Baker, R. C. | bioRxiv Science

bioRxiv2026

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

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.

microbiology↗

bioRxiv2020

Evaluation of Nanopore sequencing technology to differentiate Salmonella serotypes and serotype variants with the same or closely related antigenic formulae

Our previous study demonstrated that whole genome sequencing (WGS) data generated by Oxford Nanopore Technologies (ONT) can be used for rapid and accurate prediction of Salmnonella serotypes. However, one limitation is that established methods for WGS-based serotype prediction cannot differentiate certain serotypes and serotype variants with the same or closely related antigenic formulae. This study aimed to evaluate Nanopore sequencing and corresponding data analysis for differentiation of these serotypes and serotype variants, thus overcoming this limitation. Five workflows that combined different flow cells, library construction methods and basecaller models were evaluated and compared. The workflow that consisted of the R9 flow cell, rapid sequencing library construction kit and guppy basecaller with base modified model performed best for Single Nucleotide Polymorphism (SNP) analysis. With this workflow, as high as 99.98% matched the identity of the assembled genomes and only less than five high quality SNPs (hqSNPs) between ONT and Illumina sequencing data were achieved. SNP typing allowed differentiation of Choleraesuissensu stricto, Choleraesuis var. Kunzendorf, Choleraesuis var. Decatur, Paratyphi C, and Typhisuis that share the same antigenic formula 6,7:c:1,5. Prophage prediction further distinguished Orion var. 15+ and Orion var. 15+, 34+. Our study improves the readiness of ONT as a Salmonella subtyping and source tracking tool for food industry applications. HighlightsO_LISalmonella serotypes or serotype variants with the same antigenic formula were differentiated by SNP typing. C_LIO_LINanopore sequencing followed by phage prediction identified the Salmonella serotype variants caused by phage conversion. C_LIO_LIThe latest ONT technology is capable of high fidelity SNP typing of Salmonella. C_LI

microbiology↗