Abstract
Plasmids play a fundamental role in the evolution of bacteria by allowing them to adapt to different environments and acquire, through horizontal transfer, genes that confer resistance to different classes of antibiotics. Using the available in vitro and in silico plasmid typing systems, we analyzed a set of isolates and public genomes of K. variicola to study its plasmid diversity. The resistome, the plasmid multilocus sequence typing (pMLST), and molecular epidemiology using the MLST system were also studied. A high frequency of IncF plasmids from human isolates but lower frequency from plant isolates were found in our strain collection. In silico detection revealed 297 incompatibility (Inc) groups, but the IncFIBK (216/297) predominated in plasmids from human and environmental samples, followed by IncFIIK (89/297) and IncFIA/FIA(HI1) (75/297). These Inc groups were associated with clinically important ESBL (CTX-M-15), carbapenemases (KPC-2 and NDM-1), and colistin-resistant genes which were associated with major sequence types (ST): ST60, ST20, and ST10. In silico MOB typing showed 76% (311/404) of the genomes contained one or more of the six relaxase families with MOBF being most abundant. We identified untypeable plasmids carrying blaKPC-2, blaIMP-1, and blaSHV-187 but for which a relaxase was found; this may suggest that novel plasmid structures could be emerging in this bacterial species. The plasmid content in K. variicola has limited diversity, predominantly composed of IncFIBK plasmids dispersed in different STs. Plasmid detection using the replicon and MOB typing scheme provide a broader context of the plasmids in K. variicola. This study showed that whole-sequence-based typing provides current insights of the prevalence of plasmid types and their association with antimicrobial resistant genes in K. variicola obtained from humans and environmental niches.
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Data availability
The draft genome sequences of K. variicola 06–268, 4880, 9635, and VI were deposited in GenBank under accession numbers; NZ_CXOZ00000000.1, CXPB00000000.1, and JAGMVR000000000.1, respectively.
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Acknowledgements
The authors thank Alejandro Sánchez Pérez for his technical assistance.
Funding
This work was supported by grant 347316 FORDECYT-PRONACES from SEP-CONACyT (Secretaría de Educación Pública-Consejo Nacional de Ciencia y Tecnología).
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Conceived and designed the study: JDB, NRM, and UGR. Performed the experiments: JDB, DMG, HBC, RSR, JART, and AAV. Analyzed and interpreted the data: JDB, NRM, MD, HBC, AAV, and UGR. Contributed reagents, materials, analysis tools, or data: RSR, EAV, JART, and UGR. Wrote the paper: JDB, NRM, and UGR. Revised and edited the paper: MD, NRM, and UGR.
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The laboratory procedures carried out in this project with plant tissues were reviewed and approved by the research, biosafety, and ethics commissions of the National Institute of Public Health.
This project was exempt from review by the Ethic Commission at National Institute of Public Health because it does not involve human subjects and/or it is not an academic study and/or it does not include the analysis of data previously obtained from another study requiring the patients’ informed consent. On the other hand, the bacteria included in the study were obtained by routine procedures in each of the hospitals involved.
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Josefina Duran-Bedolla and Nadia Rodríguez-Medina have contributed equally to this research.
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Duran-Bedolla, J., Rodríguez-Medina, N., Dunn, M. et al. Plasmids of the incompatibility group FIBK occur in Klebsiella variicola from diverse ecological niches. Int Microbiol 26, 917–927 (2023). https://doi.org/10.1007/s10123-023-00346-0
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DOI: https://doi.org/10.1007/s10123-023-00346-0