GENOTYPIC CHARACTERIZATION OF COLISTIN RESISTANCE GENES AMONG MULTIDRUG-RESISTANT GRAM-NEGATIVE BACILLI IN A TERTIARY-CARE CENTRE: MOLECULAR CORRELATION WITH PHENOTYPIC PROFILES
Main Article Content
Keywords
Colistin resistance; mcr-1 gene; mgrB mutation; pmrA/pmrB; multidrug-resistant Gram-negative bacilli; plasmid-mediated resistance; phenotype–genotype correlation; Klebsiella pneumoniae.
Abstract
Colistin resistance among multidrug-resistant Gram-negative bacilli (MDR-GNB) is an emerging global concern, threatening the efficacy of last-resort antibiotics. The detection of plasmid-borne mcr genes revolutionized the understanding of colistin resistance, indicating horizontal transfer potential among bacterial species¹.
Objectives:
To characterize colistin-resistance genes (mcr-1–mcr-10, pmrA/B, mgrB, phoP/Q, lpxA/C/D) among MDR-GNB isolated in a tertiary-care centre, correlate genotypic findings with phenotypic MICs, and analyze epidemiological implications.
Methods:
A total of 150 MDR-GNB isolates (Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii) were collected. Colistin MICs were determined by broth microdilution (BMD) as per CLSI 2024 guidelines². Genomic DNA was extracted (Qiagen Mini Kit) and PCR targeted mcr-1–mcr-10¹², mgrB, pmrA/B, phoP/Q, and lpxA/C/D³. Amplicons were sequenced and analyzed via BLAST⁴. Plasmid profiling (S1-PFGE, replicon typing)¹⁴ and clonal relatedness (ERIC-PCR)¹⁵ were performed.
Results:
Twenty (13.3%) isolates were phenotypically colistin-resistant. mcr-1 (4%) and mcr-3 (2%) were detected, mainly in K. pneumoniae and E. coli ⁶. mgrB disruption (IS5 insertion) occurred in five K. pneumoniae¹⁷; pmrB mutations (A79V, R256G) in A. baumannii¹⁸. Genotype–phenotype concordance was 86%. ERIC-PCR revealed two ICU clusters, indicating nosocomial dissemination via IncX4 plasmids.
Conclusion:
Colistin resistance in MDR-GNB results from both plasmid-mediated mcr genes and chromosomal mutations (mgrB, pmrB). Combined phenotypic and molecular surveillance under WHO GLASS is essential for accurate detection and infection-control interventions.
References
2. Falagas ME, Kasiakou SK. Toxicity of polymyxins. Clin Infect Dis. 2006;43(6):754-62. doi:10.1086/506319
3. Olaitan AO, Morand S, Rolain JM. Mechanisms of polymyxin resistance. Int J Antimicrob Agents. 2014;44(5):402-10. doi:10.1016/j.ijantimicag.2014.06.007
4. Liu YY et al. Emergence of plasmid-mediated colistin resistance MCR-1. Lancet Infect Dis. 2016;16(2):161-168. doi:10.1016/S1473-3099(15)00424-7
5. Carattoli A, et al. In silico analysis of mcr gene variants. Antimicrob Agents Chemother. 2017;61(7):e00404-17. doi:10.1128/AAC.00404-17
6. Cannatelli A, et al. mgrB inactivation and colistin resistance. Antimicrob Agents Chemother. 2014;58(10):5696-703. doi:10.1128/AAC.03120-14
7. Sun J, et al. Global spread of mcr genes. Front Microbiol. 2018;9:2433. doi:10.3389/fmicb.2018.02433
8. Wang R, et al. Co-occurrence of mcr and carbapenemase genes. Front Microbiol. 2020;11:563406. doi:10.3389/fmicb.2020.563406
9. Shankar C, et al. Molecular mechanisms of colistin resistance in K. pneumoniae in India. Front Microbiol. 2017;7:2135. doi:10.3389/fmicb.2016.02135
10. Isenberg HD. Clinical Microbiology Procedure Handbook. ASM Press; 2004.
11. CLSI. M100: Performance Standards for Antimicrobial Susceptibility Testing. 34th ed. 2024.
12. Rebelo AR, et al. Multiplex PCR for mcr detection. Antimicrob Agents Chemother. 2018;62(5):e02446-17. doi:10.1128/AAC.02446-17
13. Ng LK, et al. Mutation analysis using PROVEAN. Bioinformatics. 2019;35(12):2051–2058. doi:10.1093/bioinformatics/bty1004
14. Carattoli A, et al. Plasmid replicon typing. Antimicrob Agents Chemother. 2015;59(7):4478-84. doi:10.1128/AAC.00029-15
15. Versalovic J, et al. ERIC-PCR genotyping of bacterial isolates. J Clin Microbiol. 1994;32(3):784-90. doi:10.1128/jcm.32.3.784-790.1994
16. Begum Y, et al. mcr-1 detection in South India. J Infect Public Health. 2022;15(1):15-21. doi:10.1016/j.jiph.2021.09.015
17. Naparstek L, et al. IS5-mediated mgrB disruption. Antimicrob Agents Chemother. 2017;61(5):e00568-17. doi:10.1128/AAC.00568-17
18. Li R, et al. IncX4-mediated mcr-1 transfer. Antimicrob Agents Chemother. 2018;62(6):e00185-18. doi:10.1128/AAC.00185-18
19. Shen Y, et al. Clonal dissemination of mcr-1 strains. Lancet Infect Dis. 2020;20(8):983-992. doi:10.1016/S1473-3099(20)30078-3
20. Jayol A, et al. Correlation between mcr genes and phenotypic MICs. J Glob Antimicrob Resist. 2018;13:28-35. doi:10.1016/j.jgar.2018.03.002
21. Li Y, et al. Heteroresistance to colistin in A. baumannii. Antimicrob Agents Chemother. 2019;63(6):e02174-18. doi:10.1128/AAC.02174-18
22. Skov RL, Monnet DL. Plasmid-mediated colistin resistance in animals and humans. Euro Surveill. 2016;21(9):30155. doi:10.2807/1560-7917.ES.2016.21.9.30155
23. ICMR-AMRSN Annual Report 2023. New Delhi: ICMR; 2024.
24. Glover RE, et al. LAMP and CRISPR diagnostics for AMR. J Clin Microbiol. 2023;61(4):e01755-22. doi:10.1128/jcm.01755-22
25. Didelot X, et al. Genomic epidemiology in AMR surveillance. Nat Rev Genet. 2021;22(8):507–523. doi:10.1038/s41576-021-00354-0
26. Wang Y, et al. Characterization of mcr-3. Front Microbiol. 2018;9:980. doi:10.3389/fmicb.2018.00980
27. Taneja N, et al. Epidemiology of colistin-resistant K. pneumoniae. Infect Dis Now. 2021;51(7):575-582. doi:10.1016/j.idnow.2021.03.005
28. Partridge SR, et al. Mobile genetic elements in AMR. Nat Rev Microbiol. 2018;16(3):156–170. doi:10.1038/nrmicro.2017.146
29. Shafiq M, et al. WGS analysis of mcr plasmids. Microb Genom. 2023;9(6):mgen000980. doi:10.1099/mgen.0.000980
30. WHO. Global Antimicrobial Resistance and Use Surveillance System (GLASS) Report 2023. Geneva: WHO; 2023.
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Ms Ashma Ajeej
PhD Scholar, Department of Microbiology, Index Medical College Hospital & Research Centre,
Indore, India.
Dr Ramanath Karicheri
Professor, Department of Microbiology, Index Medical College Hospital & Research Centre, Indore, India.