Genomic and phylogenetic analysis of hypervirulent Klebsiella pneumoniae ST23 in Ireland
Maria Maguire, Niall DeLappe, Ciaran Clarke, Alma Touhy, Ulrike MacDonald, Alan D. Hutson, Martin Cormican, Wendy Brennan, Genevieve Devane, Dearbháile Morris, Simone C. Coughlan, Georgios Miliotis, Thomas A. Russo, Liam P. Burke
Abstract
Hypervirulent Klebsiella pneumoniae (hv Kp ) 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 Kp sequence type 23 (ST23) in Ireland and the convergence of hypervirulent (hv) and antimicrobial resistance genotypes. Short-read sequences (PE300) for 90 K. pneumoniae ST23 isolates were generated by the Galway Reference Laboratory Services (GRLS). Isolates were from screening swabs ( n =59), invasive infections ( n =18), non-invasive sites ( n =12) and the hospital environment ( n =1). The virulence and resistance content were assessed genomically using Kleborate (v2.2.0), ABRicate (v1.0.1) and Platon (v1.6). The in vivo 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 ( bla OXA-48 / bla OXA-181 / bla 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 in vivo virulence. An established clone of hv Kp ST23 is circulating within Ireland and causing both colonization and infection of patients. The lack of reliable screening methods for hv Kp makes its detection and control in the healthcare setting challenging.