Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from 10 chickens and 9 guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (4 of them novel), of which ST155 was the most common (22/68, 32 %). These strains span four of the eight main phylogroups of E. coli, with phylogroups B1 and A being most prevalent. Nearly a third of the isolates harboured at least one antimicrobial resistance gene, while most of the ST155 isolates (14/22, 64 %) encoded resistance to ≥3 classes of clinically relevant antibiotics, as well as putative virulence factors, suggesting pathogenic potential in humans. Furthermore, hierarchical clustering revealed that several Gambian poultry strains were closely related to isolates from humans. Although the ST155 lineage is common in poultry from Africa and South America, the Gambian ST155 isolates belong to a unique cgMLST cluster comprising closely related (38–39 alleles differences) isolates from poultry and livestock from sub-Saharan Africa – suggesting that strains can be exchanged between poultry and livestock in this setting. Continued surveillance of E. coli and other potential pathogens in rural backyard poultry from sub-Saharan Africa is warranted.

中文翻译：

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冈比亚后院鸡和珍珠鸡分离的大肠杆菌的基因组多样性


冈比亚家庭普遍饲养鸡和珍珠鸡，作为负担得起的蛋白质来源。使用标准微生物技术，我们从冈比亚农村地区的 10 只鸡和 9 只珍珠鸡中获得了 68 株盲肠大肠杆菌分离株。 Illumina全基因组测序后，在分离株中检测到28种序列类型（其中4种为新序列），其中ST155是最常见的（22/68，32%）。这些菌株跨越大肠杆菌八个主要系统群中的四个，其中系统群 B1 和 A 最为普遍。近三分之一的分离株至少含有一个抗菌素耐药基因，而大多数 ST155 分离株（14/22，64%）编码对 ≥3 类临床相关抗生素的耐药性，以及假定的毒力因子，这表明在人类。此外，层次聚类显示一些冈比亚家禽品系与人类分离株密切相关。尽管 ST155 谱系在非洲和南美洲的家禽中很常见，但冈比亚 ST155 分离株属于一个独特的 cgMLST 簇，该簇包含来自撒哈拉以南非洲的家禽和牲畜的密切相关（38-39 个等位基因差异）分离株 - 这表明菌株可以在此环境中家禽和牲畜之间进行交换。有必要继续监测撒哈拉以南非洲农村后院家禽中的大肠杆菌和其他潜在病原体。