Ikumapayi, U. N. | Search bioRxiv

bioRxiv2021

Invasive atypical non-typhoidal Salmonella in The Gambia

BackgroundInvasive non-typhoidal Salmonella (iNTS) disease continues to be a significant public health problem in sub-Saharan Africa. Common clinical misdiagnosis, antimicrobial resistance, high case fatality and lack of a vaccine make iNTS a priority for global health research. Using whole genome sequence analysis of 164 invasive Salmonella isolates obtained through population-based surveillance between 2008 and 2016, we conducted genomic analysis of the serovars causing invasive Salmonella diseases in rural Gambia. ResultsThe incidence of iNTS varied over time. The proportion of atypical serovars causing disease increased over time from 40% to 65% compared to the typical serovars Enteritidis and Typhimurium decreasing from 30% to 12%. Overall iNTS case fatality was 10% with 10% fatality in cases of atypical iNTS. Genetic virulence factors were identified in 14/70 (20%) typical serovars and 45/68 (66%) of the atypical serovars and were associated with: invasion, proliferation and/or translocation (Clade A); and host colonization and immune modulation (Clade G). Among Enteritidis isolates, 33/40 were resistant to [≥]4 the antimicrobials tested, except for ciprofloxacin, to which all isolates were susceptible. Resistance was low in Typhimurium isolates, however, all16 isolates were resistant to gentamicin. ConclusionThe increase in incidence and proportion of iNTS disease caused by atypical serovars is concerning. The increased proportion of atypical serovars and the high associated case fatality may be related to acquisition of specific genetic virulence factors. These factors may provide a selective advantage to the atypical serovars. Investigations should be conducted elsewhere in Africa to identify potential changes in the distribution iNTS serovars and the extent of these virulence elements.

genomics↗

bioRxiv2020

Genomic Diversity of Escherichia coli isolates 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 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 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 commensal E. coli genomes, a group that has been traditionally underrepresented in the sequencing of this species.

ecology↗