Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity

Abstract

Antibiotic resistant Klebsiella pneumoniae is a leading public health threat and gastrointestinal carriage is an established risk factor for subsequent infections during hospitalization. Our study contributes new knowledge of risk factors for gastrointestinal carriage and the genomic population structure of K. pneumoniae colonizing humans in a representative sample of a general population in a community setting. Altogether, 2,975 participants (54% women) >40 y in the population-based Tromsø Study: Tromsø7, Norway (2015-2016) were included. Fecal samples were screened for K. pneumoniae, which were characterized using whole-genome sequencing. Risk factors for carriage were analyzed using multivariable logistic regression on data from questionnaires and the Norwegian Prescription Database. Prevalence of K. pneumoniae gastrointestinal carriage was 16.3% (95% CI 15.0-17.7, no gender difference). Risk factors associated with carriage included age ≥60 y, travel to Greece or Asia past 12 months (adjusted odds ratio 1.49, 95% CI 1.11-2.00), Crohn's disease/ulcerative colitis (2.26, 1.20-4.27), use of proton pump inhibitors (1.62, 1.18-2.22) and non-steroidal anti-inflammatory drugs past 6 months (1.38, 1.04-1.84), and antibiotic use the last month (1.73, 1.05-2.86). Prevalence was higher among those having used combinations of drug classes and decreased over time with respect to preceding antibiotic use. The K. pneumoniae population was diverse with 300 sequence types among 484 isolates distributed across four phylogroups. Only 5.2% of isolates harbored acquired resistance and 11.6% had virulence factors. Identification of risk factors for gastrointestinal carriage allows for identification of individuals that may have higher risk of extraintestinal infection during hospitalization. The findings that specific diseases and drugs used were associated with carriage show an impact of these possibly through modulating the human gut microbiota promoting colonization. The diverse population structure of carriage isolates reflects the ecologically adaptive capacity of the bacterium and challenges for vaccine prospects and the identification of reservoirs as a potential source for human colonization.

Exploring Klebsiella pneumoniae in Healthy Poultry Reveals High Genetic Diversity, Good Biofilm-Forming Abilities and Higher Prevalence in Turkeys Than Broilers

“…These isolates comprise a set of diverse K. pneumoniae , represented by many STs in both animal species. Many of these STs, such as ST13, ST17, ST35, ST37 and ST290, have previously been identified in humans ( Marcade et al, 2013 ; Safavi et al, 2020 ; Raffelsberger et al, 2021 ). A recently published study from Norway screened 2,975 healthy persons for K. pneumoniae gut carriage ( Raffelsberger et al, 2021 ), and identified a diverse population of K. pneumoniae .…”

“…Many of these STs, such as ST13, ST17, ST35, ST37 and ST290, have previously been identified in humans ( Marcade et al, 2013 ; Safavi et al, 2020 ; Raffelsberger et al, 2021 ). A recently published study from Norway screened 2,975 healthy persons for K. pneumoniae gut carriage ( Raffelsberger et al, 2021 ), and identified a diverse population of K. pneumoniae . The study also identified ST35 and ST37 among the most common STs identified in healthy Norwegians, although the occurrence of these STs were found to be only 1.9% each ( Raffelsberger et al, 2021 ).…”

“…A recently published study from Norway screened 2,975 healthy persons for K. pneumoniae gut carriage ( Raffelsberger et al, 2021 ), and identified a diverse population of K. pneumoniae . The study also identified ST35 and ST37 among the most common STs identified in healthy Norwegians, although the occurrence of these STs were found to be only 1.9% each ( Raffelsberger et al, 2021 ). In the current study, ST35 represented a major ST identified in both poultry species.…”

“…Virulence genes were detected in a relatively high fraction of the genomes, 23.2%. In the Norwegian study on healthy humans as carriers of K. pneumoniae , the detection rate of virulence factors was 11.6% ( Raffelsberger et al, 2021 ). There could be several reasons for the lower rate in humans, but in the human study other phylogroups in addition to K. pneumoniae sensu stricto were present ( Raffelsberger et al, 2021 ).…”

“…In the Norwegian study on healthy humans as carriers of K. pneumoniae , the detection rate of virulence factors was 11.6% ( Raffelsberger et al, 2021 ). There could be several reasons for the lower rate in humans, but in the human study other phylogroups in addition to K. pneumoniae sensu stricto were present ( Raffelsberger et al, 2021 ). K. pneumoniae sensu stricto has been found to be more strongly associated with virulence than other subspecies ( Holt et al, 2015 ).…”