A Novel Technique to Characterize Klebsiella pneumoniae Populations Indicates that Mono-Colonization is Associated...

Klebsiella pneumoniae and related species are a common cause of healthcare-associated infections. The gut is a major Klebsiella reservoir and gut colonization is a risk factor for developing an extraintestinal Klebsiella infection. Patients can be colonized by multiple Klebsiella strains or even species in the gut simultaneously, and there is high concordance between the gut colonizing- and infection causing- strains. The detection and characterization of colonizing strains is critical for a better understanding of the progression to infection and for developing interventions for colonized patients. However, the association between mixed or mono-colonization and subsequent infection is unknown. In this study, we developed an amplicon-based sequencing method called wzi-Seq that enables the detection and quantification of Klebsiella strains from complex samples and mixtures using the conserved capsule gene wzi as a molecular barcode. This method is highly accurate and precise with a sensitivity of 93% and specificity of 99.8% in mixtures containing as many as 58 unique wzi types. The assay was validated analytically and applied to an established case and control cohort. We determined that 63.2% (108/171) patients were mono-colonized with a single Klebsiella strain while 36.8% (63/171) had mixed colonization with multiple Klebsiella strains. Controlling for patient variables in multivariate analysis, we determined that mono-colonization was significantly (p = 0.034) associated with infection. Characterization of Klebsiella colonizing populations could improve the accuracy of assessing infection risk and enable targeted interventions to prevent these healthcare-associated infections.