Next-Generation Sequencing in the Clinical Microbiology Lab
Next-generation sequencing techniques are quickly moving into the clinical microbiology lab. ASM provides a number of resources to help you learn best practices for their application and interpretation for infectious disease diagnoses.
Last week's Bugs & Drugs post presented the benefits of using molecular technologies in diagnosing infectious diseases. "Molecular technologies" is a catch-all phrase for many different methods to look at the genetic content of a microbial infection, and one of the methods that is quickly increasing in clinical applications is next-generation sequencing (NGS). NGS itself is a term for the collective sequencing techniques and their associated analytical pipelines that have been developed since 454 pyrosequencing advanced the decades-old Sanger sequencing protocols.
Now several of the experts involved in the Report, together with ASM and the College of American Pathologists, have published an open-access update to the report. The article addresses assay design and validation using concrete examples from two separate studies, one using respiratory specimens and one using cerebrospinal fluid specimens. In addition to wet bench protocols, the article outlines important aspects of database selection and curation--aspects that can strongly influence the analytical outcome of a sequencing assay.As previously discussed on the blog, development of new clinical assays requires standardization and validation to ensure the technique providess accurate results in a variety of locations and conditions. As the technology has been developed and applied toward basic research, ASM has facilitated conversations about its transfer to clinical uses. In 2016, the American Academy of Microbiology released a Colloquium Report entitled "Applications of Clinical Microbial Next-Generation Sequencing." This Report summarized the current state of NGS in the clinic and made recommendations for further implementation.
Looking for more resources on NGS in the clinical lab? Try these reviews from the Journal of Clinical Microbiology:
- Dekker JP and Frank KM. Next-Generation Epidemiology: Using Real-Time Core Genome Multilocus Sequence Typing to Support Infection Control Policy.
- Gargis AS, Kalman L, and Lubin IM. Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories. JClinMicro Dec 2016.
- Gwinn M, MacCannell DR, and Khabbaz RF. Integrating Advanced Molecular Technologies into Public Health. JClinMicro March 2017.