Seasonality and other factors influencing hospital acquisition of multi-drug-resistant Enterobacterales colonisation: a one-year cohort study – Botswana, 2022–2023

Background: Healthcare facilities may be major reservoirs for antimicrobial resistance, particularly in low- and middle-income countries, yet data are limited on factors influencing acquisition in these settings. In this cohort study, we followed up participants who screened negative for colonisation with extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) and carbapenem-resistant Enterobacterales (CRE) on admission and assessed the incidence and risk factors for hospital acquisition of ESCrE and CRE colonisation in this population. Methods and findings: In this 12-month cohort study, we enrolled patients upon admission to a tertiary referral hospital Emergency Department in Botswana. A rectal swab was collected within 24 h of admission, and on days 3-6, 7-10, and 11-14 of hospitalisation, if still admitted. Acquisition of ESCrE and CRE was defined as a new positive swab culture in a study subject with a negative swab culture on admission. ESCrE and CRE colonisation were determined by growth on selective culture media and confirmed using automated phenotypic identification and antibiotic susceptibility testing. Associations between acquisition of ESCrE/CRE colonisation and clinical and demographic variables were analysed. Among patients with no detected colonisation at admission who remained hospitalised for ≥3 days, 81 (34.3%) and 29 (9.4%) had newly acquired ESCrE and CRE colonisation, respectively. Patients were at higher risk of ESCrE acquisition if they were hospitalised in the summer/rainy months (adjusted risk ratio, 1.49 [95% confidence interval [CI]: 1.05-2.12]). The risk of CRE acquisition was higher among patients aged