Characterization of the IncFII-IncFIB(pB171) Plasmid Carrying blaNDM-5 in Escherichia coli ST405 Clinical Isolate in Japan
Bibliographic record
Abstract
Yoko Takayama, 1, 2 Tsuyoshi Sekizuka, 3 Hidehito Matsui, 4 Yuzuru Adachi, 4 Ryotaro Eda, 5 Shin Nihonyanagi, 2 Tatsuhiko Wada, 2 Mari Matsui, 6 Satowa Suzuki, 6 Masashi Takaso, 7 Hidero Kitasato, 5 Makoto Kuroda, 3 Hideaki Hanaki 4 1Department of Infection Control and Infectious Diseases, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Kanagawa, Japan; 2Department of Infection Control and Prevention, Kitasato University Hospital, Kanagawa, Japan; 3Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan; 4Infection Control Research Center, Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan; 5Department of Microbiology, School of Allied Health Sciences, Kitasato University, Kanagawa, Japan; 6Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan; 7Department of Orthopaedic Surgery, Kitasato University School of Medicine, Kanagawa, JapanCorrespondence: Yoko Takayama 1-15-1 Kitasato, Minami-Ku, Sagamihara, Kanagawa 252-0374, JapanTel/Fax +81-42-778-9119Email yoko@med.kitasato-u.ac.jpPurpose: New Delhi metallo-β-lactamase 5 (NDM-5) shows stronger resistance to carbapenems and broad-spectrum cephalosporins than NDM-1 because NDM-5 differs from NDM-1 by two amino acid substitutions. In this study, our aim was to characterize a NDM-5-producing Escherichia coli isolate KY1497 from a patient with urinary tract infection in Japan, who had no recent history of overseas travel.Patients and Methods: NDM-5-producing E. coli isolate KY1497 was detected in the urine sample of a patient hospitalized in a tertiary hospital in Japan. The complete genome sequence of isolate KY1497 was determined by short- and long-read sequencing with hybrid assembly, followed by multilocus sequence typing (MLST), core-genome phylogeny analysis, plasmid analysis, and transconjugation experiments.Results: KY1497 was classified as ST405 by MLST, and core-genome phylogeny exhibited the closest lineage to the clinical isolates in Nepal (IOMTU605) and Canada (FDAARGOS_448). KY1497 harbors blaNDM-5 in the IncFII-IncFIB(pB171) replicon plasmid (pKY1497_1, 123,767 base pairs). Plasmid analysis suggested that the cognate plasmids of pKY1497_1 have a minor plasmid background, rather than the globally disseminated IncX3 plasmid carrying blaNDM-5. Transconjugation analysis revealed that pKY1497_1 is transmissible to the recipient E. coli J53 strain.Conclusion: We characterized a novel Inc replicon plasmid (IncFII-IncFIB[pB171]) carrying blaNDM-5 and its host E. coli strain. NDMs are associated with a high risk of infection worldwide because of their antibiotic resistance and untreatable and hard-to-treat infections. Other patients in the hospital showed negative results for carbapenem-resistant Enterobacteriaceae. As NDM-producing strains are only sporadically detected in Japan, attention should be provided to the community prevalence of NDM-producing E. coli strains to prevent nosocomial infections.Keywords: blaNDM-5, Escherichia coli, sequence type 405, IncFII, IncFIB
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".