Comparison of clinical metagenomics with 16S rDNA Sanger sequencing for the bacteriological diagnosis of culture-negative samples

Background: Currently, diagnosis of bacterial infections is based on culture, possibly followed by the amplification and sequencing (Sanger method) of the 16S rDNA - encoding gene when cultures are negative. Clinical metagenomics (CMg), i.e. the sequencing of a sample's entire nucleic acids, may allow for the identification of bacteria not detected by conventional methods. Here, we tested the performance of CMg compared to 16S rDNA sequencing (Sanger) in 50 patients with suspected bacterial infection but negative cultures. Methods: This is a prospective cohort study. Fifty patients (73 samples) with negative culture and a 16S rDNA sequencing demand (Sanger) were recruited from two sites. On the same samples, CMg was also performed and compared to 16S rDNA Sanger sequencing. Bacteria were identified using MetaPhlAn4. Results: Among the 73 samples, 20 (27.4%, 17 patients) had a clinically significant 16S rDNA Sanger sequencing result (used for patient management) while 11 (15.1%, 9 patients) were considered contaminants. At the patient level, the sensitivity of CMg was 70.1% (12/17) compared to 16S rDNA. In samples negative for 16S rDNA Sanger sequencing (n=53), CMg identified clinically-relevant bacteria in 10 samples (18.9%, 10 patients) with 14 additional bacteria. Conclusions: CMg was not 100% sensitive when compared to 16S, supporting that it may not be a suitable replacement. However, CMg did find additional bacteria in samples negative for 16S rDNA Sanger. CMg could therefore be positioned as a complementary to 16S rDNA Sanger sequencing. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by a grant from the Assistance Publique Hopitaux de Paris (Contrat de Recherche Clinique). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The project was approved by the Comite de Protection des Personnes Sud-Ouest et Outre Mer 1 on October 25, 2021 (2019-A01117-50 CPP 1-19-077 / SI 5294). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors