Forty Years of Molecular Diagnostics for Infectious Diseases

Abstract

Nearly 40 years have elapsed since the invention of the PCR, with its extremely sensitive and specific ability to detect nucleic acids via in vitro enzyme-mediated amplification. In turn, more than 2 years have passed since the onset of the coronavirus disease 2019 (COVID-19) pandemic, during which time molecular diagnostics for infectious diseases have assumed a larger global role than ever before. In this context, we review broadly the progression of molecular techniques in clinical microbiology, to their current prominence. Notably, these methods now entail both the detection and quantification of microbial nucleic acids, along with their sequence-based characterization. Overall, we seek to provide a combined perspective on the techniques themselves, as well as how they have come to shape health care at the intersection of technologic innovation, pathophysiologic knowledge, clinical/laboratory logistics, and even financial/regulatory factors.

Keywords: DNA sequencing; PCR; diagnostic molecular microbiology; magnetic beads; nucleotide array; point of care; real-time quantitative PCR; sequencing; syndromic panel.

FIG 1

Basic three-step procedure for a nucleic acid amplification assay in clinical microbiology, compromising specimen extraction, RNA/DNA amplification itself, and amplification product detection/identification. For each step (at top), different technical/procedural options employed in clinical settings use are summarized. Important classes of diagnostic technology also combine (conceptually or instrumentation-wise) the component steps together, summarized at bottom. These include qPCR/qRT-PCR, which combine amplification and detection, as well as various high-throughput automated and point-of-cate testing platforms, which segue from one step to the next through engineering features.

FIG 2

(A) Integrated themes in molecular diagnostics. A web of interconnected factors now guide the application of molecular diagnostics to infectious disease care. With examples provided here, these include advances in the diagnostic technology itself and our understanding of the pathobiology of infections and host-microbe interactions; practical and logistical considerations in both the laboratory and clinic; prominent matters of health care finance and reimbursement; and the regulatory/legal framework surrounding diagnostic testing around the world. (B) Evolution of NAAT Technology. Republished with permission from reference . POCT, point-of-care test.