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Tian C, Song J, Ren L, Huang D, Wang S, Fu L, Zhao Y, Bai Y, Fan X, Ma T, Ying J. Complete genetic characterization of carbapenem-resistant Acinetobacter johnsonii, co-producing NDM-1, OXA-58, and PER-1 in a patient source. Front Cell Infect Microbiol 2023; 13:1227063. [PMID: 37692162 PMCID: PMC10486904 DOI: 10.3389/fcimb.2023.1227063] [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: 05/22/2023] [Accepted: 07/31/2023] [Indexed: 09/12/2023] Open
Abstract
The emergence of carbapenemase-producing Acinetobacter spp. has been widely reported and become a global threat. However, carbapenem-resistant A. johnsonii strains are relatively rare and without comprehensive genetic structure analysis, especially for isolates collected from human specimen. Here, one A. johnsonii AYTCM strain, co-producing NDM-1, OXA-58, and PER-1 enzymes, was isolated from sputum in China in 2018. Antimicrobial susceptibility testing showed that it was resistant to meropenem, imipenem, ceftazidime, ciprofloxacin, and cefoperazone/sulbactam. Whole-genome sequencing and bioinformatic analysis revealed that it possessed 11 plasmids. bla OXA-58 and bla PER-1 genes were located in the pAYTCM-1 plasmid. Especially, a complex class 1 integron consisted of a 5' conserved segment (5' CS) and 3' CS, which was found to carry sul1, arr-3, qnrVC6, and bla PER-1 cassettes. Moreover, the bla NDM-1 gene was located in 41,087 conjugative plasmids and was quite stable even after 70 passages under antibiotics-free conditions. In addition, six prophage regions were identified. Tracking of closely related plasmids in the public database showed that pAYTCM-1 was similar to pXBB1-9, pOXA23_010062, pOXA58_010030, and pAcsw19-2 plasmids, which were collected from the strains of sewage in China. Concerning the pAYTCM-3 plasmids, results showed that strains were collected from different sources and their hosts were isolated from various countries, such as China, USA, Japan, Brazil, and Mexico, suggesting that a wide spread occurred all over the world. In conclusion, early surveillance is warranted to avoid the extensive spread of this high-risk clone in the healthcare setting.
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Affiliation(s)
- Chongmei Tian
- Department of Pharmacy, Shaoxing Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Shaoxing, Zhejiang, China
| | - Jianqin Song
- Department of Traditional Chinese Medicine, Hangzhou Linping District Hospital of Integrated Chinese and Western Medicine, Hangzhou, China
| | - Lingzhi Ren
- Department of Clinical Laboratory, The People’s Hospital of Zhangqiu Area, Jinan, China
| | - Delian Huang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China
| | - Siwei Wang
- Core Facility, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People’s Hospital, Quzhou, China
| | - Liping Fu
- Department of Pharmacy, Shaoxing Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Shaoxing, Zhejiang, China
| | - Yaping Zhao
- Department of Pharmacy, Shaoxing Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Shaoxing, Zhejiang, China
| | - Yongfeng Bai
- Department of Clinical Laboratory, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People’s Hospital, Quzhou, China
| | - Xueyu Fan
- Department of Clinical Laboratory, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People’s Hospital, Quzhou, China
| | - Tianhong Ma
- Department of Pharmacy, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, China
| | - Junjie Ying
- Department of Urology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People’s Hospital, Quzhou, China
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Moran RA, Liu H, Doughty EL, Hua X, Cummins EA, Liveikis T, McNally A, Zhou Z, van Schaik W, Yu Y. GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes. Microb Genom 2022; 8. [PMID: 35731562 PMCID: PMC9455709 DOI: 10.1099/mgen.0.000840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Carbapenem and other antibiotic resistance genes (ARGs) can be found in plasmids in Acinetobacter, but many plasmid types in this genus have not been well-characterized. Here we describe the distribution, diversity and evolutionary capacity of rep group 13 (GR13) plasmids that are found in Acinetobacter species from diverse environments. Our investigation was prompted by the discovery of two GR13 plasmids in A. baumannii isolated in an intensive care unit (ICU). The plasmids harbour distinct accessory genes: pDETAB5 contains blaNDM-1 and genes that confer resistance to four further antibiotic classes, while pDETAB13 carries putative alcohol tolerance determinants. Both plasmids contain multiple dif modules, which are flanked by pdif sites recognized by XerC/XerD tyrosine recombinases. The ARG-containing dif modules in pDETAB5 are almost identical to those found in pDETAB2, a GR34 plasmid from an unrelated A. baumannii isolated in the same ICU a month prior. Examination of a further 41 complete, publicly available plasmid sequences revealed that the GR13 pangenome consists of just four core but 1186 accessory genes, 123 in the shell and 1063 in the cloud, reflecting substantial capacity for diversification. The GR13 core genome includes genes for replication and partitioning, and for a putative tyrosine recombinase. Accessory segments encode proteins with diverse putative functions, including for metabolism, antibiotic/heavy metal/alcohol tolerance, restriction-modification, an anti-phage system and multiple toxin–antitoxin systems. The movement of dif modules and actions of insertion sequences play an important role in generating diversity in GR13 plasmids. Discrete GR13 plasmid lineages are internationally disseminated and found in multiple Acinetobacter species, which suggests they are important platforms for the accumulation, horizontal transmission and persistence of accessory genes in this genus.
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Affiliation(s)
- Robert A Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Haiyang Liu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, PR China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, 310016, PR China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, PR China
| | - Emma L Doughty
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, PR China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, 310016, PR China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, PR China
| | - Elizabeth A Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Tomas Liveikis
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Zhihui Zhou
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, PR China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, 310016, PR China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, PR China
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, PR China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, 310016, PR China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, PR China
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Jia H, Sun Q, Ruan Z, Xie X. Characterization of a small plasmid carrying the carbapenem resistance gene bla OXA-72 from community-acquired Acinetobacter baumannii sequence type 880 in China. Infect Drug Resist 2019; 12:1545-1553. [PMID: 31239730 PMCID: PMC6559137 DOI: 10.2147/idr.s202803] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/22/2019] [Indexed: 12/20/2022] Open
Abstract
Background Acinetobacter baumannii has emerged as an important pathogen associated with hospital- and community-acquired infections. Community-acquired A. baumannii pneumonia is characterized by a fulminant course and high mortality rates. In this study, we report the identification of a community-acquired carbapenem-resistant A. baumannii strain carrying the bla OXA-72 gene. Methods This A. baumannii isolate was recovered from a male patient diagnosed with community-acquired pneumonia, septic shock, and respiratory failure. Antimicrobial susceptibility testing were performed and the minimum inhibitory concentrations were determined by the broth microdilution method. Whole-genome sequencing was performed using both long-read MinION and short-read Illumina platforms to fully characterize the bla OXA-72-carrying plasmid of the A. baumannii A52. The in silico multilocus sequence typing and genomic epidemiological analysis of the closely related isolates were further elucidated by our recently updated BacWGSTdb server. Results The isolate was resistant to meropenem and remained susceptible to several other antimicrobial agents. Whole-genome sequencing and bioinformatics analysis indicated that this A. baumannii isolate belonged to the rare sporadic clone sequence type 880 and the bla OXA-72 gene was located on the 8,493-bp plasmid pA52-OXA-72. This plasmid exhibited only partial similarity to different OXA-72-encoding plasmids (size range: 8,771-12,056 bp) in various Acinetobacter spp. recovered from patients and other reservoirs in different countries. Conclusion This study described the first case of fulminant carbapenem-resistant community-acquired A. baumannii pneumonia caused by a rare sporadic clone in China. Adequate surveillance is warranted to monitor the emergence of A. baumannii as a community pathogen.
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Affiliation(s)
- Huiqiong Jia
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Qingyang Sun
- Department of Clinical Laboratory, The 117th hospital of People's Liberation Army, Hangzhou, People's Republic of China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Xinyou Xie
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
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Klotz P, Jacobmeyer L, Stamm I, Leidner U, Pfeifer Y, Semmler T, Prenger-Berninghoff E, Ewers C. Carbapenem-resistant Acinetobacter baumannii ST294 harbouring the OXA-72 carbapenemase from a captive grey parrot. J Antimicrob Chemother 2019; 73:1098-1100. [PMID: 29309610 DOI: 10.1093/jac/dkx490] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Peter Klotz
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, Giessen, Germany
| | - Lisa Jacobmeyer
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, Giessen, Germany
| | - Ivonne Stamm
- Vet Med Labor GmbH, Division of IDEXX Laboratories, Ludwigsburg, Germany
| | - Ursula Leidner
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, Giessen, Germany
| | - Yvonne Pfeifer
- FG13 Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Torsten Semmler
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Ellen Prenger-Berninghoff
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, Giessen, Germany
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, Giessen, Germany
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Karampatakis T, Antachopoulos C, Tsakris A, Roilides E. Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii in Greece: an extended review (2000–2015). Future Microbiol 2017; 12:801-815. [DOI: 10.2217/fmb-2016-0200] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) is endemic in Greece. CRAB initially emerged in 2000 and since then, carbapenemases still have a crucial role in CRAB appearance, except for a few cases resulting from efflux pump or outer-membrane protein mechanisms. OXA-type carbapenemases present the highest prevalence worldwide and bla OXA-23-like and bla OXA-58-like are the most important genes found; VIM-yielding CRAB have also been detected, while a single CRAB isolate producing NDM has quite recently emerged in Greece. The predominant OXA-23 producers are associated with multilocus sequence typing Pasteur scheme sequence type 2 clonal strains of the international clone II. The emergence of colistin-resistant CRAB has complicated the treatment of such infections and the interpretation of susceptibility data. Infection control measures and adjusted antimicrobial treatment strategies could confine CRAB spread. The aim of this review is to go through the molecular epidemiology of CRAB, in an endemic area and highlight its potential future evolution.
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Affiliation(s)
- Theodoros Karampatakis
- Infectious Diseases Unit, 3rd Department of Pediatrics, Medical Faculty, School of Health Sciences, Aristotle University, Hippokration General Hospital, Thessaloniki, Greece
| | - Charalampos Antachopoulos
- Infectious Diseases Unit, 3rd Department of Pediatrics, Medical Faculty, School of Health Sciences, Aristotle University, Hippokration General Hospital, Thessaloniki, Greece
| | - Athanassios Tsakris
- Microbiology Department, National & Kapodistrian University School of Medicine, Athens, Greece
| | - Emmanuel Roilides
- Infectious Diseases Unit, 3rd Department of Pediatrics, Medical Faculty, School of Health Sciences, Aristotle University, Hippokration General Hospital, Thessaloniki, Greece
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Lee CR, Lee JH, Park M, Park KS, Bae IK, Kim YB, Cha CJ, Jeong BC, Lee SH. Biology of Acinetobacter baumannii: Pathogenesis, Antibiotic Resistance Mechanisms, and Prospective Treatment Options. Front Cell Infect Microbiol 2017; 7:55. [PMID: 28348979 PMCID: PMC5346588 DOI: 10.3389/fcimb.2017.00055] [Citation(s) in RCA: 517] [Impact Index Per Article: 73.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/13/2017] [Indexed: 12/27/2022] Open
Abstract
Acinetobacter baumannii is undoubtedly one of the most successful pathogens responsible for hospital-acquired nosocomial infections in the modern healthcare system. Due to the prevalence of infections and outbreaks caused by multi-drug resistant A. baumannii, few antibiotics are effective for treating infections caused by this pathogen. To overcome this problem, knowledge of the pathogenesis and antibiotic resistance mechanisms of A. baumannii is important. In this review, we summarize current studies on the virulence factors that contribute to A. baumannii pathogenesis, including porins, capsular polysaccharides, lipopolysaccharides, phospholipases, outer membrane vesicles, metal acquisition systems, and protein secretion systems. Mechanisms of antibiotic resistance of this organism, including acquirement of β-lactamases, up-regulation of multidrug efflux pumps, modification of aminoglycosides, permeability defects, and alteration of target sites, are also discussed. Lastly, novel prospective treatment options for infections caused by multi-drug resistant A. baumannii are summarized.
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Affiliation(s)
- Chang-Ro Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Moonhee Park
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji UniversityYongin, South Korea; DNA Analysis Division, Seoul Institute, National Forensic ServiceSeoul, South Korea
| | - Kwang Seung Park
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Il Kwon Bae
- Department of Dental Hygiene, College of Health and Welfare, Silla University Busan, South Korea
| | - Young Bae Kim
- Biotechnology Program, North Shore Community College Danvers, MA, USA
| | - Chang-Jun Cha
- Department of Systems Biotechnology, College of Biotechnology and Natural Resources, Chung-Ang University Anseong, South Korea
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
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