Abstract
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.
Highlights
Escherichia coli is a highly versatile species, capable of adapting to a wide range of ecological niches and colonizing a diverse range of hosts [1, 2]
We found several sequence types (STs) associated with extraintestinal infections and/or AMR in humans: ST73, ST681, ST127, ST226, ST336, ST349 [47,48,49]
We have described the population structure of E. coli in diurnal non-human primates living in rural and urban habitats from the Gambia
Summary
Escherichia coli is a highly versatile species, capable of adapting to a wide range of ecological niches and colonizing a diverse range of hosts [1, 2]. E. coli colonizes the gastrointestinal tract as a commensal, as well as causing intestinal and extraintestinal infection [2]. E. coli is capable of colonizing the gut in non-h uman primates [3], where data from captive animals suggest that gut isolates are dominated by phylogroups B1 and A, which, in humans, encompass commensals as well as strains associated with intestinal pathology [4, 5]. E. coli strains encoding colibactin, or cytotoxic necrotizing factor 1 have been isolated. Foster-Nyarko et al, Microbial Genomics 2020;6 from healthy laboratory rhesus macaques [6], while enteropathogenic E. coli strains can – in the laboratory – cause colitis in marmosets [7], rhesus macaques infected with simian immunodeficiency virus [8] and cotton-top tamarins [9]
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