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

• Published in: The Journal of molecular diagnostics : JMD Vol. 23; no. 11; pp. 1468 - 1477
• Main Authors: Price, Travis K., Realegeno, Susan, Mirasol, Ruel, Tsan, Allison, Chandrasekaran, Sukantha, Garner, Omai B., Yang, Shangxin
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-11-2021
• Subjects: Bacterial Proteins - genetics; Base Sequence - genetics; Chaperonin 60 - genetics; Chromosome Mapping - methods; Clinical Laboratory Techniques - methods; Computational Biology - methods; Data Accuracy; Disease Outbreaks - prevention & control; DNA-Directed RNA Polymerases - genetics; Drug Resistance, Bacterial - genetics; Escherichia coli - genetics; Escherichia coli Proteins - genetics; Genes, Bacterial; High-Throughput Nucleotide Sequencing - methods; Humans; Laboratories, Clinical; Mycobacterium - classification; Mycobacterium - genetics; Mycobacterium - isolation & purification; Retrospective Studies; RNA, Ribosomal, 16S - genetics; Whole Genome Sequencing - methods
• ISSN: 1525-1578; 1943-7811
• DOI: 10.1016/j.jmoldx.2021.07.020

The application of next-generation sequencing extends from microbial identification to epidemiologic insight and antimicrobial resistance prediction. Despite this potential, the roadblock for clinical laboratories lies in implementation and validation of such complex technology and data analysis. Herein, a validation study used whole-genome sequencing (WGS) for pan-bacterial identification (ID) in a clinical laboratory, and assessed its clinical relevance. A diverse set of 125 bacterial isolates, including a subset without genus (25) and/or species (10) ID, 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 of 89) and 89% (79 of 89) of isolates were identified at the genus and species-levels, respectively. WGS also provided improved results for 71% (25/35) isolates originally reported with genus-only or descriptive IDs. Chart review identified cases in which 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 owing to unclear ID, use of antibiotics when not clinically indicated, and help with an outbreak investigation. The implementation of next-generation sequencing in a clinical microbiology setting is a challenging but necessary task. This study provides a model for the validation and implementation of bacterial ID by WGS in such a setting.