Abstract
Little is known about the genomic diversity of Escherichia coli in healthy children from sub-Saharan Africa, even though this is pertinent to understanding bacterial evolution and ecology and their role in infection. We isolated and whole-genome sequenced up to five colonies of faecal E. coli from 66 asymptomatic children aged three-to-five years in rural Gambia (n = 88 isolates from 21 positive stools). We identified 56 genotypes, with an average of 2.7 genotypes per host. These were spread over 37 seven-allele sequence types and the E. coli phylogroups A, B1, B2, C, D, E, F and Escherichia cryptic clade I. Immigration events accounted for three-quarters of the diversity within our study population, while one-quarter of variants appeared to have arisen from within-host evolution. Several isolates encode putative virulence factors commonly found in Enteropathogenic and Enteroaggregative E. coli, and 53% of the isolates encode resistance to three or more classes of antimicrobials. Thus, resident E. coli in these children may constitute reservoirs of virulence- and resistance-associated genes. Moreover, several study strains were closely related to isolates that caused disease in humans or originated from livestock. Our results suggest that within-host evolution plays a minor role in the generation of diversity compared to independent immigration and the establishment of strains among our study population. Also, this study adds significantly to the number of commensal E. coli genomes, a group that has been traditionally underrepresented in the sequencing of this species.
Highlights
Ease of culture and genetic tractability account for the unparalleled status of Escherichia coli as “the biological rock star”, driving advances in biotechnology [1], while providing critical insights into biology and evolution [2]
This study provides an overview of the within-host genomic diversity of E. coli in healthy children from a rural setting in the Gambia, West Africa
We recovered a low rate of colonisation than reported elsewhere among children of similar age groups [42], with only a third of our study samples yielding growth of E. coli
Summary
Ease of culture and genetic tractability account for the unparalleled status of Escherichia coli as “the biological rock star”, driving advances in biotechnology [1], while providing critical insights into biology and evolution [2]. E. coli is a widespread commensal, as well as a versatile pathogen, linked to diarrhoea ( in the underfives), urinary tract infection, neonatal sepsis, bacteraemia and multi-drug resistant infection in hospitals [3,4,5]. Most of what we know about E. coli stems from the investigation of laboratory strains, which fail to capture the ecology and evolution of this key organism “in the wild” [6]. We have a broad understanding of the population structure of E. coli, with eight significant phylogroups loosely linked to ecological niche and pathogenic potential (B2, D and F linked to extraintestinal infection; A and B1 linked to severe intestinal infections such as haemolytic-uraemic syndrome) [14,15,16,17]. All phylogroups can colonise the human gut, but it remains unclear how far commensals and pathogenic strains compete or collaborate—or engage in horizontal gene transfer—within this important niche [18, 19]
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