Improving the diagnosis of infection: a prospective study clarifies the role of an innovative metagenomic tool

The identification of microorganisms involved in infection is a major challenge in ensuring that patients receive optimal treatment. Recent epidemics have shown the importance of a tool capable of detecting new or unexpected pathogens and those with rapidly evolving genomes. Currently, the search for infectious agents is mostly ‘targeted’ and requires prior knowledge of the possible causes of infection. In many cases however, no microorganism is identified by first-line testing and the cause of the infection remains unknown, leading to suboptimal treatment.

Metagenomics¹ using next-generation sequencing (mNGS) can identify a wide range of pathogens, including rare or novel microorganisms. This study aims to improve use of this innovative microbial identification technique, which remains complex and costly for hospital laboratories as it requires cross-disciplinary skills ranging from specific sample preparation to bioinformatics analysis of a large number of sequences. The hospital team drew on the technical and IT skills of the Institut Pasteur’s Pathogen Discovery Laboratory² and worked to make mNGS available within the AP-HP and to practitioners in healthcare centers in mainland France and overseas.

In this study, 742 samples were collected for mNGS analysis from 523 patients between October 29, 2019 and November 7, 2022. Samples were accompanied by a mandatory prescription form completed by the physician, indicating the level of clinical suspicion of infection.

The results relate to a panel whose initial suspicion of infection was either high (63%) or low (37%). In 117 patient samples where infection was strongly suspected — i.e. 25% of samples where infection was strongly suspected according to the practitioners’ preliminary assessment — causative or potentially causative pathogens were detected.

The diagnostic yield of mNGS was particularly high in immunocompromised patients and in patients with neurological disorders where brain biopsies were available. In fact, mNGS more easily detects a causative or potentially causative pathogenic virus in brain biopsies than in cerebrospinal fluid, which is traditionally used because it is easier to obtain. Furthermore, the study showed that stool analyses could be used to investigate not only digestive disorders, but also hepatitis and various neurological symptoms.

In addition, the clinical performance of mNGS compares favorably to conventional microbiology. Together with future studies, the results of this prospective observational study will help to define the role of mNGS in decision making relating to diagnosis and treatment.

“The Microbiology Laboratory (Prof. Leruez-Ville), in conjunction with the Department of Infectious and Tropical Diseases (Prof. Lortholary and Prof. Lecuit) and the Pediatric Immunohematology and Rheumatology Department (Prof. Quartier dit Maire and Prof. Neven) at Necker-Enfants Malades Hospital (AP-HP), has developed extensive expertise in the management of immunocompromised patients prone to infections caused by unusual microorganisms. The Institut Pasteur’s Pathogen Discovery Laboratory², which was led by Prof. Marc Eloit at the time of the study, had already optimized the use of high-throughput sequencing for pathogen discovery by developing the technique for both sample preparation methods and bioinformatics analysis tools. This collaboration between Necker-Enfants Malades (AP-HP) and the Institut Pasteur was therefore well placed to identify novel causes of infection in cases where conventional techniques were missing diagnoses,” explains Dr. Anne Jamet, the study’s final author, who is head of mNGS at Necker-Enfants Malades Hospital (AP-HP) and a researcher at the Institut Necker-Enfants Malades (AP-HP).

“Our instincts have translated into reliable diagnoses in everyday practice as well as several noteworthy discoveries, including the identification of a new virus responsible for hepatitis,” adds Dr. Jacques Fourgeaud, first author of the study and lead virologist for mNGS at Necker-Enfants Malades Hospital (AP-HP).

“This sequencing-based tool is now indispensable for diagnosing patients with a suspected infection. We are now using it earlier and earlier in severe cases, particularly those involving the brain, and in immunocompromised adults and children,” says Prof. Olivier Lortholary, an infectious diseases specialist who is head of the Department of Infectious and Tropical Diseases at Necker-Enfants Malades Hospital (AP-HP) and co-author of the study.

“We’re delighted to be able to contribute to better medical care, while at the same time increasing our knowledge of infectious diseases,” adds Prof. Marc Eloit, co-last author of the study, who led the Pathogen Discovery Laboratory² until September 2023 and is now a visiting researcher at the Institut Pasteur. The study also provides an insight into the future of infection diagnostics. “The microorganisms we identify with the Necker microbiology laboratory will enable us to develop new tools to make sequencing technology faster and more accessible for front-line microbiological analysis while enhancing its potential for the discovery of new human pathogens,” says co-author Philippe Pérot, a research engineer in the Institut Pasteur’s Pathogen Discovery Laboratory² and lead for mNGS at the Institut Pasteur.

The study was funded by Necker-Enfants Malades Hospital (AP-HP) and the Institut Pasteur.

¹ Study of all genomes from a single environment and interactions between them

² The Institut Pasteur’s Pathogen Discovery Laboratory was led by Prof. Marc Eloit until August 31, 2023. Dr. Nolwenn Dheilly took over as head of the laboratory on September 1, 2023.