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.

中文翻译：

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肯尼亚 COVID-19 前后大肠杆菌和志贺氏菌的阿奇霉素耐药模式。


大肠杆菌和志贺氏菌属是撒哈拉以南非洲急性腹泻的主要细菌原因，对全球社区、旅行者和美国军队构成风险。这些病原体和其他肠道病原体的抗菌素耐药性 （AMR） 增加给临床医生带来了治疗挑战。在 COVID-19 大流行期间，不适当使用抗菌药物（例如治疗病毒性呼吸道感染）的情况有所增加。我们评估了从肯尼亚的 1,672 份 COVID-19 前 （2017-2019） 和 1,118 份 COVID-19 后 （2022-2023） 人类粪便样本中获得的 116 份大肠杆菌和 109 份志贺氏菌属分离株的 AMR 趋势。从 COVID-19 之前到之后，阿奇霉素耐药性显着增加，从 6.3% 增加到 40.4% （p = 0.001）。将来自分离株子集的 AMR 表型谱与来自全基因组测序的基因型 AMR 信息进行比较。检测到的最常见的 AMR 基因是大环内酯类 mph（A） 基因。这项研究强调了持续 AMR 监测的必要性。