibiotics10111411] [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: 10/14/2021] [Revised: 11/10/2021] [Accepted: 11/14/2021] [Indexed: 11/16/2022] Open
Abstract
The emergence of carbapenem-resistant Proteus represents a serious threat to global public health due to limited antibiotic treatment options. Here, we characterize a Proteus isolate NMG38-2 of swine origin that exhibits extensive drug resistance, including carbapenems. Whole-genome sequencing based on Illumina and MinION platforms showed that NMG38-2 contains 24 acquired antibiotic resistance genes and three plasmids, among which, pNDM_NMG38-2, a pPvSC3-like plasmid, is transferable and co-carries blaNDM-1 and lnu(G). Sequence analysis of pPvSC3-like plasmids showed that they share a conserved backbone but have a diverse accessory module with complex chimera structures bearing abundant resistance genes, which are facilitated by transposons and/or homologous recombination. The acquisition of blaNDM-1 in pNDM_NMG38-2 was due to the ISCR1-mediated integration event. Comprehensive analysis of the lnu(G)-bearing cassettes carried by bacterial plasmids or chromosomes revealed a diversification of its genetic contexts, with Tn6260 and ISPst2 elements being the leading contributors to the dissemination of lnu(G) in Enterococcus and Enterobacteriaceae, respectively. In conclusion, this study provides a better understanding of the genetic features of pPvSC3-like plasmids, which represent a novel plasmid group as a vehicle mediating the dissemination of blaNDM-1 among bacteria species. Moreover, our results highlight the central roles of Tn6260 and ISPst2 in the spread of lnu(G).
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Plasmids Shape the Current Prevalence of tmexCD1-toprJ1 among Klebsiella pneumoniae in Food Production Chains. mSystems 2021; 6:e0070221. [PMID: 34609171 PMCID: PMC8547460 DOI: 10.1128/msystems.00702-21] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The emergence of novel antimicrobial resistance genes conferring resistance to last-resort antimicrobials poses a serious challenge to global public health security. Recently, one plasmid-mediated RND family multidrug resistance efflux pump gene cluster named tmexCD1-toprJ1, which confers resistance to tigecycline, was identified in bacteria of animal and human origins. However, the comprehensive landscape of the genomic epidemiology of this novel resistance determinant remained unclear. To fill this knowledge gap, we isolated 25 tmexCD1-toprJ1-positive bacteria from 682 samples collected along the pork production chain, including swine farms, slaughterhouses, and retail pork, and characterized the positive strains systematically using antimicrobial susceptibility testing, conjugation assays, single-molecule sequencing, and genomic analyses. We found that tmexCD1-toprJ1-positive bacteria were most prevalent in slaughterhouses (7.32%), followed by retail pork (0.72%). Most of the positive strains were Klebsiella pneumoniae (23/25), followed by Proteus mirabilis (2/25). IncFIB(Mar)/IncHI1B hybrid plasmids were mainly vectors for tmexCD1-toprJ1 and dominated the horizontal dissemination of tmexCD1-toprJ1 among K. pneumoniae isolates. However, in this study, we identified the IncR plasmid as a tmexCD1-toprJ1-positive plasmid with a broad host range, which evidenced that the widespread prevalence of tmexCD1-toprJ1 is possible due to such kinds of plasmids in the future. In addition, we found diversity and heterogeneity of translocatable units containing tmexCD1-toprJ1 in the plasmids. We also investigated the genetic features of tmexCD1-toprJ1 in online databases, which led to the proposal of the umuC gene as the potential insertion site of tmexCD1-toprJ1. Collectively, this study enriches the epidemiological and genomic characterization of tmexCD1-toprJ1 and provides a theoretical basis for preventing an increase in tmexCD1-toprJ1 prevalence. IMPORTANCE Tigecycline, the first member of the glycylcycline class of antibacterial agents, is frequently used to treat complicated infections caused by multidrug-resistant Gram-positive and Gram-negative bacteria. The emergence of a novel plasmid-mediated efflux pump, TmexCD1-ToprJ1, conferring resistance to multiple antimicrobials, including tigecycline, poses a huge risk to human health. In this study, we investigated the prevalence of tmexCD1-toprJ1-positive strains along the food production chain and found that tmexCD1-toprJ1 was mainly distributed in IncFIB(Mar)/HI1B hybrid plasmids of K. pneumoniae. We also observed a potential risk of transmission of such plasmids along the pork processing chain, which finally may incur a threat to humans. Furthermore, the IncFIB(Mar)/HI1B tmexCD1-toprJ1-positive plasmids with a limited host range and specific insertion sites of tmexCD1-toprJ1 are strong evidence to prevent a fulminant epidemic of tmexCD1-toprJ1 among diverse pathogens. The mobilization and dissemination of tmexCD1-toprJ1, especially when driven by plasmids, deserve sustained attention and investigations.
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McDonald JP, Quiros DR, Vaisman A, Mendez AR, Reyelt J, Schmidt M, Gonzalez M, Woodgate R. CroS R391 , an ortholog of the λ Cro repressor, plays a major role in suppressing polV R391 -dependent mutagenesis. Mol Microbiol 2021; 116:877-889. [PMID: 34184328 PMCID: PMC8460599 DOI: 10.1111/mmi.14777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 12/26/2022]
Abstract
When subcloned into low-copy-number expression vectors, rumAB, encoding polVR391 (RumA'2 B), is best characterized as a potent mutator giving rise to high levels of spontaneous mutagenesis in vivo. This is in dramatic contrast to the poorly mutable phenotype when polVR391 is expressed from the native 88.5 kb R391, suggesting that R391 expresses cis-acting factors that suppress the expression and/or the activity of polVR391 . Indeed, we recently discovered that SetRR391 , an ortholog of λ cI repressor, is a transcriptional repressor of rumAB. Here, we report that CroSR391 , an ortholog of λ Cro, also serves as a potent transcriptional repressor of rumAB. Levels of RumA are dependent upon an interplay between SetRR391 and CroSR391 , with the greatest reduction of RumA protein levels observed in the absence of SetRR391 and the presence of CroSR391 . Under these conditions, CroSR391 completely abolishes the high levels of mutagenesis promoted by polVR391 expressed from low-copy-number plasmids. Furthermore, deletion of croSR391 on the native R391 results in a dramatic increase in mutagenesis, indicating that CroSR391 plays a major role in suppressing polVR391 mutagenesis in vivo. Inactivating mutations in CroSR391 therefore have the distinct possibility of increasing cellular mutagenesis that could lead to the evolution of antibiotic resistance of pathogenic bacteria harboring R391.
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Affiliation(s)
- John P. McDonald
- Laboratory of Genomic IntegrityNational Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
| | - Dominic R. Quiros
- Laboratory of Genomic IntegrityNational Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
| | - Alexandra Vaisman
- Laboratory of Genomic IntegrityNational Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
| | | | - Jan Reyelt
- Gen‐H Genetic Engineering Heidelberg GmbHHeidelbergGermany
- Present address:
AGC Biologics GmbHHeidelbergGermany
| | - Marlen Schmidt
- Gen‐H Genetic Engineering Heidelberg GmbHHeidelbergGermany
| | | | - Roger Woodgate
- Laboratory of Genomic IntegrityNational Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
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A Novel SXT/R391 Integrative and Conjugative Element Carries Two Copies of the blaNDM-1 Gene in Proteus mirabilis. mSphere 2021; 6:e0058821. [PMID: 34378988 PMCID: PMC8386438 DOI: 10.1128/msphere.00588-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The rapid spread of the blaNDM-1 gene is a major public health concern. Here, we describe the multidrug-resistant Proteus mirabilis strain XH1653, which contains a novel SXT/R391 integrative and conjugative element (ICE), harboring two tandem copies of blaNDM-1 and 21 other resistance genes. XH1653 was resistant to all antibiotics tested, apart from aztreonam. Whole-genome data revealed that two copies of blaNDM-1 embedded in the ISCR1 element are located in HS4 of the novel ICE, which we named ICEPmiChnXH1653. A circular intermediate of ICEPmiChnXH1653 was detected by PCR, and conjugation experiments showed that the ICE can be transferred to the Escherichia coli strain EC600 with frequencies of 1.5 × 10-7. In the recipient strain, the ICE exhibited a higher excision frequency and extrachromosomal copy number than the ICE in the donor strain. We also observed that the presence of ICEPmiChnXH1653 has a negative impact on bacterial fitness and leads to changes in the transcriptome of the host. In vitro evolution experiments under nonselective conditions showed that the two tandem copies of the ISCR1 element and the ISVsa3 element can be lost during repeated laboratory passage. This is the first report of a novel SXT/R391 ICE carrying two tandem copies of blaNDM-1, which also illustrates the role that ICEs may play as platforms for the accumulation and transmission of antibiotic resistance genes. IMPORTANCE The occurrence of carbapenemase-producing Proteus mirabilis, especially those strains producing NDM-1 and its variants, is a major public health concern worldwide. The integrative conjugative element (ICE) plays an important role in horizontal acquisition of resistance genes. In this study, we characterized a novel SXT/R391 ICE from a clinical P. mirabilis isolate that we named ICEPmiChnXH1653, which contains two tandem copies of the carbapenemase gene blaNDM-1. We performed an integrative approach to gain insights into different aspects of ICEPmiChnXH1653 evolution and biology and observed that ICEPmiChnXH1653 obtained the carbapenemase gene blaNDM-1 by ISCR1-mediated homologous recombination. Our study reveals that the transmission of blaNDM-1 by ISCR1 elements or ICEs may be an important contributor to the carbapenem resistance development across species, which could improve our understanding of horizontal gene transfer in clinical environments.
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Zheng XR, Sun YH, Zhu JH, Wu SL, Ping C, Fang LX, Jiang HX. Two novel bla NDM-1-harbouring transposons on pPrY2001-like plasmids coexisting with a novel cfr-encoding plasmid in food animal source Enterobacteriaceae. J Glob Antimicrob Resist 2021; 26:222-226. [PMID: 34245899 DOI: 10.1016/j.jgar.2021.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/27/2021] [Accepted: 06/13/2021] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES This study reports identification of the carbapenemase-encoding gene from carbapenem-resistant Enterobacterales from food animals. METHODS A total of 40 bacterial isolates recovered from 475 faecal swabs obtained on one farm were tested for the presence of the blaNDM-1 gene by PCR. Species identification of three blaNDM-1-positive strains was conducted by MALDI-TOF/MS. Antimicrobial susceptibility testing was performed by broth microdilution. Transferability of the blaNDM-1 and cfr genes was determined by filter mating. The genetic environment of blaNDM-1 and cfr was analysed by whole-genome sequencing. RESULTS Two Proteus mirabilis (JPM24 and YPM35) and one Providencia rettgeri (YPR25) carried blaNDM-1. The blaNDM-1 genes were located on conjugable pPrY2001-like plasmids often reported to carry important antimicrobial resistance genes (ARGs). YPR25 and YPM35 shared two almost identical conjugable plasmids, one carrying blaNDM-1 and the other cfr. The blaNDM-1 gene in YPR25 (same as YPM35) and JPM24 was located in two novel transposons, designated Tn6922 and Tn6923, respectively. Tn6922 and Tn6923 carried 14 and 7 ARGs, respectively, and both contained multiple copies of IS26 in the same direction, with a high degree of similarity. Additionally, cfr was located on a plasmid with an unreported high frequency of conjugative transfer in YPR25 (same as YPM35). CONCLUSION We identified two novel blaNDM-1-containing transposons (Tn6922 and Tn6923) present on pPrY2001-like plasmids. The pPrY2001-like blaNDM-1 plasmids coexisted with a novel cfr plasmid, and both could transfer at high frequency, highlighting the importance of continuous surveillance of multiresistant Enterobacterales of animal origin that can serve as a reservoir for ARGs.
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Affiliation(s)
- Xing-Run Zheng
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Yin-Huan Sun
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Jia-Hang Zhu
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Si-Li Wu
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Cai Ping
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Liang-Xing Fang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Hong-Xia Jiang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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Moser AI, Viaggi V, Mauri C, Carattoli A, Luzzaro F, Endimiani A. An XDR Proteus vulgaris isolate hosting a novel blaNDM-1- and armA-carrying plasmid. J Antimicrob Chemother 2021; 76:1938-1941. [PMID: 33891008 DOI: 10.1093/jac/dkab111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aline I Moser
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Valentina Viaggi
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Carola Mauri
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | | | - Francesco Luzzaro
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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Characterization of TMexCD3-TOprJ3, an RND-Type Efflux System Conferring Resistance to Tigecycline in Proteus mirabilis, and Its Associated Integrative Conjugative Element. Antimicrob Agents Chemother 2021; 65:e0271220. [PMID: 33875423 DOI: 10.1128/aac.02712-20] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The emergence and transmission of novel antimicrobial resistance genes pose a great threat to public health globally. Recently, the plasmid-encoding RND efflux pump TMexCD1-TOprJ1 in Klebsiella pneumoniae was reported to reduce the sensitivity of multiple antimicrobials. Here, we identified a pandrug-resistant Proteus mirabilis isolate that harbored the novel tmexCD3-toprJ3 gene cluster located on SXT/R391 ICE. This study expands current knowledge of the transfer mechanisms of tmexCD1-toprJ1-like gene clusters among P. mirabilis isolates and warrants further genomic epidemiology investigations.
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Luo X, Yin Z, Zeng L, Hu L, Jiang X, Jing Y, Chen F, Wang D, Song Y, Yang H, Zhou D. Chromosomal Integration of Huge and Complex bla NDM-Carrying Genetic Elements in Enterobacteriaceae. Front Cell Infect Microbiol 2021; 11:690799. [PMID: 34211858 PMCID: PMC8239412 DOI: 10.3389/fcimb.2021.690799] [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: 04/04/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
In this study, a detailed genetic dissection of the huge and complex blaNDM-carrying genetic elements and their related mobile genetic elements was performed in Enterobacteriaceae. An extensive comparison was applied to 12 chromosomal genetic elements, including six sequenced in this study and the other six from GenBank. These 12 genetic elements were divided into five groups: a novel IME Tn6588; two related IMEs Tn6523 (SGI1) and Tn6589; four related ICEs Tn6512 (R391), Tn6575 (ICEPvuChnBC22), Tn6576, and Tn6577; Tn7 and its derivatives Tn6726 and 40.7-kb Tn7-related element; and two related IMEs Tn6591 (GIsul2) and Tn6590. At least 51 resistance genes, involved in resistance to 18 different categories of antibiotics and heavy metals, were found in these 12 genetic elements. Notably, Tn6576 carried another ICE Tn6582. In particular, the six blaNDM-carrying genetic elements Tn6588, Tn6589, Tn6575, Tn6576, Tn6726, and 40.7-kb Tn7-related element contained large accessory multidrug resistance (MDR) regions, each of which had a very complex mosaic structure that comprised intact or residual mobile genetic elements including insertion sequences, unit or composite transposons, integrons, and putative resistance units. Core blaNDM genetic environments manifested as four different Tn125 derivatives and, notably, two or more copies of relevant Tn125 derivatives were found in each of Tn6576, Tn6588, Tn6589, and 40.7-kb Tn7-related element. The huge and complex blaNDM-carrying genetic elements were assembled from complex transposition and homolog recombination. Firstly identified were eight novel mobile elements, including three ICEs Tn6576, Tn6577, and Tn6582, two IMEs, Tn6588 and Tn6589, two composite transposons Tn6580a and Tn6580b, and one integron In1718.
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Affiliation(s)
- Xinhua Luo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lijun Zeng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,The Fifth Medical Center, Chinese Peoples Liberation Army General Hospital, Beijing, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaoyuan Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ying Jing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fangzhou Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dongguo Wang
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated With Taizhou University, Taizhou, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria. Clin Microbiol Rev 2021; 34:e0018820. [PMID: 34076490 DOI: 10.1128/cmr.00188-20] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Seven mobile oxazolidinone resistance genes, including cfr, cfr(B), cfr(C), cfr(D), cfr(E), optrA, and poxtA, have been identified to date. The cfr genes code for 23S rRNA methylases, which confer a multiresistance phenotype that includes resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A compounds. The optrA and poxtA genes code for ABC-F proteins that protect the bacterial ribosomes from the inhibitory effects of oxazolidinones. The optrA gene confers resistance to oxazolidinones and phenicols, while the poxtA gene confers elevated MICs or resistance to oxazolidinones, phenicols, and tetracycline. These oxazolidinone resistance genes are most frequently found on plasmids, but they are also located on transposons, integrative and conjugative elements (ICEs), genomic islands, and prophages. In these mobile genetic elements (MGEs), insertion sequences (IS) most often flanked the cfr, optrA, and poxtA genes and were able to generate translocatable units (TUs) that comprise the oxazolidinone resistance genes and occasionally also other genes. MGEs and TUs play an important role in the dissemination of oxazolidinone resistance genes across strain, species, and genus boundaries. Most frequently, these MGEs also harbor genes that mediate resistance not only to antimicrobial agents of other classes, but also to metals and biocides. Direct selection pressure by the use of antimicrobial agents to which the oxazolidinone resistance genes confer resistance, but also indirect selection pressure by the use of antimicrobial agents, metals, or biocides (the respective resistance genes against which are colocated on cfr-, optrA-, or poxtA-carrying MGEs) may play a role in the coselection and persistence of oxazolidinone resistance genes.
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Song Z, Zuo L, Li C, Tian Y, Wang H. Copper Ions Facilitate the Conjugative Transfer of SXT/R391 Integrative and Conjugative Element Across Bacterial Genera. Front Microbiol 2021; 11:616792. [PMID: 33603719 PMCID: PMC7884315 DOI: 10.3389/fmicb.2020.616792] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/22/2020] [Indexed: 12/16/2022] Open
Abstract
Copper can persist stably in the environment for prolonged periods. Except for inducing antibiotic resistance in bacteria, copper ions (Cu2+) can facilitate the horizontal transfer of plasmid DNA. However, whether and how Cu2+ can accelerate the conjugative transfer of SXT/R391 integrative and conjugative element (ICE) is still largely unknown. In this study, Proteus mirabilis ChSC1905, harboring an SXT/R391 ICE that carried 21 antibiotic resistance genes (ARGs), was used as a donor, and Escherichia coli EC600 was used as a recipient. Cu2+, at subinhibitory and environmentally relevant concentrations (1–10 μmol/L), significantly accelerated the conjugative transfer of SXT/R391 ICE across bacterial genera (from P. mirabilis to E. coli) (p < 0.05). The combined analyses of phenotypic tests and genome-wide sequencing indicated that reactive oxygen species (ROS) production and cell membrane permeability were critical in the enhanced conjugative transfer of SXT/R391 ICE. Furthermore, the expression of genes related to cell adhesion and ATP synthesis was also significantly upregulated on exposure to Cu2+ at a concentration of 5 μmol/L. This study clarified the potential mechanisms of Cu2+ to promote the conjugative transfer of SXT/R391 ICE, revealing the potential risk imposed by Cu2+ on the horizontal transfer of SXT/R391 ICE-mediated ARGs.
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Affiliation(s)
- Zhou Song
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lei Zuo
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Cui Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yiming Tian
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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