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Volume 10, Issue 2

Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant causing invasive infections in the USA Open Access

Abstract

Despite the notable clinical impact, recent molecular epidemiology regarding third-generation-cephalosporin-resistant (3GC-R) in the USA remains limited. We performed whole-genome sequencing of 3GC-R bacteraemia isolates collected from March 2016 to May 2022 at a tertiary care cancer centre in Houston, TX, USA, using Illumina and Oxford Nanopore Technologies platforms. A comprehensive comparative genomic analysis was performed to dissect population structure, transmission dynamics and pan-genomic signatures of our 3GC-R . population. Of the 178 3GC-R bacteraemias that occurred during our study time frame, we were able to analyse 153 (86 %) bacteraemia isolates, 126 initial and 27 recurrent isolates. While isolates belonging to the widely prevalent clonal group (CG) 258 were rarely observed, the predominant CG, 307, accounted for 37 (29 %) index isolates and displayed a significant correlation (Pearson correlation test value=0.03) with the annual frequency of 3GC-R . bacteraemia. Interestingly, only 11 % (4/37) of CG307 isolates belonged to the commonly detected ‘Texas-specific’ clade that has been observed in previous Texas-based antimicrobial-resistance surveillance studies. We identified nearly half of our CG307 isolates (=18) belonged to a novel, monophyletic CG307 sub-clade characterized by the chromosomally encoded and unique accessory genome content. This CG307 sub-clade was detected in various regions of the USA, with genome sequences from 24 additional strains becoming recently available in the National Center for Biotechnology Information (NCBI) SRA database. Collectively, this study underscores the emergence and dissemination of a distinct CG307 sub-clade that is a prevalent cause of 3GC-R . bacteraemia among cancer patients seen in Houston, TX, and has recently been isolated throughout the USA.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): accessory genome , clonal group 307 , multidrug-resistant K. pneumoniae surveillance , nosocomial transmission and third-generation-cephalosporin-resistant Klebsiella pneumoniae
Funding
This study was supported by the:
  • National Institute of Allergy and Infectious Diseases (Award P01AI152999)
    • Principle Award Recipient: SamuelA Shelburne
  • National Institute of Allergy and Infectious Diseases (Award R21AI151536)
    • Principle Award Recipient: SamuelA Shelburne
  • National Institute of Allergy and Infectious Diseases (Award T32 AI141349)
    • Principle Award Recipient: WilliamCharles Shropshire
  • Peter and Cynthia Hu scholarship
    • Principle Award Recipient: Chin-TingWu
  • Dell Family Fund for the School of Health Professional scholarship
    • Principle Award Recipient: SelvalakshmiSelvaraj Anand
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2024-02-26
2024-04-27
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Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA
M Gen 10, 001201 (2024); https://doi.org/10.1099/mgen.0.001201
/content/journal/mgen/10.1099/mgen.0.001201
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