Genomic and phylogenetic analysis of hypervirulent Klebsiella pneumoniae ST23 in Ireland

Hypervirulent <i>Klebsiella pneumoniae</i> (hv<i>Kp</i>) has emerged as a pathogen of global concern associated with invasive community-acquired infections. The combination of hypervirulence and carbapenem resistance can result in severe and difficult-to-treat infections. This retrospective study aimed to investigate the spread of hv<i>Kp</i> sequence type 23 (ST23) in Ireland and the convergence of hypervirulent (hv) and antimicrobial resistance genotypes. Short-read sequences (PE300) for 90 <i>K. pneumoniae</i> ST23 isolates were generated by the Galway Reference Laboratory Services (GRLS). Isolates were from screening swabs (<i>n</i>=59), invasive infections (<i>n</i>=18), non-invasive sites (<i>n</i>=12) and the hospital environment (<i>n</i>=1). The virulence and resistance content were assessed genomically using Kleborate (v2.2.0), ABRicate (v1.0.1) and Platon (v1.6). The <i>in vivo</i> virulence of the isolates was assessed using a murine model. All isolates were genotypically hv with 88/90 isolates having a maximal Kleborate virulence score of 5 including carriage of key genes. Eighty-two per cent of isolates (74/90) carried a carbapenemase gene (<i>bla</i> _OXA-48/<i>bla</i> _OXA-181/<i>bla</i> _NDM-1), and 42% carried resistance genes to 3 or more antimicrobial classes. Core genomic delineation revealed the isolates to be clonal with similar resistance and virulence profiles. Two distinct clusters of Irish isolates were detected consisting of 82/90 of the isolates. Isolates associated with carriage and infection demonstrated similar <i>in vivo</i> virulence. An established clone of hv<i>Kp</i> ST23 is circulating within Ireland and causing both colonization and infection of patients. The lack of reliable screening methods for hv<i>Kp</i> makes its detection and control in the healthcare setting challenging.