Abstract
We recently identified clonal complex 10 (CC10) Escherichia coli as the predominant clonal group in two populations of healthy Australian food-production pigs. CC10 are highly successful, colonizing humans, food-production animals, fresh produce and environmental niches. Furthermore, E. coli within CC10 are frequently drug resistant and increasingly reported as human and animal extra-intestinal pathogens. In order to develop a high-resolution global phylogeny and determine the repertoire of antimicrobial-resistance genes, virulence-associated genes and plasmid types within this clonal group, we downloaded 228 publicly available CC10 short-read genome sequences for comparison with 20 porcine CC10 we have previously described. Core genome single nucleotide polymorphism phylogeny revealed a highly diverse global phylogeny consisting of multiple lineages that did not cluster by geography or source of the isolates. Australian porcine strains belonged to several of these divergent lineages, indicative that CC10 is present in these animals due to multiple colonization events. Differences in resistance gene and plasmid carriage between porcine strains and the global collection highlighted the role of lateral gene transfer in the evolution of CC10 strains. Virulence profiles typical of extra-intestinal pathogenic E. coli were present in both Australian porcine strains and the broader collection. As both the core phylogeny and accessory gene characteristics appeared unrelated to the geography or source of the isolates, it is likely that the global expansion of CC10 is not a recent event and may be associated with faecal carriage in humans.
Highlights
Escherichia coli is both a successful commensal and a serious pathogen affecting human and animal health, and is the most frequently isolated Gram-negative pathogen impacting human health [1]
As both the core phylogeny and accessory gene characteristics appeared unrelated to the geography or source of the isolates, it is likely that the global expansion of clonal complex 10 (CC10) is not a recent event and may be associated with faecal carriage in humans
We recently described the phylogeny, virulence-associated gene (VAG) and antimicrobial resistance (AMR) gene (ARG) carriage in a collection of 103 E. coli genome sequences derived from the faeces of healthy Australian pigs [16]
Summary
Escherichia coli is both a successful commensal and a serious pathogen affecting human and animal health, and is the most frequently isolated Gram-negative pathogen impacting human health [1]. Severe outbreaks of drug-resistant InPEC disease, such as the O104 : H4 outbreak in 2011, are well documented, as well as the global dissemination of resistant ExPEC clones, such as ST131 [5,6,7] Responses to such events are reactive, and come after significant financial and human cost is incurred.
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