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Mutations in two component system (PhoPQ and PmrAB) in colistin resistant Klebsiella pneumoniae from North Indian tertiary care hospital

The Journal of Antibiotics volume 74, pages 450–457 (2021)Cite this article

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Abstract

Colistin resistance in Gram negative bacteria is mainly attributed to chromosomal mutations in Two Component Systems(TCS) PhoPQ and PmrAB and plasmid-borne genes(mcr and its variants). The aim of this study was to understand the molecular basis of colistin resistance in Klebsiella pneumoniae and determine clonal transmission, in a North Indian tertiary care hospital over a 2.5 year period. Antimicrobial susceptibility was determined by Vitek and colistin resistance was confirmed by broth microdilution. Carbapenemases(blaKPC, blaVIM, blaIMP, blaNDM, blaOXA-48) and mcr-1 screening was done by PCR. Mutations in chromosomal genes mgrB, phoP, phoQ, pmrA, pmrB were analysed. Sequence typing was performed by Multilocus sequence typing(MLST). OXA-48 was detected in thirteen isolates while three isolates co-expressed OXA-48 and NDM. The mcr-1 gene was absent in all 16 isolates. Deleterious mutations in mgrB included insertion sequences IS903 and ISkpn26 and a premature stop codon. A total of 18 point mutations were identified in PhoPQ and PmrAB TCS; of which, novel mutations were reported in phoQ (K46E, L322V, D152N, F373L, R249G), pmrB (P159R) and pmrA (D149L). Six different sequence types ST231, ST147, ST395, ST42, ST14 and ST101 were identified. Phylogenetic analysis showed that sequence types ST14, ST395 and ST147 are closely related to ST101 and all identified sequence types had a common ancestor ST231. Colistin resistance in K. pneumoniae was attributed to mutations in PhoPQ and PmrAB TCS, while location specific distribution of strains indicates clonal transmission. The results of this study will help in formulation of effective infection prevention and antimicrobial development strategies.

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Acknowledgements

The authors would like to express their gratitude to Prof. Pallab Ray, Post Graduate Institute of Medical Education and Research, Chandigarh, India and Prof. Balaji Veeraraghavan, Department of Clinical Microbiology, Christian Medical College, Vellore, India for providing  mcr-1 positive strain and carbapenemases positive strains respectively. Part of these results has also been presented as a poster at the AIIMS ASM-2020 conference in New Delhi, India in October 2020.

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Authors and Affiliations

  1. Department of Microbiology, Hamdard Institute of Medical Sciences and Research, Jamia Hamdard, New Delhi, 110062, India

    Pushpa Kumari Nirwan & Mridu Dudeja

  2. Department of Education and Research, Artemis Hospitals, Sector 51, Gurgaon, Haryana, 122001, India

    Pushpa Kumari Nirwan, Nirupama Chatterjee & Namita Jaggi

  3. Department of Microbiology, Artemis Hospitals, Sector 51, Gurgaon, Haryana, 122001, India

    Rajesh Panwar & Namita Jaggi

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  1. Pushpa Kumari Nirwan
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  5. Namita Jaggi
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Contributions

All authors contributed to the study conception and design. PKN—Study design, Laboratory methods, data analysis and manuscript writing; NC—Study design, Laboratory methods; manuscript correction RP—Isolate collection and Antibiotic susceptibility testing; MD and NJ—Study design and manuscript correction. All authors read and approved the final manuscript.

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Correspondence to Namita Jaggi.

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The study protocol was approved by Artemis Hospital Institutional Ethics Committee (AHS-IEC Reg No: ECR/53/Inst/HR/2013/RR-16). Waiver for consent was obtained as microbiological samples were considered a part of standard care procedures and keeping patient identity anonymous in the study. All authors provide their consent for publication.

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Nirwan, P.K., Chatterjee, N., Panwar, R. et al. Mutations in two component system (PhoPQ and PmrAB) in colistin resistant Klebsiella pneumoniae from North Indian tertiary care hospital. J Antibiot 74, 450–457 (2021). https://doi.org/10.1038/s41429-021-00417-2

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