title: KlebSeq, a Diagnostic Tool for Surveillance, Detection, and Monitoring of Klebsiella pneumoniae.
abstract: Health care-acquired infections (HAIs) kill tens of thousands of people each year and add significantly to health care 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 caused an urgent public health crisis. In the health care environment, patient colonization by 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 report, we describe the design and validation of KlebSeq, a highly informative screening tool that detects Klebsiella species and identifies clinically important strains and characteristics by 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, and 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 health care staff of the risk of infection and outbreak potential. KlebSeq also serves as a model for next-generation molecular tools for public health and health care, as expansion of this tool can be used for several other HAI agents or applications.
authors: Translational Genomics Research Institute, Flagstaff, Arizona, USA jbowers@tgen.org.
authors: Jolene R
authors: JR
authors: Bowers
authors: Translational Genomics Research Institute, Flagstaff, Arizona, USA.
authors: Darrin
authors: D
authors: Lemmer
authors: Microbial Genetics and Genomics, Flagstaff, Arizona, USA.
authors: Jason W
authors: JW
authors: Sahl
authors: Microbial Genetics and Genomics, Flagstaff, Arizona, USA.
authors: Talima
authors: T
authors: Pearson
authors: Translational Genomics Research Institute, Flagstaff, Arizona, USA.
authors: Elizabeth M
authors: EM
authors: Driebe
authors: Banner Health, Phoenix, Arizona, USA.
authors: Bette
authors: B
authors: Wojack
authors: Banner Health, Phoenix, Arizona, USA.
authors: Michael A
authors: MA
authors: Saubolle
authors: Translational Genomics Research Institute, Flagstaff, Arizona, USA.
authors: David M
authors: DM
authors: Engelthaler
authors: Translational Genomics Research Institute, Flagstaff, Arizona, USA Microbial Genetics and Genomics, Flagstaff, Arizona, USA.
authors: Paul
authors: P
authors: Keim
mesh_terms: D003428:Cross Infection / Q000175:diagnosis*; D024881:Drug Resistance, Bacterial; D062665:Epidemiological Monitoring; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D007710:Klebsiella Infections / Q000175:diagnosis*; D007711:Klebsiella pneumoniae / Q000235:genetics / Q000302:isolation & purification*; D008403:Mass Screening / Q000379:methods*; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D037521:Virulence Factors / Q000032:analysis
chemical_list: D037521:Virulence Factors