Genomic characterization of carbapenem and colistin-resistant Klebsiella pneumoniae isolates from humans and dogs

Ruttana Pachanon; Nwai Oo Khine; Nathita Phumthanakorn; Thidathip Wongsurawat; Waree Niyomtham; Tanittha Chatsuwan; David J Hampson; Nuvee Prapasarakul

doi:10.3389/fvets.2024.1386496

Genomic characterization of carbapenem and colistin-resistant Klebsiella pneumoniae isolates from humans and dogs

Front Vet Sci. 2024 May 21:11:1386496. doi: 10.3389/fvets.2024.1386496. eCollection 2024.

Authors

Ruttana Pachanon¹, Nwai Oo Khine¹, Nathita Phumthanakorn², Thidathip Wongsurawat³, Waree Niyomtham¹, Tanittha Chatsuwan⁴, David J Hampson⁵, Nuvee Prapasarakul^{1

6}

Affiliations

¹ Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.
² Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand.
³ Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
⁴ Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
⁵ School of Veterinary Medicine, Murdoch University, Perth, WA, Australia.
⁶ Center of Excellence in Diagnosis and Monitoring of Animal Pathogens (DMAP), Bangkok, Thailand.

Abstract

Introduction: Carbapenem and colistin-resistant Enterobacteriaceae, including Klebsiella pneumoniae, have become a growing global concern, posing a significant threat to public health. Currently, there is limited information about the genetic background of carbapenem and colistin-resistant K. pneumoniae isolates infecting humans and dogs in Thailand. This study aimed to characterize carbapenem and colistin-resistant genes in six resistant K. pneumoniae clinical isolates (three from humans and three from dogs) which differed in their pulse field gel electrophoresis profiles.

Methods: Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), antimicrobial susceptibility testing, and whole-genome sequencing were employed to identify and analyze the isolates.

Results and discussion: All six isolates were carbapenemase-producing K. pneumoniae isolates with chromosomally carried bla_SHV, fosA, oqxA and oqxB genes, as well as nine to 21 virulence genes. The isolates belonged to five multilocus sequence types (STs): one isolate from a human and one from a dog belonged to ST16, with the other two human isolates being from ST340 and ST1269 and the other two dog isolates were ST147 and ST15. One human isolate and two dog isolates harbored the same bla_OXA-232 gene on the ColKP3 plasmid, and one dog isolate carried the bla_OXA-48 gene on the IncFII plasmid. Notably, one human isolate exhibited resistance to colistin mediated by the mcr-3.5 gene carried on the IncFII plasmid, which co-existed with resistance determinants to other antibiotics, including aminoglycosides and quinolones. In conclusion, this study provides a comprehensive characterization of both chromosome- and plasmid-mediated carbapenem and colistin resistance in a set of K. pneumoniae clinical isolates from unrelated humans and dogs in Thailand. The similarities and differences found contribute to our understanding of the potential widescale dissemination of these important resistance genes among clinical isolates from humans and animals, which in turn may contribute to outbreaks of emerging resistant clones in hospital settings.

Keywords: Klebsiella pneumoniae; carbapenem resistance; colistin resistance; plasmid-mediated resistance; whole genome analysis.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study was funded by the Thailand Science Research and Innovation Fund Chulalongkorn University (CU_FRB65_hea (87)_192_31_11) and C2F Postdoctoral Scholarship, Chulalongkorn University. The open access fee for this article was paid by the Office of Research Affairs, Chulalongkorn University.