Genomic diversity of <i>Escherichia coli</i> from healthy children in rural Gambia

Little is known about the genomic diversity of Escherichia coli in healthy children from sub-Saharan Africa, even though this pertinent to understanding bacterial evolution and ecology their role infection. We isolated whole-genome sequenced up five colonies faecal E. 66 asymptomatic aged three-to-five years rural Gambia (n = 88 isolates 21 positive stools). identified 56 genotypes, with an average 2.7 genotypes per host. These were spread over 37 seven-allele sequence types phylogroups A, B1, B2, C, D, E, F cryptic clade I. Immigration events accounted for three-quarters within our study population, while one-quarter variants appeared have arisen within-host evolution. Several encode putative virulence factors commonly found Enteropathogenic Enteroaggregative coli, 53% resistance three or more classes antimicrobials. Thus, resident these may constitute reservoirs virulence- resistance-associated genes. Moreover, several strains closely related that caused disease humans originated livestock. Our results suggest plays a minor generation compared independent immigration establishment among population. Also, adds significantly number commensal genomes, group has been traditionally underrepresented sequencing species.