Genome analysis of an OXA-48-producing carbapenem- and colistin-resistant Klebsiella pneumoniae sequence type 11 clone isolated from an inpatient

Background: Colistin is one of the last-resort therapeutic antibiotics used to control carbapenem-resistant Klebsiella pneumoniae. However, the emergence of colistin-resistant strains with high mortality and morbidity has become a new challenge. Therefore, it is crucial to characterize the genotypic features of carbapenem- and colistin-resistant K. pneumoniae (CCKP) isolates to implement public health intervention strategies. Methods: In this study, we analyzed the whole genome of an OXA-48-producing CCKP strain for molecular characterization of antimicrobial resistance (AMR) as well as comparative genome and plasmid analysis. Results: The whole-genome analysis showed that IRAN-43 genome possessed 140 contigs with 5,585,691 bp length, GC content of 56.9% and N50 score of 200,728. Multi-locus sequence typing (MLST) analysis showed that this K. pneumoniae strain belonged to sequence type (ST) 11. Single amino acid substitutions associated with colistin resistance were found in PhoP (D150G), PmrB (R256G) and RamA (I25T). In addition, two plasmids harboring qnrS1, tetR, tetB (plasmid-1) and bla(OXA-48) (plasmid-2) were discovered. No plasmid-mediated colistin resistance (mcr) genes were detected. Integrative conjugative element of K. pneumoniae (ICEKp)4 variant was detected as well as cps locus length of 22,156 bp encoding 17 open reading frames (ORFs) which belonged to K. pneumoniae capsular locus (KL)15-1. Conclusion: CCKP has been increasingly reporting from Iran. High frequency of antibiotic resistance genes among ST11 suggests that stricter control measures are needed to prevent the spread of this clone in hospital settings.

Automated summary

The study analyzed a carbapenem- and colistin-resistant Klebsiella pneumoniae strain producing OXA-48, identifying single amino acid substitutions associated with colistin resistance and discovering two plasmids carrying specific genes. The increasing reports of CCKP in Iran highlight the need for stricter control measures to prevent the spread of this clone.