Validation, Implementation, and Clinical Utility of Whole Genome Sequence-Based Bacterial Identification in the Clinical Microbiology Laboratory

The application of next-generation sequencing (NGS) extends from microbial identification to epidemiological insight and antimicrobial resistance prediction. Despite this potential, the roadblock for clinical labs lies in implementation and validation of such complex technology and data analysis. Here, we describe a validation study of using whole-genome sequencing (WGS) for pan-bacterial identification (ID) in a clinical laboratory setting, and discuss the clinical relevance. A diverse set of 125 bacterial isolates, including a subset of isolates without genus (25) and/or species (10) IDs, were analyzed by de novo assembly and reference genome mapping. The 16S rRNA, rpoB, and groEL genes were used for ID. Using WGS, 100% (89/89) and 89% (79/89) of isolates were identified to the genus and species-levels, respectively. WGS also provided improved results for the majority of isolates (25/35) that were originally reported with genus-only or descriptive IDs. Chart review identified cases where improved genus and/or species level ID by WGS may have had a positive impact on patient care. Reasons included the use of an ineffective antibiotic due to unclear ID, use of antibiotics when not clinically indicated, and help with an outbreak investigation. The implementation of NGS in a clinical microbiology setting is a challenging but necessary task. Our study provides a model for the validation and implementation of bacterial ID by WGS in such a setting.