SECTION 2FINDINGS AND RECOMMENDATIONS

Key Finding 2.1 Multiplex panels and MALDITOF MS are the main sources of competition for NGS, with MALDI-TOF MS being primarily for the identification of isolated, cultured colonies. Some multiplex PCR panels that are currently available can detect an array of pathogens without requiring a pure culture. MALDI-TOF MS has been incorporated into clinical laboratories, while NGS still remains more of a “service model.” The turnaround time for MALDI-TOF MS is minutes once a pure culture has been obtained. MALDI-TOF MS has proven to be useful for the identification of organisms from pure culture with the assistance of a reference database. A key advantage of NGS is the option to perform de novo genome assembly, which does not require a genomic reference or prior knowledge of the target organism, but organism identification still requires a reference database.

Key Recommendation 2.1 In order for NGS-based assays to become commonplace in the clinical microbiology laboratory, there is a need for the development of “turnkey” solutions for all phases of testing (i.e., sample preparation, sequencing, data analysis, and result interpretation). The ultimate goal of diagnostic NGS is to place a direct clinical specimen from any matrix into the NGS workflow and generate an actionable result within a reasonable time frame. Continued efforts for direct clinical sample sequencing should be pursued.

Key Finding 2.2 There are platform-dependent errors associated with different sequencing chemistries, and thus, the base calling/error rate sensitivities and specificities of sequencing platforms cannot be directly compared to those of other types of DNA technologies.

Key Recommendation 2.2 It is recommended that a distinction be made between diagnostic clinical specificity/sensitivity and analytical specificity/sensitivity when discussing a clinical microbiological NGS test. The qualifiers of “diagnostic clinical” and “analytical” are not interchangeable, and confusion can arise when reporting a laboratory test result (27). More efforts are also needed to understand the mutation rates and population structures of commonly encountered clinical pathogens in relationship to their effects on NGS sensitivity and specificity.