Prevalence, risk factors and genetic characterisation of extended-spectrum beta-lactamase and carbapenemase-producing Enterobacteriaceae (ESBL-E and CPE): a community-based cross-sectional study, the Netherlands, 2014 to 2016

Background: The epidemiology of carriage of extended-spectrum beta-lactamase-producing (ESBL-E) and carbapenemase-producing Enterobacteriaceae (CPE) in the general population is unknown. Aim: In this observational study, the prevalence and risk factors for intestinal ESBL-E and CPE carriage in the Dutch general population were determined. ESBL-E were characterised. Methods: From 2014 to 2016, ca2,000 residents were invited monthly to complete a questionnaire and provide a faecal sample, which was tested for ESBL-E. The first 1,758 samples were also tested for CPE. Risk factors for ESBL-E carriage were identified by multivariable logistic regression analysis. ESBL-E isolates underwent whole genome sequencing. Results: Of 47,957 individuals invited, 4,177(8.7%) completed the questionnaire and provided a faecal sample. ESBL-E were detected in 186 (4.5%) individuals, resulting in an adjusted prevalence of 5.0%(95% confidence interval(CI):3.4-6.6%). Risk factors were: born outside the Netherlands (odds ratio (OR):1.99; 95%CI:1.16-4.54), eating in restaurants >20 times/year(OR: 1.70; 95% CI: 1.04-2.76), antibiotic use 6 months ago (OR: 2.05; 95%CI: 1.05-4.03), swimming in sea/ocean < 12 months ago (OR:1.63; 95%CI:1.11-2.39), travelling to Africa (OR:3.03; 95%CI:1.23-7.46) or Asia (OR: 2.00; 95% CI: 1.02-3.90) <12 months ago, and not changing kitchen towels daily (OR: 2.19; 95%CI:1.24-3.87). The last had the largest population attributable risk (PAR) (47.5%). Eighty-four of 189 (44.4%) ESBL-E isolates carried bla(CTX-M-15).Escherichia coli isolates belonged to 70 different sequence types (ST)s, of which ST131(42/178 isolates; 23.6%) was most prevalent. Associations were observed between lncFIA plasmids and ST131 and bla(CTX-M-)(27), and between Incl1 and ST88 and bla(CTX-M-1). No CPE were detected. Conclusions: The prevalence of ESBL-E carriage in the Netherlands' community-dwelling population is 5.0%. Identified risk factors were mostly travelling (particularly to Asia and Africa) and kitchen hygiene. CPE were not detected.