Azithromycin Resistance Patterns in <i>Escherichia coli</i> and <i>Shigella</i> before and after COVID-19, Kenya

Escherichia coli and Shigella spp. are leading bacterial causes of acute diarrhea in sub-Saharan Africa and pose risks to global communities, travelers, and the US military. Increasing antimicrobial resistance (AMR) in those and other enteric pathogens creates treatment challenges for clinicians. Inappropriate use of antimicrobial drugs, such as azithromycin for viral respiratory infections, increased during the COVID-19 pandemic. We evaluated AMR trends of 116 E. coli and 109 Shigella spp. isolates obtained from 1,672 pre-COVID-19 (2017-2019) and 1,118 post-COVID-19 (2022-2023) human fecal samples from Kenya. Azithromycin resistance increased significantly from before to after COVID-19, from 6.3% to 40.4% (p = 0.001). Phenotypic AMR profiles from a subset of isolates were compared with genotypic AMR information derived from whole genome sequencing. The most common AMR gene detected was the macrolide mph(A) gene. This study highlights the need for continued AMR surveillance.