Resistome of carbapenem- and colistin-resistant Klebsiella pneumoniae clinical isolates

Abstract

The emergence and dissemination of carbapenemases, bacterial enzymes able to inactivate most β-lactam antibiotics, in Enterobacteriaceae is of increasing concern. The concurrent spread of resistance against colistin, an antibiotic of last resort, further compounds this challenge further. Whole-genome sequencing (WGS) can play a significant role in the rapid and accurate detection/characterization of existing and emergent resistance determinants, an essential aspect of public health surveillance and response activities to combat the spread of antimicrobial resistant bacteria. In the current study, WGS data was used to characterize the genomic content of antimicrobial resistance genes, including those encoding carbapenemases, in 10 multidrug-resistant Klebsiella pneumoniae isolates from Pakistan. These clinical isolates represented five sequence types: ST11 (n = 3 isolates), ST14 (n = 3), ST15 (n = 1), ST101 (n = 2), and ST307 (n = 1). Resistance profiles against 25 clinically-relevant antimicrobials were determined by broth microdilution; resistant phenotypes were observed for at least 15 of the 25 antibiotics tested in all isolates except one. Specifically, 8/10 isolates were carbapenem-resistant and 7/10 isolates were colistin-resistant. The blaNDM-1 and blaOXA-48 carbapenemase genes were present in 7/10 and 5/10 isolates, respectively; including 2 isolates carrying both genes. No plasmid-mediated determinants for colistin resistance (e.g. mcr) were detected, but disruptions and mutations in chromosomal loci (i.e. mgrB and pmrB) previously reported to confer colistin resistance were observed. A blaOXA-48-carrying IncL/M-type plasmid was found in all blaOXA-48-positive isolates. The application of WGS to molecular epidemiology and surveillance studies, as exemplified here, will provide both a more complete understanding of the global distribution of MDR isolates and a robust surveillance tool useful for detecting emerging threats to public health.

Emerging high-risk ST101 and ST307 carbapenem-resistant Klebsiella pneumoniae clones from bloodstream infections in Southern Italy

“…Interestingly, we also identified many plasmids in the characterized isolates, especially IncF-type and although, according to Lomonaco et al [37], these mutations seem not to be related to colistin resistance. However, these two isolates showed phenotypic resistance to colistin.…”

“…Moreover, ST101 is a high-risk for mediating further spread of carbapenem resistance [34,35]. In Italy, this ST has generally been reported as sporadic [7,10,11,16,17,32], with higher prevalence when the studied strains were isolated from any infection site [34,36,37]. We found that approximately 18% of the characterized strains belonged to ST101, while no isolates belonging to this ST were identified in the report of Calia et al in Southern Italy [28].…”

Emerging high-risk ST101 and ST307 carbapenem-resistant Klebsiella pneumoniae clones from bloodstream infections in Southern Italy

“…Traditionally, colistin resistance in KP is associated with mutations in chromosomal genes [43]. Among the isolates characterized in our study, two carried the L213M substitutions in the chromosomal pmrB gene, although, according to Lomonaco et al [37], these mutations seem not to be related to colistin resistance. However, these two isolates showed phenotypic resistance to colistin.…”

Tracking short-term changes in the genetic diversity and antimicrobial resistance of OXA-232-producing Klebsiella pneumoniae ST14 in clinical settings

“…Klebsiella pneumoniae ST14 is a major reservoir for bla OXA-232 and sometimes co-harbours bla NDM-1 [6e8]. Moreover, it has been encountered in neonatal and paediatric infections along with other plasmid-mediated antimicrobial-resistance genes, including bla KPC-2 , bla CTX-M- 15 and aac(6ʹ)Ib-cr, suggesting that this species evolves by obtaining extra plasmids in clinical environments in which diverse genes are present [9].…”