When tests don’t fit the rules: regulatory challenges for agnostic metagenomic next-generation sequencing in infectious diseases diagnostics

ABSTRACT Metagenomic next-generation sequencing (mNGS) enables agnostic detection of bacteria, viruses, fungi, and parasites from clinical specimens. Patient access is restricted due to their current regulatory classification as Laboratory Developed Tests, which are offered by a limited number of laboratories. While patient access may be expanded through Food and Drug Administration authorization of mNGS-based in vitro diagnostics, some regulatory requirements for achieving this classification can be challenging to apply due to the agnostic nature of mNGS. For example, existing guidelines recommend organism-by-organism performance characterization similar to targeted molecular tests involving fixed analytes with stable detection thresholds. This mini-review synthesizes validation and regulatory challenges unique to mNGS-based diagnostics and describes how laboratories and developers currently navigate available pathways. We focus on core analytical and clinical validation challenges, including discussion on the central role of bioinformatics pipelines and reference databases. We then summarize practical considerations for regulatory engagement, labeling, clinical-facing reporting, and alignment of mNGS assays to existing quality system frameworks. Finally, we outline future oversight considerations, including the need to distinguish mNGS from multiplexed PCR paradigms and the potential value of modular, component-based regulatory approaches that separately evaluate reagents, instruments, software, and databases, enabling system-level oversight rather than organism-by-organism validation. Together, these considerations aim to support risk-appropriate, scalable oversight, and accelerate adoption of mNGS in clinical microbiology.