Genomic diversity ofEscherichia coliisolates from healthy children in rural Gambia

Little is known about the genomic diversity ofEscherichia coliin 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 faecalE. colifrom 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 theE. coliphylogroups A, B1, B2, C, D, E, F andEscherichiacryptic 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 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 than independent immigration and the establishment of strains among our study population. Also, this study adds significantly to the number of commensalE. coligenomes, a group that has been traditionally underrepresented in the sequencing of this species.