Abstract
Carbapenem resistant Klebsiella pneumoniae causing severe infection resulting in morbidity and mortality have become a global health concern. K. pneumoniae with sequence type ST147 is an international high-risk clonal lineage, genomic studies have been done on K. pneumoniae ST147 isolated from clinical origin but genomic data for environmental K. pneumoniae ST147 is very scarce. Herein, K. pneumoniae IITR008, an extensively drug resistant and potentially hypervirulent bacterium, was isolated from Triveni Sangam, the confluence of three rivers where religious congregations are organized. Phenotypic, genomic and comparative genomic analysis of strain IITR008 was performed. Antibiotic susceptibility profiling revealed resistance to 9 different classes of antibiotics including ß-lactams, ß-lactam combination agents, carbapenem, aminoglycoside, macrolide, quinolones, cephams, phenicol, and folate pathway antagonists and was found to be susceptible to only tetracycline. The strain IITR008 possesses hypervirulence genes namely, iutA and iroN in addition to numerous virulence factors coding for adherence, regulation, iron uptake, secretion system and toxin. Both the IITR008 chromosome and plasmid pIITR008_75 possess a plethora of clinically relevant antibiotic-resistant genes (ARGs) including blaCTX-M-15, blaTEM-1, and blaSHV-11, corroborating the phenotypic resistance. Comparative genomic analysis with other ST147 K. pneumoniae provided insights on the phylogenetic clustering of IITR008 with a clinical strain isolated from a patient in Czech with recent travel history in India and other clinical strains isolated from India and Pakistan. According to the ‘One Health’ perspective, surveillance of antibiotic resistance in the environment is crucial to impede its accelerated development in diverse ecological niches.
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The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.
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Authors are grateful to the Director, CSIR-IITR for necessary facilities provided to conduct the research. DS thank CSIR for providing CSIR-SRF fellowship.
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This work was partially funded and supported by institutional grants received from the Council of Scientific & Industrial Research—Indian Institute of Toxicology Research (CSIR-IITR). This manuscript carries the CSIR-IITR communication number: IITR/SEC/MS/2023/58.
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Conceptualization: Natesan Manickam; Methodology: Deeksha Singh, Natesan Manickam; Formal analysis: Deeksha Singh Natesan Manickam, Shilpee Pal, Srikrishna Subramanian; Writing-original draft preparation: Deeksha Singh; Writing-review and editing: Deeksha Singh, Natesan Manickam, Shilpee Pal, Srikrishna Subramanian; Funding acquisition: Natesan Manickam; Validation: Deeksha Singh, Natesan Manickam, Srikrishna Subramanian; and Supervision: Natesan Manickam, Srikrishna Subramanian. All authors have read and approved the manuscript.
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Singh, D., Pal, S., Subramanian, S. et al. Comparative genomics of an extensively drug resistant strain Klebsiella pneumoniae IITR008 with international high-risk clonal lineage ST147 isolated from river water. Antonie van Leeuwenhoek 117, 57 (2024). https://doi.org/10.1007/s10482-024-01955-z
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DOI: https://doi.org/10.1007/s10482-024-01955-z