Bacterial Whole Genome Sequencing on the Illumina iSeq 100 for Clinical and Public Health Laboratories

Abstract

Bacterial whole-genome sequencing (WGS) provides clinical and public health laboratories an unprecedented level of information on species identification, antimicrobial resistance, and epidemiologic typing. However, multiple barriers to widespread adoption still exist. This research describes bacterial WGS using the Illumina iSeq 100 instrument to overcome some of these barriers. Using an in-house, high-quality single-nucleotide polymorphism analysis pipeline and a commercial whole-genome multilocus sequence typing program, the sequencing of Acinetobacter baumannii, Burkholderia cepacia, Clostridioides difficile, Enterococcus faecalis, Escherichia coli, Pseudomonas aeruginosa, Serratia marcescens, and Staphylococcus aureus isolates was validated. The genome coverage range was 17Â to 149Â, with a mean of 59Â. The limit of detection for single-nucleotide polymorphisms was 30Â. Overall platform base calling accuracy was >99.999%. Reproducibility and repeatability of base calling inferred from whole-genome multilocus sequence typing was species dependent and ranged from >97% similarity for P. aeruginosa to >99.9% similarity for S. aureus. Resistance gene and multilocus sequence typing allele identification was 100% concordant with expected results. A simple, modified library preparation reduces the per-sample cost by half to give overall theoretical sample costs ranging from approximately $50 to $100 for library preparation and sequencing. The iSeq 100 provides a cost-effective and easy-to-use platform for clinical and public health laboratories to sequence bacterial isolates for a wide range of potential applications.

A simplified, amplicon-based method for whole genome sequencing of human respiratory syncytial viruses

“…A limitation of this study is that although we have demonstrated that tiling amplicons generated by this approach can be sequenced either on the Illumina iSeq platform or on the long-read ONT MinION platform, we characterized this new method mostly using an Illumina platform and only several RSV whole genomes were sequenced on the ONT platform. An advantage of using the Illumina DNA preparation kits is that saturation-based DNA normalization is performed when doing on-bead tagmentation 27 . Therefore, up to 48 NGS libraries were pooled for a multiplex sequencing on an Illumina iSeq device in this study, without individual library quantitation and normalization.…”

Intensification in Genetic Information and Acquisition of Resistant Genes in Genome of Acinetobacter baumannii: A Pan-Genomic Analysis

“…Whole-genome sequencing (WGS) provides deep knowledge regarding species identification, antimicrobial resistance, and epidemiological typing of organisms to researchers. It helps in the identification of new drug targets and the development of new drugs [ 11 ]. The ability of WGS to distinguish the strains that differ by even a single nucleotide provides high-resolution information [ 12 ].…”

Emergence of multi-drug-resistant Mycobacterium tuberculosis in Niger: A snapshot based on whole-genome sequencing

“…Second generation high throughput sequencing technologies (such as the Illumina iSeq 100 System) mean it is now possible to perform whole genome sequencing (WGS) of M . tuberculosis [ 6 ]. Current genomic data showed that MTBC comprises nine human-adapted lineages (lineages 1–9) [ 4 , 7 – 10 ].…”