1
|
Jing Y, Yu S, Li Z, Ma J, Wang L, Yu L, Song Z, Chen H, Wu Z, Luo X. Coexistence of a novel chromosomal integrative and mobilizable element Tn7548 with two bla KPC-2-carrying plasmids in a multidrug-resistant Aeromonas hydrophila strain K522 from China. J Glob Antimicrob Resist 2024; 37:157-164. [PMID: 38552873 DOI: 10.1016/j.jgar.2024.03.006] [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: 10/26/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 06/21/2024] Open
Abstract
OBJECTIVES Herein, we detected one multidrug-resistant Aeromonas hydrophila strain K522 co-carrying two blaKPC-2 genes together with a novel chromosomal integrative and mobilizable element (IME) Tn7548 from China. To reveal the genetic characteristics of the novel reservoir of blaKPC-2 and IME in Aeromonas, a detailed genomic characterization of K522 was performed, and a phylogenetic analysis of Tn7412-related IMEs was carried out. METHODS Carbapenemases were detected by using the immunocolloidal gold technique and antimicrobial susceptibility was tested by using VITEK 2. The whole-genome sequences of K522 were analysed using phylogenetics, detailed dissection, and comparison. RESULTS Strain K522 carried a Tn7412-related chromosomal IME Tn7548 and three resistance plasmids pK522-A-KPC, pK522-B-KPC, and pK522-MOX. A phylogenetic tree of 82 Tn7412-related IMEs was constructed, and five families of IMEs were divided. These IMEs shared four key backbone genes: int, repC, and hipAB, and carried various profiles of antimicrobial resistance genes (ARGs). pK522-A-KPC and pK522-B-KPC carried blaKPC-2 and belonged to IncG and unclassified type plasmid, respectively. The blaKPC-2 regions of these two plasmids were the truncated version derived from Tn6296, resulting in the carbapenem resistance of K522. CONCLUSION We first reported A. hydrophila harbouring a novel Tn7412-related IME Tn7548 together with two blaKPC-2 carrying plasmids and a MDR plasmid. Three of these four mobile genetic elements (MGEs) discovered in A. hydrophila K522 were novel. The emergence of novel MGEs carrying ARGs indicated the rapid evolution of the resistance gene vectors in A. hydrophila under selection pressure and would contribute to the further dissemination of various ARGs in Aeromonas.
Collapse
Affiliation(s)
- Ying Jing
- Department of Clinical Laboratory Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Sufei Yu
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Zhaolun Li
- Department of Clinical Laboratory Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Jie Ma
- Department of Clinical Laboratory Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Luwei Wang
- Department of Clinical Laboratory Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Lianhua Yu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Zhiwei Song
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Huimin Chen
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Zhenghai Wu
- Department of Clinical Laboratory Medicine, Traditional Chinese Medicine Hospital of Huangyan, Taizhou, China
| | - Xinhua Luo
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China.
| |
Collapse
|
2
|
Luo X, Dong F, Dai P, Xu M, Yu L, Hu D, Feng J, Zhang J, Jing Y. Coexistence of blaKPC-2 and blaNDM-1 in one IncHI5 plasmid confers transferable carbapenem resistance from a clinical isolate of Klebsiella michiganensis in China. J Glob Antimicrob Resist 2023; 35:104-109. [PMID: 37714378 DOI: 10.1016/j.jgar.2023.09.006] [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: 04/09/2023] [Revised: 08/23/2023] [Accepted: 09/03/2023] [Indexed: 09/17/2023] Open
Abstract
OBJECTIVES This study firstly identified an IncHI5 plasmid pK254-KPC_NDM co-carrying two different class carbapenemase genes blaKPC-2 and blaNDM-1 in Klebsiella michiganensis K254. METHODS The strain K254 was sequenced by high-throughput genome sequencing. A detailed genomic and phenotypic characterization of pK254-KPC_NDM was performed. RESULTS pK254-KPC_NDM displayed the conserve IncHI5 backbone and carried a resistant accessory region: Tn1696-related transposon Tn7414 containing blaKPC-2 and blaNDM-1. A sequence comparison was applied to a collection of four Tn1696-related transposons (Tn7414-Tn7417) harbouring carbapenemase genes. For all these four transposons, the blaNDM-1 was carried by Tn125 derivatives within three different mobile genetic elements. Tn7414 further acquired another carbapenemase gene, blaKPC-2, because of the integration of the local blaKPC-2 genetic environment from Tn6296, resulting in the high-level carbapenem resistance of K. michiganensis K254. The conjugal transfer and plasmid stability experiments confirmed that pK254-KPC_NDM could be transferred intercellularly and keep the stable vertical inheritance in different bacteria, which would contribute to the further dissemination of multiple carbapenemase genes and enhance the adaption and survival of K. michiganensis under complex and diverse antimicrobial selection pressures. CONCLUSION This study was the first to report the K. michiganensis isolate coharbouring blaKPC-2 and blaNDM-1 in the Tn1696-related transposon in IncHI5 plasmid. The emergence of novel transposons simultaneously carrying multiple carbapenemase genes might contribute to the further dissemination of high-level carbapenem resistance in the isolates of the hospital settings and pose new challenges for the treatment of nosocomial infection.
Collapse
Affiliation(s)
- Xinhua Luo
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, China
| | - Fang Dong
- Department of Clinical Laboratory Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Piaopiao Dai
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, China
| | - Mengqiao Xu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, China
| | - Lianhua Yu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, China
| | - Dakang Hu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, China
| | - Jiao Feng
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Jin Zhang
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, China
| | - Ying Jing
- Department of Clinical Laboratory Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China.
| |
Collapse
|
3
|
Jia J, Huang L, Zhang L, Sheng Y, Chu W, Xu H, Xu A. Genomic characterization of two carbapenem-resistant Serratia marcescens isolates causing bacteremia: Emergence of KPC-2-encoding IncR plasmids. Front Cell Infect Microbiol 2023; 13:1075255. [PMID: 36844412 PMCID: PMC9945258 DOI: 10.3389/fcimb.2023.1075255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/10/2023] [Indexed: 02/11/2023] Open
Abstract
The occurrence and transmission of carbapenemase-producing-Enterobacterales (CPE) on a global scale has become a major issue. Clinical reports are rarely providing information on the genomic and plasmid features of carbapenem-resistant Serratia marcescens. Our objective was to investigate the resistance and transmission dynamics of two carbapenem-resistant S. marcescens that are resistant to carbapenem and have caused bacteremia in China. Blood specimens were taken from two individuals with bacteremia. Multiplex PCR was employed to identify genes that code for carbapenemase. Antimicrobial susceptibility tests and plasmid analysis were conducted on S. marcescens isolates SM768 and SM4145. The genome of SM768 and SM4145 were completely sequenced using NovaSeq 6000-PE150 and PacBio RS II platforms. Antimicrobial resistance genes (ARGs) were predicted using the ResFinder tool. S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and southern blotting were employed to analyze plasmids. Two S. marcescens that produced KPC-2 were identified from bloodstream infections. The antimicrobial susceptibility testing demonstrated that both of the isolates had a resistance to various antibiotics. The whole-genome sequence (WGS) and plasmid analysis revealed the presence of bla KPC-2-bearing IncR plasmids and multiple plasmid-borne antimicrobial resistance genes in the isolates. Our comparative plasmid analysis suggested that the two IncR plasmids identified in this study could be derived from a common ancestor. Our findings revealed the emergence of bla KPC-2-bearing IncR plasmid in China, which could be a hindrance to the transmission of KPC-2-producing S. marcescens in clinical settings.
Collapse
Affiliation(s)
- Junli Jia
- Department of Respiratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lisha Huang
- Department of Respiratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Long Zhang
- Department of Respiratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanbing Sheng
- Department of Respiratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Weili Chu
- Department of Respiratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Aiguo Xu
- Department of Respiratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,*Correspondence: Aiguo Xu,
| |
Collapse
|
4
|
Li Y, Liu Q, She J, Qiu Y, Dai X, Zhang L. IS26-mediated in vivo acquisition of blaKPC-2 in an ST11-K64 Klebsiella pneumoniae isolate from a senile inpatient. J Antimicrob Chemother 2023; 78:550-553. [PMID: 36508324 DOI: 10.1093/jac/dkac420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/20/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- Ying Li
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan Province 646000, China.,Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Qian Liu
- Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Sichuan, Luzhou, China
| | - Junping She
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Yichuan Qiu
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Xiaoyi Dai
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Luhua Zhang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| |
Collapse
|
5
|
Jing Y, Yin Z, Wang P, Guan J, Chen F, Wang L, Li X, Mu X, Zhou D. A Genomic and Bioinformatics View of the Classification and Evolution of Morganella Species and Their Chromosomal Accessory Genetic Elements Harboring Antimicrobial Resistance Genes. Microbiol Spectr 2022; 10:e0265021. [PMID: 35196820 PMCID: PMC8865565 DOI: 10.1128/spectrum.02650-21] [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: 12/16/2021] [Accepted: 02/01/2022] [Indexed: 11/20/2022] Open
Abstract
In this study, draft-genome sequencing was conducted for 60 Chinese Morganella isolates, and furthermore, 12 of them were fully sequenced. Then, a total of 166 global sequenced Morganella isolates, including the above 60, were collected to perform average nucleotide identity-based genomic classification and core single nucleotide polymorphism-based phylogenomic analysis. A genome sequence-based species classification scheme for Morganella was established, and accordingly, the two conventional Morganella species were redefined as two complexes and further divided into four and two genospecies, respectively. At least 88 acquired antimicrobial resistance genes (ARGs) were disseminated in these 166 isolates and were prevalent mostly in the isolates from hospital settings. IS26/IS15DI, IS10 and IS1R, and Tn3-, Tn21-, and Tn7-subfamily unit transposons were frequently presented in these 166 isolates. Furthermore, a detailed sequence comparison was applied to 18 Morganella chromosomal accessory genetic elements (AGEs) from the fully sequenced 12 isolates, together with 5 prototype AGEs from GenBank. These 23 AGEs were divided into eight different groups belonging to composite/unit transposons, transposable prophages, integrative and mobilizable elements, and integrative and conjugative elements, and they harbored at least 52 ARGs involved in resistance to 15 categories of antimicrobials. Eleven of these 23 AGEs acquired large accessory modules, which exhibited complex mosaic structures and contained many antimicrobial resistance loci and associated ARGs. Integration of ARG-containing AGEs into Morganella chromosomes would contribute to the accumulation and dissemination of ARGs in Morganella and enhance the adaption and survival of Morganella under complex and diverse antimicrobial selection pressures. IMPORTANCE This study presents a comprehensive genomic epidemiology analysis on global sequenced Morganella isolates. First, a genome sequence-based species classification scheme for Morganella is established with a higher resolution and accuracy than those of the conventional scheme. Second, the prevalence of accessory genetic elements (AGEs) and associated antimicrobial resistance genes (ARGs) among Morganella isolates is disclosed based on genome sequences. Finally, a detailed sequence comparison of eight groups of 23 AGEs (including 19 Morganella chromosomal AGEs) reveals that Morganella chromosomes have evolved to acquire diverse AGEs harboring different profiles of ARGs and that some of these AGEs harbor large accessory modules that exhibit complex mosaic structures and contain a large number of ARGs. Data presented here provide a deeper understanding of the classification and evolution of Morganella species and also those of ARG-containing AGEs in Morganella at the genomic scale.
Collapse
Affiliation(s)
- Ying Jing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jiayao Guan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fangzhou Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lingling Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xinyue Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaofei Mu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| |
Collapse
|
6
|
Hua X, Liang Q, Deng M, He J, Wang M, Hong W, Wu J, Lu B, Leptihn S, Yu Y, Chen H. BacAnt: A Combination Annotation Server for Bacterial DNA Sequences to Identify Antibiotic Resistance Genes, Integrons, and Transposable Elements. Front Microbiol 2021; 12:649969. [PMID: 34367079 PMCID: PMC8343408 DOI: 10.3389/fmicb.2021.649969] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/31/2021] [Indexed: 11/22/2022] Open
Abstract
Whole genome sequencing (WGS) of bacteria has become a routine method in diagnostic laboratories. One of the clinically most useful advantages of WGS is the ability to predict antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in bacterial sequences. This allows comprehensive investigations of such genetic features but can also be used for epidemiological studies. A plethora of software programs have been developed for the detailed annotation of bacterial DNA sequences, such as rapid annotation using subsystem technology (RAST), Resfinder, ISfinder, INTEGRALL and The Transposon Registry. Unfortunately, to this day, a reliable annotation tool of the combination of ARGs and MGEs is not available, and the generation of genbank files requires much manual input. Here, we present a new webserver which allows the annotation of ARGs, integrons and transposable elements at the same time. The pipeline generates genbank files automatically, which are compatible with Easyfig for comparative genomic analysis. Our BacAnt code and standalone software package are available at https://github.com/xthua/bacant with an accompanying web application at http://bacant.net.
Collapse
Affiliation(s)
- Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qian Liang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China.,National Medical Products Administration Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou, China
| | - Min Deng
- Department of Infectious Diseases, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Jintao He
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Meixia Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China.,National Medical Products Administration Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou, China
| | - Wenjie Hong
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China.,National Medical Products Administration Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou, China
| | - Jun Wu
- Lin'an Center for Disease Control and Prevention, Lin'an, China
| | - Bian Lu
- Xiaoshan Center for Disease Control and Prevention, Hangzhou, China
| | - Sebastian Leptihn
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang University-University of Edinburgh Institute, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huan Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China.,National Medical Products Administration Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou, China
| |
Collapse
|
7
|
Wang X, Xiao W, Li L, Jing M, Sun M, Chang Y, Qu Y, Jiang Y, Xu Q. Analysis of the molecular characteristics of a blaKPC-2-harbouring untypeable plasmid in Serratia marcescens. Int Microbiol 2021; 25:237-244. [PMID: 34232406 DOI: 10.1007/s10123-021-00172-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Serratia marcescens has attracted increasing attention worldwide as a neglected opportunistic pathogen of public health concern, especially due to its antimicrobial resistance features, which usually cause nosocomial infections in immunocompromised or critically ill patients. METHODS In our study, four carbapenem-resistant Serratia marcescens (CRSM) clinical isolates were characterized in our hospital from February 2018 to May 2018. The conjugation experiment confirmed the transferability of the carbapenem resistance gene. The types of carbapenem resistance genes were detected by PCR. The homology of the strains was analysed by pulsed field gel electrophoresis (PFGE). The characteristics of the plasmid and environment of carbapenem resistance genes were analysed after whole genome sequencing was performed. Then, we compared the amino acid sequence of the replication initiation protein and constructed a dendrogram by the neighbour-joining method. RESULTS All four isolates showed carbapenem resistance conferred by a blaKPC-2-harbouring plasmid. They had exactly the same bands confirmed by PFGE and were defined as the homologous strains. The blaKPC-2 genes in all of the isolates were located in a 42,742 bp plasmid, which was located in the core region of antibiotic resistance and was composed of Tn3 family transposons, recombinant enzyme genes, ISKpn6 and ISKpn27. The core region of antibiotic resistance formed a 'Tn3-ISKpn6-blaKPC-ISKpn27-Tn3' structure, which was an independent region as a movable element belonging to transposon Tn6296 and its derivatives. The plasmid had a similar skeleton to incX6 plasmids and a similar amino acid sequence to the replication initiation protein. The plasmid was defined as an untypeable blaKPC-2-harbouring plasmid named the 'IncX6-like' plasmid. CONCLUSION The four CRSM isolates were mainly clonally disseminated with a blaKPC-2-harbouring plasmid in our hospital. The pKPC-2-HENAN1602 plasmid (CP047392) in our study was first reported in Serratia marcescens, which belongs to an untypeable group named the 'IncX6-like' plasmid. The carbapenem-resistant gene structure surrounding blaKPC-2 as a sole accessory module can be acquired by horizontal gene transfer and might lead to serious nosocomial infection.
Collapse
Affiliation(s)
- Xiaokun Wang
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Weiqiang Xiao
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Lu Li
- Department of Anesthesiology and Perioperative Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Min Jing
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Mingyue Sun
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Yanmin Chang
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Yuanye Qu
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Yu Jiang
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Qingxia Xu
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China. .,Department of Zhengzhou Key Laboratory of Digestive Tumor Markers, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China.
| |
Collapse
|
8
|
Czerwonka G, Gmiter D, Durlik-Popińska K. Draft Genome of Proteus mirabilis Serogroup O18 Elaborating Phosphocholine-Decorated O Antigen. Front Cell Infect Microbiol 2021; 11:620010. [PMID: 33842384 PMCID: PMC8027243 DOI: 10.3389/fcimb.2021.620010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/02/2021] [Indexed: 11/13/2022] Open
Abstract
Proteus mirabilis is a pathogenic, Gram-negative, rod-shaped bacterium that causes ascending urinary tract infections. Swarming motility, urease production, biofilm formation, and the properties of its lipopolysaccharide (LPS) are all factors that contribute to the virulence of this bacterium. Uniquely, members of the O18 serogroup elaborate LPS molecules capped with O antigen polymers built of pentasaccharide repeats; these repeats are modified with a phosphocholine (ChoP) moiety attached to the proximal sugar of each O unit. Decoration of the LPS with ChoP is an important surface modification of many pathogenic and commensal bacteria. The presence of ChoP on the bacterial envelope is correlated with pathogenicity, as decoration with ChoP plays a role in bacterial adhesion to mucosal surfaces, resistance to antimicrobial peptides and sensitivity to complement-mediated killing in several species. The genome of P. mirabilis O18 is 3.98 Mb in size, containing 3,762 protein-coding sequences and an overall GC content of 38.7%. Annotation performed using the RAST Annotation Server revealed genes associated with choline phosphorylation, uptake and transfer. Moreover, amino acid sequence alignment of the translated licC gene revealed it to be homologous to LicC from Streptococcus pneumoniae encoding CTP:phosphocholine cytidylyltransferase. Recognized homologs are located in the O antigen gene clusters of Proteus species, near the wzx gene encoding the O antigen flippase, which translocates lipid-linked O units across the inner membrane. This study reveals the genes potentially engaged in LPS decoration with ChoP in P. mirabilis O18.
Collapse
Affiliation(s)
- Grzegorz Czerwonka
- Institute of Biology, Jan Kochanowski University in Kielce, Kielce, Poland
| | - Dawid Gmiter
- Institute of Biology, Jan Kochanowski University in Kielce, Kielce, Poland
| | | |
Collapse
|
9
|
Liu X, Zou D, Wang C, Zhang X, Pei D, Liu W, Li Y. Evaluation of loop-mediated isothermal amplification assays for rapid detection of blaKPC producing Serratia spp. in clinical specimens: A prospective diagnostic accuracy study. Exp Ther Med 2021; 21:308. [PMID: 33717251 PMCID: PMC7885079 DOI: 10.3892/etm.2021.9739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/10/2020] [Indexed: 11/12/2022] Open
Abstract
The prevalence of carbapenem-resistant Serratia spp. is increasing owing to the propagation of β lactamase Klebsiella pneumoniae carbapenemase (blaKPC) and it has become one of the major global health concerns. As effective therapies for such resistant pathogens are limited, there is a great need for the rapid and sensitive characterization of the pathogen. In the present study, a loop-mediated isothermal amplification (LAMP) method for the rapid detection of Serratia spp. with blaKPC in pure cultures and clinical specimens was developed. A calcein indicator and real-time turbidity recording system were used to assess the LAMP reaction. The LAMP assay was compared with conventional PCR and real-time PCR kits for the target pathogen. The desired amplification was achieved using selected primers and detection was possible using both the calcein indicator method and the real-time turbity recording system at 65˚C for 60 min. The sensitivity of the detection system for blaKPC-producing Serratia spp. reached a detection limit of 3.92 pg/µl DNA, which was 10 times more sensitive than conventional PCR. Specificity testing indicated that the primers were highly specific. Compared with conventional culture methods and real-time PCR, the LAMP assay was more sensitive, easier for laboratory staff to master and less influenced by the clinical specimen matrix. In conclusion, a LAMP assay for blaKPC-producing Serratia spp. that permitted rapid, sensitive and economical detection for this pathogen was successfully developed. Comparisons with alternative methods indicated that the LAMP assay was more feasible in a clinical setting.
Collapse
Affiliation(s)
- Xinwei Liu
- Department of Clinical Laboratory, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, Henan 450002, P.R. China
| | - Dayang Zou
- Institute for Disease Prevention and Control, People's Liberation Army, Beijing 100071, P.R. China
| | - Chunxia Wang
- Department of Clinical Laboratory, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, Henan 450002, P.R. China
| | - Xiaoqian Zhang
- Department of Clinical Laboratory, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, Henan 450002, P.R. China
| | - Dongxu Pei
- Department of Clinical Laboratory, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, Henan 450002, P.R. China
| | - Wei Liu
- Institute for Disease Prevention and Control, People's Liberation Army, Beijing 100071, P.R. China
| | - Yongwei Li
- Department of Clinical Laboratory, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, Henan 450002, P.R. China
| |
Collapse
|
10
|
Chen Q, Lin Y, Li Z, Lu L, Li P, Wang K, Yang L, Ma H, Li P, Song H. Characterization of a New Transposon, Tn 6696, on a bla NDM- 1-Carrying Plasmid From Multidrug-Resistant Enterobacter cloacae ssp. dissolvens in China. Front Microbiol 2020; 11:525479. [PMID: 33042048 PMCID: PMC7522282 DOI: 10.3389/fmicb.2020.525479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 08/18/2020] [Indexed: 12/04/2022] Open
Abstract
Background Enterobacter cloacae is an opportunistic pathogen which is responsible for serious nosocomial infections. A gene which plays an important role in resistance to carbapenems is the New Delhi metallo-β-lactamase 1 (NDM-1). Currently, the spread of NDM-1-producing E. cloacae strains is a serious public threat. Methods A multidrug-resistant E. cloacae ssp. dissolvens strain CBG15936 was recovered in 2017 in Guangzhou, China. PCR, S1-pulsed-field gel electrophoresis, and Southern blotting were performed to locate the blaNDM–1 gene. Susceptibility testing and conjugation experiments were also performed. Illumina HiSeq and Nanopore sequencers were used to perform whole-genome sequencing. Results Strain CBG15936 belongs to ST932 and is resistant to carbapenems. The blaNDM–1 gene was found on a ∼62-kb plasmid, which has a conjugation frequency of 1.68 × 10–3 events per donor cell. Genome sequencing and analysis revealed that the NDM-1-carrying IncN1 plasmid contained a new transposon Tn6696, which consists of an intact qnrS1-carrying Tn6292 element, an inverted 8.3-kb Tn3000 remnant, ISkpn19, ΔtnpA, and IS26. Conclusion A new transposon, Tn6696, has been detected on a blaNDM–1-carrying plasmid recovered from multidrug-resistant E. cloacae ssp. dissolvens CBG15936 from China. This finding provides a new perspective regarding the potential for blaNDM–1 to undergo horizontal transfer among drug-resistant bacteria.
Collapse
Affiliation(s)
- Qichao Chen
- Center for Disease Control and Prevention of People's Liberation Army, Beijing, China
| | - Yanfeng Lin
- Center for Disease Control and Prevention of People's Liberation Army, Beijing, China.,Academy of Military Medical Sciences, Beijing, China
| | - Zhonghong Li
- Center for Disease Control and Prevention of People's Liberation Army, Beijing, China.,College of Environmental and Chemical Engineering, Nanchang Hangkong University, Nanchang, China
| | - Lanfen Lu
- Department of Laboratory Diagnosis, Sun Yat-sen University Affiliated Zhongshan Hospital, Zhongshan, China
| | - Peihan Li
- Center for Disease Control and Prevention of People's Liberation Army, Beijing, China.,Academy of Military Medical Sciences, Beijing, China
| | - Kaiying Wang
- Center for Disease Control and Prevention of People's Liberation Army, Beijing, China.,Academy of Military Medical Sciences, Beijing, China
| | - Lang Yang
- Center for Disease Control and Prevention of People's Liberation Army, Beijing, China.,Academy of Military Medical Sciences, Beijing, China
| | - Hui Ma
- The Sixth Medical Center of People's Liberation Army General Hospital, Beijing, China
| | - Peng Li
- Center for Disease Control and Prevention of People's Liberation Army, Beijing, China
| | - Hongbin Song
- Center for Disease Control and Prevention of People's Liberation Army, Beijing, China
| |
Collapse
|
11
|
Prussing C, Snavely EA, Singh N, Lapierre P, Lasek-Nesselquist E, Mitchell K, Haas W, Owsiak R, Nazarian E, Musser KA. Nanopore MinION Sequencing Reveals Possible Transfer of bla KPC-2 Plasmid Across Bacterial Species in Two Healthcare Facilities. Front Microbiol 2020; 11:2007. [PMID: 32973725 PMCID: PMC7466660 DOI: 10.3389/fmicb.2020.02007] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/29/2020] [Indexed: 11/13/2022] Open
Abstract
Carbapenemase-producing Enterobacteriaceae are a major threat to global public health. Klebsiella pneumoniae carbapenemase (KPC) is the most commonly identified carbapenemase in the United States and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different species. Here we describe the results of an epidemiological investigation of KPC-producing bacteria at two healthcare facilities. Using a combination of short-read and long-read whole-genome sequencing, we identified an identical 44 kilobase plasmid carrying the bla KPC-2 gene in four bacterial isolates belonging to three different species (Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli). The isolates in this investigation were collected from patients who were epidemiologically linked in a region in which KPC was uncommon, suggesting that the antibiotic resistance plasmid was transmitted between these bacterial species. This investigation highlights the importance of long-read sequencing in investigating the relatedness of bacterial plasmids, and in elucidating potential plasmid-mediated outbreaks caused by antibiotic resistant bacteria.
Collapse
Affiliation(s)
- Catharine Prussing
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Emily A. Snavely
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Navjot Singh
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | | | - Kara Mitchell
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Wolfgang Haas
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Rita Owsiak
- Maine Center for Disease Control and Prevention, Department of Health and Human Services, Augusta, ME, United States
| | - Elizabeth Nazarian
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Kimberlee A. Musser
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| |
Collapse
|
12
|
Liu Z, Chu W, Li X, Tang W, Ye J, Zhou Q, Guan S. Genomic Features and Virulence Characteristics of a Community-Acquired Bloodstream Infection-Causing Hypervirulent Klebsiella pneumoniae ST86 Strain Harboring KPC-2-Encoding IncX6 Plasmid. Microb Drug Resist 2020; 27:360-368. [PMID: 32716252 DOI: 10.1089/mdr.2019.0394] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The emergence and spread of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) is causing worldwide concern. Sequence type (ST) 86 K. pneumoniae, a major hvKP clone, is rarely resistant to carbapenem. In this study, we report the genomic features and virulence characteristics of a community-acquired bloodstream infection (CA-BSI)-causing CR-hvKP ST86 strain (KPN55602). This strain is resistant to carbapenem but sensitive to amikacin, gentamicin, tigecycline, and colistin. According to in vitro and in vivo virulence assessments, it was classified as hypervirulent. Whole-genome sequencing revealed that KPN55602 has a single 5.13 Mb chromosome and two plasmids. The chromosome of KPN55602 is phylogenetically similar to those of other sequenced ST86 strains. The incompatibility (Inc) group HI1B plasmid pK55602_1, harboring a set of virulence genes, was classified as a virulence plasmid. The IncX6 plasmid pK55602_2, carrying blaKPC-2, was transferable through conjugation and is highly homologous to all five sequenced blaKPC-bearing IncX6 plasmids. In conclusion, to our knowledge, this is the first report of a CA-BSI-causing CR-hvKP ST86 strain harboring an exogenous blaKPC-2-bearing IncX6 plasmid, supplementing existing knowledge on the CR-hvKP evolutionary scenario. The IncX6 plasmid may be an important vehicle for blaKPC, and its horizontal transfer may have led to CR-hvKP evolution in the community setting.
Collapse
Affiliation(s)
- Zhou Liu
- Department of Laboratory Medicine and The Second Hospital of Anhui Medical University, Hefei, China
| | - Wenwen Chu
- Department of Laboratory Medicine and The Second Hospital of Anhui Medical University, Hefei, China
| | - Xin Li
- Department of Laboratory Medicine and The Second Hospital of Anhui Medical University, Hefei, China
| | - Wei Tang
- Department of Laboratory Medicine and The Second Hospital of Anhui Medical University, Hefei, China
| | - Jun Ye
- Department of Infectious Disease, The Second Hospital of Anhui Medical University, Hefei, China
| | - Qiang Zhou
- Department of Laboratory Medicine and The Second Hospital of Anhui Medical University, Hefei, China
| | - Shihe Guan
- Department of Laboratory Medicine and The Second Hospital of Anhui Medical University, Hefei, China
| |
Collapse
|
13
|
Sun Q, Feng J, Tong Y, Liang L, Zhai F, Xiang R. Genomic characterization of Inc pA1763-KPC: IncFII K7 type plasmids p13294-KPC and pA1966-NR from Klebsiella pneumoniae. Future Microbiol 2020; 15:713-721. [PMID: 32431175 DOI: 10.2217/fmb-2020-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To characterize two plasmids p13294-KPC and pA1966-NR from clinical Klebsiella pneumoniae strains. Materials & methods: Plasmids p13294-KPC and pA1966-NR were fully sequenced and then detailed genomic analysis was performed in this work. The antimicrobial resistance phenotypes were determined. Results: p13294-KPC and pA1966-NR displayed IncpA1763-KPC:IncFIIK7 dual-replicon structures. The backbone of these two plasmids were closely related to each other. p13294-KPC contained two accessory modules, namely ΔISKpn25 and blaKPC-2 region, and the blaKPC-2 region carried a range of mobile elements and resistance gene blaKPC-2. while pA1966-NR contained four individual IS elements in its backbone and carried no resistance genes. Conclusion: This study provided a deeper insight into the genomic characterization of IncpA1763-KPC: IncFIIK7 type plasmids p13294-KPC and pA1966-NR.
Collapse
Affiliation(s)
- Qifeng Sun
- Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jiao Feng
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, China.,State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing, 100071, China
| | - Yigang Tong
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing, 100071, China
| | - Luhua Liang
- Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Fei Zhai
- Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Rongwu Xiang
- Shenyang Pharmaceutical University, Shenyang, 110016, China
| |
Collapse
|
14
|
Bandy A. Ringing bells: Morganella morganii fights for recognition. Public Health 2020; 182:45-50. [PMID: 32169625 DOI: 10.1016/j.puhe.2020.01.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 01/12/2020] [Accepted: 01/27/2020] [Indexed: 10/24/2022]
Abstract
OBJECTIVES The global increase in rare opportunistic microbial infections is alarming. The current review was undertaken to study the diversified disease spectrum, pathogenicity, and resistance patterns of Morganella morganii. STUDY DESIGN This study is a review of the diversified disease spectrum of M. morganii. METHODS The articles used in this review were all extracted from PubMed and Google Scholar, using the terms 'M. morganii', 'prevalence', 'virulence factors', 'infections', 'resistance pattern', and 'genomics'. This review includes original articles, reviews, and case reports focusing on M. morganii, hospital-based prevalence studies, and studies on resistance in M. morganii published between 1906 and April 2019. Articles published in English, French, Spanish, and Chinese were reviewed. RESULTS M. morganii has had a significant impact as a clinical pathogen and the pace of its occurrence and the increase in its resistance rates puts this bacterium on the path to becoming the next 'superbug'. These developments not only impact M. morganii, but as a result of gene and plasmid transfer evolution, other clinical pathogens have been able to acquire their diverse intrinsic and acquired virulence genes. Its vast host range raises concerns around its capacity to generate new infections through novel symbiotic relationships. CONCLUSIONS M. morganii opportunism is being increasingly reported across the globe. This bacterium is accumulating intrinsic and acquired multidrug resistance genes, resulting in increased morbidity and mortality rates for M. morganii infections and complicating its treatment. M. morganii should be recognized as a clinically significant pathogen, and clinicians should place this microorganism in the list of causative possibilities during patient care. It is important for both the infection control activities in hospitals and in public health sector.
Collapse
Affiliation(s)
- Altaf Bandy
- College of Medicine, Jouf University, PO Box: 2014, Sakaka, Al Jouf, Saudi Arabia.
| |
Collapse
|
15
|
Hala S, Antony CP, Alshehri M, Althaqafi AO, Alsaedi A, Mufti A, Kaaki M, Alhaj-Hussein BT, Zowawi HM, Al-Amri A, Pain A. First report of Klebsiella quasipneumoniae harboring bla KPC-2 in Saudi Arabia. Antimicrob Resist Infect Control 2019; 8:203. [PMID: 31890159 PMCID: PMC6923860 DOI: 10.1186/s13756-019-0653-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/14/2019] [Indexed: 12/20/2022] Open
Abstract
Background Nosocomial infections caused by multi-drug resistant Enterobacteriaceae are a global public health threat that ought to be promptly identified, reported, and addressed accurately. Many carbapenem-resistant Enterobacteriaceae-associated genes have been identified in Saudi Arabia but not the endemic Klebsiella pneumoniae carbapenemases (KPCs), which are encoded by blaKPC-type genes. KPCs are known for their exceptional spreading potential. Methods We collected n = 286 multi-drug resistant (MDR) Klebsiella spp. isolates as part of screening for resistant patterns from a tertiary hospital in Saudi Arabia between 2014 and 2018. Antimicrobial susceptibility testing was carried out using both VITEK II and the broth microdilution of all collected isolates. Detection of resistance-conferring genes was carried out using Illumina whole-genome shotgun sequencing and PacBio SMRT sequencing protocols. Results A Carbapenem-resistant Enterobacteriaceae (CRE) Klebsiella quasipneumoniae subsp. similipneumoniae strain was identified as a novel ST-3510 carrying a blaKPC-2 carbapenemase encoding gene. The isolate, designated as NGKPC-421, was obtained from shotgun Whole Genome Sequencing (WGS) surveillance of 286 MDR Klebsiella spp. clinical isolates. The NGKPC-421 isolate was collected from a septic patient in late 2017 and was initially misidentified as K. pneumoniae. The sequencing and assembly of the NGKPC-421 genome resulted in the identification of a putative ~ 39.4 kb IncX6 plasmid harboring a blaKPC-2 gene, flanked by transposable elements (ISKpn6-blaKPC-2–ISKpn27). Conclusion This is the first identification of a KPC-2-producing CRE in the Gulf region. The impact on this finding is of major concern to the public health in Saudi Arabia, considering that it is the religious epicenter with a continuous mass influx of pilgrims from across the world. Our study strongly highlights the importance of implementing rapid sequencing-based technologies in clinical microbiology for precise taxonomic classification and monitoring of antimicrobial resistance patterns.
Collapse
Affiliation(s)
- Sharif Hala
- 1Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Clinical Microbiology Department, King Abdullah International Medical Research Centre - Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia.,3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Chakkiath Paul Antony
- 1Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,7Red Sea Research Center, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mohammed Alshehri
- Clinical Microbiology Department, King Abdullah International Medical Research Centre - Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia.,3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Abdulhakeem O Althaqafi
- 3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia.,WHO Collaborating Centre for Infection Prevention and Control, and GCC Center for Infection Control, Riyadh, Saudi Arabia
| | - Asim Alsaedi
- 3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia.,WHO Collaborating Centre for Infection Prevention and Control, and GCC Center for Infection Control, Riyadh, Saudi Arabia
| | - Areej Mufti
- 3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Mai Kaaki
- 3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | | | - Hosam M Zowawi
- Clinical Microbiology Department, King Abdullah International Medical Research Centre - Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia.,3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia.,WHO Collaborating Centre for Infection Prevention and Control, and GCC Center for Infection Control, Riyadh, Saudi Arabia.,5UQ Centre for Clinical Research, Herston, Queensland, The University of Queensland, Queensland, Australia
| | - Abdulfattah Al-Amri
- 3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Arnab Pain
- 1Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,6Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Thuwal, Japan
| |
Collapse
|
16
|
Characterization of a Multidrug-Resistant Porcine Klebsiella pneumoniae Sequence Type 11 Strain Coharboring bla KPC-2 and fosA3 on Two Novel Hybrid Plasmids. mSphere 2019; 4:4/5/e00590-19. [PMID: 31511369 PMCID: PMC6739495 DOI: 10.1128/msphere.00590-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The global dissemination of carbapenem resistance genes is of great concern. Animals are usually considered a reservoir of resistance genes and an important source of human infection. Although carbapenemase-producing Enterobacteriaceae strains of animal origin have been reported increasingly, blaKPC-2-positive strains from food-producing animals are still rare. In this study, we first describe the isolation and characterization of a carbapenem-resistant Klebsiella pneumoniae ST11 isolate, strain K15, which is of pig origin and coproduces KPC-2 and FosA3 via two novel hybrid plasmids. Furthermore, our findings highlight that this ST11 Klebsiella pneumoniae strain K15 is most likely of human origin and could be easily transmitted back to humans via direct contact or food intake. In light of our findings, significant attention must be paid to monitoring the prevalence and further evolution of blaKPC-2-carrying plasmids among the Enterobacteriaceae strains of animal origin. The occurrence of carbapenemase-producing Enterobacteriaceae (CPE) poses a considerable risk for public health. The gene for Klebsiella pneumoniae carbapenemase-2 (KPC-2) has been reported in many countries worldwide, and KPC-2-producing strains are mainly of human origin. In this study, we identified two novel hybrid plasmids that carry either blaKPC-2 or the fosfomycin resistance gene fosA3 in the multiresistant K. pneumoniae isolate K15 of swine origin in China. The blaKPC-2-bearing plasmid pK15-KPC was a fusion derivative of an IncF33:A−:B− incompatibility group (Inc) plasmid and chromosomal sequences of K. pneumoniae (CSKP). A 5-bp direct target sequence duplication (GACTA) was identified at the boundaries of the CSKP, suggesting that the integration might have been due to a transposition event. The blaKPC-2 gene on pK15-KPC was in a derivative of ΔTn6296-1. The multireplicon fosA3-carrying IncN-IncR plasmid pK15-FOS also showed a mosaic structure, possibly originating from a recombination between an epidemic fosA3-carrying pHN7A8-like plasmid and a pKPC-LK30-like IncR plasmid. Stability tests demonstrated that both novel hybrid plasmids were stably maintained in the original host without antibiotic selection but were lost from the transformants after approximately 200 generations. This is apparently the first description of a porcine sequence type 11 (ST11) K. pneumoniae isolate coproducing KPC-2 and FosA3 via pK15-KPC and pK15-FOS, respectively. The multidrug resistance (MDR) phenotype of this high-risk K. pneumoniae isolate may contribute to its spread and its persistence. IMPORTANCE The global dissemination of carbapenem resistance genes is of great concern. Animals are usually considered a reservoir of resistance genes and an important source of human infection. Although carbapenemase-producing Enterobacteriaceae strains of animal origin have been reported increasingly, blaKPC-2-positive strains from food-producing animals are still rare. In this study, we first describe the isolation and characterization of a carbapenem-resistant Klebsiella pneumoniae ST11 isolate, strain K15, which is of pig origin and coproduces KPC-2 and FosA3 via two novel hybrid plasmids. Furthermore, our findings highlight that this ST11 Klebsiella pneumoniae strain K15 is most likely of human origin and could be easily transmitted back to humans via direct contact or food intake. In light of our findings, significant attention must be paid to monitoring the prevalence and further evolution of blaKPC-2-carrying plasmids among the Enterobacteriaceae strains of animal origin.
Collapse
|
17
|
Kopotsa K, Osei Sekyere J, Mbelle NM. Plasmid evolution in carbapenemase-producing Enterobacteriaceae: a review. Ann N Y Acad Sci 2019; 1457:61-91. [PMID: 31469443 DOI: 10.1111/nyas.14223] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/22/2019] [Accepted: 07/26/2019] [Indexed: 12/17/2022]
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) have been listed by the WHO as high-priority pathogens owing to their high association with mortalities and morbidities. Resistance to multiple β-lactams complicates effective clinical management of CRE infections. Using plasmid typing methods, a wide distribution of plasmid replicon groups has been reported in CREs around the world, including IncF, N, X, A/C, L/M, R, P, H, I, and W. We performed a literature search for English research papers, published between 2013 and 2018, reporting on plasmid-mediated carbapenem resistance. A rise in both carbapenemase types and associated plasmid replicon groups was seen, with China, Canada, and the United States recording a higher increase than other countries. blaKPC was the most prevalent, except in Angola and the Czech Republic, where OXA-181 (n = 50, 88%) and OXA-48-like (n = 24, 44%) carbapenemases were most prevalent, respectively; blaKPC-2/3 accounted for 70% (n = 956) of all reported carbapenemases. IncF plasmids were found to be responsible for disseminating different antibiotic resistance genes worldwide, accounting for almost 40% (n = 254) of plasmid-borne carbapenemases. blaCTX-M , blaTEM , blaSHV , blaOXA-1/9 , qnr, and aac-(6')-lb were mostly detected concurrently with carbapenemases. Most reported plasmids were conjugative but not present in multiple countries or species, suggesting limited interspecies and interboundary transmission of a common plasmid. A major limitation to effective characterization of plasmid evolution was the use of PCR-based instead of whole-plasmid sequencing-based plasmid typing.
Collapse
Affiliation(s)
- Katlego Kopotsa
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa.,National Health Laboratory Service, Tshwane Division, Department of Medical Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| |
Collapse
|
18
|
Abstract
While the description of resistance to quinolones is almost as old as these antimicrobial agents themselves, transferable mechanisms of quinolone resistance (TMQR) remained absent from the scenario for more than 36 years, appearing first as sporadic events and afterward as epidemics. In 1998, the first TMQR was soundly described, that is, QnrA. The presence of QnrA was almost anecdotal for years, but in the middle of the first decade of the 21st century, there was an explosion of TMQR descriptions, which definitively changed the epidemiology of quinolone resistance. Currently, 3 different clinically relevant mechanisms of quinolone resistance are encoded within mobile elements: (i) target protection, which is mediated by 7 different families of Qnr (QnrA, QnrB, QnrC, QnrD, QnrE, QnrS, and QnrVC), which overall account for more than 100 recognized alleles; (ii) antibiotic efflux, which is mediated by 2 main transferable efflux pumps (QepA and OqxAB), which together account for more than 30 alleles, and a series of other efflux pumps (e.g., QacBIII), which at present have been sporadically described; and (iii) antibiotic modification, which is mediated by the enzymes AAC(6')Ib-cr, from which different alleles have been claimed, as well as CrpP, a newly described phosphorylase.
Collapse
|
19
|
Assessing genetic diversity and similarity of 435 KPC-carrying plasmids. Sci Rep 2019; 9:11223. [PMID: 31375735 PMCID: PMC6677891 DOI: 10.1038/s41598-019-47758-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/22/2019] [Indexed: 01/01/2023] Open
Abstract
The global spread and diversification of multidrug-resistant Gram-negative (MRGN) bacteria poses major challenges to healthcare. In particular, carbapenem-resistant Klebsiella pneumoniae strains have been frequently identified in infections and hospital-wide outbreaks. The most frequently underlying resistance gene (blaKPC) has been spreading over the last decade in the health care setting. blaKPC seems to have rapidly diversified and has been found in various species and on different plasmid types. To review the progress and dynamics of this diversification, all currently available KPC plasmids in the NCBI database were analysed in this work. Plasmids were grouped into 257 different representative KPC plasmids, of which 79.4% could be clearly assigned to incompatibility (Inc) group or groups. In almost half of all representative plasmids, the KPC gene is located on Tn4401 variants, emphasizing the importance of this transposon type for the transmission of KPC genes to other plasmids. The transposons also seem to be responsible for the occurrence of altered or uncommon fused plasmid types probably due to incomplete transposition. Moreover, many KPC plasmids contain genes that encode proteins promoting recombinant processes and mutagenesis; in consequence accelerating the diversification of KPC genes and other colocalized resistance genes.
Collapse
|
20
|
Schweizer C, Bischoff P, Bender J, Kola A, Gastmeier P, Hummel M, Klefisch FR, Schoenrath F, Frühauf A, Pfeifer Y. Plasmid-Mediated Transmission of KPC-2 Carbapenemase in Enterobacteriaceae in Critically Ill Patients. Front Microbiol 2019; 10:276. [PMID: 30837980 PMCID: PMC6390000 DOI: 10.3389/fmicb.2019.00276] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/01/2019] [Indexed: 11/25/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) cause health care-associated infections worldwide, and they are of severe concern due to limited treatment options. We report an outbreak of KPC-2-producing CRE that was caused by horizontal transmission of a promiscuous plasmid across different genera of bacteria and hospitals in Germany. Eleven isolates (8 Citrobacter freundii, 2 Klebsiella oxytoca, and 1 Escherichia coli) were obtained from seven critically ill patients during the six months of the outbreak in 2016. One patient developed a CRE infection while the other six patients were CRE-colonized. Three patients died in the course of the hospital stay. Six of the seven patients carried the same C. freundii clone; one K. oxytoca clone was found in two patients, and one patient carried E. coli and C. freundii. Molecular analysis confirmed the presence of a conjugative, blaKPC-2-carrying 70 kb-IncN plasmid in C. freundii and E. coli and an 80 kb-IncN plasmid in K. oxytoca. All transconjugants harbored either the 70 or 80 kb plasmid with blaKPC-2, embedded within transposon variant Tn4401g. Whole genome sequencing and downstream bioinformatics analyses of all plasmid sequences showed an almost perfect match when compared to a blaKPC-2-carrying plasmid of a large outbreak in another German hospital two years earlier. Differences in plasmid sizes and open reading frames point to the presence of inserted mobile genetic elements. There are few outbreak reports worldwide on the transmission of blaKPC-2-carrying plasmids across different bacterial genera. Our data suggest a regional and supraregional spread of blaKPC-2-carrying IncN-plasmids harboring the Tn4401g isoform in Germany.
Collapse
Affiliation(s)
- Christian Schweizer
- Department of Infection Control/Internal Medicine, Paulinenkrankenhaus, Berlin, Germany.,Department of Infection Control, German Heart Center Berlin, Berlin, Germany
| | - Peter Bischoff
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Jennifer Bender
- Robert Koch Institute, FG13 Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Manfred Hummel
- Department of Infection Control/Internal Medicine, Paulinenkrankenhaus, Berlin, Germany
| | - Frank-Rainer Klefisch
- Department of Infection Control/Internal Medicine, Paulinenkrankenhaus, Berlin, Germany
| | - Felix Schoenrath
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, Berlin, Germany.,Partner Site Berlin, DZHK: German Centre for Cardiovascular Research, Berlin, Germany
| | - Andre Frühauf
- Robert Koch Institute, FG13 Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Yvonne Pfeifer
- Robert Koch Institute, FG13 Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| |
Collapse
|
21
|
Gmiter D, Czerwonka G, Drewnowska JM, Swiecicka I, Kaca W. Draft Genome Sequences of Proteus mirabilis K1609 and K670: A Model Strains for Territoriality Examination. Curr Microbiol 2018; 76:144-152. [PMID: 30448962 PMCID: PMC6373192 DOI: 10.1007/s00284-018-1598-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 11/12/2018] [Indexed: 11/26/2022]
Abstract
Proteus mirabilis is a pathogenic Gram-negative bacterium characterized by its ability to swarm across surfaces, which frequently leads to colonization of the urinary tract and causes severe infections. P. mirabilis strains are also well known from their self-recognition phenomenon, referred to as Dienes phenomenon. In this study, we present novel aspect of self-recognition, which is a hierarchy in terms of strains territoriality. We report the draft genome sequences of P. mirabilis K1609 and K670 strains exhibiting the strongest and the weakest territoriality, respectively. Our results indicated that K1609 is closely related to strain BB2000, a model system for self-recognition, comparing with the K670. We annotated genes associated with recognition of kin and swarming initiation control and indicated polymorphisms by which observed differences in territoriality might results from. The phenotypic and genomic features of both strains reveal their application as a model organisms for studying not only the mechanisms of kin-recognition but also strains territoriality, thus providing new approach to the phenomenon. Availability of these genome sequences may facilitate understanding of the interactions between P. mirabilis strains.
Collapse
Affiliation(s)
- Dawid Gmiter
- Department of Microbiology, Jan Kochanowski University, 15 Swietokrzyska Street, 25-406, Kielce, Poland.
| | - Grzegorz Czerwonka
- Department of Microbiology, Jan Kochanowski University, 15 Swietokrzyska Street, 25-406, Kielce, Poland
| | - Justyna Malgorzata Drewnowska
- Departament of Microbiology, Institute of Biology, University of Bialystok, 1J Ciolkowskiego Street, 15-245, Bialystok, Poland
| | - Izabela Swiecicka
- Departament of Microbiology, Institute of Biology, University of Bialystok, 1J Ciolkowskiego Street, 15-245, Bialystok, Poland
- Laboratory of Applied Microbiology, University of Bialystok, 1J Ciolkowskiego Street, 15-245, Bialystok, Poland
| | - Wieslaw Kaca
- Department of Microbiology, Jan Kochanowski University, 15 Swietokrzyska Street, 25-406, Kielce, Poland
| |
Collapse
|