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Wang N, Zheng X, Leptihn S, Li Y, Cai H, Zhang P, Wu W, Yu Y, Hua X. Characteristics and phylogenetic distribution of megaplasmids and prediction of a putative chromid in Pseudomonas aeruginosa. Comput Struct Biotechnol J 2024; 23:1418-1428. [PMID: 38616963 PMCID: PMC11015739 DOI: 10.1016/j.csbj.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/16/2024] Open
Abstract
Research on megaplasmids that contribute to the spread of antimicrobial resistance (AMR) in Pseudomonas aeruginosa strains has grown in recent years due to the now widely used technologies allowing long-read sequencing. Here, we systematically analyzed distinct and consistent genetic characteristics of megaplasmids found in P. aeruginosa. Our data provide information on their phylogenetic distribution and hypotheses tracing the potential evolutionary paths of megaplasmids. Most of the megaplasmids we found belong to the IncP-2-type, with conserved and syntenic genetic backbones carrying modules of genes associated with chemotaxis apparatus, tellurite resistance and plasmid replication, segregation, and transmission. Extensively variable regions harbor abundant AMR genes, especially those encoding β-lactamases such as VIM-2, IMP-45, and KPC variants, which are high-risk elements in nosocomial infection. IncP-2 megaplasmids act as effective vehicles transmitting AMR genes to diverse regions. One evolutionary model of the origin of megaplasmids claims that chromids can develop from megaplasmids. These chromids have been characterized as an intermediate between a megaplasmid and a chromosome, also containing core genes that can be found on the chromosome but not on the megaplasmid. Using in silico prediction, we identified the "PABCH45 unnamed replicon" as a putative chromid in P. aeruginosa, which shows a much higher similarity and closer phylogenetic relationship to chromosomes than to megaplasmids while also encoding plasmid-like partition genes. We propose that such a chromid could facilitate genome expansion, allowing for more rapid adaptations to novel ecological niches or selective conditions, in comparison to megaplasmids.
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Affiliation(s)
- Nanfei Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuan Zheng
- Department of Nephrology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Sebastian Leptihn
- HMU Health and Medical University, Am Anger 64/73 – 99084, Erfurt, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF) Translational Phage-Network, Inhoffenstraße 7 – 38124, Braunschweig, Germany
- University of Southern Denmark,Department of Biochemistry and Molecular Biology, Campusvej 55 – 5230, Odense, Denmark
| | - Yue Li
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Heng Cai
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Piaopiao Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenhao Wu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Yuan M, Nie L, Huang Z, Xu S, Qiu X, Han L, Kang Y, Li F, Yao J, Li Q, Li H, Li D, Zhu X, Li Z. Capture of armA by a novel ISCR element, ISCR28. Int J Antimicrob Agents 2024; 64:107250. [PMID: 38908532 DOI: 10.1016/j.ijantimicag.2024.107250] [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: 04/11/2023] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 06/24/2024]
Abstract
ISCR28 is a fully functional and active member of the IS91-like family of insertion sequences. ISCR28 is 1,708-bp long and contains a 1,293-bp long putative open reading frame that codes a transposase. Sixty ISCR28-containing sequences from GenBank generated 27 non-repeat genetic contexts, all of which represented naturally occurring biological events that had occurred in a wide range of gram-negative organisms. Insertion of ISCR28 into target DNA preferred the presence of a 5'-GXXT-3' sequence at its terIS (replication terminator) end. Loss of the first 4 bp of its oriIS (origin of replication) likely caused ISCR28 to be trapped in ISApl1-based transposons or similar structures. Loss of terIS and fusion with a mobile element upstream likely promoted co-transfer of ISCR28 and the downstream resistance genes. ArmA and its downstream intact ISCR28 can be excised from recombinant pKD46 plasmids forming circular intermediates, further elucidating its activity as a transposase.
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Affiliation(s)
- Min Yuan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lu Nie
- Department of Laboratory Medicine, The First People's Hospital of Foshan, Foshan, Guangdong, China
| | - Zhenzhou Huang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuai Xu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaotong Qiu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lichao Han
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yutong Kang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fang Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiang Yao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qixin Li
- Department of Laboratory Medicine, The First People's Hospital of Foshan, Foshan, Guangdong, China
| | - Huan Li
- Central and Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, China
| | - Dan Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiong Zhu
- Central and Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, China.
| | - Zhenjun Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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Chen Y, Xiang G, Liu P, Zhou X, Guo P, Wu Z, Yang J, Chen P, Huang J, Liao K. Prevalence and molecular characteristics of ceftazidime-avibactam resistance among carbapenem-resistant Pseudomonas aeruginosa clinical isolates. J Glob Antimicrob Resist 2024; 36:276-283. [PMID: 38295902 DOI: 10.1016/j.jgar.2024.01.014] [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: 08/21/2023] [Revised: 12/06/2023] [Accepted: 01/09/2024] [Indexed: 02/20/2024] Open
Abstract
OBJECTIVES Resistance against ceftazidime-avibactam (CZA) in carbapenem-resistant Pseudomonas aeruginosa (CRPA) is emerging. This study was aimed at detecting the prevalence and molecular characteristics of CZA-resistant CRPA clinical isolates in Guangdong Province, China. METHODS The antimicrobial susceptibility profile of these strains was determined. A subset of 16 CZA-resistant CRPA isolates was analysed by whole-genome sequencing (WGS). Genetic surroundings of carbapenem resistance genes and pan-genome-wide association analysis were further studied. RESULTS Of the 250 CRPA isolates, CZA resistance rate was 6.4% (16/250). The minimum inhibitory concentration (MIC) of CZA range was from 0.25 to >256 mg/L. MIC50 and MIC90 were 2/4 and 8/4 mg/L, respectively. Among the 16 CZA-resistant CRPA strains, 31.3% (5/16) of them carried class B carbapenem resistance genes, including blaIMP-4, blaIMP-45, and blaVIM-2, located on IncP-2 megaplasmids or chromosomes, respectively. Pan-genome-wide association analysis of accessory genes for CZA-susceptible or -resistant CRPA isolates showed that PA1874, a hypothetical protein containing BapA prefix-like domain, was enriched in CZA-resistant group significantly. CONCLUSIONS Class B carbapenem resistance genes play important roles in CZA resistance. Meanwhile, the PA1874 gene may be a novel mechanism involving in CZA resistance. It is necessary to continually monitor CZA-resistant CRPA isolates.
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Affiliation(s)
- Yili Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Guoxiu Xiang
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pingjuan Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xianling Zhou
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Penghao Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhongwen Wu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Juhua Yang
- Vision Medicals Co., Ltd, Guangzhou, China
| | - Peisong Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Junqi Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Organ Transplant Centre, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China; Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China.
| | - Kang Liao
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
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Eladawy M, Thomas JC, Hoyles L. Phenotypic and genomic characterization of Pseudomonas aeruginosa isolates recovered from catheter-associated urinary tract infections in an Egyptian hospital. Microb Genom 2023; 9:001125. [PMID: 37902186 PMCID: PMC10634444 DOI: 10.1099/mgen.0.001125] [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: 07/20/2023] [Accepted: 10/12/2023] [Indexed: 10/31/2023] Open
Abstract
Catheter-associated urinary tract infections (CAUTIs) represent one of the major healthcare-associated infections, and Pseudomonas aeruginosa is a common Gram-negative bacterium associated with catheter infections in Egyptian clinical settings. The present study describes the phenotypic and genotypic characteristics of 31 P. aeruginosa isolates recovered from CAUTIs in an Egyptian hospital over a 3 month period. Genomes of isolates were of good quality and were confirmed to be P. aeruginosa by comparison to the type strain (average nucleotide identity, phylogenetic analysis). Clonal diversity among the isolates was determined; eight different sequence types were found (STs 244, 357, 381, 621, 773, 1430, 1667 and 3765), of which ST357 and ST773 are considered to be high-risk clones. Antimicrobial resistance (AMR) testing according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines showed that the isolates were highly resistant to quinolones [ciprofloxacin (12/31, 38.7 %) and levofloxacin (9/31, 29 %) followed by tobramycin (10/31, 32.5 %)] and cephalosporins (7/31, 22.5 %). Genotypic analysis of resistance determinants predicted all isolates to encode a range of AMR genes, including those conferring resistance to aminoglycosides, β-lactamases, fluoroquinolones, fosfomycin, sulfonamides, tetracyclines and chloramphenicol. One isolate was found to carry a 422 938 bp pBT2436-like megaplasmid encoding OXA-520, the first report from Egypt of this emerging family of clinically important mobile genetic elements. All isolates were able to form biofilms and were predicted to encode virulence genes associated with adherence, antimicrobial activity, anti-phagocytosis, phospholipase enzymes, iron uptake, proteases, secretion systems and toxins. The present study shows how phenotypic analysis alongside genomic analysis may help us understand the AMR and virulence profiles of P. aeruginosa contributing to CAUTIs in Egypt.
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Affiliation(s)
- Mohamed Eladawy
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Jonathan C. Thomas
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Lesley Hoyles
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
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Wang N, Lei T, Zhu Y, Li Y, Cai H, Zhang P, Leptihn S, Zhou J, Ke H, Gao B, Feng Y, Hua X, Qu T. Characterization of two novel VIM-type metallo-β-lactamases, VIM-84 and VIM-85, associated with the spread of IncP-2 megaplasmids in Pseudomonas aeruginosa. Microbiol Spectr 2023; 11:e0154423. [PMID: 37707305 PMCID: PMC10580930 DOI: 10.1128/spectrum.01544-23] [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: 04/17/2023] [Accepted: 07/17/2023] [Indexed: 09/15/2023] Open
Abstract
This study aimed to characterize two novel VIM-type metallo-β-lactamases, VIM-84 and VIM-85, and reveal the important role of the IncP-2 type megaplasmids in the spread of antimicrobial resistance (AMR) genes. VIM-84 and VIM-85 were encoded by two novel genes bla VIM-84 and bla VIM-85 which showed similarity to bla VIM-24. Both bla VIM-84 and bla VIM-85 are harbored into class 1 integrons embedded into the Tn1403 transposon. The bla VIM-85 gene was identified in a megaplasmid, which was related to 17 megaplasmid sequences with sizes larger than 430 kb, deposited previously in Genbank. A comparative analysis of complete plasmid sequences showed highly similar backbone regions and various AMR genes. A phylogenetic tree revealed that these megaplasmids, which were widely distributed globally, were vehicles for the spread of AMR genes. The bla VIM-24, bla VIM-84, and bla VIM-85 genes were cloned into pGK1900, and the recombinant vectors were further transformed into Escherichia coli DH5α and Pseudomonas aeruginosa PAO1. The antimicrobial susceptibility test of the cloning strains showed high levels of resistance to β-lactams while they remained susceptible to aztreonam. Enzymatic tests revealed that both, VIM-84 and VIM-85, exhibited higher activity in hydrolyzing β-lactams compared to VIM-24. A D117N mutation found in VIM-24 affected binding to the antibiotics. IMPORTANCE The metallo-β-lactamases-producing Pseudomonas aeruginosa strains play an important role in hospital outbreaks and the VIM-type enzyme is the most prevalent in European countries. Two novel VIM-type enzymes in our study, VIM-84 and VIM-85, have higher levels of resistance to β-lactams and greater hydrolytic activities for most β-lactams compared with VIM-24. Both bla VIM-84 and bla VIM-85 are harbored into class 1 integrons embedded into the Tn1403 transposon. Notably, the genes bla VIM-85 are carried by three different IncP-2-type megaplasmids which are distributed locally and appear responsible for the spread of antimicrobial resistance genes in hospital settings.
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Affiliation(s)
- Nanfei Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tailong Lei
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiwei Zhu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yue Li
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Heng Cai
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Piaopiao Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Sebastian Leptihn
- Department of Biochemistry, Health and Medical University, Erfurt, Germany
- Department of Antimicrobial Biotechnology, Fraunhofer Institute for Cell Therapy & Immunology, Leipzig, Germany
| | - Junxin Zhou
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huanhuan Ke
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bo Gao
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Feng
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang, China
| | - Tingting Qu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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Chauviat A, Meyer T, Favre-Bonté S. Versatility of Stenotrophomonas maltophilia: Ecological roles of RND efflux pumps. Heliyon 2023; 9:e14639. [PMID: 37089375 PMCID: PMC10113797 DOI: 10.1016/j.heliyon.2023.e14639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
S. maltophilia is a widely distributed bacterium found in natural, anthropized and clinical environments. The genome of this opportunistic pathogen of environmental origin includes a large number of genes encoding RND efflux pumps independently of the clinical or environmental origin of the strains. These pumps have been historically associated with the uptake of antibiotics and clinically relevant molecules because they confer resistance to many antibiotics. However, considering the environmental origin of S. maltophilia, the ecological role of these pumps needs to be clarified. RND efflux systems are highly conserved within bacteria and encountered both in pathogenic and non-pathogenic species. Moreover, their evolutionary origin, conservation and multiple copies in bacterial genomes suggest a primordial role in cellular functions and environmental adaptation. This review is aimed at elucidating the ecological role of S. maltophilia RND efflux pumps in the environmental context and providing an exhaustive description of the environmental niches of S. maltophilia. By looking at the substrates and functions of the pumps, we propose different involvements and roles according to the adaptation of the bacterium to various niches. We highlight that i°) regulatory mechanisms and inducer molecules help to understand the conditions leading to their expression, and ii°) association and functional redundancy of RND pumps and other efflux systems demonstrate their complex role within S. maltophilia cells. These observations emphasize that RND efflux pumps play a role in the versatility of S. maltophilia.
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Characterization of a Conjugative Multidrug Resistance IncP-2 Megaplasmid, pPAG5, from a Clinical Pseudomonas aeruginosa Isolate. Microbiol Spectr 2022; 10:e0199221. [PMID: 35171033 PMCID: PMC8849076 DOI: 10.1128/spectrum.01992-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The spread of resistance genes via horizontal plasmid transfer plays a significant role in the formation of multidrug-resistant (MDR) Pseudomonas aeruginosa strains. Here, we identified a megaplasmid (ca. 513 kb), designated pPAG5, which was recovered from a clinical multidrug-resistant P. aeruginosa PAG5 strain. The pPAG5 plasmid belonged to the IncP-2 incompatibility group. Two large multidrug resistance regions (MDR-1 and MDR-2) and two heavy metal resistance operons (merEDACPTR and terZABCDE) were identified in the pPAG5 plasmid. Genetic analysis demonstrated that the formation of MDR regions was mediated by several homologous recombination events. Further conjugation assays identified that pPAG5 could be transferred to P. aeruginosa but not Escherichia coli. Antimicrobial susceptibility testing on transconjugants demonstrated that pPAG5 was capable of transferring resistance genes to transconjugants and producing a multidrug-resistant phenotype. Comparative analysis revealed that pPAG5 and related plasmids shared an overall similar backbone, including genes essential for replication (repA), partition (par), and conjugal transfer (tra). Further phylogenetic analysis showed that pPAG5 was closely related to plasmids pOZ176 and pJB37, both of which are members of the IncP-2-type plasmid group. IMPORTANCE The emergence and spread of plasmid-associated multidrug resistance in bacterial pathogens is a key global threat to public health. It is important to understand the mechanisms of the formation and evolution of these plasmids in patients, hospitals, and the environment. In this study, we detailed the genetic characteristics of a multidrug resistance IncP-2 megaplasmid, pPAG5, and investigated the formation of its MDR regions and evolution. To the best of our knowledge, plasmid pPAG5 is the largest multidrug resistance plasmid ever sequenced in the Pseudomonas genus. Our results may provide further insight into the formation of multidrug resistance plasmids in bacteria and the molecular evolution of plasmids.
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Shi Y, Zhang Y, Wu X, Zhang H, Yang M, Tian Z. Potential dissemination mechanism of the tetC gene in Aeromonas media from the aerobic biofilm reactor under oxytetracycline stresses. J Environ Sci (China) 2021; 105:90-99. [PMID: 34130843 DOI: 10.1016/j.jes.2020.12.038] [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: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 06/12/2023]
Abstract
The tetC gene has been found to be one of the most widely distributed tetracycline resistance (tet) genes in various environmental niches, but the detailed dissemination mechanisms are still largely unknown. In the present study, 11 tetC-containing Aeromonas media strains were isolated from an aerobic biofilm reactor under oxytetracycline stresses, and the genome of one strain was sequenced using the PacBio RSII sequencing approach to reveal the genetic environment of tetC. The tetC gene was carried by an IS26 composite transposon, named Tn6434. The tetC-carrying Tn6434 structure was detected in all of the A. media strains either in a novel plasmid pAeme2 (n=9) or other DNA molecules (n=2) by PCR screening. The NCBI database searching result shows that this structure was also present in the plasmids or chromosomes of other 13 genera, indicating the transferability of Tn6434. Inverse PCR and sequencing confirmed that Tn6434 can form a circular intermediate and is able to incorporate into a preexisting IS26 element, suggesting that Tn6434 might be responsible for the dissemination of tetC between different DNA molecules. This study will be helpful in uncovering the spread mechanism of tet genes in water environments.
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Affiliation(s)
- Yanhong Shi
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Xiangyang Wu
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Hong Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhe Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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Jiang X, Yin Z, Yuan M, Cheng Q, Hu L, Xu Y, Yang W, Yang H, Zhao Y, Zhao X, Gao B, Dai E, Song Y, Zhou D. Plasmids of novel incompatibility group IncpRBL16 from Pseudomonas species. J Antimicrob Chemother 2021; 75:2093-2100. [PMID: 32395746 DOI: 10.1093/jac/dkaa143] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/18/2020] [Accepted: 03/22/2020] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES To dissect genomic features of IncpRBL16 plasmids from Pseudomonas. METHODS An extensive genomic comparison was applied to all 17 available sequenced IncpRBL16 plasmids, including 8 sequenced in this study and another 2 sequenced in two of our previous studies. RESULTS Conserved IncpRBL16 backbone markers repAIncpRBL16 together with its iterons, parB2-parA, che, pil and ter were present in all 17 plasmids. At least 18 regions or sites across IncpRBL16 genomes exhibited major modular differences, including insertion of accessory modules, deletion of backbone regions surrounding insertion sites and substitution of multiple-gene backbone regions. Ten plasmids carried a sole IncpRBL16 replicon, while exogenous acquisition of an auxiliary replicon (located in an accessory module) besides the primary IncpRBL16 replicon was observed in each of the remaining seven plasmids. The 17 IncpRBL16 plasmids carried at least 71 different accessory modules, notably including Tn1403-related regions, Tn7-family transposons, Tn6571-family transposons, integrative and conjugative elements, and integrative and mobilizable elements. There were a total of 40 known resistance genes, which were involved in resistance to 15 categories of antibiotics and heavy metals, notably including blaIMP-9, blaIMP-45, blaVIM-2, blaDIM-2, blaOXA-246, blaPER-1, aphA and armA. CONCLUSIONS Different IncpRBL16 plasmids contain different profiles of accessory modules and thus diverse collections of resistance genes. To the best of our knowledge, this is the first report of fully sequenced blaOXA-246-carrying (p12939-PER) and blaPER-1-carrying (p12939-PER and pA681-IMP) IncpRBL16 plasmids and also that of 14 novel (first identified in this study) and additionally 31 newly named (first designated in this study, but with previously determined sequences) mobile elements.
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Affiliation(s)
- Xiaoyuan Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Min Yuan
- State Key Laboratory of Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Qiaoxiang Cheng
- Department of Laboratory Medicine, the Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei 050021, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yanan Xu
- Department of Laboratory Medicine, the Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei 050021, China
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yuee Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Xiaodong Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Bo Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Erhei Dai
- Department of Laboratory Medicine, the Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei 050021, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
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10
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Urbanowicz P, Bitar I, Izdebski R, Baraniak A, Literacka E, Hrabák J, Gniadkowski M. Epidemic Territorial Spread of IncP-2-Type VIM-2 Carbapenemase-Encoding Megaplasmids in Nosocomial Pseudomonas aeruginosa Populations. Antimicrob Agents Chemother 2021; 65:e02122-20. [PMID: 33526490 PMCID: PMC8097432 DOI: 10.1128/aac.02122-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/25/2021] [Indexed: 11/20/2022] Open
Abstract
In 2003 to 2004, the first five VIM-2 metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa (MPPA) isolates with an In4-like integron, In461 (aadB-blaVIM-2-aadA6), on conjugative plasmids were identified in three hospitals in Poland. In 2005 to 2015, MPPA expanded much in the country, and as many as 80 isolates in a collection of 454 MPPA (∼18%) had In461, one of the two most common MBL-encoding integrons. The organisms occurred in 49 hospitals in 33 cities of 11/16 main administrative regions. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) classified them into 55 pulsotypes and 35 sequence types (STs), respectively, revealing their remarkable genetic diversity overall, with only a few small clonal clusters. S1 nuclease/hybridization assays and mating of 63 representative isolates showed that ∼85% of these had large In461-carrying plasmids, ∼350 to 550 kb, usually self-transmitting with high efficiency (∼10-1 to 10-2 per donor cell). The plasmids from 19 isolates were sequenced and subjected to structural and single-nucleotide-polymorphism (SNP)-based phylogenetic analysis. These formed a subgroup within a family of IncP-2-type megaplasmids, observed worldwide in pseudomonads from various environments and conferring resistance/tolerance to multiple stress factors, including antibiotics. Their microdiversity in Poland arose mainly from acquisition of different accessory fragments, as well as new resistance genes and multiplication of these. Short-read sequence and/or PCR mapping confirmed the In461-carrying plasmids in the remaining isolates to be the IncP-2 types. The study demonstrated a large-scale epidemic spread of multidrug resistance plasmids in P. aeruginosa populations, creating an epidemiological threat. It contributes to the knowledge on IncP-2 types, which are interesting research objects in resistance epidemiology, environmental microbiology, and biotechnology.
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Affiliation(s)
- Paweł Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Ibrahim Bitar
- Biomedical Center, Faculty of Medicine in Plzen, Charles University, Plzen, Czech Republic
| | - Radosław Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Anna Baraniak
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Elżbieta Literacka
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - Jaroslav Hrabák
- Biomedical Center, Faculty of Medicine in Plzen, Charles University, Plzen, Czech Republic
| | - Marek Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
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11
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Zhang X, Wang L, Li D, Li P, Yuan L, Yang F, Guo Q, Wang M. An IncP-2 plasmid sublineage associated with dissemination of blaIMP-45 among carbapenem-resistant Pseudomonas aeruginosa. Emerg Microbes Infect 2021; 10:442-449. [PMID: 33620296 PMCID: PMC7971254 DOI: 10.1080/22221751.2021.1894903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
IMP-45, a variant of IMP-9, is one of the dominant metallo-β-lactamases (MBLs) in clinical carbapenem-resistant Pseudomonas aeruginosa (CRPA) isolates in China. The aim of this study was to investigate the distribution and mechanism of dissemination of blaIMP-45. MBL genes were detected by PCR in 173 non-duplicate CRPA isolates collected from Hospital HS in Shanghai and 605 P. aeruginosa isolates from a multicenter surveillance of blaIMP-45 in China. In total, 17 IMP-45-producers (14 from Hospital HS and 3 from other hospitals) were identified. Molecular typing identified an outbreak of 11 IMP-45-producing ST508 CRPA in the ICU of Hospital HS. Conjugation assays and whole genome sequencing were conducted among IMP-45-producers. Genomic comparison revealed that 16 blaIMP-45-carrying plasmids (9 from this study and 7 from GenBank) shared a similar backbone with IncP-2 blaIMP-9-carrying plasmid pOZ176 but lacked repA-oriV-parAB region. repA2 gene was presented in pOZ176, blaIMP-45-carrying plasmids (17 from this study and 7 from GenBank) and 15 megaplasmids from GenBank. Phylogenetic analysis of repA2 showed that most blaIMP-45-carrying plasmids were clustered into a sublineage separate from the one containing pOZ176. This IncP-2 plasmid sublineage contributed to the dissemination of blaIMP-45 among genetically diverse P. aeruginosa and recruited multiple resistance genes during its evolution.
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Affiliation(s)
- Xuefei Zhang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Leilei Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Dan Li
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Pei Li
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Lili Yuan
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Fan Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Infection Control Unit, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Qinglan Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
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12
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Evolution of IS26-bounded pseudo-compound transposons carrying the tet(C) tetracycline resistance determinant. Plasmid 2020; 112:102541. [DOI: 10.1016/j.plasmid.2020.102541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/13/2022]
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13
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Huyan J, Tian Z, Zhang Y, Zhang H, Shi Y, Gillings MR, Yang M. Dynamics of class 1 integrons in aerobic biofilm reactors spiked with antibiotics. ENVIRONMENT INTERNATIONAL 2020; 140:105816. [PMID: 32474215 DOI: 10.1016/j.envint.2020.105816] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/10/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Class 1 integrons are strongly associated with the dissemination of antibiotic resistance in bacteria. However, little is known about whether the presence of antibiotics affects the abundance of integrons and antibiotic resistance genes during biological wastewater treatment. To explore the roles of class 1 integrons in spreading antibiotic resistance genes in environmental compartments, the dynamics of integrons were followed in biofilm reactors treating synthetic wastewater respectively spiked with streptomycin (STM) and oxytetracycline (OTC). The relative abundance of the integron-integrase gene (intI1) increased 12 or 29-fold respectively when treated with STM or OTC, under incrementally increasing dosage regimes from 0 to 50 mg L-1. Significant increases in intI1 abundance initially occurred at an antibiotic dose of 0.1 mg L-1. At the beginning of the experiment, 51% to 64% of integrons carried no gene cassettes. In STM and OTC spiked systems, there was a significant increase in the proportion of integrons that contained resistance gene cassettes, particularly at intermediate and higher antibiotic concentrations. Gene cassettes encoding resistance to aminoglycosides, trimethoprim, beta-lactam, erythromycin, and quaternary ammonium compounds were all detected in the treated systems. Three tetracycline resistance genes (tetA, tetC, tetG) were significantly correlated with the abundance of intI1 (p < 0.01), despite no tet resistance being present as a gene cassette. Genome sequencing of isolates showed synteny between the tet resistance genes and intI1, mediated through linkage to transposable elements including Tn3, IS26 and ISCR3. Class 1 integrons appeared to be under positive selection in the presence of antibiotics, and might have actively acquired new gene cassettes during the experiment.
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Affiliation(s)
- Jiaoqi Huyan
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of the Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing 100049, China
| | - Zhe Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of the Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of the Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing 100049, China.
| | - Hong Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yanhong Shi
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of the Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing 100049, China.
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14
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Cazares A, Moore MP, Hall JPJ, Wright LL, Grimes M, Emond-Rhéault JG, Pongchaikul P, Santanirand P, Levesque RC, Fothergill JL, Winstanley C. A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas. Nat Commun 2020; 11:1370. [PMID: 32170080 PMCID: PMC7070040 DOI: 10.1038/s41467-020-15081-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 02/13/2020] [Indexed: 11/10/2022] Open
Abstract
Multidrug resistance (MDR) represents a global threat to health. Here, we used whole genome sequencing to characterise Pseudomonas aeruginosa MDR clinical isolates from a hospital in Thailand. Using long-read sequence data we obtained complete sequences of two closely related megaplasmids (>420 kb) carrying large arrays of antibiotic resistance genes located in discrete, complex and dynamic resistance regions, and revealing evidence of extensive duplication and recombination events. A comprehensive pangenomic and phylogenomic analysis indicates that: 1) these large plasmids comprise an emerging family present in different members of the Pseudomonas genus, and associated with multiple sources (geographical, clinical or environmental); 2) the megaplasmids encode diverse niche-adaptive accessory traits, including multidrug resistance; 3) the accessory genome of the megaplasmid family is highly flexible and diverse. The history of the megaplasmid family, inferred from our analysis of the available database, suggests that members carrying multiple resistance genes date back to at least the 1970s.
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Affiliation(s)
- Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Matthew P Moore
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - James P J Hall
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK
| | - Laura L Wright
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Macauley Grimes
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | | | | | | | - Roger C Levesque
- Institute for Integrative and Systems Biology (IBIS), University Laval, Quebec City, QC, Canada
| | - Joanne L Fothergill
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
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15
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Emergence of a Plasmid-Encoded Resistance-Nodulation-Division Efflux Pump Conferring Resistance to Multiple Drugs, Including Tigecycline, in Klebsiella pneumoniae. mBio 2020; 11:mBio.02930-19. [PMID: 32127452 PMCID: PMC7064769 DOI: 10.1128/mbio.02930-19] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In an era of increasing concerns about antimicrobial resistance, tigecycline is likely to have a critically important role in the treatment of carbapenem-resistant Enterobacteriaceae, the most problematic pathogens in human clinical settings—especially carbapenem-resistant K.pneumoniae. Here, we identified a new plasmid-borne RND-type tigecycline resistance determinant, TMexCD1-TOprJ1, which is widespread among K. pneumoniae isolates from food animals. tmexCD1-toprJ1 appears to have originated from the chromosome of a Pseudomonas species and may have been transferred onto plasmids by adjacent site-specific integrases. Although tmexCD1-toprJ1 still appears to be rare in human clinical isolates, considering the transferability of the tmexCD1-toprJ1 gene cluster and the broad substrate spectrum of TMexCD1-TOprJ1, further dissemination of this mobile tigecycline resistance determinant is possible. Therefore, from a “One Health” perspective, measures are urgently needed to monitor and control its further spread. The current low prevalence in human clinical isolates provides a precious time window to design and implement measures to tackle this. Transporters belonging to the chromosomally encoded resistance-nodulation-division (RND) superfamily mediate multidrug resistance in Gram-negative bacteria. However, the cotransfer of large gene clusters encoding RND-type pumps from the chromosome to a plasmid appears infrequent, and no plasmid-mediated RND efflux pump gene cluster has yet been found to confer resistance to tigecycline. Here, we identified a novel RND efflux pump gene cluster, designated tmexCD1-toprJ1, on plasmids from five pandrug-resistant Klebsiella pneumoniae isolates of animal origin. TMexCD1-TOprJ1 increased (by 4- to 32-fold) the MICs of tetracyclines (including tigecycline and eravacycline), quinolones, cephalosporins, and aminoglycosides for K.pneumoniae, Escherichia coli, and Salmonella. TMexCD1-TOprJ1 is closely related (64.5% to 77.8% amino acid identity) to the MexCD-OprJ efflux pump encoded on the chromosome of Pseudomonas aeruginosa. In an IncFIA plasmid, pHNAH8I, the tmexCD1-toprJ1 gene cluster lies adjacent to two genes encoding site-specific integrases, which may have been responsible for its acquisition. Expression of TMexCD1-TOprJ1 in E. coli resulted in increased tigecycline efflux and in K. pneumoniae negated the efficacy of tigecycline in an in vivo infection model. Expression of TMexCD1-TOprJ1 reduced the growth of E. coli and Salmonella but not K. pneumoniae. tmexCD1-toprJ1-positive Enterobacteriaceae isolates were rare in humans (0.08%) but more common in chicken fecal (14.3%) and retail meat (3.4%) samples. Plasmid-borne tmexCD1-toprJ1-like gene clusters were identified in sequences in GenBank from Enterobacteriaceae and Pseudomonas strains from multiple continents. The possibility of further global dissemination of the tmexCD1-toprJ1 gene cluster and its analogues in Enterobacteriaceae via plasmids may be an important consideration for public health planning.
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16
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Pincus NB, Bachta KER, Ozer EA, Allen JP, Pura ON, Qi C, Rhodes NJ, Marty FM, Pandit A, Mekalanos JJ, Oliver A, Hauser AR. Long-term Persistence of an Extensively Drug-Resistant Subclade of Globally Distributed Pseudomonas aeruginosa Clonal Complex 446 in an Academic Medical Center. Clin Infect Dis 2019; 71:1524-1531. [PMID: 31583403 PMCID: PMC7486844 DOI: 10.1093/cid/ciz973] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 09/30/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a major challenge in the treatment of infections caused by Pseudomonas aeruginosa. Highly drug-resistant infections are disproportionally caused by a small subset of globally distributed P. aeruginosa sequence types (STs), termed "high-risk clones." We noted that clonal complex (CC) 446 (which includes STs 298 and 446) isolates were repeatedly cultured at 1 medical center and asked whether this lineage might constitute an emerging high-risk clone. METHODS We searched P. aeruginosa genomes from collections available from several institutions and from a public database for the presence of CC446 isolates. We determined antibacterial susceptibility using microbroth dilution and examined genome sequences to characterize the population structure of CC446 and investigate the genetic basis of AMR. RESULTS CC446 was globally distributed over 5 continents. CC446 isolates demonstrated high rates of AMR, with 51.9% (28/54) being multidrug-resistant (MDR) and 53.6% of these (15/28) being extensively drug-resistant (XDR). Phylogenetic analysis revealed that most MDR/XDR isolates belonged to a subclade of ST298 (designated ST298*) of which 100% (21/21) were MDR and 61.9% (13/21) were XDR. XDR ST298* was identified repeatedly and consistently at a single academic medical center from 2001 through 2017. These isolates harbored a large plasmid that carries a novel antibiotic resistance integron. CONCLUSIONS CC446 isolates are globally distributed with multiple occurrences of high AMR. The subclade ST298* is responsible for a prolonged epidemic (≥16 years) of XDR infections at an academic medical center. These findings indicate that CC446 is an emerging high-risk clone deserving further surveillance.
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Affiliation(s)
- Nathan B Pincus
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kelly E R Bachta
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA,Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jonathan P Allen
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA,Present address: Department of Microbiology and Immunology, Loyola University, Chicago, CTRE 218, 2160 S. First Ave. Maywood, IL 60153
| | - Olivia N Pura
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Chao Qi
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Nathaniel J Rhodes
- Department of Pharmacy Practice, Chicago College of Pharmacy, Midwestern University, Downers Grove, Illinois, USA,Pharmacometrics Center of Excellence, Chicago College of Pharmacy, Midwestern University, Downers Grove, Illinois, USA,Department of Pharmacy, Northwestern Memorial Hospital, Chicago, Illinois, USA
| | - Francisco M Marty
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Alisha Pandit
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - John J Mekalanos
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitari Son Espases, Institut d’Investigació Sanitaria Illes Balears, Palma de Mallorca, Spain
| | - Alan R Hauser
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA,Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA,Correspondence: A. R. Hauser, 303 E. Chicago Ave., Ward 6–035, Chicago, IL 60611 ()
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17
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Weiser R, Green AE, Bull MJ, Cunningham-Oakes E, Jolley KA, Maiden MCJ, Hall AJ, Winstanley C, Weightman AJ, Donoghue D, Amezquita A, Connor TR, Mahenthiralingam E. Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes. Microb Genom 2019; 5:e000276. [PMID: 31170060 PMCID: PMC6700666 DOI: 10.1099/mgen.0.000276] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/24/2019] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa is a highly versatile, antibiotic-resistant Gram-negative bacterium known for causing opportunistic infections and contamination of industrial products. Despite extensive genomic analysis of clinical P. aeruginosa strains, no genomes exist for preservative-tolerant industrial strains. A unique collection of 69 industrial isolates was assembled and compared to clinical and environmental strains; 16 genetically distinct industrial strains were subjected to array tube genotyping, multilocus sequence typing and whole-genome sequencing. The industrial strains possessed high preservative tolerance and were dispersed widely across P. aeruginosa as a species, but recurrence of strains from the same lineage within specific industrial products and locations was identified. The industrial P. aeruginosa genomes (mean=7.0 Mb) were significantly larger than those of previously sequenced environmental (mean=6.5 Mb; n=19) and clinical (mean=6.6 Mb; n=66) strains. Complete sequencing of the P. aeruginosa industrial strain RW109, which encoded the largest genome (7.75 Mb), revealed a multireplicon structure including a megaplasmid (555 265 bp) and large plasmid (151 612 bp). The RW109 megaplasmid represented an emerging plasmid family conserved in seven industrial and two clinical P. aeruginosa strains, and associated with extremely stress-resilient phenotypes, including antimicrobial resistance and solvent tolerance. Here, by defining the detailed phylogenomics of P. aeruginosa industrial strains, we show that they uniquely possess multireplicon, megaplasmid-bearing genomes, and significantly greater genomic content worthy of further study.
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Affiliation(s)
- Rebecca Weiser
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Angharad E. Green
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
- University of Liverpool, Institute of Infection and Global Health, Liverpool, UK
| | - Matthew J. Bull
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Edward Cunningham-Oakes
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Keith A. Jolley
- Department of Zoology, The Tinbergen Building, University of Oxford, Oxford, UK
| | - Martin C. J. Maiden
- Department of Zoology, The Tinbergen Building, University of Oxford, Oxford, UK
| | - Amanda J. Hall
- University of Liverpool, Institute of Infection and Global Health, Liverpool, UK
| | - Craig Winstanley
- University of Liverpool, Institute of Infection and Global Health, Liverpool, UK
| | - Andrew J. Weightman
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Denise Donoghue
- Unilever Research and Development, Port Sunlight, Wirral, UK
| | - Alejandro Amezquita
- Unilever Research and Development, Safety and Environmental Assurance Centre, Colworth House, Sharnbrook, Bedford, UK
| | - Thomas R. Connor
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
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18
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Jing Y, Jiang X, Yin Z, Hu L, Zhang Y, Yang W, Yang H, Gao B, Zhao Y, Zhou D, Wang C, Luo Y. Genomic diversification of IncR plasmids from China. J Glob Antimicrob Resist 2019; 19:358-364. [PMID: 31216492 DOI: 10.1016/j.jgar.2019.06.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/02/2019] [Accepted: 06/10/2019] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES The aim of this study was to perform a detailed genomic characterisation of IncR plasmids from China. METHODS Three IncR plasmids (p13190-tetA, p02085-tetA and p30860-tetA) from clinical isolates ofKlebsiella pneumoniae, Citrobacter freundii and Enterobacter cloacae, respectively, were fully sequenced using high-throughput genome sequencing and were compared with five previously sequenced IncR plasmids (pHN84KPC, pSH-01, pK245, pKPC_P16 and pKPC-LK30) from China. RESULTS The eight IncR plasmids from China possessed conserved IncR backbones composed of repB, parAB, umuCD, retA and resD. Resistance accessory modules integrated into the IncR backbones included multidrug resistance (MDR) regions in p30860-tetA, p02085-tetA, p13190-tetA and pK245, blaKPC-2 regions in pHN84KPC, pKPC-LK30 and pKPC_P16, and the ΔTn1721-sil region in pSH-01. These resistance accessory modules were inserted at a site between retA and vagD, resulting in loss of the backbone genes vagCD in some of the plasmids. The resistance accessory modules differed dramatically from one another and carried distinct profiles of resistance markers. In particular, all of p13190-tetA, p02085-tetA, p30860-tetA, pHN84KPC, pSH-01 and pK245 carried tetracycline resistance tet gene modules, and the carbapenemase gene blaKPC-2 was identified in pHN84KPC, pKPC-LK30 and pKPC_P16. In addition, one or more regions responsible for plasmid replication and/or maintenance were found in some of the resistance accessory modules, facilitating stable replication of corresponding IncR plasmids at steady-state copy numbers. CONCLUSIONS This detailed comparative genomics analysis of IncR plasmids from China provides a deeper insight into the diversification and evolution of IncR plasmids.
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Affiliation(s)
- Ying Jing
- Medical Laboratory Center, General Hospital of People's Liberation Army, Beijing 100085, China; School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China.
| | - Xiaoyuan Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Ying Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Bo Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Yuee Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Chengbin Wang
- Medical Laboratory Center, General Hospital of People's Liberation Army, Beijing 100085, China; School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China.
| | - Yanping Luo
- Medical Laboratory Center, General Hospital of People's Liberation Army, Beijing 100085, China.
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