KlebSeq: A Diagnostic Tool for Surveillance, Detection, and Monitoring of Klebsiella pneumoniae

Healthcare-acquired infections (HAIs) kill tens of thousands of people each year and add significantly to healthcare costs. Multidrug resistant and epidemic strains are a large proportion of HAI agents, and multidrug resistant strains of Klebsiella pneumoniae, a leading HAI agent, have become an urgent public health crisis. In the healthcare environment, patient colonization of K. pneumoniae precedes infection, and transmission via colonization leads to outbreaks. Periodic patient screening for K. pneumoniae colonization has the potential to curb the number of HAIs. In this study, we describe the design and validation of KlebSeq, a highly informative screening tool that detects Klebsiella species and identifies clinically important strains and characteristics using highly multiplexed amplicon sequencing without a live culturing step. We demonstrate the utility of this tool on several complex specimen types including urine, wound swabs and tissue, several types of respiratory, and fecal specimens, showing K. pneumoniae species and clonal group identification and antimicrobial resistance and virulence profiling, including capsule typing. Use of this amplicon sequencing tool to screen patients for Klebsiella carriage could inform healthcare staff of the risk of infection and outbreak potential. KlebSeq also serves as a model of next generation molecular tools for public health and healthcare, as expansion of this tool can be used for several other HAI agents or applications.