Impact of databases on genomic survey of Salmonella antimicrobial resistance and virulence factor functional genes across the African continent

Abstract

Tracking the antimicrobial resistance potential of foodborne bacteria remains relevant today due to the potential for functional availability and horizontal transfer of relevant genes across species. We conducted a study of AMR potential across 4,552 Salmonella enterica isolates submitted to the NCBI Sequence Read Archive from the African continent. After assembling raw fastq data to high quality and contiguity, AMR genes, virulence factors, and plasmids and other mobile elements were predicted with the ABRicate software suite across multiple AMR databases. Prevalence of AMR genes in countries did not correlate with the number of Salmonella isolates sequenced. Isolates carrying functional genes were also classified by FAO food categories, identifying land animals meat and poultry and dairy as the primary sources of AMR genes amongst Salmonella isolates in Africa. The trends of AMR presence varied across different databases; whereas, the overall AMR genes per isolate for the same database did not vary substantially. Genomic comparison by k-mer analysis suggests most sampled isolates are not closely related within or across countries. Due to the low likelihood of cross border transmission, epidemiological reasons for AMR transmission within Salmonella in the five countries with highest prevalence of AMR genes are not identifiable presently.