Clinical use of WGS: Cost-effective in-house approach

Abstract In-house Whole-Genome Sequencing (WGS) has been proven to significantly reduce costs and improve operational efficiency compared to reference laboratory services for bacterial and mycobacterial identification. At AdventHealth Orlando, a 12-month cost analysis was conducted following the implementation of an in-house WGS protocol designed to replace send-out services for organism identification. Long-read sequencing was selected for its simplicity, customization, and minimal instrumentation needs. WGS provides broader genomic coverage. The workflow employed the ZymoBIOMICS MagBead 96 DNA Kit (Zymo Research) for DNA extraction, followed by library preparation using the Rapid Ligation Kit, and sequencing on the Flongle flow-cell and MK1C sequencer (Oxford Nanopore). The in-house protocol, colony-to-result, enables multiplexing of six isolates per flow-cell. Samples were sequenced on Tuesdays and Thursdays. The standardized protocol ensures scalability and adaptability, accounting reagents, instruments, and labor costs. From October-2022 to September-2023, 93 bacterial and 667 mycobacterial isolates were sent to reference laboratories, costing $364 and $369 per isolate, respectively, including shipping. Post-implementation (October-2023 to September-2024), 78 bacterial and 705 mycobacterial isolates were processed in-house at $63 per isolate, saving $230,646. Return on investment was achieved within one month. Turnaround time improved from an average of 9 days to 48 hours. Following these results, we transitioned to the GridION sequencer (Oxford Nanopore) while maintaining the same workflow and enabling expanded capabilities. Additionally, clinically significant mold identification, has been implemented using a similar protocol. This study highlights the cost-effectiveness, scalability, and operational improvements of in-house WGS, offering a model for other clinical laboratories seeking efficiency and broader identification capabilities.