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Moon BY, Ali MS, Kim S, Kang HS, Kang YJ, Kim JM, Moon DC, Lim SK. Prevalence and molecular characteristics of carbapenem-resistant Escherichia coli isolated from dogs in South Korea. J Vet Sci 2024; 25:e67. [PMID: 39363655 PMCID: PMC11450394 DOI: 10.4142/jvs.24164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/25/2024] [Accepted: 08/13/2024] [Indexed: 10/05/2024] Open
Abstract
IMPORTANCE Carbapenem-resistant Enterobacteriaceae are emerging as a global public health risk. Therefore, assessing the prevalence of carbapenem-resistant Escherichia coli (CRE) in both humans and animals is important. OBJECTIVE We aimed to ascertain the occurrence and characteristics of CRE isolated from companion animals, dogs and cats. METHODS E. coli strains were tested for antimicrobial susceptibility using the broth microdilution technique. Antimicrobial resistance genes were detected by polymerase chain reaction and sequencing analysis. The molecular characteristics of CRE were determined using multi-locus sequence typing, replicon typing, and pulsed-field gel electrophoresis (PFGE). RESULTS In total, 13 CRE isolates (0.13%) were identified from dogs possessing blaNDM-5 along with β-lactamase genes, mostly blaCMY-2 (92.2%) and blaTEM-1 (53.8%). The commonly observed mutations were S83L and D87N in gyrA, S80I in parC, and S458A in parE. CRE carried non-beta-lactam resistance genes, with the majority being tet(B) (100%), sul (84.6%), and aac(3)-II (53.8%). Nine different PFGE patterns (P1-P9), IncX3-type plasmids (69.2%), and ST410 (84.6%) were predominantly detected. CONCLUSIONS AND RELEVANCE This investigation provides significant insight into the prevalence and molecular characteristics of blaNDM-5-carrying E. coli in dogs. The co-existence of blaNDM-5 and other antimicrobial resistance genes in E. coli potentially poses severe health hazards to humans.
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Affiliation(s)
- Bo-Youn Moon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Md Sekendar Ali
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Seunghoe Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Hee-Seung Kang
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Ye-Ji Kang
- Division of Health Hazard Response, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - Jae-Myung Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Dong-Chan Moon
- Centre for Infectious Diseases Research, Korea Centers for Disease Control and Prevention, Cheongju 28159, Korea.
| | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea.
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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; 30:938-941. [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] [MESH Headings] [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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Tian X, Zhang L, Li C, Xia D, Ying J. Genome sequence of a sequence type 1 NDM-5-producing carbapenem-resistant Klebsiella pneumoniae in China. J Glob Antimicrob Resist 2024; 38:271-274. [PMID: 38789084 DOI: 10.1016/j.jgar.2024.05.001] [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: 12/30/2023] [Revised: 04/23/2024] [Accepted: 05/01/2024] [Indexed: 05/26/2024] Open
Abstract
OBJECTIVES The emergence of carbapenem-resistant Klebsiella pneumoniae presents significant health challenges. Here, we present the structural genome sequence of an NDM-5-producing K. pneumoniae (HZKP2) in China. METHODS Antimicrobial susceptibility tests were conducted via broth microdilution. Whole-genome sequencing was performed for genomic analysis. Wzi and capsular polysaccharide (KL) were analysed using Kaptive. Resistance genes, virulence factors, and comparative genomics analyses were also conducted. Multilocus sequence typing (MLST), replicons type, and core genome MLST analysis were further conducted using BacWGSTdb server. RESULTS HZKP2 was resistant to cefepime, ceftazidime, ciprofloxacin, ciprofloxacin, meropenem, and ertapenem. It harboured fosA, blaSHV-187, oqxA, oqxB, sul1, dfrA1, tet(A), floR, aph(6)-Id, aph(3'')-Ib, sul2, blaCTX-M-55, and blaNDM-5. Based on the RAST results, 5563 genes that belonged to 398 subsystems were annotated. The complete genome sequence of HZKP2 was characterized as ST1, wzi 19, and KL19, 5 five contigs totalling 5 654 446 bp, including one chromosome and four plasmids. Further analysis found that blaNDM-5 was located in a 46 161 bp IncX3 plasmid (pHZKP2-3). The genetic structure of blaNDM-5 gene was ISKox3-IS26-bleMBL-blaNDM-5-IS5-ISAb125-IS3000. Further analysis revealed that insertion sequences mediated the dissemination of blaNDM-5 from other species of Enterobacterales. Phylogenetic analysis showed that the closest relative was from a human stool specimen in China, which differed by 53 core genome MLST alleles. CONCLUSIONS Our study provides the first structural perspective of the ST1 K. pneumoniae isolate producing NDM-5 in China. These results could provide valuable insights into the genetic characteristics, antimicrobial resistance mechanisms, and transmission dynamics of carbapenem-resistant K. pneumoniae in clinical settings.
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Affiliation(s)
- Xuebin Tian
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lu Zhang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Chun Li
- Department of Archives, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Daozong Xia
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Junjie Ying
- Department of Urology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China.
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Pan F, Xu Q, Jiang C, Du Q, Yu F, Chen P, Zhang H. Genomic characterisation of bla NDM-5-IncX3 plasmid in an ST4 Klebsiella aerogenes clinical isolate. J Glob Antimicrob Resist 2024; 37:81-85. [PMID: 38460750 DOI: 10.1016/j.jgar.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 01/24/2024] [Accepted: 02/11/2024] [Indexed: 03/11/2024] Open
Abstract
OBJECTIVES The dissemination of New Delhi metallo-β-lactamase-5 (NDM-5) among various species of Enterobacterales has attracted serious global attention. Here, we characterise the genomic characterisation of blaNDM-5-IncX3 plasmid (pNDM-KA3) in an ST4 Klebsiella aerogenes (KA3) strain isolated from a neonate with pneumonia. METHODS Antimicrobial susceptibility and multilocus sequence typing was performed for the KA3. The plasmid conjugation assay and plasmid stability of the KA3 (pNDM-KA3) were also analysed. The pNDM-KA3 plasmid was further analysed by whole-genome sequencing and comparative analysis to determine the genetic environment of blaNDM-5. RESULTS The KA3 strain belongs to ST4 and shows high resistance to β-lactam antibiotics, including carbapenems, but is susceptible to ciprofloxacin, amikacin, tigecycline, and colistin. The pNDM-KA3 was successfully transferred to the recipient E. coli J53 and showed strong stability in K. aerogenes. Genomic sequencing revealed that the pNDM-KA3 plasmid was assigned to plasmid incompatibility group X3 with 43367 bp, and a conserved structure sequence of △IS3000-△ISAba125-IS5-blaNDM-5-bleMBL- trpF-dsbC-IS26 was detected upstream and downstream of the blaNDM-5 gene. Further analysis revealed that insertion sequences mediated the dissemination of blaNDM-5 from other species of Enterobacterales. The pNDM-KA3 showed high similarity to blaNDM-5-harbouring plasmids in other species of Enterobacterales, with these plasmids carrying genes for replication (repB), partitioning (parA and parB), stability (hns), and conjugative transfer (virB and virD). CONCLUSIONS Continued monitoring for the dissemination of blaNDM-5 among uncommon Enterobacterales species should be further reinforced.
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Affiliation(s)
- Fen Pan
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Xu
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Cong Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qingqing Du
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fangyuan Yu
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Pengcheng Chen
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China..
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Menezes J, Frosini SM, Amaral AJ, Loeffler A, Pomba C. Dissemination of bla NDM-5-carrying IncX3-type plasmid among non-clonal Escherichia coli strains colonising a dog with a skin infection caused by a carbapenem-resistant Klebsiella pneumoniae, United Kingdom. J Infect Public Health 2023; 16 Suppl 1:190-193. [PMID: 37926593 DOI: 10.1016/j.jiph.2023.10.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023] Open
Abstract
A successful outcome of a post-surgical wound infection management by a carbapenem-resistant Klebsiella pneumoniae is described in a dog. Four multidrug-resistant and carbapenem-resistant Escherichia coli strains belonging to ST410 (n = 1) and ST648 (n = 3) were isolated from faecal samples and nasal swabs of this dog at admission to a veterinary hospital in the United Kingdom, and one month after discharge. Whole-genome sequencing analysis suggests dissemination of a 46,161-bp IncX3 blaNDM-5-carrying plasmid among E. coli strains from the different lineages. In this study, the E. coli ST648 strains were virtually identical to each other (5 SNPs difference) indicating dissemination and persistence of this clone over time and across different anatomical sites in the same dog maybe due to the prolonged antimicrobial therapy. The carbapenemase carrying plasmid also showed homology with other publicly available plasmid sequences from Asian countries. These results suggests that plasmids may be a major vehicle in mediating the dissemination of carbapenem-resistance. Further studies investigating the selection and flow of plasmids carrying important resistance genes amongst companion animals are needed as it may further contaminate other environments posing a threat to public health.
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Affiliation(s)
- Juliana Menezes
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal; Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Lisbon, Portugal
| | - Siân-Marie Frosini
- Department of Clinical Science and Services, Royal Veterinary College, Hertfordshire, United Kingdom
| | - Andreia J Amaral
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal; Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Lisbon, Portugal; Science and Technology School, University of Évora, Évora, Portugal
| | - Anette Loeffler
- Department of Clinical Science and Services, Royal Veterinary College, Hertfordshire, United Kingdom
| | - Constança Pomba
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal; Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Lisbon, Portugal.
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Kyung SM, Lee JH, Lee ES, Hwang CY, Yoo HS. Whole genome structure and resistance genes in carbapenemase-producing multidrug resistant ST378 Klebsiella pneumoniae. BMC Microbiol 2023; 23:323. [PMID: 37924028 PMCID: PMC10623767 DOI: 10.1186/s12866-023-03074-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND Carbapenemase-producing Klebsiella pneumoniae (CPKP) is one of the most dangerous multidrug-resistant (MDR) pathogens in human health due to its widespread circulation in the nosocomial environment. CPKP carried by companion dogs, which are close to human beings, should be considered a common threat to public health. However, CPKP dissemination through companion animals is still under consideration of major diagnosis and surveillance systems. METHODS Two CPKP isolates which were genotyped to harbor bla NDM-5-encoding IncX3 plasmids, were subjected to the whole-genome study. Whole bacterial DNA was isolated, sequenced, and assembled with Oxford Nanopore long reads and corrected with short reads from the Illumina NovaSeq 6000 platform. The whole-genome structure and positions of antimicrobial resistance (AMR) genes were identified and visualized using CGView. Worldwide datasets were downloaded from the NCBI GenBank database for whole-genome comparative analysis. The whole-genome phylogenetic analysis was constructed using the identified whole-chromosome SNP sites from K. pneumoniae HS11286. RESULTS As a result of the whole-genome identification, 4 heterogenous plasmids and a single chromosome were identified, each carrying various AMR genes. Multiple novel structures were identified from the AMR genes, coupled with mobile gene elements (MGE). The comparative whole-genome epidemiology revealed that ST378 K. pneumoniae is a novel type of CPKP, carrying a higher prevalence of AMR genes. CONCLUSIONS The characterized whole-genome analysis of this study shows the emergence of a novel type of CPKP strain carrying various AMR genes with variated genomic structures. The presented data in this study show the necessity to develop additional surveillance programs and control measures for a novel type of CPKP strain.
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Affiliation(s)
- Su Min Kyung
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jun Ho Lee
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Eun-Seo Lee
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Cheol-Yong Hwang
- Department of Veterinary Dermatology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Han Sang Yoo
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.
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Kyung SM, Lee J, Lee ES, Hwang CY, Yoo HS. Genomic molecular epidemiology of carbapenemase-producing Escherichia coli ST410 isolates by complete genome analysis. Vet Res 2023; 54:72. [PMID: 37658425 PMCID: PMC10472685 DOI: 10.1186/s13567-023-01205-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/04/2023] [Indexed: 09/03/2023] Open
Abstract
The circulation of carbapenemase-producing Escherichia coli (CPEC) in our society is a serious concern for vulnerable patients in nosocomial environments. However, the genomic epidemiology of the circulation of CPEC bacteria among companion animals remains largely unknown. In this study, epidemiological analysis was conducted using complete genome identification of CPEC ST410 isolates obtained from companion animals. To estimate the genomic distance and relatedness of the isolates, a total of 37 whole-genome datasets of E. coli ST410 strains were downloaded and comparatively analysed. As a result of the analysis, the genomic structure of the chromosomes and plasmids was identified, revealing the genomic positions of multiple resistance and virulence genes. The isolates in this study were grouped into the subclade H24/RxC, with fimH24, and substituted quinolone resistance-determining regions (QRDRs) and multiple beta-lactamases, including extended-spectrum β-lactamase (ESBL) and carbapenemase. In addition, the in silico comparison of the whole-genome datasets revealed unidentified ST410 H24/Rx subgroups, including either high pathogenicity islands (HPIs) or H21 serotypes. Considering the genetic variations and resistance gene dissemination of the isolates carried by companion animals, future approaches for preventive measurement must include the "One Health" perspective for public health in our society.
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Affiliation(s)
- Su Min Kyung
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Junho Lee
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Eun-Seo Lee
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Cheol-Yong Hwang
- Department of Veterinary Dermatology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Han Sang Yoo
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.
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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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