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Volume 6, Issue 9

Genomic diversity of isolates from non-human primates in the Gambia Open Access

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 isolates from four species of non-human primates in the Gambia: (=22), (=14), (=6) and (=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 . 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 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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Escherichia coli , Extraintestinal pathogenic E. coli , Non-human primates and phylogenomic diversity
Funding
This study was supported by the:
  • Biotechnology and Biological Sciences Research Council (Award BB/R012504/1)
    • Principle Award Recipient: Mark John Pallen
© 2020 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2020-09-14
2024-04-25
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Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia
M Gen 6, e000428 (2020); https://doi.org/10.1099/mgen.0.000428
/content/journal/mgen/10.1099/mgen.0.000428
/content/journal/mgen/10.1099/mgen.0.000428
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