β-Lactamase and Macrolide Resistance Gene Carriage in Escherichia coli Isolates Among Children Discharged From Inpatient Care in Western Kenya: A Cross-sectional Study

Abstract

Background Antimicrobial resistance (AMR) is a global threat to infectious disease control, particularly among recently hospitalized children. We sought to determine the prevalence and mitigating factors of resistance in enteric Escherichia coli among children discharged from health facilities in western Kenya. Methods Between June 2016 and November 2019, children aged 1-59 months were enrolled at the point of discharge from hospital. E. coli was isolated by microbiological culture from rectal swabs at baseline. β-lactamases and macrolide resistance-conferring genes were detected by PCR. The modified Poisson regression model was used to assess the predictors mph(A) and CTX-M-type ESBL. Results Of the 238 children whose E. coli isolates were tested, 91 (38.2%) and 109 (45.8%) had detectable CTX-M-type ESBL and mph(A) genes, respectively. Antibiotic treatment during hospitalization (adjusted prevalence ratio [aPR]=2.47; 95%CI:1.12-5.43, p=0.025), length of hospitalization (aPR=1.42; 95%CI:1.00-2.01, p=0.052), and the practice of open defecation (aPR=2.47; 95%CI:1.40-4.36, p=0.002) were independent predictors for CTX-M-type ESBL and for mph(A) genes. Pneumococcal vaccination was associated with a 43% lower likelihood of CTX-M-type ESBL (aPR=0.57; 95%CI:0.38-0.85, p=0.005), whilst measles vaccination was associated with a 32% lower likelihood of mph(A) gene (aPR=0.68; 95%CI:0.49-0.93, p=0.017) in E. coli isolates. Conclusions Among children discharged from hospital, history of vaccination, shorter hospital stay, lack of in-hospital antibiotic exposure and improved sanitation were associated with lower likelihood of AMR genes. AMR control programs should consider strategies beyond antimicrobial stewardship, including improvements in sanitation, increased vaccine coverage and the development of novel vaccines, to mitigate the continued spread of AMR.