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Background <p>Dogs are one of the most popular companion animals in the UK, with an estimated 13.5 million within UK households. Within these households, human-animal physical interactions may lead to inter-species bacterial sharing, including <i>Escherichia coli</i>. <i>E. coli</i> is an opportunistic pathogen with a broad host range and can contribute to the spread of antimicrobial resistance (AMR). This work aimed to understand the extent of <i>E. coli</i> co-occurrence between hosts within the same household, and between dogs and humans.</p> Results <p><i>E. coli</i> was non-selectively cultured from faecal samples obtained from 24 households with at least one human (<i>n</i> = 31) and one dog (<i>n</i> = 27) sample available at the same timepoint. Up to eight presumptive <i>E. coli</i> colonies were selected per sample and underwent short read whole genome sequencing. In total, 217 <i>E. coli</i> genomes were classified into 53 known sequence types (STs) and one unknown ST. Within samples, up to four different STs were present within each human and up to three different STs within a dog. Using a five single nucleotide polymorphism (SNP) threshold, there were 20 <i>E. coli</i> co-occurrences between hosts, including the same and different host species. Four instances involved potential cross-species co-occurrence within the same household. A genome-wide association study using a combined unitig and gene presence and absence approach identified one gene significantly more common in human derived samples; in silico characterisation revealed this gene is likely to have a function related to Type-F conjugative transfer system pilin assembly. Overall, 48.8% of the genomes had at least one genetic determinant associated with AMR, and 17.5% were classified as multidrug resistant. <i>E. coli</i> from humans carried more AMR determinants than <i>E. coli</i> from dogs.</p> Conclusion <p>There was limited evidence of <i>E. coli</i> co-occurrence between different host species within households, and only one host-associated genetic feature. Humans harboured <i>E. coli</i> associated with more AMR determinants than those from dogs, suggesting that <i>E. coli</i> from humans presented a larger AMR source and AMR risk to other hosts in this dataset. Our findings can help inform risk analysis of <i>E. coli</i> sharing and transmission between humans and their companion dogs.</p>

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Whole genome comparative analysis shows limited Escherichia coli co-occurrence within co-habiting humans and dogs

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年8月4日

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  • Gabriel Astorga,
  • Samuel J. Bloomfield,
  • John Wain,
  • Leonardo de Oliveira Martins,
  • Dipali Singh,
  • Sumeet K. Tiwari,
  • George M. Savva,
  • Anette Loeffler,
  • Juliana Menezes,
  • Constança Pomba,
  • Siân Marie Frosini,
  • Alison E. Mather

摘要

Background

Dogs are one of the most popular companion animals in the UK, with an estimated 13.5 million within UK households. Within these households, human-animal physical interactions may lead to inter-species bacterial sharing, including Escherichia coli. E. coli is an opportunistic pathogen with a broad host range and can contribute to the spread of antimicrobial resistance (AMR). This work aimed to understand the extent of E. coli co-occurrence between hosts within the same household, and between dogs and humans.

Results

E. coli was non-selectively cultured from faecal samples obtained from 24 households with at least one human (n = 31) and one dog (n = 27) sample available at the same timepoint. Up to eight presumptive E. coli colonies were selected per sample and underwent short read whole genome sequencing. In total, 217 E. coli genomes were classified into 53 known sequence types (STs) and one unknown ST. Within samples, up to four different STs were present within each human and up to three different STs within a dog. Using a five single nucleotide polymorphism (SNP) threshold, there were 20 E. coli co-occurrences between hosts, including the same and different host species. Four instances involved potential cross-species co-occurrence within the same household. A genome-wide association study using a combined unitig and gene presence and absence approach identified one gene significantly more common in human derived samples; in silico characterisation revealed this gene is likely to have a function related to Type-F conjugative transfer system pilin assembly. Overall, 48.8% of the genomes had at least one genetic determinant associated with AMR, and 17.5% were classified as multidrug resistant. E. coli from humans carried more AMR determinants than E. coli from dogs.

Conclusion

There was limited evidence of E. coli co-occurrence between different host species within households, and only one host-associated genetic feature. Humans harboured E. coli associated with more AMR determinants than those from dogs, suggesting that E. coli from humans presented a larger AMR source and AMR risk to other hosts in this dataset. Our findings can help inform risk analysis of E. coli sharing and transmission between humans and their companion dogs.