Leveraging illumina iSeq100 for whole genome sequencing of Salmonella Typhi for a resource-limited setting

Bacterial whole-genome-sequencing improves our understanding of epidemiology and pathogenesis of infections. It also 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 with strategic use of available platforms. Therefore, this study aimed at performing and evaluating the whole-genome-sequencing of S Typhi using Illumina iSeq100. Six banked isolates of S Typhi were selected, extracted, confirmed by qPCR and then sequenced in Illumina iSeq100 at 200pM. The consensus was generated by mapping onto S. Typhi CT18. These consensus genomes and their 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 (breadth and depth) of the genomes from this study were compared to the same genomes sequenced using HiSeq/NextSeq. The average coverage breadth (96.81%) and depth (63.75x) of genomes sequenced in iSeq100 were comparable to that of HiSeq/NextSeq (breadth: 98.72% and depth: 69.87x). The genotypes detected, the number of SNPs and genetic determinants of AMR genes were identical across platforms. The data from bacterial whole-genome-sequencing using the iSeq100 is equally informative when compared to some high-end sequencers. Thus, this study advocates for optimum utlisation of available platforms such as iSeq100.