Metagenomic next-generation sequencing for pneumocystis jirovecii pneumonia in patients with connective tissue disease

Background:Accurate diagnosis of Pneumocystis jirovecii pneumonia(PJP)is challenging,and the delayed diagnosis of PJP is associated with high mortality in patients with connective tissue disease(CTD).Metagenomic next-generation sequencing(mNGS)technology facilitates etiological diagnosis of various infectious diseases,with promising application in diagnosing PJP.This study aimed to investigate the value of mNGS using bronchoalveolar lavage fluid(BALF)for diagnosing PJP infection.Methods:Data from 55 patients with CTD and suspected pulmonary infection was retrospectively collected and analysed.A PJP group and non-PJP group were formed.The clinical manifestations,laboratory test results,treatment methods,and outcomes were summarized.BALF mNGS results were compared with traditional pathogen tests(TPT)and serum 1,3-beta-D-glucan(BDG)testing.Results:The mean age of PJP patients was 54 years,and 59%(10/17)of the patients were female.A significant difference was found between the average daily dose of prednisone administered to the PJP group and non-PJP group(25 mg vs.16 mg,P<0.001).The PJP group had a significantly higher incidence of dyspnoea(88%[15/17]vs.16%[6/38],P<0.001)and elevated serum BDG level(167.73 vs.30.67 pg/mL,P<0.001).BALF mNGS was more sensitive than both TPT(100%[95%confidence interval{CI}:77.1%-100%]vs.11.8%[95%CI:2.1%-37.7%],P<0.001)and serum BDG(100%[95%CI:77.1%-100%]vs.85.7%[95%CI:42%-99.2%],P<0.001).BALF mNGS was more specific than serum BDG(89.5%[95%CI:74.3%-96.6%]vs.46.7%[95%CI:22.3%-72.6%],P=0.493).Co-infection with cytomegalovirus(CMV)was more common in the PJP patients than in the non-PJP patients(59%[10/17]vs.11%[4/38],respectively,P<0.001).Conclusion:BALF mNGS technology is highly effective for diagnosing PJP in patients with CTD and identifying co-infections.

Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique

Many viruses can cause respiratory diseases in humans.Although great advances have been achieved in methods of diagnosis,it remains challenging to identify pathogens in unexplained pneumonia(UP) cases.In this study,we applied next-generation sequencing(NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province,China.A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS.An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples.Human rhinovirus C was the virus most frequently detected and was identified in seven samples.Human measles virus,adenovirus B 55 and coxsackievirus A10 were also identified.Metagenomic sequencing also provided virus genomic sequences,which enabled genotype characterization and phylogenetic analysis.For cases of multiple infection,metagenomic sequencing afforded information regarding the quantity of each virus in the sample,which could be used to evaluate each viruses' role in the disease.Our study highlights the potential of metagenomic sequencing for pathogen identification in UP cases.

mNGS-based dynamic pathogen monitoring for accurate diagnosis and treatment of severe pneumonia caused by fungal infections

Metagenomic next-generation sequencing(mNGs)has been widely applied to identify pathogens associated with infectious diseases.However,limited studies have explored the use of mNGs-based dynamic pathogen monitoring in intensive care unit patients with severe pneumonia.Here,we present a clinical case of an 86-year-old male patient with severe pneumonia caused by a fungal infection.During the clinical treatment,four mNGS analyses were performed within two consecutive weeks.Various respiratory fungal pathogens,including Candida orthopsilosis,Candida albicans,and Aspergillus fumigatus were detected by mNGS of bronchoalveolar lavage fluid(BALF).Based on conventional pathogen identification and clinical symptoms,the patient was diagnosed with severe pneumonia caused by a fungal infection.The abundance of fungal species decreased gradually in response to antifungal and empirical therapies,and the fungal infections were effectively con-trolled.In summary,our results demonstrated that mNGS could effectively identify pathogens in patients with severe pneumonia.Additionally,dynamic pathogen monitoring based on mNGS could assist in the precise diag-nosis of complex infections and may facilitate rapid induction of the most appropriate therapy.