Antimicrobial resistance (AMR) is a global threat, including in sub-Saharan Africa. However, little is known about the genetics of resistant bacteria in the region. In Malawi, there is growing concern about increasing rates of antimicrobial resistance to most empirically used antimicrobials. The highly drug resistant Escherichia coli sequence type (ST) 131, which is associated with the extended spectrum β-lactamase blaCTX-M-15 , has been increasing in prevalence globally. Previous data from isolates collected between 2006 and 2013 in southern Malawi have revealed the presence of ST131 and the blaCTX-M-15 gene in the country. We performed whole genome sequencing (WGS) of 58 clinical E. coli isolates at Kamuzu Central Hospital, a tertiary care centre in central Malawi, collected from 2012 to 2018. We used Oxford Nanopore Technologies (ONT) sequencing, which was performed in Malawi. We show that ST131 is observed more often (14.9% increasing to 32.8%) and that the blaCTX-M-15 gene is occurring at a higher frequency (21.3% increasing to 44.8%). Phylogenetics indicates that isolates are highly related between the central and southern geographic regions and confirms that ST131 isolates are contained in a single group. All AMR genes, including blaCTX-M-15 , were widely distributed across sequence types. We also identified an increased number of ST410 isolates, which in this study tend to carry a plasmid-located copy of blaCTX-M-15 gene at a higher frequency than blaCTX-M-15 occurs in ST131. This study confirms the expanding nature of ST131 and the wide distribution of the blaCTX-M-15 gene in Malawi. We also highlight the feasibility of conducting longitudinal genomic epidemiology studies of important bacteria with the sequencing done on site using a nanopore platform that requires minimal infrastructure.

中文翻译：

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马拉维利隆圭三级转诊中心分离出的大肠杆菌的基因组流行病学


抗菌素耐药性 (AMR) 是一个全球性威胁，包括撒哈拉以南非洲地区。然而，人们对该地区耐药细菌的遗传学知之甚少。在马拉维，人们越来越担心大多数经验使用的抗菌药物的耐药率不断上升。高度耐药的大肠杆菌序列类型 (ST) 131 与超广谱 β-内酰胺酶bla CTX-M-15相关，在全球范围内的患病率不断增加。之前从 2006 年至 2013 年在马拉维南部收集的分离株获得的数据显示，该国存在 ST131 和bla CTX-M-15基因。我们对马拉维中部三级护理中心 Kamuzu 中心医院 2012 年至 2018 年收集的 58 个临床大肠杆菌分离株进行了全基因组测序 (WGS)。我们使用了在马拉维进行的牛津纳米孔技术 (ONT) 测序。我们发现 ST131 的出现频率更高（从 14.9% 增加到 32.8%），并且bla CTX-M-15基因的出现频率更高（从 21.3% 增加到 44.8%）。系统发育表明中部和南部地理区域之间的分离株高度相关，并证实 ST131 分离株包含在一个组中。所有 AMR 基因，包括bla CTX-M-15 ，广泛分布于序列类型中。 我们还发现了数量增加的 ST410 分离株，在本研究中，这些分离株往往携带bla CTX-M-15基因的质粒定位副本，其频率高于 ST131 中出现的bla CTX-M-15 。这项研究证实了 ST131 的扩展性质以及bla CTX-M-15基因在马拉维的广泛分布。我们还强调了对重要细菌进行纵向基因组流行病学研究的可行性，并使用需要最少基础设施的纳米孔平台进行现场测序。