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Peng K, Liu YX, Sun X, Wang Q, Song L, Wang Z, Li R. Large-scale bacterial genomic and metagenomic analysis reveals Pseudomonas aeruginosa as potential ancestral source of tigecycline resistance gene cluster tmexCD-toprJ. Microbiol Res 2024; 285:127747. [PMID: 38739956 DOI: 10.1016/j.micres.2024.127747] [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: 01/23/2024] [Revised: 04/04/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND The global dissemination of the multidrug resistance efflux pump gene cluster tmexCD-toprJ has greatly weakened the effects of multiple antibiotics, including tigecycline. However, the potential origin and transmission mechanisms of the gene cluster remain unclear. METHODS Here, we concluded a comprehensive bioinformatics analysis on integrated 73,498 bacterial genomes, including Pseudomonas spp., Klebsiella spp., Aeromonas spp., Proteus spp., and Citrobacter spp., along with 1,152 long-read metagenomic datasets to trace the origin and propagation of tmexCD-toprJ. RESULTS Our results demonstrated that tmexCD-toprJ was predominantly found in Pseudomonas aeruginosa sourced from human hosts in Asian countries and North American countries. Phylogenetic and genomic feature analyses showed that tmexCD-toprJ was likely evolved from mexCD-oprJ of some special clones of P. aeruginosa. Furthermore, metagenomic analysis confirmed that P. aeruginosa is the only potential ancestral bacterium for tmexCD-toprJ. A putative mobile genetic structure harboring tmexCD-toprJ, int-int-hp-hp-tnfxB-tmexCD-toprJ, was the predominant genetic context of tmexCD-toprJ across various bacterial genera, suggesting that the two integrase genes play a pivotal role in the horizontal transmission of tmexCD-toprJ. CONCLUSIONS Based on these findings, it is almost certain that the tmexCD-toprJ gene cluster was derived from P. aeruginosa and further spread to other bacteria.
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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
| | - Yong-Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Xinran Sun
- 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
| | - Luyang Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, 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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Jian C, Ye C, Guo T, Hao J, Ding Y, Xiao X, Xie W, Zeng Z, Liu J. Emergence of aztreonam/avibactam and tigecycline-resistant Pseudomonas putida group Co-producing bla IMP-1, bla AFM-4 and bla OXA-1041 with a novel sequence type ST268 in Southwestern China. Microb Pathog 2024; 192:106668. [PMID: 38697232 DOI: 10.1016/j.micpath.2024.106668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/04/2024]
Abstract
OBJECTIVES The emergence of carbapenem-resistant Pseudomonas putida (CRPP) has raised public awareness. This study investigated two strains from the Pseudomonas putida group that were resistant to carbapenem, tigecycline, and aztreonam-avibactam (ATM-AVI), with a focus on their microbial and genomic characteristics. METHODS We assessed the antibiotic resistance profile using broth dilution, disk diffusion, and E-test methods. Efflux pump phenotype testing and real-time quantitative PCR were employed to evaluate efflux pump activity in tigecycline resistance, while polymerase chain reaction was utilized to detect common carbapenem genes. Additionally, whole-genome sequencing was performed to analyze genomic characteristics. The transferability of blaIMP-1 and blaAFM-4 was assessed through a conjugation experiment. Furthermore, growth kinetics and biofilm formation were examined using growth curves and crystal violet staining. RESULTS Both strains demonstrated resistance to carbapenem, tigecycline, and ATM-AVI. Notably, NMP can restore sensitivity to tigecycline. Subsequent analysis revealed that they co-produced blaIMP-1, blaAFM-4, tmexCD-toprJ, and blaOXA-1041, belonging to a novel sequence type ST268. Although they were closely related on the phylogenetic tree, they exhibited different levels of virulence. Genetic environment analysis indicated variations compared to prior studies, particularly regarding the blaIMP-1 and blaAFM-4 genes, which showed limited horizontal transferability. Moreover, it was observed that temperature exerted a specific influence on their biological factors. CONCLUSION We initially identified two P. putida ST268 strains co-producing blaIMP-1, blaAFM-4, blaOXA-1041, and tmexCD-toprJ. The resistance to tigecycline and ATM-AVI can be attributed to the presence of multiple drug resistance determinants. These findings underscore the significance of P. putida as a reservoir for novel antibiotic resistance genes. Therefore, it is imperative to develop alternative antibiotic therapies and establish effective monitoring of bacterial resistance.
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Affiliation(s)
- Chunxia Jian
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China; Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China; Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, China.
| | - Caihong Ye
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China; Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China; Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, China.
| | - Tongtong Guo
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China; Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China; Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, China.
| | - Jingchen Hao
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China; Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China; Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, China.
| | - Yinhuan Ding
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China; Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China; Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, China.
| | - Xue Xiao
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China; Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China; Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, China.
| | - Wenchao Xie
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China; Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China; Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, China.
| | - Zhangrui Zeng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China; Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China; Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, China.
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China; Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China; Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, China.
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Ma L, Qu Y, Wang W, Wang D. Characterization of Klebsiella pneumoniae carrying the blaNDM-1 gene in IncX3 plasmids and the rare In1765 in an IncFIB-IncHI1B plasmid. Front Cell Infect Microbiol 2024; 13:1324846. [PMID: 38274736 PMCID: PMC10808583 DOI: 10.3389/fcimb.2023.1324846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Background Today, the blaNDM gene is widely distributed on several plasmids from a variety of Gram-negative bacteria, primarily in transposons and gene cassettes within their multidrug-resistant (MDR) regions. This has led to the global dissemination of the blaNDM gene. Methods The determination of class A beta-lactamase, class B and D carbapenemases was performed according to the recommendations of the Clinical and Laboratory Standards Institute (CLSI). Antimicrobial susceptibility testing was performed using both the BioMerieux VITEK2 system and antibiotic paper diffusion methods. Plasmid transfer was then evaluated by conjugation experiments and plasmid electroporation assays. To comprehensively analyze the complete genome of K. pneumoniae strain F11 and to investigate the presence of mobile genetic elements associated with antibiotic resistance and virulence genes, Nanopore and Illumina sequencing platforms were used, and bioinformatics methods were applied to analyze the obtained data. Results Our findings revealed that K. pneumoniae strain F11 carried class A beta-lactamase and classes B+D carbapenemases, and exhibited resistance to commonly used antibiotics, particularly tigecycline and ceftazidime/avibactam, due to the presence of relevant resistance genes. Plasmid transfer assays demonstrated successful recovery of plasmids pA_F11 and pB_F11, with average conjugation frequencies of 2.91×10-4 and 1.56×10-4, respectively. However, plasmids pC_F11 and pD_F11 failed in both conjugation and electroporation experiments. The MDR region of plasmid pA_F11 contained rare In1765, TnAs2, and TnAs3 elements. The MDR2 region of plasmid pB_F11 functioned as a mobile genetic "island" and lacked the blaNDM-1 gene, serving as a "bridge" connecting the early composite structure of bleMBL and blaNDM-1 to the recent composite structure. Additionally, the MDR1 region of plasmid pB_F11 comprised In27, TnAs1, TnAs3, and Tn2; and plasmid pC_F11 harbored the recent composite structure of bleMBL and blaNDM-1 within Tn3000 which partially contained partial Tn125. Conclusion This study demonstrated that complex combinations of transposons and integron overlaps, along with the synergistic effects of different drug resistance and virulence genes, led to a lack of effective therapeutic agents for strain F11, therefore its dissemination and prevalence should be strictly controlled.
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Affiliation(s)
- Liman Ma
- School of Medicine, Taizhou University, Taizhou, Zhejiang, China
- Department of Central Laboratory, Taizhou Municipal Hospital affiliated with Taizhou University, Taizhou, Zhejiang, China
| | - Ying Qu
- Department of Clinical Medicine Laboratory, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang, China
| | - Wenji Wang
- Department of Central Laboratory, Taizhou Municipal Hospital affiliated with Taizhou University, Taizhou, Zhejiang, China
- School of Life Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Dongguo Wang
- School of Medicine, Taizhou University, Taizhou, Zhejiang, China
- Department of Central Laboratory, Taizhou Municipal Hospital affiliated with Taizhou University, Taizhou, Zhejiang, China
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Yao H, Zhang T, Peng K, Peng J, Liu X, Xia Z, Chi L, Zhao X, Li S, Chen S, Qin S, Li R. Conjugative plasmids facilitate the transmission of tmexCD2-toprJ2 among carbapenem-resistant Klebsiella pneumoniae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167373. [PMID: 37758131 DOI: 10.1016/j.scitotenv.2023.167373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/23/2023] [Accepted: 09/24/2023] [Indexed: 10/02/2023]
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a great threat to global public health. The emergence of tmexCD-toprJ greatly weakened the efficacy of tigecycline in the treatment of CRKP infections. In this study, we did a comprehensive investigation of the prevalence and genomic features of tmexCD-toprJ in clinical CRKP from 2018 to 2020 in Henan province, China. The results demonstrated tmexCD-toprJ was at a low prevalence in CRKP from patients (7/2031, 0.34 %). Among the seven tmexCD-toprJ positive CRKP, KP18-29 that carried tmexCD1-toprJ1, blaNDM-1 and mcr-8.2 was resistant to tigecycline, carbapenem and colistin simultaneously. While, tmexCD2-toprJ2 together with one or two carbapenemase genes were detected in the remaining strains. Four strains (KP18-231, KP18-2110-2, KP19-3023 and KP19-3088) isolated at different times but shared the same sequence type (ST) 2667 exhibited high genomic similarity, indicating the clonal dissemination of CRKP ST2667 co-producing KPC-2 and TMexCD-TOprJ. Notably, conjugative transmission of the IncFrepB(R1701) plasmid co-harboring tmexCD2-toprJ2 and blaKPC-2 among clinical CRKP isolates belonging to different STs (ST2667, ST978 and ST147) revealed further propagation of tmexCD-toprJ among K. pneumoniae. Such IncFrepB(R1701) plasmids pose a substantial threat to public health due to their mobile resistance to both tigecycline and carbapenem. Online data mining showed isolates carried both carbapenemase genes and tmexCD-toprJ were dominantly isolated from humans, and isolates of animal origins usually carried mcr genes and tmexCD-toprJ, suggesting that these critical resistance genes co-existed in diverse niches. Global surveillance of K. pneumoniae co-harboring tmexCD-toprJ and mcr/carbapenemase genes in various settings with a One Health strategy was warranted.
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Affiliation(s)
- Hong Yao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Tingting Zhang
- XNA Platform, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Kai Peng
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Junke Peng
- XNA Platform, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Xu Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ziwei Xia
- XNA Platform, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Leizi Chi
- XNA Platform, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaoyu Zhao
- XNA Platform, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Shihong Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Shangshang Qin
- XNA Platform, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China.
| | - Ruichao Li
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China.
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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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Zhu J, Lv J, Zhu Z, Wang T, Xie X, Zhang H, Chen L, Du H. Identification of TMexCD-TOprJ-producing carbapenem-resistant Gram-negative bacteria from hospital sewage. Drug Resist Updat 2023; 70:100989. [PMID: 37480594 DOI: 10.1016/j.drup.2023.100989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/14/2023] [Accepted: 07/05/2023] [Indexed: 07/24/2023]
Abstract
Carbapenems and tigecycline are crucial antimicrobials for the treatment of gram-negative bacteria infections. Recently, a novel resistance-nodulation-division (RND) efflux pump gene cluster, tmexCD-toprJ, which confers resistance to tigecycline, has been discovered in animals and clinical isolates. It was reported that hospital sewage could act as a reservoir for gram-negative bacteria with high antimicrobial resistance genes. In this study, we analyzed 84 isolates of carbapenem-resistant gram-negative bacteria (CR-GNB) from hospital sewage, and identified five isolates of TMexCD-ToprJ-producing CR-GNB, including one Raoultella ornithinolytica isolate and four Pseudomonas spp. isolates. All these five isolates carried at least one carbapenem resistance gene and were resistant to multiple antibiotics. Multiple tmexCD-toprJ clusters were detected, including tmexC2D2-toprJ2, tmexC3D3-toprJ3, tmexC3.2D3.3-toprJ1b and tmexC3.2D3-toprJ1b. Among these clusters, the genetic construct of tmexC3.2D3-toprJ1b showed 2-fold higher minimum inhibitory concentration (MIC) of tigecycline than other three variants. In addition, it was found that the tmexCD-toprJ gene cluster was originated from Pseudomonas spp. and mainly located on Tn6855 variants inserted in the same umuC-like genes on chromosomes and plasmids. This unit co-localized with blaIMP or blaVIM on IncHI5-, IncpJBCL41- and IncpSTY-type plasmids in the five isolates of TMCR-GNB. The IncHI5- and IncpSTY-type plasmids had the ability to conjugal transfer to E. coli J53 and P. aeruginosa PAO1, highlighting the potential risk of transfer of tmexCD-toprJ from Pseudomonas spp. to Enterobacterales. Importantly, genomic analysis showed that similar tmexCD-toprJ-harboring IncHI5 plasmids were also detected in human samples, suggesting transmission between environmental and human sectors. The emergence of TMCR-GNB from hospital sewage underscores the need for ongoing surveillance of antimicrobial resistance genes, particularly the novel resistance genes such as the tmexCD-toprJ gene clusters in the wastewater environment.
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Affiliation(s)
- Jie Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, PR China
| | - Jingnan Lv
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, PR China; MOE Key Laboratory of Geriatric Diseases and Immunology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Zhichen Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, PR China
| | - Tao Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, PR China
| | - Xiaofang Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, PR China
| | - Haifang Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, PR China
| | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ, USA; Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, PR China; MOE Key Laboratory of Geriatric Diseases and Immunology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215123, PR China.
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Liu C, Du P, Yang P, Zheng J, Yi J, Lu M, Shen N. Emergence and Inter- and Intrahost Evolution of Pandrug-Resistant Klebsiella pneumoniae Coharboring tmexCD1-toprJ1, blaNDM-1, and blaKPC-2. Microbiol Spectr 2023; 11:e0278622. [PMID: 36719204 PMCID: PMC10100677 DOI: 10.1128/spectrum.02786-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 01/09/2023] [Indexed: 02/01/2023] Open
Abstract
Klebsiella pneumoniae is capable of acquiring various exogenous genetic elements and subsequently conferring high antimicrobial resistance. Recently, a plasmid-mediated RND family multidrug efflux pump gene cluster, tmexCD1-toprJ1, was discovered in K. pneumoniae. In this study, we analyzed tigecycline-resistant K. pneumoniae isolates from patients from surveillance from 2017 to 2021. In addition to phenotype detection, including growth curves, plasmid transferability and stability, hypermucoviscosity, biofilm formation, and serum survival, by whole-genome sequencing, we analyzed the phylogenetic relationships of the isolates harboring tmexCD1-toprJ1 and discovered the composition of plasmids carrying tmexCD1-toprJ1. In total, we discovered that 12 tigecycline-resistant isolates from 5 patients possessed tmexCD1-toprJ1, designated sequence type 22 (ST22) and ST3691. An ST11 isolate harbored a partial tmexD1, and a complete toprJ1 (tmexC1 was lost) was tigecycline sensitive. All the ST22 tigecycline-resistant isolates coharbored tmexCD1-toprJ1, blaNDM-1, and blaKPC-2. tmexCD1-toprJ1 was encoded by a novel IncU plasmid in ST22 and an IncFIB/HI1B plasmid in ST3691, which presented differences in mobility and stability. Interestingly, isolates from the same patients presented heteroresistance to tigecycline, not only among isolates from different specimens but also those from the same sample, which might be attributed to the differential expression of tmexCD1-toprJ1 due to the dynamic genetic heterogeneity caused by relocating tmexCD1-toprJ1 close to the replication origin of plasmid. Here, we reported the emergence of K. pneumoniae isolates coharboring tmexCD1-toprJ1, blaNDM-1, and blaKPC-2. The results highlight the impact of in vivo genetic heterogeneity of tmexCD1-toprJ1-carrying elements on the in vivo variation of tigecycline resistance, which might have notable influences on antimicrobial treatment. IMPORTANCE Pandrug-resistant (PDR) Klebsiella pneumoniae poses a great challenge to public health, and tigecycline is an essential choice for antimicrobial treatment. In this study, we reported the emergence of PDR K. pneumoniae coharboring tmexCD1-toprJ1, blaNDM-1, and blaKPC-2, which belongs to ST22 and ST3691. By whole-genome analysis, we reconstructed the evolutionary map of the ST22 ancestor to become the PDR superbug by acquiring multiple genetic elements encoding tmexCD1-toprJ1 or blaNDM-1. Importantly, the genetic contexts of tmexCD1-toprJ1 among the ST22 isolates are different and present with various mobilities and stabilities. Furthermore, we also discovered the heterogeneity of tigecycline resistance during long-term infection of ST22, which might be attributed to the differential expression of tmexCD1-toprJ1 due to the dynamic genetic heterogeneity caused by relocating tmexCD1-toprJ1 close to the replication origin of plasmid. This study tracks the inter- and intrahost microevolution of the superbug PDR K. pneumoniae and highlights the importance of timely monitoring of the variation of pathogens during antimicrobial treatment.
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Affiliation(s)
- Chao Liu
- Department of Infectious Disease, Peking University Third Hospital, Beijing, China
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | | | - Ping Yang
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Jiajia Zheng
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Juan Yi
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Ming Lu
- Department of Infectious Disease, Peking University Third Hospital, Beijing, China
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Ning Shen
- Department of Infectious Disease, Peking University Third Hospital, Beijing, China
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
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Dong N, Liu C, Hu Y, Lu J, Zeng Y, Chen G, Chen S, Zhang R. Emergence of an Extensive Drug Resistant Pseudomonas aeruginosa Strain of Chicken Origin Carrying blaIMP-45, tet(X6), and tmexCD3- toprJ3 on an Inc pRBL16 Plasmid. Microbiol Spectr 2022; 10:e0228322. [PMID: 36301093 PMCID: PMC9769874 DOI: 10.1128/spectrum.02283-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/13/2022] [Indexed: 01/06/2023] Open
Abstract
This study reports an extensively drug resistant Pseudomonas aeruginosa strain PA166-2 which was of chicken origin and carrying blaIMP-45, tet(X6) and tmexCD3-toprJ3 on a single plasmid. The strain was characterized by antimicrobial susceptibility testing, resistance gene screening, conjugation assay, whole-genome sequencing, and bioinformatics analysis. Strain PA166-2 was resistant to tigecycline and carbapenems. It belonged to ST313 and carried a plasmid pPA166-2-MDR, which belongs to the incompatibility group IncpRBL16. pPA166-2-MDR harbored a 78 Kb multidrug resistance (MDR) region carrying an array of antimicrobial resistance genes, including blaIMP-45, tet(X6), and tmexCD3-toprJ3. The gene blaIMP-45 was inserted into the backbone of plasmid pPA166-2-MDR within a class 1 integron, In786. tmexCD3-toprJ3 in plasmid pPA166-2-MDR was inserted in umuC, constituting the genetic context of ISCfr1-tnfxB3-tmexC3-tmexD3-toprJ3-△umuC. The genetic context of tet(X6) in this plasmid was identical to that of other reported plasmid-borne tet(X) variants, namely, tet(X6)-abh-guaA-ISVsa3. To the best of our knowledge, this is the first report of the cooccurrence of blaIMP-45, tet(X6), and tmexCD3-toprJ3 in one plasmid in Pseudomonas sp. The emergence of plasmid-mediated tigecycline resistance genes tmexCD3-toprJ3 and tet(X6), as well as carbapenemase genes from chickens expanded the global transmission of vital resistance genes. Findings from us and from others indicate that plasmids of the incompatibility group IncpRBL16 may serve as a reservoir for carbapenem and tigecycline resistance determinants. IMPORTANCE Pseudomonas aeruginosa is an opportunistic pathogen that causes infections that are difficult to treat. This study reported, for the first time, the occurrence of last-resort antibiotic resistance determinants blaIMP-45, tet(X6), and tmexCD3-toprJ3 on a single plasmid in P. aeruginosa from chickens. The P. aeruginosa strain belonged to ST313 and was resistant to last-line antibiotics, namely, carbapenems and tigecycline. The plasmid carrying the last-line resistance genes belonged to the incompatibility group IncpRBL16, which was reported to contain different profiles of accessory modules and thus carried diverse collections of resistance genes. The emergence of plasmid-mediated tigecycline resistance genes tmexCD3-toprJ3 and tet(X6), as well as carbapenemase genes, from chickens expanded the global transmission of vital resistance genes. The results in this study highlighted that IncpRBL16 plasmids may serve as a reservoir for the dissemination of resistance genes. Control measures should be implemented to prevent the further dissemination of such strains.
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Affiliation(s)
- Ning Dong
- Department of Medical Microbiology, School of Biology and Basic Medical Science, Medical College of Soochow University, Suzhou, China
- Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Soochow University, Suzhou, China
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Congcong Liu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Yanyan Hu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Jiayue Lu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Yu Zeng
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Gongxiang Chen
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
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Anyanwu MU, Nwobi OC, Okpala COR, Ezeonu IM. Mobile Tigecycline Resistance: An Emerging Health Catastrophe Requiring Urgent One Health Global Intervention. Front Microbiol 2022; 13:808744. [PMID: 35979498 PMCID: PMC9376449 DOI: 10.3389/fmicb.2022.808744] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/24/2022] [Indexed: 01/13/2023] Open
Abstract
Mobile tigecycline resistance (MTR) threatens the clinical efficacy of the salvage antibiotic, tigecycline (TIG) used in treating deadly infections in humans caused by superbugs (multidrug-, extensively drug-, and pandrug-resistant bacteria), including carbapenem- and colistin-resistant bacteria. Currently, non-mobile tet(X) and mobile plasmid-mediated transmissible tet(X) and resistance-nodulation-division (RND) efflux pump tmexCD-toprJ genes, conferring high-level TIG (HLT) resistance have been detected in humans, animals, and environmental ecosystems. Given the increasing rate of development and spread of plasmid-mediated resistance against the two last-resort antibiotics, colistin (COL) and TIG, there is a need to alert the global community on the emergence and spread of plasmid-mediated HLT resistance and the need for nations, especially developing countries, to increase their antimicrobial stewardship. Justifiably, MTR spread projects One Health ramifications and portends a monumental threat to global public and animal health, which could lead to outrageous health and economic impact due to limited options for therapy. To delve more into this very important subject matter, this current work will discuss why MTR is an emerging health catastrophe requiring urgent One Health global intervention, which has been constructed as follows: (a) antimicrobial activity of TIG; (b) mechanism of TIG resistance; (c) distribution, reservoirs, and traits of MTR gene-harboring isolates; (d) causes of MTR development; (e) possible MTR gene transfer mode and One Health implication; and (f) MTR spread and mitigating strategies.
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Affiliation(s)
- Madubuike Umunna Anyanwu
- Microbiology Unit, Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, University of Nigeria, Nsukka, Nigeria
- *Correspondence: Madubuike Umunna Anyanwu,
| | - Obichukwu Chisom Nwobi
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Nigeria, Nsukka, Nigeria
| | - Charles Odilichukwu R. Okpala
- Department of Functional Food Products Development, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- Charles Odilichukwu R. Okpala,
| | - Ifeoma M. Ezeonu
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria
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10
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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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Dong H, Li Y, Cheng J, Xia Z, Liu W, Yan T, Chen F, Wang Z, Li R, Shi J, Qin S. Genomic Epidemiology Insights on NDM-Producing Pathogens Revealed the Pivotal Role of Plasmids on blaNDM Transmission. Microbiol Spectr 2022; 10:e0215621. [PMID: 35225688 PMCID: PMC9049954 DOI: 10.1128/spectrum.02156-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/30/2022] [Indexed: 12/14/2022] Open
Abstract
Incidences of nosocomial infections mediated by New Delhi metallo-β-lactamase (NDM) enzyme-producing Enterobacterales are increasing globally, resulting in a great burden to public health. The carbapenem-resistant Enterobacterales (CRE) were collected from Henan, China during 2013-2016. The blaNDM-positive strains were characterized using PCR, antimicrobial susceptibility testing, conjugation assay, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), Southern blot, whole-genome sequencing (WGS), and bioinformatics analysis. Eighty-one NDM-producing strains were identified among 391 nonduplicate CRE strains. Among them, four strains cocarried mcr and blaNDM genes, and two carried blaIMP-4 and blaNDM genes. The coexistence of blaNDM-5 and mcr-9 in Enterobacter hormaechei was found for the first time. In total, four blaNDM subtypes were identified. Among them, blaNDM-1 and blaNDM-5 were predominant. There was an obvious increasing trend in blaNDM-5 from 2013 to 2016. Thirteen different bacterial species were found among the 81 strains, and Escherichia coli was the dominant strain. blaNDM genes were located on nine different Inc-type plasmids, most of them on the IncX3 plasmids, except for the Pr-15-2-50 strain, which was located on the chromosome. We characterized two novel plasmids: the IncHI5-like plasmid carrying blaNDM-9 found in K. pneumonia, and the IncI1 blaNDM-5-positive plasmid. These findings provide the genomic basis for the widespread transmission of blaNDM and pave the way for the formulation of more effective monitoring and control methods. IMPORTANCE To control the emergence and transmission of CRE, it is important to perform retrospective genomic investigations. It is important to evaluate the plasmid diversity, genetic environment, and evolutionary relationships of the blaNDM-positive clinical strains in the early transmission stages. This study conducted an in-depth analysis of blaNDM-positive pathogens during a 4-year period using different methods for observing the high prevalence and active transmission of blaNDM-positive CRE. Moreover, we also explored the coexistence of the blaNDM and mcr, a clinically important mobile colistin resistance gene. This study shows that the prevalence of blaNDM-positive pathogens in Henan is high and the isolation rates increase each year. Moreover, plasmid-mediated horizontal transfer plays an important role in blaNDM dissemination. The co-occurrence of multiple resistance genes highlighted a long-lasting evolutionary pathway. Therefore, we have suggested the long-term continuous surveillance of clinical pathogens carrying blaNDM to learn the future transmission trend and curb the public health risk caused by CRE.
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Affiliation(s)
- Huiyue Dong
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Yan 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
| | - Jing Cheng
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Ziwei Xia
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Wentian Liu
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Tingting Yan
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Fangfang Chen
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, 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
- Institute of Comparative Medicine, 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
| | - Jinjin Shi
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
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12
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Wang X, Sun N, Liu X, Li F, Sun J, Huang J, Li R, Wang L. Small clone dissemination of tmexCD1-toprJ1-carrying Klebsiella pneumoniae isolates in a chicken farm. J Glob Antimicrob Resist 2022; 29:105-112. [DOI: 10.1016/j.jgar.2022.02.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 10/19/2022] Open
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13
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Sun S, Wang Q, Jin L, Guo Y, Yin Y, Wang R, Bi L, Zhang R, Han Y, Wang H. Identification of multiple transfer units and novel subtypes of tmexCD-toprJ gene clusters in clinical carbapenem-resistant Enterobacter cloacae and Klebsiella oxytoca. J Antimicrob Chemother 2021; 77:625-632. [PMID: 34893837 DOI: 10.1093/jac/dkab434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/25/2021] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Tigecycline is a last-resort antibiotic used to treat lethal infections caused by carbapenem-resistant Enterobacterales; however, plasmid-borne tigecycline resistance tmexCD-toprJ gene clusters can confer tigecycline resistance. The aim of the study was to identify novel subtypes and the spread of tmexCD-toprJ. METHODS Five non-duplicate isolates of different species, carrying tmexCD-toprJ gene clusters or novel subtypes, were isolated from patients across China between November 2018 and June 2019. WGS was performed using Illumina and Nanopore platforms. A phylogenetic tree was constructed using a dataset of 77 sequences carrying the tmexCD-toprJ gene clusters, 72 of which were downloaded from NCBI with a blastn identity cut-off of 95%. RESULTS We detected six different transfer units and two novel subtypes (tmexC1D1.2-toprJ1 and tmexC2D2.2-toprJ2) of the tmexCD-toprJ gene clusters. Among the six transfer units, three were mediated by IS26, while the rest were presumably mediated by Tn5393, hypothetical integrases (xerD-hp clusters-umuC-integrases-tnfxB2-tmexC2D2-toprJ2-umuC) and hypothetical units (hp-hp-hp-tnfxB2-tmexC2D2.2-toprJ2-ΔTn5393-Tn6292). Moreover, two tmexCD-toprJ-like gene clusters co-located on the same plasmid with blaNDM in five isolates. Phylogenetic analysis revealed that tmexCD-toprJ gene clusters may have originated in Pseudomonas spp., being mainly distributed in Pseudomonas spp. and Klebsiella spp. (64/77). Most tmexCD-toprJ gene clusters in Enterobacterales were located on plasmids, indicating that the gene clusters have a high inter-species transfer risk after transfer to Enterobacterales. CONCLUSIONS In summary, to the best of our knowledge, this is the first report of tmexCD-toprJ gene clusters being isolated from Enterobacter cloacae and Klebsiella oxytoca, revealing that these multiple transfer units should be further studied because of their clinical significance.
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Affiliation(s)
- Shijun Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Qi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Longyang Jin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yifan Guo
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Lei Bi
- Department of Clinical Laboratory, Zibo Central Hospital, Shandong, China
| | - Renfei Zhang
- Department of Clinical Laboratory, The Third Hospital of Mianyang, Sichuan Mental Health Center, Sichuan, China
| | - Yungang Han
- Department of Clinical Laboratory, Henan Provincial Chest Hospital, Henan, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
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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: 9] [Impact Index Per Article: 3.0] [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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Liu Z, Chen R, Xu P, Wang Z, Li R. Characterization of a bla NDM-1-Bearing IncHI5-Like Plasmid From Klebsiella pneumoniae of Infant Origin. Front Cell Infect Microbiol 2021; 11:738053. [PMID: 34660344 PMCID: PMC8517479 DOI: 10.3389/fcimb.2021.738053] [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] [Received: 07/08/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
The spread of plasmid-mediated carbapenem-resistant clinical isolates is a serious threat to global health. In this study, an emerging NDM-encoding IncHI5-like plasmid from Klebsiella pneumoniae of infant patient origin was characterized, and the plasmid was compared to the available IncHI5-like plasmids to better understand the genetic composition and evolution of this emerging plasmid. Clinical isolate C39 was identified as K. pneumoniae and belonged to the ST37 and KL15 serotype. Whole genome sequencing (WGS) and analysis revealed that it harbored two plasmids, one of which was a large IncHI5-like plasmid pC39-334kb encoding a wide variety of antimicrobial resistance genes clustered in a single multidrug resistance (MDR) region. The blaNDM-1 gene was located on a ΔISAba125-blaNDM-1-bleMBL-trpF-dsbC structure. Comparative genomic analysis showed that it shared a similar backbone with four IncHI5-like plasmids and the IncHI5 plasmid pNDM-1-EC12, and these six plasmids differed from typical IncHI5 plasmids. The replication genes of IncHI5-like plasmids shared 97.06% (repHI5B) and 97.99% (repFIB-like) nucleotide identity with those of IncHI5 plasmids. Given that pNDM-1-EC12 and all IncHI5-like plasmids are closely related genetically, the occurrence of IncHI5-like plasmid is likely associated with the mutation of the replication genes of pNDM-1-EC12-like IncHI5 plasmids. All available IncHI5-like plasmids harbored 262 core genes encoding replication and maintenance functions and carried distinct MDR regions. Furthermore, 80% of them (4/5) were found in K. pneumoniae from Chinese nosocomial settings. To conclude, this study expands our knowledge of the evolution history of IncHI5-like plasmids, and more attention should be paid to track the evolution pathway of them among clinical, animal, and environmental settings.
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Affiliation(s)
- Ziyi Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Ruifei Chen
- Department of Clinical Laboratory, Henan Provincial People's Hospital, Zhengzhou, China.,Department of Clinical Laboratory of Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China
| | - Poshi Xu
- Department of Clinical Laboratory, Henan Provincial People's Hospital, Zhengzhou, China.,Department of Clinical Laboratory of Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, 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, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
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Wang CZ, Gao X, Lv LC, Cai ZP, Yang J, Liu JH. Novel tigecycline resistance gene cluster tnfxB3-tmexCD3-toprJ1b in Proteus spp. and Pseudomonas aeruginosa, co-existing with tet(X6) on an SXT/R391 integrative and conjugative element. J Antimicrob Chemother 2021; 76:3159-3167. [PMID: 34508611 DOI: 10.1093/jac/dkab325] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/05/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To characterize a novel MDR efflux pump gene cluster tnfxB3-tmexCD3-toprJ1b carried by Proteus spp. and Pseudomonas aeruginosa strains from chickens. METHODS Antimicrobial susceptibility testing, conjugation and WGS were performed to characterize tnfxB3-tmexCD3-toprJ1b-positive isolates. Cloning and reverse transcription-quantitative PCR were performed to investigate the function of tnfxB3-tmexCD3-toprJ1b. RESULTS The WGS data revealed that a novel efflux pump gene cluster, tnfxB3-tmexCD3-toprJ1b, was identified on the chromosome of the Proteus cibarius strain SDQ8C180-2T, where an SXT/R391-family integrative and conjugative element (ICE) was found to co-carry tet(X6) and tnfxB3-tmexCD3-toprJ1b. Further retrospective analysis found two other tnfxB3-tmexCD3-toprJ1b variants in a Proteus mirabilis isolate and a P. aeruginosa isolate, respectively. tmexCD3-toprJ1b and its variants increased the MICs of tigecycline (8-fold) and other antibiotics (2-8-fold) in Escherichia coli host strains. The TNfxB3 protein down-regulated the expression of the tmexCD3-toprJ1b operon. Moreover, genetic-context analyses showed that tnfxB3-tmexCD3-toprJ1b together with adjacent integrase genes appeared to compose a transferable module 'int1-like+int2-like+hp1+hp2+ISCfr1+tnfxB3-tmexCD3-toprJ1b', which was inserted into the umuC-like gene of this ICE. Further analysis of the tnfxB3-tmexCD3-toprJ1b-harbouring sequences deposited in GenBank revealed similar transferable modules inserted into umuC-like genes in plasmids or chromosomes of Klebsiella pneumoniae, Pseudomonas spp. and Aeromonas spp., implying that these modules could be transferred across different bacterial species. CONCLUSIONS To the best of our knowledge, this is the first identification of a novel tigecycline gene cluster, tmexCD3-toprJ1b, which co-exists with tet(X6) within an ICE. More attention should be paid to the co-transfer of these two tigecycline resistance determinants via an ICE to other Gram-negative bacteria.
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Affiliation(s)
- Cheng-Zhen Wang
- College of Veterinary Medicine, Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xun Gao
- College of Veterinary Medicine, Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Lu-Chao Lv
- College of Veterinary Medicine, Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Zhong-Peng Cai
- College of Veterinary Medicine, Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Jun Yang
- College of Veterinary Medicine, Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Jian-Hua Liu
- College of Veterinary Medicine, Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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