Metagenomics sequencing in infection diagnosis: clinical applications

Abstract

By performing a literature review, to identify categories of patients in whom metagenomics sequencing has demonstrated potential clinical relevance in the diagnosis of infections, highlighting the practical applications, benefits and limitations of this method in the context of different clinical scenarios for further adaptation of clinical and laboratory diagnostic protocols. The study is descriptive and analytical. A literature review was conducted, using literature from open access databases. English language papers relevant to the proposed research topic published in the last 5 years were selected according to the inclusion criteria.

Metagenomics sequencing (mNGS) is an innovative technology that has revolutionized traditional clinical diagnostics on multiple levels. It can be used for the simultaneous identification of multiple pathogens such as bacteria, viruses, fungi and parasites in clinical samples. The application of metagenomics would bring considerable benefits even in cases of rare infections with unknown etiology or pathogens that are difficult to culture. This study demonstrates how this new technology can be used for meaningful clinical diagnostics in microbiology. Patients with lower respiratory tract infections represent a category of patients for whom the use of mNGS brings several benefits, this technology has an overall higher sensitivity for pathogen detection compared to the culture method and is a necessary complement to conventional microbiologic tests. Sepsis is a major public health challenge and the use of mNGS for this category of patients can shorten the total hospitalization time and reduce mortality. Metagenomics sequencing technology is also useful for patients with central nervous system infections, the use of mNSG for those patients has a higher detection rate but the highest diagnostic yield is observed when combining mNGS with conventional methods. Metagenomics offers significant benefits in the detection of pathogens also in patients with deep cervical space abscesses, with a superior detection rate and sensitivity, allowing early initiation of antimicrobial therapy, improved prognosis and reduced consumption of medical resources. Metagenomics provides a complete, rapid and accurate identification of pathogens, significantly improving treatment, mainly when traditional methods are insufficient. Based on the studies presented in this article we can conclude that the application of metagenomics for patients with lower respiratory tract infections, sepsis, central nervous system infections and cervical deep space infections has a very high potential to reduce morbidity, mortality and health care costs.