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 bacterial infections and allows comprehensive investigation on virulence, evolution and resistance mechanisms. Nepal, in recent times, has seen some increase in sequencing capabilities but faces numerous hurdles for optimum utilization. However, these hurdles can be alleviated with use of Illumina iSeq100. Therefore, this study aimed at performing whole genome sequencing of bacteria isolated utilizing the iSeq100 platform. For this study, 6 banked Salmonella enterica serovar Typhi bacterial isolates were selected. These isolates were extracted for DNA, confirmed by qPCR and then, their libraries were prepared. The libaries were checked and loaded in Illumina iSeq100 at loading concentration of 200pM. The consensus was generated from the raw genomic data by reference-based assembly, mapping onto S. Typhi CT18. These consensus genomes and coverage parameters were compared to data from using HiSeq and NextSeq. The raw reads were also evaluated using pathogenwatch (v22.3.8) to observe for 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 Illumina HiSeq and NextSeq. The average coverage width (96.81%) and depth (63.75x) of genomes sequenced in iSeq100 were comparable to that of HiSeq (width: 98.72% and depth: 69.87x). When the genomes sequenced were compared, 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 other high-end sequencers. Therefore, the primary goal of this study is to advocate for optimum utlisation of iSeq100 while still ensuring a high standard of quality. This optimum utilization would create capacity to fill critical surveillance gaps.