Community carriage of ESBL-producing Escherichia coli and Klebsiella pneumoniae: a cross-sectional study of risk factors and comparative genomics of carriage and clinical isolates

• Published in: mSphere
• Main Authors: Niclas Raffelsberger, Dorota Julia Buczek, Kristian Svendsen, Lars Småbrekke, Anna Kaarina Pöntinen, Iren H. Löhr, Lotte Leonore Eivindsdatter Andreassen, Gunnar Skov Simonsen, Arnfinn Sundsfjord, Kirsten Gravningen, Ørjan Samuelsen
• Format: Article in Journal/Newspaper
• Language: English
• Published: American Society for Microbiology 2023
• Subjects: Escherichia coli; Klebsiella pneumoniae; extended-spectrum β-lactamase; antimicrobial resistance; carriage; risk factors; Microbiology; QR1-502; Norway; Tromsø
• Online Access: https://doi.org/10.1128/msphere.00025-23; https://doaj.org/article/92fbb9207ddf431b88472033122999bf

ABSTRACT The global prevalence of infections caused by extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) is increasing, and for Escherichia coli, observations indicate that this is partly driven by community-onset cases. The ESBL-E population structure in the community is scarcely described, and data on risk factors for carriage are conflicting. Here, we report the prevalence and population structure of fecal ESBL-producing E. coli and Klebsiella pneumoniae (ESBL-Ec/Kp) in a general adult population, examine risk factors, and compare carriage isolates with contemporary clinical isolates. Fecal samples obtained from 4,999 participants (54% women) ≥40 years in the seventh survey of the population-based Tromsø Study, Norway (2015, 2016), were screened for ESBL-Ec/Kp. In addition, we included 118 ESBL-Ec clinical isolates from the Norwegian surveillance program in 2014. All isolates were whole-genome sequenced. Risk factors associated with carriage were analyzed using multivariable logistic regression. ESBL-Ec gastrointestinal carriage prevalence was 3.3% [95% confidence interval (CI) 2.8%–3.9%, no sex difference] and 0.08% (0.02%–0.20%) for ESBL-Kp. For ESBL-Ec, travel to Asia was the only independent risk factor (adjusted odds ratio 3.46, 95% CI 2.18–5.49). E. coli ST131 was most prevalent in both collections. However, the ST131 proportion was significantly lower in carriage (24%) versus clinical isolates (58%, P < 0.001). Carriage isolates were genetically more diverse with a higher proportion of phylogroup A (26%) than clinical isolates (5%, P < 0.001), indicating that ESBL gene acquisition occurs in a variety of E. coli lineages colonizing the gut. STs commonly related to extraintestinal infections were more frequent in clinical isolates also carrying a higher prevalence of antimicrobial resistance, which could indicate clone-associated pathogenicity. IMPORTANCE ESBL-Ec and ESBL-Kp are major pathogens in the global burden of antimicrobial resistance. However, there is a gap in knowledge ...