Use of Diagnostic Metagenomics in the Clinical Microbiology Laboratory

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Figure 1.
Sites of current and future mNGS diagnostics. Blue represents sterile sites. Black represents nonsterile sites. BAL, bronchoalveolar lavage; cfDNA, cell-free DNA; CNS, central nervous system; CSF, cerebral spinal fluid; UTI, urinary tract infection.

Table 1.

mNGS steps and needed skillsets

Step of mNGS	Associated/Needed Skills	Automated or Streamlined Solutions Available
Nucleic acid extraction	1. Knowledge of molecular workflow 2. Molecular sample handling techniques	Automation
Complementary DNA creation (for RNA libraries)	Same as previously mentioned, including handling and manipulation of RNA	None
Library preparation	1. Knowledge of molecular workflow 2. Molecular/micropipetting techniques 3. Understanding of NGS methodology and calculations 4. Critical thinking/troubleshooting of NGS preparation steps	Automation
Instrument operation	Experience or proper training	None
Quality control	Critical thinking/troubleshooting of NGS preparation steps	None
Read/data analysis	All of the previously mentioned items, including bioinformatics training and programming knowledge	Web-based commercial pipeline
Data interpretation	1. All of the previously mentioned items, including experience and involvement in the test validation 2. Medical Director review, chart review, consultation, and sign-out	Establishment of positive/negative pipeline criteria