Emergence of KPC-3-and OXA-181-producing ST13 and ST17 Klebsiella pneumoniae in Portugal: genomic insights on national and international dissemination

Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) strains are of particular concern, especially strains with mobilizable carbapenemase genes such as bla(KPC), bla(NDM) or bla(OXA-48), given that carbapenems are usually the last line drugs in the beta-lactam class and, resistance to this sub-class is associated with increased mortality and frequently co-occurs with resistance to other antimicrobial classes. Objectives To characterize the genomic diversity and international dissemination of CRKP strains from tertiary care hospitals in Lisbon, Portugal. Methods Twenty CRKP isolates obtained from different patients were subjected to WGS for species confirmation, typing, drug resistance gene detection and phylogenetic reconstruction. Two additional genomic datasets were included for comparative purposes: 26 isolates (ST13, ST17 and ST231) from our collection and 64 internationally available genomic assemblies (ST13). Results By imposing a 21 SNP cut-off on pairwise comparisons we identified two genomic clusters (GCs): ST13/GC1 (n = 11), all bearing bla(KPC-3), and ST17/GC2 (n = 4) harbouring bla(OXA-181) and bla(CTX-M-15) genes. The inclusion of the additional datasets allowed the expansion of GC1/ST13/KPC-3 to 23 isolates, all exclusively from Portugal, France and the Netherlands. The phylogenetic tree reinforced the importance of the GC1/KPC-3-producing clones along with their rapid emergence and expansion across these countries. The data obtained suggest that the ST13 branch emerged over a decade ago and only more recently did it underpin a stronger pulse of transmission in the studied population. Conclusions This study identifies an emerging OXA-181/ST17-producing strain in Portugal and highlights the ongoing international dissemination of a KPC-3/ST13-producing clone from Portugal.

Automated summary

This study characterized the genomic diversity and international dissemination of CRKP strains from tertiary care hospitals in Lisbon, Portugal. Two genomic clusters, ST13/GC1 and ST17/GC2, were identified. Additionally, an emerging OXA-181/ST17-producing strain in Portugal and the ongoing international dissemination of a KPC-3/ST13-producing clone were highlighted.