Abstract
Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of K. pneumoniae genome data. Here we introduce Kleborate, a tool for analysing genomes of K. pneumoniae and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available Klebsiella genomes, including clinical isolates from a pan-European study of carbapenemase-producing Klebsiella, highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type K. pneumoniae from gut metagenomes.
Highlights
Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcareassociated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases
Our goal was to develop a single tool that can rapidly extract genotype information that is clinically relevant to K. pneumoniae and other members of the species complex in order to support genomic epidemiology and surveillance
We have previously reported genotyping schemes for the acquired K. pneumoniae virulence loci ybt, clb, iuc and iro[34,35], and K and O antigen typing implemented in the software Kaptive[36]
Summary
Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcareassociated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Klebsiella pneumoniae bacteria commonly colonize the mammalian gut, but are recognized as a major public health threat due to their ability to cause severe infections in healthcare settings and their association with antimicrobial resistance (AMR)[1,2]. Treatment of healthcare-associated (HA) K. pneumoniae infections is often limited by multidrug resistance (MDR) resulting from the accumulation of horizontally acquired AMR genes and mutations in core genes[2]. Invasive community-acquired infections are generally associated with so-called hypervirulent K. pneumoniae (hvKp) and are most commonly reported in East and Southeast Asia, or in individuals with East Asian ancestry[12]. The convergence of AMR and virulence in K. pneumoniae potentiates invasive and difficult-to-treat infections, and at least one fatal outbreak has been documented in China where carbapenemaseproducing hvKp are increasingly common[20,21,22,23,24]
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