Advancing infection diagnosis: Study on innovative metagenomic tool

France's clinical metagenomics: A study on performance


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Scientists from Necker-Enfants Malades Hospital and collaborators studied the role of genetic characterization in infection diagnosis. Using next-gen sequencing, they explored non-targeted metagenomics for optimal treatment.

Published in Lancet Microbe on December 1, 2023, the study addresses challenges in identifying infectious agents, emphasizing the need for a tool capable of detecting new pathogens and those with rapidly evolving genomes. The current ‘targeted’ approach often falls short, leaving the cause of infection unknown and leading to suboptimal treatment.”

Using advanced sequencing (mNGS), this study explores the broad identification capabilities of metagenomics in detecting various pathogens, including rare or novel microorganisms.

The aim is to enhance the application of this innovative microbial identification technique. While complex and costly, the study, conducted by the hospital team in collaboration with Institut Pasteur, seeks to make mNGS more accessible in hospital labs and healthcare centers across France. The study analyzed 742 samples from 523 patients between October 29, 2019, and November 7, 2022, with accompanying physician-prescribed forms indicating clinical suspicion of infection.

In samples with high initial infection suspicion (63%), metagenomics showed a diagnostic yield of 25%, detecting causative pathogens. It performed exceptionally well in immunocompromised and neurologically-disordered patients, especially with brain biopsies. Brain biopsies surpassed cerebrospinal fluid in virus detection.

Stool analyses proved effective for digestive, hepatitis, and neurological issues. Notably, metagenomics matched or outperformed traditional microbiology. From a prospective study, these findings contribute to defining metagenomics’ role in diagnosis and treatment decisions.

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) explains, “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 Prof. Marc Eloit led 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.

“We’re excited to improve medical care and enhance infectious disease knowledge,” said Prof. Marc Eloit, co-last author of the study. The findings offer insights into the future of infection diagnostics, aiding tool development for faster and accessible sequencing. Philippe Pérot, co-author and lead for mNGS at Institut Pasteur, highlights the potential for discovering new pathogens. The study, funded by Necker-Enfants Malades Hospital and Institut Pasteur, paves the way for advanced genomic analysis in infectious disease research.

In conclusion, this study sheds light on the potential of mNGS in improving infection diagnosis, paving the way for future advancements in genomic analysis and the discovery of new pathogens.

Journal reference:

  1. Jacques Fourgeaud, Béatrice Regnault, et al., Performance of clinical metagenomics in France: a prospective observational study. The Lancet. DOI: 10.1016/S2666-5247(23)00244-6.


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