Human Gut Colonisation by the Klebsiella pneumoniae Species Complex: Detection, Duration, Dynamics, and Microbiota Associations

• Main Author: Lindstedt, Kenneth
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: UiT The Arctic University of Norway 2024
• Subjects: Klebsiella pneumoniae; qPCR; whole metagenomic sequencing; gastrointestinal colonization; sequence type; longitudinal; colonization resistance; antimicrobial resistance; DOKTOR-003; Tromsø
• Online Access: https://hdl.handle.net/10037/33627

The Klebsiella pneumoniae Species Complex (KpSC) is an important group of human pathogens, of which, Klebsiella pneumoniae is most clinically important and frequently associated with antimicrobial resistance (AMR). K. pneumoniae gastrointestinal tract (GIT) colonisation is a key infection risk factor and hub for AMR dissemination. Here we investigated and compared the ZKIR-qPCR and whole metagenomic sequencing (WMS) for KpSC detection, quantification, and sequence type (ST) analysis from faecal samples. These tools were then applied to samples from 108 community-based adults recruited from the general population in Tromsø municipality, collected monthly for six months, to investigate the duration, dynamics, host- and microbiota-associations of KpSC GIT colonisation. In paper I, we demonstrated the ZKIR-qPCR had the highest sensitivity, positive in 52/52 KpSC culture-positive samples, and 11/51 and 23/47 culture-negative samples, using a direct-faecal and culture-enrichment method, respectively. WMS had lower sensitivity and was inclined to false positives at low KpSC abundances. Both tools accurately quantified KpSC abundance. Paper II showed WMS performed accurate KpSC ST detection, agreeing with single colony whole genome sequencing in 44/49 and 46/49 culture-enriched faecal samples using two bioinformatic tools, StrainGE and mSWEEP, respectively. Both tools could detect within-sample ST diversity and StrainGE could recreate accurate phylogenetic relationships between closely related strains. In paper III, we found 27.1%, 69.4%, and 3.5% of participants were persistent (positive in all samples), transient (positive one to five times), or non-carriers of the KpSC, respectively. Persistent carriers had a significantly higher KpSC GIT abundance and tended to retain the same ST for multiple months. KpSC GIT abundance associated positively with increased Bacteroides and Phocaeicola, and negatively with Bifidobacterium, Alistipes, Akkermansia, and multiple Bacillota (Firmicutes). Participant age, travel abroad, and ...