Carbapenemase-producing hypervirulent Klebsiella pneumoniae in Alberta, Canada, 2016-2024

Hypervirulent Klebsiella pneumoniae (hvKp) can cause invasive community-acquired infections in healthy adults. HvKp is usually susceptible to most antibiotics; however, multi-drug resistance, including to carbapenems, is emerging. This is especially concerning due to the combination of disease severity and antibiotic resistance. Recent reports of the ST23 lineage of hvKp has raised alarms globally, making reporting of these cases significant.

Carbapenemase-producing K. pneumoniae (CP-Kp) in Alberta, Canada were screened for the presence of hypervirulence genes associated with the hypervirulent phenotype. A hypermucoviscous string test was performed on all isolates, and genomes were sequenced using both Illumina NextSeq and Oxford Nanopore Technologies platforms. The presence of hypervirulence-associated genes (ybt, clb, iuc, iro, rmpA/A2) in the assembled genomes was determined.

Eight different sequence types (ST) were observed among the 16 cases identified, including several global high-risk lineages (ST11, ST15, ST231, ST147, and ST395) and one hypervirulent lineage (ST23). Carbapenemase genes included bla _NDM-1 (n = 1), bla _OXA-48-type (n = 7), or both bla _NDM + bla _OXA-48-type (n = 8). The ST23 isolate harboured ybt and clb on the chromosome, iro and iuc on a 229.9 kb IncFIB,IncHI1B virulence plasmid, and bla _OXA-48 on a 92.3 kb IncFIA,IncFII plasmid. Almost half of the isolates co-harboured virulence genes and a carbapenemase (bla _NDM-1, n = 4 or bla _NDM-5, n = 3) on the same plasmid, creating hybrid plasmids. Phenotypically, however, 81% of isolates (n = 13) were string test-negative.

These data highlights the presence of high-risk lineages of hvKp in the Canadian landscape, as well as the first report of ST23 in Canada.