Duration and dynamics of Klebsiella pneumoniae species complex gut carriage in a community-based adult population cohort

Abstract

Klebsiella pneumoniae species complex (KpSC) is a group of closely related bacterial species including Klebsiella pneumoniae sensu stricto known as a major human opportunistic pathogen associated with healthcare. KpSC gut carriage is a major risk factor for clinical infections and elderly people (≥60y) are at the risk of KpSC gut colonisation. This master project investigated the presence, duration and dynamics of KpSC gut carriage among a community-based general adult population (n=108, 62% female; ≥47 y), recruited from the previous Tromsø7 Cross-sectional KpSC Carriage Study, during six months (September 2021 to March 2022). Monthly faecal samples were screened for KpSC by ZKIR-qPCR, and whole metagenome sequencing (WMS) was used for microbiome analysis and ST typing by StrainGE. qPCR confirmed the majority of the population being transient carriers (76.5%), a minority of the population were non-carriers (9.1%), and few were chronic carriers (14.1%). Alpha diversity analysis did not show any significant difference among the three KpSC carriage groups. Alpha diversity significantly decreased with increased KpSC relative abundance in the age group below 60y. The chronic carriers were significantly older than the transient carriers. Evaluation of StrainGE tool for analysing KpSC phylogenetic relationships from metagenome samples revealed that StrainGE accurately identified two out of the three phylogeny relations. Furthermore, ST analysis by StrainGE identified a highly diverse KpSC population with 13 STs and two phylogroups detected in 41 metagenome samples from seven participants (one transient and six chronic carriers). Three out of the six chronic carriers retained a single ST in all six months. This study indicates that there might be an association of gut colonisation with KpSC with age and gut microbiome. The accuracy of StrainGE suggests that it might be a useful tool in epidemiological surveillance and outbreak investigation using metagenomic samples. The diversity of KpSC in gut colonisation highlights the niche-specific adaptive capacity of the KpSC members and the challenges for the development of decolonisation strategies.