RESUMO
INTERESTS OF CLINICAL METAGENOMICS IN INFECTIOUS DISEASES. Clinical metagenomics (CM) is a cutting-edge molecular biology technique that is now a valuable diagnostic tool for microbiologists. It enables the detection of all microorganisms present in a sample, without any prior assumption or bias. The CM approach can be applied to various types of samples and involves multiple steps, such as extraction, library preparation, Next Generation Sequencing, and bioinformatics analysis. CM has been implemented in the diagnosis of various conditions, including infections of the central nervous system, respiratory, digestive, ocular, skin infection, and sepsis. Moreover, CM provides a comprehensive analysis of the microbiome present in the sample, microbial transcripts, and the host response in a single analysis. However, further studies are necessary to determine its place in the diagnostic algorithm. Besides diagnosis, CM has proven useful in identifying resistance to antimicrobial treatments and in epidemiology. Although the cost of CM is still higher than conventional methods, the emergence of more affordable sequencers and commercial tests will enable its implementation in a larger number of laboratories in the future.
INTÉRÊTS DE LA MÉTAGÉNOMIQUE CLINIQUE EN INFECTIOLOGIE. La métagénomique clinique (MgC) est un nouvel outil de biologie moléculaire dans l'arsenal diagnostique des microbiologistes. Elle permet de détecter sans a priori tous les micro-organismes présents. Utilisable sur tous types de prélèvements, elle nécessite plusieurs étapes (extraction, préparation des banques, séquençage par next generation sequencing, analyses bio-informatiques). Son utilisation en diagnostic a été décrite dans différentes pathologies (infections du système nerveux central, infections respiratoires, digestives, oculaires, cutanées et en cas de sepsis). En une seule analyse, la MgC permet également d'étudier le microbiome présent dans le prélèvement, d'analyser les transcrits microbiens et d'étudier la réponse de l'hôte. Sa place dans l'algorithme diagnostique doit faire l'objet d'études supplémentaires. En sus du diagnostic, la MgC a démontré son utilité dans la recherche de résistance aux traitements antimicrobiens, mais également en épidémiologie. Malgré les progrès visant à réduire les coûts, la MgC reste encore à l'heure actuelle plus coûteuse que les méthodes conventionnelles. La mise sur le marché de séquenceurs plus accessibles ainsi que le développement de tests commerciaux permettront l'utilisation de la MgC dans un plus grand nombre de laboratoires dans les années futures.
Assuntos
Anti-Infecciosos , Doenças Transmissíveis , Microbiota , Sepse , Humanos , Doenças Transmissíveis/diagnóstico , Microbiota/genética , Metagenômica/métodosRESUMO
BACKGROUND: The dynamics of SARS-CoV-2 alpha variant shedding and immune responses at the nasal mucosa remain poorly characterised. METHODS: We measured infectious viral release, antibodies and cytokines in 426 PCR+ nasopharyngeal swabs from individuals harboring non-alpha or alpha variants. FINDINGS: With both lineages, viral titers were variable, ranging from 0 to >106 infectious units. Rapid antigenic diagnostic tests were positive in 94% of samples with infectious virus. 68 % of individuals carried infectious virus within two days after onset of symptoms. This proportion decreased overtime. Viable virus was detected up to 14 days. Samples containing anti-spike IgG or IgA did not generally harbor infectious virus. Ct values were slightly but not significantly lower with alpha. This variant was characterized by a fast decrease of infectivity overtime and a marked release of 13 cytokines (including IFN-b, IP-10 and IL-10). INTERPRETATION: The alpha variant displays modified viral decay and cytokine profiles at the nasopharyngeal mucosae during symptomatic infection. FUNDING: This retrospective study has been funded by Institut Pasteur, ANRS, Vaccine Research Institute, Labex IBEID, ANR/FRM and IDISCOVR, Fondation pour la Recherche Médicale.