Leveraging Illumina iSeq100 for Whole Genome Sequencing of Salmonella Typhi: a practical approach for resource-limited setting

Bacterial whole-genome-sequencing helps to improve our understanding of epidemiology and pathogenesis of infections and allows comprehensive investigation on virulence, evolution and resistance mechanisms. Nepal, recently, has seen some increase in sequencing capabilities but faces hurdles for optimum utilisation. However, these hurdles could be alleviated using Illumina iSeq100. Therefore, this study aimed at performing whole-genome-sequencing of bacteria utilising iSeq100. Six banked isolates of S Typhi bacterial were selected, extracted for DNA, confirmed by qPCR and then sequenced in Illumina iSeq100 at 200pM. The consensus was generated by reference-based assembly, mapping onto S . Typhi CT18. These consensus genomes and coverage parameters were compared to data from HiSeq and NextSeq. The raw reads were also evaluated using pathogenwatch to observe genotype, mutations and resistance genes. The coverage parameters (coverage width and depth) of the genomes from this study were compared to same genomes sequenced using HiSeq/NextSeq. The average coverage width (96.81%) and depth (63.75x) of genomes sequenced in iSeq100 were comparable to that of HiSeq/NextSeq (width: 98.72% and depth: 69.87x). The genotypes detected, number of SNPs and genetic determinants of AMR genes were identical. The data from bacterial whole-genome-sequencing using the Illumina iSeq100 is equally informative when compared to some high-end sequencers. Thus, the primary goal of this study is to advocate for optimum utlisation of iSeq100, still ensuring for a high-quality data.