Klebsiella pneumoniae (Kp) is an opportunistic pathogen and leading cause of hospital-associated infections. Intensive care unit (ICU) patients are particularly at risk. Kp is part of the healthy human microbiome, providing a potential reservoir for infection. However, the frequency of gut colonization and its contribution to infections are not well characterized.
We conducted a one-year prospective cohort study in which 498 ICU patients were screened for rectal and throat carriage of Kp shortly after admission. Kp isolated from screening swabs and clinical diagnostic samples were characterized using whole genome sequencing and combined with epidemiological data to identify likely transmission events.
Kp carriage frequencies were estimated at 6% (95% CI, 3%-8%) amongst ICU patients admitted direct from the community, and 19% (95% CI, 14% - 51%) amongst those with recent healthcare contact. Gut colonisation on admission was significantly associated with subsequent infection (infection risk 16% vs 3%, OR=6.9, p<0.001), and genome data indicated matching carriage and infection isolates in 80% of isolate pairs. Five likely transmission chains were identified, responsible for 12% of Kp infections in ICU. 49% of Kp infections were caused by the patients' own unique strain, and 48% of screened patients with infections were positive for prior colonisation.
These data confirm Kp colonisation is a significant risk factor for infection in ICU, and indicate ~50% of Kp infections result from patients' own microbiota. Screening for colonisation on admission could limit risk of infection in the colonised patient and others.