Increasing contact between humans and non-human primates provides an opportunity for the transfer of potential pathogens or antimicrobial resistance between host species. We have investigated genomic diversity and antimicrobial resistance in Escherichia coli isolates from four species of non-human primates in the Gambia: Papio papio (n=22), Chlorocebus sabaeus (n=14), Piliocolobus badius (n=6) and Erythrocebus patas (n=1). We performed Illumina whole-genome sequencing on 101 isolates from 43 stools, followed by nanopore long-read sequencing on 11 isolates. We identified 43 sequence types (STs) by the Achtman scheme (ten of which are novel), spanning five of the eight known phylogroups of E. coli . The majority of simian isolates belong to phylogroup B2 – characterized by strains that cause human extraintestinal infections – and encode factors associated with extraintestinal disease. A subset of the B2 strains (ST73, ST681 and ST127) carry the pks genomic island, which encodes colibactin, a genotoxin associated with colorectal cancer. We found little antimicrobial resistance and only one example of multi-drug resistance among the simian isolates. Hierarchical clustering showed that simian isolates from ST442 and ST349 are closely related to isolates recovered from human clinical cases (differences in 50 and 7 alleles, respectively), suggesting recent exchange between the two host species. Conversely, simian isolates from ST73, ST681 and ST127 were distinct from human isolates, while five simian isolates belong to unique core-genome ST complexes – indicating novel diversity specific to the primate niche. Our results are of planetary health importance, considering the increasing contact between humans and wild non-human primates.

中文翻译：

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从冈比亚非人类灵长类动物中分离出的大肠杆菌的基因组多样性。


人类和非人类灵长类动物之间接触的增加为宿主物种之间潜在病原体或抗菌药物耐药性的转移提供了机会。我们研究了冈比亚四种非人类灵长类动物中分离出的大肠杆菌的基因组多样性和抗菌药物耐药性：狒狒( n =22)、 Chlorocebus sabaeus ( n =14)、 Piliocolobus badius ( n =6) 和Erythrocebus patas ( n =1)。我们对 43 份粪便中的 101 个分离株进行了 Illumina 全基因组测序，随后对 11 个分离株进行了纳米孔长读长测序。我们通过 Achtman 方案鉴定了 43 种序列类型 (ST)（其中 10 种是新的），涵盖了大肠杆菌8 个已知系统群中的 5 个。大多数猿猴分离株属于系统群 B2（其特征是引起人类肠外感染的菌株），并编码与肠外疾病相关的因子。 B2 菌株的一个子集（ST73、ST681 和 ST127）携带pks基因组岛，编码大肠杆菌素，这是一种与结直肠癌相关的基因毒素。我们在猿猴分离株中发现了很少的抗菌药物耐药性，并且只有一个具有多重耐药性的例子。层次聚类显示，来自 ST442 和 ST349 的猿猴分离株与从人类临床病例中回收的分离株密切相关（分别有 50 个和 7 个等位基因的差异），表明这两个宿主物种之间最近发生过交换。 相反，来自 ST73、ST681 和 ST127 的猿猴分离株与人类分离株不同，而 5 个猿猴分离株属于独特的核心基因组 ST 复合体，这表明灵长类动物生态位特有的新多样性。考虑到人类与野生非人类灵长类动物之间的接触不断增加，我们的研究结果对地球健康具有重要意义。