1
|
Shi Q, Hu H, Yu Q, Huang W, Wang Y, Quan J, Zhou J, Weng R, Zhang P, Meng Y, Liu H, Jiang Y, Yu Y, Du X. Chromosomal integration and plasmid fusion occurring in ST20 carbapenem-resistant Klebsiella pneumoniae isolates coharboring blaNDM-1 and blaIMP-4 induce resistance transmission and fitness variation. Emerg Microbes Infect 2024; 13:2339942. [PMID: 38584569 PMCID: PMC11022923 DOI: 10.1080/22221751.2024.2339942] [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: 01/14/2024] [Accepted: 04/03/2024] [Indexed: 04/09/2024]
Abstract
To investigate the epidemiology of ST20 carbapenem-resistant Klebsiella pneumoniae (CRKP) in China, and further explore the genomic characteristics of blaIMP-4 and blaNDM-1 coharboring isolates and plasmid contributions to resistance and fitness. Seven ST20 CRKP isolates were collected nationwide, and antimicrobial susceptibility testing was performed. Antimicrobial resistance genes, virulence genes, and plasmid replicons were identified via whole-genome sequencing, and clonality assessed via core-genome multilocus sequence typing. Furthermore, we found four dual-metallo-β-lactamases (MBL)-harbouring isolates, the gene location was detected by Southern blotting, and plasmid location analysis showed that blaIMP-4 was located on a separate plasmid, a self-conjugative fusion plasmid, or the bacterial chromosome. These isolates were subjected to long-read sequencing, the presence of blaIMP-4 in different locations was identified by genomic comparison, and transposon units were detected via inverse PCR. We subsequently found that blaIMP-4 on the fusion plasmid and bacterial chromosome was formed via intact plasmid recombination by the IS26 and ltrA, respectively, and the circular transposon unit was related to cointegration, however, blaIMP-4 in different locations did not affect the gene stability. The blaNDM-1-harbouring plasmid contributed to the increased resistance to β-lactams and shortened survival lag time which was revealed in plasmid cured isolates. In summary, the K. pneumoniae ST20 clone is a high-risk resistant clone. With the use of ceftazidime/avibactam, MBL-positive isolates, especially dual-MBL-harbouring isolates, should be given additional attention.
Collapse
Affiliation(s)
- Qiucheng Shi
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Huangdu Hu
- Center for General Practice Medicine, Department of Infectious Diseases, Zhejiang Provincial People’s Hospital, Hangzhou Medical College Affiliated People’s Hospital, Hangzhou, People’s Republic of China
| | - Qian Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Weiyi Huang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yinping Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Jingjing Quan
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Junxin Zhou
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Rui Weng
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Ping Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yan Meng
- Department of Clinical Laboratory, Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Haiyang Liu
- Center of Laboratory Medicine, Zhejiang Provincial People’s Hospital, Hangzhou Medical College Affiliated People’s Hospital, Hangzhou, People’s Republic of China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Xiaoxing Du
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| |
Collapse
|
2
|
Singh D, Pal S, Subramanian S, Manickam N. Comparative genomics of an extensively drug resistant strain Klebsiella pneumoniae IITR008 with international high-risk clonal lineage ST147 isolated from river water. Antonie Van Leeuwenhoek 2024; 117:57. [PMID: 38491220 DOI: 10.1007/s10482-024-01955-z] [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: 08/14/2023] [Accepted: 02/26/2024] [Indexed: 03/18/2024]
Abstract
Carbapenem resistant Klebsiella pneumoniae causing severe infection resulting in morbidity and mortality have become a global health concern. K. pneumoniae with sequence type ST147 is an international high-risk clonal lineage, genomic studies have been done on K. pneumoniae ST147 isolated from clinical origin but genomic data for environmental K. pneumoniae ST147 is very scarce. Herein, K. pneumoniae IITR008, an extensively drug resistant and potentially hypervirulent bacterium, was isolated from Triveni Sangam, the confluence of three rivers where religious congregations are organized. Phenotypic, genomic and comparative genomic analysis of strain IITR008 was performed. Antibiotic susceptibility profiling revealed resistance to 9 different classes of antibiotics including ß-lactams, ß-lactam combination agents, carbapenem, aminoglycoside, macrolide, quinolones, cephams, phenicol, and folate pathway antagonists and was found to be susceptible to only tetracycline. The strain IITR008 possesses hypervirulence genes namely, iutA and iroN in addition to numerous virulence factors coding for adherence, regulation, iron uptake, secretion system and toxin. Both the IITR008 chromosome and plasmid pIITR008_75 possess a plethora of clinically relevant antibiotic-resistant genes (ARGs) including blaCTX-M-15, blaTEM-1, and blaSHV-11, corroborating the phenotypic resistance. Comparative genomic analysis with other ST147 K. pneumoniae provided insights on the phylogenetic clustering of IITR008 with a clinical strain isolated from a patient in Czech with recent travel history in India and other clinical strains isolated from India and Pakistan. According to the 'One Health' perspective, surveillance of antibiotic resistance in the environment is crucial to impede its accelerated development in diverse ecological niches.
Collapse
Affiliation(s)
- Deeksha Singh
- Environmental Biotechnology Laboratory, Environmental Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Shilpee Pal
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Srikrishna Subramanian
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Natesan Manickam
- Environmental Biotechnology Laboratory, Environmental Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
| |
Collapse
|
3
|
Huo T, Kong Z, Dong G, Zhao S, Liu X, Jiang F. Clone dissemination of IncX3 plasmid carrying bla NDM-1 in ST76 carbapenem resistance Klebsiella pneumoniae and bactericidal efficiency of aztreonam combined with avibactam in vitro and in vivo. J Glob Antimicrob Resist 2024; 36:244-251. [PMID: 38272211 DOI: 10.1016/j.jgar.2023.12.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/11/2023] [Accepted: 12/24/2023] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVES The rapid spread of the New Delhi Metal-β-lactamase-1 (NDM-1) gene in Klebsiella pneumoniae poses a substantial challenge to pediatric therapeutic care. Here, we aimed to characterise the IncX3-type plasmid carrying the blaNDM-1 gene in ST76 carbapenem resistance K. pneumoniae (CRKP) strains and assess the in vitro and in vivo bactericidal efficacy of Aztreonam (ATM) combined with Avibactam (AVI) (ATM+AVI) against CRKP. METHODS The broth microdilution method and PCR were used to detect antimicrobial susceptibility and antibiotic resistance genes. Genetic relatedness was determined using Pulsed-Field Gel Electrophoresis (PFGE) and Multilocus Sequence Typing (MLST). The plasmid conjugation assay was used to verify the transmissibility of drug-resistant plasmids. Whole-Genome Sequencing (WGS) was employed to elucidate the genomic attributes of the genes. The Fractional Inhibitory Concentration (FIC) was calculated based on the checkerboard titration assay to determine the antimicrobial effect of ATM+AVI. The time-kill curve assay and a mouse anti-infection model were used to investigate the in vitro and in vivo bactericidal efficiency of ATM+AVI. RESULTS Seven blaNDM-1-producing strains were found to be highly resistant to carbapenems, and they all belonged to the same sequence type (ST76) and were classified into the same PFGE clusters with an 89.1% similarity. The conjugation assay showed that the blaNDM-1-carrying plasmid was successfully transferred to Escherichia coli 600, resulting in transconjugants with carbapenem antibiotic resistance. A 54-kb IncX3 plasmid (pNDM-XZA88) carried the blaNDM-1 gene located on a Tn125 transposon-like element structure, demonstrating the transferability of resistance genes. Genome comparative analysis revealed that pNDM-XZA88 was highly similar to pCQ17 × 3 and pRor-30818cz and had relatively conserved backbones and variable accessory regions compared to the other four plasmids (pC39-334 kb, pNDM-1-DY1928, pNDM-K725, and pNDM-Z244). The checkerboard titration and time-kill curve assays revealed that the ATM+AVI combination therapy exerted significant bactericidal efficacy against the blaNDM-1-producing strains in vitro. The ATM+AVI combination also significantly reduced the bacterial burden in a mouse infection model constructed using the blaNDM-1-producing K. pneumoniae. CONCLUSION This study demonstrated the clone dissemination of blaNDM-1-harboring IncX3 plasmids among the ST76 K. pneumoniae isolated from pediatric patients. Therefore, more attention should be paid to preventing this high-risk clone from harming pediatric patients. Moreover, we deduced that the ATM+AVI combination therapy is an effective strategy for treating blaNDM-1-producing K. pneumoniae.
Collapse
Affiliation(s)
- Tianqun Huo
- Department of Orthopaedics, Changzhou Hospital Affiliated to Nanjing University of Chinese Medicine, Changzhou, China
| | - Ziyan Kong
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, China
| | - Guokai Dong
- Department of Forensic Medicine, Jiangsu Medical Engineering Research Center of Gene Detection, Xuzhou Medical University, Xuzhou, China
| | - Shulong Zhao
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Xuemei Liu
- Department of Laboratory Medicine, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Fei Jiang
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.
| |
Collapse
|
4
|
Liu C, Dong N, Zhang Y, Sun Q, Huang Y, Cai C, Chen G, Zhang R. Phenotypic and genomic characteristics of clinical IMP-producing Klebsiella spp. Isolates in China. COMMUNICATIONS MEDICINE 2024; 4:25. [PMID: 38383740 PMCID: PMC10881498 DOI: 10.1038/s43856-024-00439-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND IMP-producing Klebsiella spp. (IMPKsp) strains have spread globally, including in China. Currently, the prevalence and genomic characterization of IMPKsp is largely unknown nationwide. Here we aimed to provide a general overview of the phenotypic and genomic characteristics of IMPKsp strains. METHODS 61 IMPKsp strains were obtained from 13 provinces in China during 2016-2021. All strains were tested for their susceptibility to antimicrobial agents by the microdilution broth method and sequenced with Illumina next-generation sequencing. We performed conjugation experiments on thirteen representative strains which were also sequenced by Oxford nanopore sequencing technology to characterize blaIMP-encoding plasmids. RESULTS We find that all IMPKsp strains display multidrug-resistant (MDR) phenotypes. All strains belong to 27 different STs. ST307 emerges as a principal IMP-producing sublineage. blaIMP-4 is found to be the major isoform, followed by blaIMP-38. Seven incompatibility types of blaIMP-encoding plasmids are identified, including IncHI5 (32/61, 52.5%), IncN-IncR (10/61, 16.4%), IncFIB(K)-HI1B (7/61, 11.5%), IncN (5/61, 8.2%), IncN-IncFII (2/61, 3.3%), IncFII (1/61, 1.6%) and IncP (1/61, 1.6%). The strains carrying IncHI5 and IncN plasmids belong to diverse ST types, indicating that these two plasmids may play an important role in the transmission of blaIMP genes among Klebsiella spp. strains. CONCLUSIONS Our results highlight that multi-clonal transmission, multiple genetic environments and plasmid types play a major role in the dissemination process of blaIMP genes among Klebsiella spp. IncHI5 type plasmids have the potential to be the main vectors mediating the spread of the blaIMP genes in Klebsiella spp.
Collapse
Affiliation(s)
- Congcong Liu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Ning Dong
- Department of Medical Microbiology, School of Biology and Basic Medical Science, Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Yanyan Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Qiaoling Sun
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Yonglu Huang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Chang Cai
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Gongxiang Chen
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.
| |
Collapse
|
5
|
Chen SJ, Zhang WQ, Lin YL, Zeng YB, Chen ST, Wu S, Xun Z, Yang B. High Prevalence of Carbapenem-Resistant Enterobacterales Colonization Among Intensive Care Unit Patients in a Tertiary Hospital, China. Microb Drug Resist 2023; 29:568-575. [PMID: 37733305 DOI: 10.1089/mdr.2023.0056] [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] [Indexed: 09/22/2023] Open
Abstract
Intestinal colonization with carbapenem-resistant Enterobacterales (CRE) has been shown as a significant risk factor for subsequent CRE infections, especially in intensive care units (ICUs). The aim of this study was to determine the prevalence of intestinal CRE colonization among ICU patients in a Chinese tertiary hospital. Fecal sample screenings for CRE were performed on ICU patients weekly. Antibiotic-susceptibility profile of CRE strains was determined using the Vitek-2 analysis system and broth microdilution method. The carbapenemases of all isolates were determined by phenotypes and genotypes. Clonal relatedness was analyzed by pulsed-field gel electrophoresis (PFGE). Whole-genome sequencing was used to identify the multilocus sequence type (ST), plasmid replicons, and insertion sequences (ISs) of isolates. The overall colonization rate of CRE was 40.4% (82/203). A total of 84 CRE strains were detected, mostly with Klebsiella pneumoniae (92.9%). Antibiotic susceptibility testing profile revealed that 84 CRE strains were resistant to most antibiotics except for tigecycline and colistin. The carbapenemase-encoding genes including blaKPC-2, blaNDM-1, and blaIMP-4 were detected, and blaKPC-2 was the predominant genotype (90.8%). A total of 9 STs were identified among 84 CRE strains, and ST11 was the most common type (83.3%). A variety of mobile genetic elements, including plasmids and ISs, were detected via online tool prediction. PFGE analysis of the 78 K. pneumoniae strains showed 8 different pulsotypes, and pulsotype A was highly prevalent. This study found that the prevalence of CRE colonization was alarmingly high in the ICU, and that effective infection control measures are urgently needed to prevent the dissemination of CRE.
Collapse
Affiliation(s)
- Shan-Jian Chen
- Department of Laboratory Medicine, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wei-Qing Zhang
- Department of Laboratory Medicine, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yu-Lan Lin
- Department of Laboratory Medicine, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yong-Bin Zeng
- Department of Laboratory Medicine, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Shou-Tao Chen
- Department of Laboratory Medicine, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Shu Wu
- Department of Laboratory Medicine, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zhen Xun
- Department of Laboratory Medicine, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Bin Yang
- Department of Laboratory Medicine, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| |
Collapse
|
6
|
Gao Y, Du P, Zhang P, Wang J, Liu Z, Fanning S, Wang Z, Li R, Bai L. Dynamic evolution and transmission of a bla NDM-1-bearing fusion plasmid in a clinical Escherichia coli. Microbiol Res 2023; 275:127450. [PMID: 37454426 DOI: 10.1016/j.micres.2023.127450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
Plasmids are the main driving forces for the rapid dissemination of blaNDM-1. In recent years, blaNDM-1-carrying fusion plasmids have been frequently reported. However, the evolutionary patterns of blaNDM-1-carrying fusion plasmids remain largely unknown. Herein, we reported a blaNDM-1-bearing fusion plasmid pZX35-269k possessing IncFII and IncA/C2 replicons from clinical ST349 E. coli 13ZX35. The backbone of pZX35-269k was structurally unstable, which was manifested in different types of structural dissociation during conjugation and passage, thereby forming various daughter plasmids. Moreover, the same events were observed in the clinical setting as well. We found that pZX35-269k exhibited highly identical to two plasmids (pZX30-70k and pZX30-192k) in 13ZX30, both of which were isolated from the same hospital. Sequence analysis highlighted that two plasmids in 13ZX30 evolved from pZX35-269k through homologous recombination of a 4856-bp fragment. Collectively, this study confirmed the transmission and structural evolution of a blaNDM-1-bearing fusion plasmid in both laboratory and clinical settings, and provided clear evidence of plasmid spread and evolution in clinical settings. Such versatile plasmids may represent a potential risk for the public health.
Collapse
Affiliation(s)
- Yanyun Gao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, People's Republic of China
| | - Pengcheng Du
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, People's Republic of China
| | - Pei Zhang
- National Health Commission Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Juan Wang
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, 22, Yangling 712100 Shaanxi, People's Republic of China
| | - Ziyi Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, People's Republic of China
| | - Séamus Fanning
- National Health Commission Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China; UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - 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 Province, People's Republic of 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 Province, People's Republic of China.
| | - Li Bai
- National Health Commission Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China.
| |
Collapse
|
7
|
Abou-assy RS, Aly MM, Amasha RH, Jastaniah S, Alammari F, Shamrani M. Carbapenem Resistance Mechanisms, Carbapenemase Genes Dissemination , and Laboratory Detection Methods: A Review. INTERNATIONAL JOURNAL OF PHARMACEUTICAL RESEARCH AND ALLIED SCIENCES 2023. [DOI: 10.51847/wqutf4vfuo] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
8
|
Jia P, Jia X, Zhu Y, Liu X, Yu W, Li R, Li X, Kang M, Xu Y, Yang Q. Emergence of a Novel NDM-5-Producing Sequence Type 4523 Klebsiella pneumoniae Strain Causing Bloodstream Infection in China. Microbiol Spectr 2022; 10:e0084222. [PMID: 35993711 PMCID: PMC9603328 DOI: 10.1128/spectrum.00842-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/24/2022] [Indexed: 12/30/2022] Open
Abstract
Klebsiella pneumoniae is a significant infectious pathogen that causes bloodstream infections. This study aimed to genetically characterize a novel sequence type 4523 (ST4523) multidrug-resistant (MDR) K. pneumoniae strain recovered from the blood of a 79-year-old Chinese female patient with severe pneumonia and chronic obstructive pulmonary disease who ultimately died of the infection. The susceptibility testing results showed that strain 18SHX180 is nonsusceptible to cephalosporin, carbapenems, combinations of β-lactam and β-lactamase inhibitors, levofloxacin, and colistin and is only susceptible to amikacin. The phylogenetic structure showed that strain 18SHX180 belongs to a novel sequence type, ST4523, and capsule serotype K111. ST4523 is closely related to ST11, the most dominant clone of clinical carbapenem-resistant K. pneumoniae in China. ST4523 has 2 single-base variants in mdh and phoE. 18SHX180 showed medium virulence in Galleria mellonella and a mouse intraperitoneal infection model. PacBio Sequel and Illumina sequencing were performed to analyze the genetic characterization of 18SHX180, which contains 2 plasmids (pSHX180-NDM5 and pSHX180-1). pSHX180-NDM5 exhibits 86% coverage and 100% identity with 3 blaNDM-5-carrying plasmids and contains an additional region coding for the frmRAB operon, which permits bacteria to sense and detoxify formaldehyde. pSHX180-1 is responsible for the MDR phenotype: it carries 11 categories of genes for antimicrobial resistance [aadA16, aph(3″)-Ib, aph(6)-Id, blaSHV-182, blaTEM-1A, qacE, aac(6')-Ib-cr, mph(A), floR, qnrB6, arr-3, sul, sul2], all of which are associated with transposons and integrons located in three accessory resistance regions. The novel ST4523 K. pneumoniae strain could threaten the control of antimicrobial resistance, and its discovery calls attention to the genetic evolution of bacteria. IMPORTANCE Klebsiella pneumoniae is a significant infectious pathogen causing bloodstream infections. Due to the dissemination of carbapenemase genes, the incidence of carbapenem-resistant K. pneumoniae (CRKP) has increased, with high morbidity and mortality rates in immunocompromised patients. Here, we reported a novel ST4523 blaNDM-5-bearing CRKP strain initially recovered from a 79-year-old female who died of both a lower respiratory tract infection and bloodstream infection. We also describe the genetic and phenotypic characteristics of this strain. This study provides important insights into the genetic evolution of ST11 K. pneumoniae.
Collapse
Affiliation(s)
- Peiyao Jia
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Xinmiao Jia
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Ying Zhu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Xiaoyu Liu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Wei Yu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Rui Li
- Department of Laboratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Xue Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Department of Clinical Laboratory, Beijing Anzhen Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Mei Kang
- Laboratory of Clinical Microbiology, Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Yingchun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Qiwen Yang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| |
Collapse
|
9
|
Sydow K, Eger E, Schwabe M, Heiden SE, Bohnert JA, Franzenburg S, Jurischka C, Schierack P, Schaufler K. Geno- and Phenotypic Characteristics of a Klebsiella pneumoniae ST20 Isolate with Unusual Colony Morphology. Microorganisms 2022; 10:microorganisms10102063. [PMID: 36296341 PMCID: PMC9606995 DOI: 10.3390/microorganisms10102063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/10/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
Klebsiella pneumoniae is a common member of the intestinal flora of vertebrates. In addition to opportunistic representatives, hypervirulent (hvKp) and antibiotic-resistant K. pneumoniae (ABR-Kp) occur. While ABR-Kp isolates often cause difficult-to-treat diseases due to limited therapeutic options, hvKp is a pathotype that can infect healthy individuals often leading to recurrent infection. Here, we investigated the clinical K. pneumoniae isolate PBIO3459 obtained from a blood sample, which showed an unusual colony morphology. By combining whole-genome and RNA sequencing with multiple in vitro and in vivo virulence-associated assays, we aimed to define the respective Klebsiella subtype and explore the unusual phenotypic appearance. We demonstrate that PBIO3459 belongs to sequence type (ST)20 and carries no acquired resistance genes, consistent with phenotypic susceptibility tests. In addition, the isolate showed low-level virulence, both at genetic and phenotypic levels. We thus suggest that PBIO3459 is an opportunistic (commensal) K. pneumoniae isolate. Genomic comparison of PBIO3459 with closely related ABR-Kp ST20 isolates revealed that they differed only in resistance genes. Finally, the unusual colony morphology was mainly associated with carbohydrate and amino acid transport and metabolism. In conclusion, our study reveals the characteristics of a Klebsiella sepsis isolate and suggests that opportunistic representatives likely acquire and accumulate antibiotic resistances that subsequently enable their emergence as ABR-Kp pathogens.
Collapse
Affiliation(s)
- Katharina Sydow
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
| | - Elias Eger
- Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Michael Schwabe
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
| | - Stefan E. Heiden
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
| | - Jürgen A. Bohnert
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Christoph Jurischka
- Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, 01968 Senftenberg, Germany
| | - Peter Schierack
- Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, 01968 Senftenberg, Germany
| | - Katharina Schaufler
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
- Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
- Correspondence: ; Tel.: +49-3834-420-4869
| |
Collapse
|