Genomic diversity of Escherichia coli from healthy children in rural Gambia

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.

Prevalence, Risk Factors, and Genetic Characterization of Extended-Spectrum Beta-Lactamase Escherichia coli Isolated From Healthy Pregnant Women in Madagascar

“…The molecular analysis of the isolates revealed a great variety of strains in all the sampling locations which was also observed in other developing countries (Stoesser et al, 2015;Ramadan et al, 2020;Foster-Nyarko et al, 2021). The majority were from commensal phylogenetic groups A with STc10 being the most frequent clonal complex detected.…”

Faecal carriage of ESBL producing and colistin resistant Escherichia coli in avian species over a 2-year period (2017-2019) in Zimbabwe

“…Epidemiological studies have shown a close genetic relationship between commensal E. coli, APEC and human ExPEC (Foster-Nyarko et al, 2021a). A substantial overlap of phylogenetic groups has been observed between the APEC in this study (A, B1 and unknown) and human ExPEC results (B2 and D) observed from a study by Lee et al, 2016(Lee et al, 2016.…”

Escherichia coli and Pseudomonas aeruginosa Isolated From Urine of Healthy Bovine Have Potential as Emerging Human and Bovine Pathogens

“…The five genomes are all representatives of the B1 phylotype. E. coli strains belonging to this phylotype have been isolated from the bladders of women with UTI and urge urinary incontinence ( Garretto et al, 2020 ) as well as commensal strains from the human GI tract ( Massot et al, 2016 ; Foster-Nyarko et al, 2021 ) and bovine GI tract ( Arimizu et al, 2019 ). In comparison with other bovine isolates, the bovine urinary isolates are most similar to each other ( Supplementary Figure 1 ), and when compared to human urinary isolates, the core genomes of the five bovine urinary E. coli strains most closely resemble each other ( Figure 1 ).…”