Automated whole genome sequencing platform for bacterial strain typing in clinical microbiology laboratories

Nosocomial outbreaks impact patient safety and place an economic burden on healthcare facilities. Laboratory testing plays a crucial role in outbreak investigation and guides containment efforts. In recent years, whole genome sequencing (WGS) methods have replaced traditional typing methods due to higher resolution and simplified workflows. Though an improvement from previous methods, bacterial WGS is time-consuming with manual DNA extraction and library preparation and long sequencing times for paired-end sequence data. Here, a fully automated library preparation and sequencing solution, the Clear Dx^TM WGS platform (Clear Labs, San Carlos, CA), was compared to a more manual library preparation and sequencing approach using 226 isolates representing 18 bacterial species. Sequence data were analyzed using SeqSphere+ (Ridom, Münster, Germany), and the results of the two methods were compared. Of the 224 isolate sequences analyzed, 222 (99%) showed concordant isolate groupings, and, overall, the results of the two approaches were statistically similar by comparison of distance matrices. The automated workflow reduced turnaround time by 16-19 h and eliminated 3 h of manual labor while decreasing costs by an estimated 34%-57% depending on the number of isolates run. This study demonstrates the advantages of integrating automation into bacterial WGS workflows.IMPORTANCEAn automated platform for bacterial nucleic acid extraction and whole genome sequencing was compared to a manual method for bacterial strain typing. The two approaches yielded nearly equivalent results, with the automated approach providing improvement in turnaround time and cost, with less manual pipetting.