Diagnostic value of metagenomic next-generation sequencing using bronchoalveolar lavage fluid samples for pathogen detection in children with severe or refractory pneumonia
Notice bibliographique
Résumé
ABSTRACT Pneumonia is the leading cause of morbidity and mortality in children and needs rapid and accurate pathogenic diagnosis. The aim of this study was to evaluate the diagnostic value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMTs) for pathogen detection in children with severe or refractory pneumonia. In this retrospective study, the clinical data of 127 children with severe or refractory pneumonia admitted to the respiratory department from June 2021 to March 2022 were analyzed. BALF mNGS and CMTs were utilized for pathogen diagnosis and comparison of their detection performance for different pathogens. The pathogenic diagnosis rate was 95.28% (121/127) by combining mNGS and CMTs. mNGS had significantly higher overall (96.06% vs 72.44%, P < 0.001), bacterial (69.29% vs 12.60%, P < 0.001), and fungal (11.81% vs 3.15%, P = 0.009) detection rates than CMTs. However, there was no significant difference of detection rates between them for respiratory viruses (33.86% vs 33.75%, P = 0.99) and Mycoplasma pneumoniae (48.03% vs 45.67%, P = 0.71). The sensitivities of mNGS for total pathogens, bacteria, and fungi were 99.17%, 100%, and 87.50%, respectively, which were higher than those of CMTs. CMTs for M. pneumoniae had the highest sensitivity (91.23%) compared with mNGS (89.47%) and multiplex PCR (88.57%). For respiratory viruses, mNGS and mPCR had similar sensitivities (97.67% vs 96.43%). mNGS was superior to CMTs in bacterial and fungal detection, while it was comparable to multiplex PCR for the detection of M. pneumoniae and respiratory viruses. Different detection methods should be rationalized for different pathogens. IMPORTANCE This study on 127 patients with severe and refractory pneumonia showed that mNGS was significantly superior to CMTs in terms of bacterial and fungal detection. We also found that multiplex PCR assay was comparable to mNGS for the detection of Mycoplasma pneumoniae and respiratory viruses and may have greater application advantages in combination with CMTs, such as M. pneumoniae IgM. For severe and refractory pneumonia, or when empiric treatment is not effective, collecting BALF for mNGS can help to quickly identify the causative organisms at an early stage. It is also important to choose more appropriate methods or combinations for different pathogens.
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Comment cette classification a été obtenuedéplier
Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule tête enseignante, pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».