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Harada K, Miyamoto T, Sugiyama M, Asai T. First report of a bla NDM-5-carrying Escherichia coli sequence type 12 isolated from a dog with pyometra in Japan. J Infect Chemother 2024:S1341-321X(24)00048-5. [PMID: 38369122 DOI: 10.1016/j.jiac.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/25/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
Carbapenemase-producing Enterobacterales (CPE) are a serious concern in human clinical settings. Companion animal-origin CPE have been only rarely identified in several countries, but they have not yet been identified in Japan. In this study, we present the first case of a canine infected with CPE in Japan. The patient was hospitalized due to pyometra. The pus discharged from the patient's uterus was subjected to bacteriological analysis. As a result, E. coli was identified in the pus and exhibited resistance to piperacillin, amoxicillin-clavulanic acid, cefazolin, ceftazidime, cefepime, meropenem, amikacin, and sulfamethoxazole-trimethoprim and susceptibility to aztreonam, minocycline, and levofloxacin. Results of the sodium mercaptoacetic acid double-disk synergy test showed that the E. coli isolate was positive for metallo-β-lactamases. Next-generation sequencing identified the blaNDM-5 gene, which was located in the IncFII-type plasmid together with blaTEM-1b, rmtB, aadA2, bleMBL, sul1, qacE, and dfrA12. The case was treated successfully with doxycycline and orbifloxacin. Our finding emphasizes that close attention should be paid to the significance of CPE harboring multidrug-resistance plasmid in companion animals, based on the perspective of One Health approach in Japan as well as in other countries.
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Affiliation(s)
- Kazuki Harada
- Laboratory of Veterinary Internal Medicine, Tottori University, Minami 4-101, Koyama, Tottori, 680-8550, Japan.
| | - Tadashi Miyamoto
- Miyamoto Animal Hospital, 2265-8, Kurokawa, Yamaguchi, 753-0851, Japan
| | - Michiyo Sugiyama
- Department of Applied Veterinary Science, The United Graduate School of Veterinary Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Tetsuo Asai
- Department of Applied Veterinary Science, The United Graduate School of Veterinary Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
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2
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Jia C, Wang Z, Huang C, Teng L, Zhou H, An H, Liao S, Liu Y, Huang L, Tang B, Yue M. Mobilome-driven partitions of the resistome in Salmonella. mSystems 2023; 8:e0088323. [PMID: 37855620 PMCID: PMC10734508 DOI: 10.1128/msystems.00883-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Antimicrobial resistance (AMR) has become a significant global challenge, with an estimated 10 million deaths annually by 2050. The emergence of AMR is mainly attributed to mobile genetic elements (MGEs or mobilomes), which accelerate wide dissemination among pathogens. The interaction between mobilomes and AMR genes (or resistomes) in Salmonella, a primary cause of diarrheal diseases that results in over 90 million cases annually, remains poorly understood. The available fragmented or incomplete genomes remain a significant limitation in investigating the relationship between AMR and MGEs. Here, we collected the most extensive closed Salmonella genomes (n = 1,817) from various sources across 58 countries. Notably, our results demonstrate that resistome transmission between Salmonella lineages follows a specific pattern of MGEs and is influenced by external drivers, including certain socioeconomic factors. Therefore, targeted interventions are urgently needed to mitigate the catastrophic consequences of Salmonella AMR.
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Affiliation(s)
- Chenghao Jia
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
| | - Zining Wang
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Chenghu Huang
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Lin Teng
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
| | - Haiyang Zhou
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Hongli An
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Sihao Liao
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
| | - Yuhao Liu
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Linlin Huang
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
| | - Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Min Yue
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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3
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Mohamed HS, Galal L, Hayer J, Benavides JA, Bañuls AL, Dupont C, Conquet G, Carrière C, Dumont Y, Didelot MN, Michon AL, Jean-Pierre H, Aboubaker MH, Godreuil S. Genomic epidemiology of carbapenemase-producing Gram-negative bacteria at the human-animal-environment interface in Djibouti city, Djibouti. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167160. [PMID: 37730061 DOI: 10.1016/j.scitotenv.2023.167160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
The emergence of carbapenem resistance is a major public health threat in sub-Saharan Africa but remains poorly understood, particularly at the human-animal-environment interface. This study provides the first One Health-based study on the epidemiology of Carbapenemase-Producing Gram-Negative Bacteria (CP-GNB) in Djibouti City, Djibouti, East Africa. In total, 800 community urine samples and 500 hospital specimens from humans, 270 livestock fecal samples, 60 fish samples, and 20 water samples were collected and tested for carbapenem resistance. The overall estimated CP-GNB prevalence was 1.9 % (32/1650 samples) and specifically concerned 0.3 % of community urine samples, 2.8 % of clinical specimens, 2.6 % of livestock fecal samples, 11.7 % of fish samples, and 10 % of water samples. The 32 CP-GNB included 19 Escherichia coli, seven Acinetobacter baumannii, five Klebsiella pneumoniae, and one Proteus mirabilis isolate. Short-read (Illumina) and long-read (Nanopore) genome sequencing revealed that carbapenem resistance was mainly associated with chromosomal carriage of blaNDM-1, blaOXA-23, blaOXA-48, blaOXA-66, and blaOXA-69 in A. baumannii, and with plasmid carriage in Enterobacterales (blaNDM-1 and blaOXA-181 in E. coli, blaNDM-1, blaNDM-5 and blaOXA-48 in K. pneumoniae, and blaNDM-1 in P. mirabilis). Moreover, 17/32 CP-GNB isolates belonged to three epidemic clones: (1) A. baumannii sequence type (ST) 1697,2535 that showed a distribution pattern consistent with intra- and inter-hospital dissemination; (2) E. coli ST10 that circulated at the human-animal-environment interface; and (3) K. pneumoniae ST147 that circulated at the human-environment interface. Horizontal exchanges probably contributed to carbapenem resistance dissemination in the city, especially the blaOXA-181-carrying ColKP3-IncX3 hybrid plasmid that was found in E. coli isolates belonging to different STs. Our study highlights that despite a relatively low CP-GNB prevalence in Djibouti City, plasmids harboring carbapenem resistance circulate in humans, animals and environment. Our findings stress the need to implement preventive and control measures for reducing the circulation of this potentially emerging public health threat.
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Affiliation(s)
- Hasna Saïd Mohamed
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; Hôpital Général Peltier de Djibouti, Djibouti ville, Djibouti; Laboratoire de Biologie Médicale de la Mer Rouge, Djibouti City, Djibouti
| | - Lokman Galal
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France.
| | - Juliette Hayer
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Julio A Benavides
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; Doctorado en Medicina de la Conservación y Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
| | - Anne-Laure Bañuls
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; LMI DRISA, Montpellier, France
| | - Chloé Dupont
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Guilhem Conquet
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Christian Carrière
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Yann Dumont
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Marie-Noëlle Didelot
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Anne-Laure Michon
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Hélène Jean-Pierre
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Mohamed Houmed Aboubaker
- Laboratoire de Biologie Médicale de la Mer Rouge, Djibouti City, Djibouti; Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti City 696, Djibouti
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; Jeune Equipe Associée à l'IRD (JEAI), FASORAM, Montpellier, France
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Li H, Sun L, Qiao H, Sun Z, Wang P, Xie C, Hu X, Nie T, Yang X, Li G, Zhang Y, Wang X, Li Z, Jiang J, Li C, You X. Polymyxin resistance caused by large-scale genomic inversion due to IS 26 intramolecular translocation in Klebsiella pneumoniae. Acta Pharm Sin B 2023; 13:3678-3693. [PMID: 37719365 PMCID: PMC10501869 DOI: 10.1016/j.apsb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/11/2023] [Accepted: 06/06/2023] [Indexed: 09/19/2023] Open
Abstract
Polymyxin B and polymyxin E (colistin) are presently considered the last line of defense against human infections caused by multidrug-resistant Gram-negative organisms such as carbapenemase-producer Enterobacterales, Acinetobacter baumannii, and Klebsiella pneumoniae. Yet resistance to this last-line drugs is a major public health threat and is rapidly increasing. Polymyxin S2 (S2) is a polymyxin B analogue previously synthesized in our institute with obviously high antibacterial activity and lower toxicity than polymyxin B and colistin. To predict the possible resistant mechanism of S2 for wide clinical application, we experimentally induced bacterial resistant mutants and studied the preliminary resistance mechanisms. Mut-S, a resistant mutant of K. pneumoniae ATCC BAA-2146 (Kpn2146) induced by S2, was analyzed by whole genome sequencing, transcriptomics, mass spectrometry and complementation experiment. Surprisingly, large-scale genomic inversion (LSGI) of approximately 1.1 Mbp in the chromosome caused by IS26 mediated intramolecular transposition was found in Mut-S, which led to mgrB truncation, lipid A modification and hence S2 resistance. The resistance can be complemented by plasmid carrying intact mgrB. The same mechanism was also found in polymyxin B and colistin induced drug-resistant mutants of Kpn2146 (Mut-B and Mut-E, respectively). This is the first report of polymyxin resistance caused by IS26 intramolecular transposition mediated mgrB truncation in chromosome in K. pneumoniae. The findings broaden our scope of knowledge for polymyxin resistance and enriched our understanding of how bacteria can manage to survive in the presence of antibiotics.
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Affiliation(s)
- Haibin Li
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Lang Sun
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Han Qiao
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zongti Sun
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Penghe Wang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Chunyang Xie
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xinxin Hu
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Tongying Nie
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xinyi Yang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Guoqing Li
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Youwen Zhang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xiukun Wang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhuorong Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100050, China
| | - Jiandong Jiang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100050, China
| | - Congran Li
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xuefu You
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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Rong F, Liu Z, Yang P, Wu F, Sun Y, Sun X, Zhou J. Epidemiological and Molecular Characteristics of bla NDM-1 and bla KPC-2 Co-Occurrence Carbapenem-Resistant Klebsiella pneumoniae. Infect Drug Resist 2023; 16:2247-2258. [PMID: 37090038 PMCID: PMC10120834 DOI: 10.2147/idr.s400138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 04/01/2023] [Indexed: 04/25/2023] Open
Abstract
Objective Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged and spread worldwide. It can usually cause a serious threat complicating treatment options in clinical settings. However, treatment options are limited. The present study investigates the prevalence and genetic characteristics of bla NDM-1 and bla KPC-2 co-harboring clinical isolates of Klebsiella pneumoniae. Methods In this study, Multiplex polymerase chain reaction (PCR) was performed to detect the carbapenem-resistant genes, and the broth microdilution method was used to determine the minimum inhibitory concentrations (MICs) of antibacterial drugs. The transferability of carbapenem-resistant phenotypes was examined using filter mating assays. Overall, we used Illumina sequencing to evaluate the epidemiological and molecular characteristics of bla NDM-1 and bla KPC-2 (genes encoding carbapenemase) co-occurrence in CRKP strains. Results All strains exhibited resistance to carbapenems and other antibiotics. However, they were still susceptible to polymyxin E. Among them, 18 isolates were positive for bla KPC-2, bla NDM-1, and multiple virulence determinants, such as genes encoding the virulence factor aerobactin, yersiniabactin, and the regulator of the mucoid phenotype (rmpA and rmpA2). Whole genome sequencing revealed that the 18 CRKP strains belonged to ST11 and capsular serotype KL64, and could be grouped into two evolutionary branches. Furthermore, these strains displayed hypervirulence potential since all of them carried pLVPK-like plasmid. Conclusion These findings suggested that ST11-KL64 CRKP strains are major threats in terms of nosocomial infections in this hospital. Hence, new strategies should be urgently developed to monitor, diagnose, and treat this high-risk CRKP clone.
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Affiliation(s)
- Fang Rong
- Department of General Practice, The Affiliated Hospital of Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Graduate School Department of Dalian Medical University, Dalian, Liaoning, 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, People’s Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
| | - Pengbin Yang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
| | - Feng Wu
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
| | - Yu Sun
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
| | - Xuewei Sun
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
| | - Jun Zhou
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Correspondence: Jun Zhou, Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou, Jiangsu, 225009, People’s Republic of China, Email
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Gotoh K, Hagiya H, Iio K, Yamada H, Matsushita O, Otsuka F. Detection of Enterobacter cloacae complex strain with a bla NDM-1-harboring plasmid from an elderly resident at a long-term care facility in Okayama, Japan. J Infect Chemother 2022; 28:1697-1699. [PMID: 36049614 DOI: 10.1016/j.jiac.2022.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/31/2022] [Accepted: 08/22/2022] [Indexed: 10/15/2022]
Abstract
Amidst the global spread of antimicrobial resistance, New Delhi metallo-β-lactamase (NDM)-type carbapenemase-producing Enterobacterales (CPE) remain uncommon in Japan, and the detection of such highly drug-resistant organisms is limited to inbound cases. There is little evidence regarding the prevalence of NDM β-lactamase gene (blaNDM)-harboring CPE in the domestic community, especially in the provincial cities of Japan. Herein, we report the isolation of a blaNDM-1-harboring plasmid in Enterobacter cloacae complex strain isolated from an elderly woman without a history of traveling abroad who had resided in a long-term care facility in Okayama, Japan. The multidrug-resistant blaNDM-harboring CPE isolate was detected in a stool sample of the patient during routine screening at admission. We performed whole-genome sequencing analysis of the isolate using MiSeq (Illumina) and MinION (Oxford Nanopore Technologies) platforms. The isolate was identified as sequence type 171, which has predominantly been reported in the United States and China. The blaNDM-1 gene was encoded on the 46,161 bp IncX3 plasmid, with sequence similarity to plasmids of similar size isolated from individuals in China. Collectively, the genomic data suggest that an imported CPE isolate may have spread among healthy individuals in the regional area of Japan.
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Affiliation(s)
- Kazuyoshi Gotoh
- Department of Bacteriology, Okayama University, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Japan
| | - Hideharu Hagiya
- Department of General Medicine, Okayama University, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Japan.
| | - Koji Iio
- Microbiology Division, Clinical Laboratory, Okayama University Hospital, Japan
| | - Haruto Yamada
- Department of Clinical Laboratory, Okayama City Hospital, Japan
| | - Osamu Matsushita
- Department of Bacteriology, Okayama University, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Japan
| | - Fumio Otsuka
- Department of General Medicine, Okayama University, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Japan; Microbiology Division, Clinical Laboratory, Okayama University Hospital, Japan
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Rodrigues C, Desai S, Passet V, Gajjar D, Brisse S. Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147. Microb Genom 2022; 8. [PMID: 35019836 PMCID: PMC8914359 DOI: 10.1099/mgen.0.000737] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The rapid emergence of multidrug-resistant Klebsiella pneumoniae is being driven largely by the spread of specific clonal groups (CGs). Of these, CG147 includes 7-gene multilocus sequence typing (MLST) sequence types (STs) ST147, ST273 and ST392. CG147 has caused nosocomial outbreaks across the world, but its global population dynamics remain unknown. Here, we report a pandrug-resistant ST147 clinical isolate from India (strain DJ) and define the evolution and global emergence of CG147. Antimicrobial-susceptibility testing following European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines and genome sequencing (Illumina and Oxford Nanopore Technologies, Unicycler assembly) were performed on strain DJ. Additionally, we collated 217 publicly available CG147 genomes [National Center for Biotechnology Information (NCBI), May 2019]. CG147 evolution was inferred within a temporal phylogenetic framework (beast) based on a recombination-free sequence alignment (Roary/Gubbins). Comparative genomic analyses focused on resistance and virulence genes and other genetic elements (BIGSdb, Kleborate, PlasmidFinder, phaster, ICEfinder and CRISPRCasFinder). Strain DJ had a pandrug-resistance phenotype. Its genome comprised the chromosome, seven plasmids and one linear phage-plasmid. Four carbapenemase genes were detected: blaNDM-5 and two copies of blaOXA-181 in the chromosome, and a second copy of blaNDM-5 on an 84 kb IncFII plasmid. CG147 genomes carried a mean of 13 acquired resistance genes or mutations; 63 % carried a carbapenemase gene and 83 % harboured blaCTX-M. All CG147 genomes presented GyrA and ParC mutations and a common subtype I-E CRISPR-Cas system. ST392 and ST273 emerged in 2005 and 1995, respectively. ST147, the most represented phylogenetic branch, was itself divided into two main clades with distinct capsular loci: KL64 (74 %, DJ included, emerged in 1994 and disseminated worldwide, with carbapenemases varying among world regions) and KL10 (20 %, emerged in 2002, predominantly found in Asian countries, associated with carbapenemases NDM and OXA-48-like). Furthermore, subclades within ST147-KL64 differed at the yersiniabactin locus, OmpK35/K36 mutations, plasmid replicons and prophages. The absence of IncF plasmids in some subclades was associated with a possible activity of a CRISPR-Cas system. K. pneumoniae CG147 comprises pandrug-resistant or extensively resistant isolates, and carries multiple and diverse resistance genes and mobile genetic elements, including chromosomal blaNDM-5. Its emergence is being driven by the spread of several phylogenetic clades marked by their own genomic features and specific temporo–spatial dynamics. These findings highlight the need for precision surveillance strategies to limit the spread of particularly concerning CG147 subsets.
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Affiliation(s)
- Carla Rodrigues
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Université de Paris, Paris, France
| | - Siddhi Desai
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Virginie Passet
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Université de Paris, Paris, France
| | - Devarshi Gajjar
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Université de Paris, Paris, France
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Uechi K, Tohya M, Tada T, Tome T, Takahashi A, Kinjo T, Maeda S, Kirikae T, Fujita J. Emergence of a multidrug-resistant plasmid encoding bla NDM-1, bla OXA-420 and armA in a clinical isolate of Acinetobacter variabilis in Japan. J Med Microbiol 2021; 70. [PMID: 34431761 DOI: 10.1099/jmm.0.001395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter variabilis (formerly genospecies 15 sensu Tjernberg and Ursing) has been isolated from humans and animals and was proposed to be a novel species in 2015. A multidrug-resistant A. variabilis isolate, RYU24, was obtained in 2012 from an inpatient in Okinawa, Japan, with no record of overseas travel. The isolate was resistant to carbapenems, aminoglycosides and ciprofloxacin, with minimum inhibitory concentrations (MICs) of 32 µg ml-1 for imipenem and meropenem; > 1024 µg ml-1 for amikacin, arbekacin, gentamicin and tobramycin; and 8 µg ml-1 for ciprofloxacin. The isolate was found to harbour a 68-kbp plasmid carrying bla NDM-1, which encodes New Delhi metallo-β-lactamase-1 (NDM-1); bla OXA-420, which encodes an OXA-58-like carbapenemase and; armA, which encodes ArmA 16S rRNA methylase conferring pan-aminoglycoside resistance. To our knowledge, this is the first report of a plasmid harbouring the three major drug-resistance genes, bla NDM-1, bla OXA-420 and armA.
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Affiliation(s)
- Kohei Uechi
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan.,Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Mari Tohya
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Tatsuya Tada
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Takaaki Tome
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Ami Takahashi
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Takeshi Kinjo
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Shiro Maeda
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Teruo Kirikae
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Jiro Fujita
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
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Sugawara Y, Akeda Y, Hagiya H, Zin KN, Aye MM, Takeuchi D, Matsumoto Y, Motooka D, Nishi I, Tomono K, Hamada S. Characterization of bla NDM-5-harbouring Klebsiella pneumoniae sequence type 11 international high-risk clones isolated from clinical samples in Yangon General Hospital, a tertiary-care hospital in Myanmar. J Med Microbiol 2021; 70. [PMID: 34038339 DOI: 10.1099/jmm.0.001348] [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] [Indexed: 11/18/2022] Open
Abstract
Fifteen Klebsiella pneumoniae isolates harbouring bla NDM genes were identified from blood and sputum specimens of patients at a tertiary-care facility (Yangon General Hospital, Yangon, Myanmar) in 2018. Two of the isolates belonged to sequence type (ST) 11, an international high-risk clone. Whole-genome sequencing and phylogenetic analyses revealed that these two isolates were clustered together with other ST11 isolates originating from other countries. The isolates harboured the bla NDM-5 gene on an IncFII-type plasmid that is prevalent among carbapenemase-producing Enterobacteriaceae in Yangon but has rarely been found in other ST11 isolates. Our data suggests the regional presence of the ST11 international high-risk clone and its acquisition of an endemic bla NDM-5-carrying plasmid.
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Affiliation(s)
- Yo Sugawara
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yukihiro Akeda
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, Suita, Japan.,Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hideharu Hagiya
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Khwar Nyo Zin
- Clinical Laboratory Department, Yangon General Hospital, Yangon, Myanmar
| | - Mya Mya Aye
- Bacteriology Research Division, Department of Medical Research, Yangon, Myanmar
| | - Dan Takeuchi
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Isao Nishi
- Laboratory for Clinical Investigation, Osaka University Hospital, Suita, Japan
| | - Kazunori Tomono
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Shigeyuki Hamada
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
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10
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Akeda Y. Current situation of carbapenem-resistant Enterobacteriaceae and Acinetobacter in Japan and Southeast Asia. Microbiol Immunol 2021; 65:229-237. [PMID: 33913535 DOI: 10.1111/1348-0421.12887] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/18/2021] [Accepted: 04/21/2021] [Indexed: 11/30/2022]
Abstract
In the recent years, issues related to drug-resistant bacteria have evolved worldwide, and various countermeasures have been taken to control their spread. Among a wide variety of drug-resistant bacterial species, carbapenem-resistant Gram-negative bacteria, including carbapenem-resistant Enterobacteriaceae (CRE) and carbapenem-resistant Acinetobacter baumannii (CRAb), are those for which countermeasures are particularly important. Carbapenems are the last resort antibiotics for any bacterial infection; therefore, infectious diseases caused by these drug-resistant bacteria are difficult to treat. In the case of CRE, since carbapenemases responsible for carbapenem resistance are mostly encoded on transmissible plasmids, it is known that susceptible bacteria can easily become carbapenem-resistant by transfer of plasmids between Enterobacteriaceae. In addition, Enterobacteriaceae are common bacterial species found in the guts of animals, including humans. Acinetobacter is ubiquitously isolated in the environment. Due to these characteristics, it is quite difficult to prevent the intrusion of multi-drug resistant pathogens in hospitals. Therefore, effective countermeasures should be developed and utilized against such dangerous pathogens based on molecular epidemiological analyses. In this review, there are also some examples presented on how to manage to monitor and control those troublesome drug-resistant bacteria conducted in Japan and Southeast Asia.
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Affiliation(s)
- Yukihiro Akeda
- Division of Infection Control and Prevention, Osaka University Hospital, Osaka University, Osaka, Japan.,Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, Osaka, Japan.,Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
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11
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Trends and molecular characteristics of carbapenemase-producing Enterobacteriaceae in Japanese hospital from 2006 to 2015. J Infect Chemother 2020; 26:667-671. [PMID: 32222331 DOI: 10.1016/j.jiac.2020.02.002] [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: 10/05/2019] [Revised: 01/23/2020] [Accepted: 02/05/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND The increasing number of carbapenemase-producing Enterobacteriaceae (CPE) has become a global problem. Most carbapenemases detected in Japan are imipenemase, which is an imipenem-degrading enzyme with low ability; thus, CPE could have been overlooked. Therefore, this study aimed to detect and analyze CPE, without overlooking CPE showing the low minimum inhibitory concentration phenotype. METHODS CPE screening was conducted on 531 ceftazidime-resistant Enterobacteriaceae isolated from Kitasato University Hospital during 2006-2015. We confirmed the presence of the carbapenemase genes (blaIMP, blaVIM, blaKPC, blaNDM, and blaOXA-48) by multiplex polymerase chain reaction. The detected CPE strains were analyzed by antimicrobial susceptibility testing, multilocus sequence typing, conjugal experiments, replicon typing, and plasmid profiling by restriction enzyme treatment. RESULTS The CPE detection rate in Kitasato University Hospital within the past 10 years was 0.0003% (nine CPE strains). These nine CPE strains were identified to harbor 8 blaIMP-1 or 1 blaNDM-5. The CPE strains consisted of five species including Klebsiella pneumoniae and Citrobacter freundii. Six of eight blaIMP-1 were coded by IncHI2 plasmid, and the other two were coded by IncA/C plasmid. Plasmid profiling revealed that K. pneumoniae and C. freundii isolated from the same patient harbored the same plasmid. CONCLUSION The CPE detection rate in this study was significantly lower than those previously reported in Japan. In one case, IncA/C plasmid transmission through different bacterial species within the body was speculated. Although the number of CPE detected was low, these results indicated that the resistance plasmid could spread to other bacterial species.
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Wang Z, Li M, Shen X, Wang L, Liu L, Hao Z, Duan J, Yu F. Outbreak of blaNDM-5-Harboring Klebsiella pneumoniae ST290 in a Tertiary Hospital in China. Microb Drug Resist 2019; 25:1443-1448. [PMID: 31334685 DOI: 10.1089/mdr.2019.0046] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) has posed a great threat to public health. Among 133 nonduplicated CRKP isolates collected between September 2016 and November 2017 in a tertiary hospital in China, 89 (89/133, 66.9%) and 31 (31/133, 23.3%) were positive for blaNDM-5 and blaKPC-2. Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) revealed that ST290 represented the majority of NDM-5 producers (67/89, 75.3%) and PFGE cluster E accounted for 50 (50/67, 74.6%) ST290 isolates from the burn ward, suggesting that K. pneumoniae ST290 clone carrying blaNDM-5 resulted in an outbreak in this hospital. Whole genome sequencing of the plasmid carrying blaNDM-5 showed that the resistance gene blaNDM-5 was located in a ∼49 kb multireplicon plasmid with a peculiar insertion of ISKpn19 of the IncX3-type plasmid. To the best of our knowledge, this is the first report of outbreak of K. pneumoniae ST290 clone carrying blaNDM-5.
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Affiliation(s)
- Zhengzheng Wang
- Department of Clinical Laboratory, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Meilan Li
- Emergency Intensive Care Unit, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaofei Shen
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Liangxing Wang
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Li Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhihao Hao
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jingjing Duan
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fangyou Yu
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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13
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Ko KS. Antibiotic-resistant clones in Gram-negative pathogens: presence of global clones in Korea. J Microbiol 2018; 57:195-202. [PMID: 30552629 DOI: 10.1007/s12275-019-8491-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 12/26/2022]
Abstract
Antibiotic resistance is a global concern in public health. Antibiotic-resistant clones can spread nationally, internationally, and globally. This review considers representative antibiotic-resistant Gram-negative bacterial clones-CTX-M- 15-producing ST131 in Escherichia coli, extended-spectrum ß-lactamase-producing ST11 and KPC-producing ST258 in Klebsiella pneumoniae, IMP-6-producing, carbapenem-resistant ST235 in Pseudomonas aeruginosa, and OXA-23-producing global clone 2 in Acinetobacter baumannii-that have disseminated worldwide, including in Korea. The findings highlight the urgency for systematic monitoring and international cooperation to suppress the emergence and propagation of antibiotic resistance.
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Affiliation(s)
- Kwan Soo Ko
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea.
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