Metagenomic Next-Generation Sequencing for Pathogenic Diagnosis and Antibiotic Management of Severe Community-Acquired Pneumonia in Immunocompromised Adults

Abstract

BackgroundMetagenomic next-generation sequencing (mNGS) is a promising technique for pathogens diagnosis. However, application of mNGS in immunocompromised adults with severe community-acquired pneumonia (SCAP) is relatively limited.MethodsWe retrospectively reviewed 23 immunocompromised and 21 immunocompetent SCAP patients with mNGS detection from April 2019 to December 2019. The performances of pathogenic diagnosis and subsequently antibiotic adjustment in immunocompromised SCAP patients were compared to immunocompetent SCAP patients. The defined by days of therapy (DOT) method was used for estimate daily antibiotic use.ResultsThere was a significant difference in the diagnostic positivity rate between mNGS and conventional test in both groups (P<0.001). Compared to immunocompetent patients, more mixed pathogens in immunocompromised patients were found (P=0.023). Before the availability of mNGS, the DOTs in immunocompromise patients were higher than immunocompetent patients (3.0 [3.0, 4.0] vs. 3.0 [2.0, 3.0], P=0.013). Compared to immunocompetent patients, immunocompromised patients had fewer full pathogen covered empirical antibiotic therapy (14.7% vs. 57.1%, P=0.022), more adjustments of antibiotic treatment (87.0%) vs. 57.1%, P=0.027). More than a half (13 of 23) SCAP patients in immunosuppressed group had reduced or downgraded antibiotic adjustments based on the results.ConclusionsmNGS may be a useful technique for detecting mixed pathogens and personalized antibiotic treatment in immunocompromised SCAP patients.

Evaluation of Metagenomic and Targeted Next-Generation Sequencing Workflows for Detection of Respiratory Pathogens from Bronchoalveolar Lavage Fluid Specimens

“…Adjunctive use also involves diagnostic stewardship, and use with standard microbiology testing in select populations may be the most beneficial. The performance of NGS workflows is enhanced when samples from specific patient populations, such as those who are immunocompromised, are studied ( 26 – 29 ).…”

Diagnostic Value of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluid for the Diagnosis of Suspected Pneumonia in Immunocompromised Patients

“…More polymicrobial infections were found in immunocompromised patients in comparison with immunocompetent patients (20). Peng etc(6) reported that more than half of microbiologically con rmed pneumonia having mixed infections.…”

Case Report: Community-Acquired Legionella gormanii Pneumonia in an Immunocompetent Patient Detected by Metagenomic Next-Generation Sequencing

“…Metagenomic next-generation sequencing (mNGS) can directly identify the pathogens' sequences in clinical samples and has been applied in clinical infectious disease diagnostics including pneumonia (5)(6)(7). Here, we report a case of severe community-acquired pneumonia in a 53-year-old man, in which the conventional pathogen-detecting tests were all negative including legionella urinary antigen test, while a great amount of DNA (7,957 in a total of 21,977,576 sequences) and RNA (3,443 in a total of 12,763,560 sequences) sequences of Legionella gormanii in bronchoalveolar lavage fluid were identified by mNGS. After quinolones antibiotic therapy, the patient recovered.…”