Clinical Utility of In-house Metagenomic Next-generation Sequencing for the Diagnosis of Lower Respiratory Tract Infections and Analysis of the Host Immune Response.

BACKGROUND: Only few pathogens that cause lower respiratory tract infections (LRTIs) can be identified due to limitations of traditional microbiological methods and the complexity of the oropharyngeal normal flora. Metagenomic next-generation sequencing (mNGS) has the potential to solve this problem. METHODS: This prospective observational study sequentially enrolled 93 patients with LRTI and 69 patients without LRTI who visited Peking University People's Hospital in 2019. Pathogens in bronchoalveolar lavage fluid (BALF) specimens were detected using mNGS (DNA and RNA) and traditional microbiological assays. Human transcriptomes were compared between LRTI and non-LRTI, bacterial and viral LRTI, and tuberculosis and nontuberculosis groups. RESULTS: Among 93 patients with LRTI, 20%, 35%, and 65% of cases were detected as definite or probable pathogens by culture, all microbiological tests, and mNGS, respectively. Our in-house BALF mNGS platform had an approximately 2-working-day turnaround time and detected more viruses and fungi than the other methods. Taking the composite reference standard as a gold standard, it had a sensitivity of 66.7%, specificity of 75.4%, positive-predictive value of 78.5%, and negative-predictive value of 62.7%. LRTI-, viral LRTI-, and tuberculosis-related differentially expressed genes were respectively related to immunity responses to infection, viral transcription and response to interferon-γ pathways, and perforin 1 and T-cell receptor B variable 9. CONCLUSIONS: Metagenomic DNA and RNA-seq can identify a wide range of LRTI pathogens, with improved sensitivity for viruses and fungi. Our in-host platform is likely feasible in the clinic. Host transcriptome data are expected to be useful for the diagnosis of LRTIs.

[A study of in vitro activity of daptomycin against 2679 Gram-positive cocci].

OBJECTIVE: To evaluate the in vitro activity of daptomycin against 2679 Gram-positive cocci. METHODS: A total of 2679 non-duplicate Gram-positive cocci isolates were collected from 17 teaching hospitals during January, 2010 and December, 2011. The minimal inhibitory concentrations (MICs) of daptomycin and other anti-microbial agents against 4 Gram-positive cocci were determined by micro-broth dilution method and agar dilution respectively. The data of drug susceptibility were analyzed by WHONET5.6 software. RESULTS: Methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative Staphylococci (MRSCoN) detection rates were 45.8% and 84.2%, respectively. The susceptibility rates of sulfamethoxazole, chloramphenicol, erythromycin, tetracycline, clindamycin and rifampicin against MRSA were 93.1%, 85.5%, 13.8%, 26.6%, 63.2% and 50.0%, respectively. The susceptibility rates of daptomycin, vancomycin and linezolid against MRSA and MRSCoN were all 100.0%. The daptomycin MIC50 and MIC90 of MRSCoN and MRSA were 0.5 mg/L. The high level gentamicin resistance rate of 513 Enterococci isolates was 56.9%. The susceptibility rates of chloramphenicol and tetracycline were 76.0% and 44.1%, respectively. The susceptibility rates of tigecycline and daptomycin reached 100.0%. The MIC50 and MIC90 of daptomycin against 17 vancomycin-resistant Enterococci (VRE) were both 2 mg/L. The susceptibility rates of daptomycin against Streptococcus pneumoniae and ß-hemolytic Streptococcus were 100.0%. The prevalence of penicillin-nonsusceptible Streptococcus pneumoniae (PNSSP) was 63.1%. The MIC50 and MIC90 of daptomycin against PNSSP were 0.125 mg/L and 0.25 mg/L, respectively according to the breakpoint of oral penicillin. The MIC50 and MIC90 daptomycin against ß-hemolytic Streptococci were 0.008 mg/L and 0.032 mg/L. CONCLUSIONS: Daptomycin have excellent in vitro activity against common Gram-positive cocci, including multi-drug resistant bacteria. It may be a good choice for clinicians to treat drug-resistant Gram-positive cocci.