Faecal colonization with extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in rural Burkina Faso.
Valia D., Karama I., Ingelbeen B., Garba Z., van Kleef E., Lompo P., Tiendrebeogo EW., Kaboré B., Kiemdé F., Yougbare S., Tiendrebeogo AL., Van Puyvelde S., Prizzon A., Vandenbroucke A-T., Argudín MA., Kabamba BM., Jacobs J., Tinto H., van der Sande MAB., Robert A., Rodriguez-Villalobos H.
OBJECTIVES: The burden of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) is increasing globally and is often linked to community-acquisition in low-resource settings. In sub-Saharan Africa, occurrence of antimicrobial resistance (AMR) in rural areas remains understudied despite anticipated higher risks. We investigated the epidemiology and genetic characteristics of ESBL-E in rural Burkina Faso. METHODS: In a community-based cross-sectional survey (May 2021 to May 2022), participants were randomly selected in two health catchment areas, and through face-to-face interviews, field workers collected data on hygiene, animal presence, household characteristics, and healthcare use. Stool samples were also collected for ESBL-E screening. Prevalence of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) and extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-KP) was estimated, and associated factors were assessed. Based on resistance profiles and PCR screening, selected isolates underwent whole genome sequencing. RESULTS: Among 1482 participants, ESBL-E prevalence was 61.3% (58.8-63.7%); ESBL-EC prevalence was 53.0% (50.5-55.5%), and ESBL-KP prevalence was 22.3% (20.3-24.5%). Colonization was more common in the rainy season than in the dry season (70.2% vs. 53.6%, p < 0.001) and among individuals not washing hands with soap before meals (62.5% vs. 49.0%, p < 0.001). Ciprofloxacin resistance exceeded 65% in both species. The predominant extended-spectrum β-lactamase gene was blaCTX-M-15 (47.3% in ESBL-EC and 19.9% in ESBL-KP), with one ESBL-EC isolate carrying blaNDM-5. Incompatibility group F (IncF) plasmids predominated, and plasmid-mediated quinolone resistance genes (qnr, aac(6')-ib-cr and oqxAB) were frequently codetected with extended-spectrum β-lactamase genes. CONCLUSIONS: ESBL-E prevalence was high and was associated with poor hygiene and seasonal variation. Higher rainy season prevalence was not explained by reported antibiotic use and may reflect increased environmental exposure risks, which requires further exploration. Improving hygiene standards and establishing community-level AMR surveillance can provide effective steps toward mitigating AMR burden in rural sub-Saharan Africa.