Clinical usefulness of metagenomic next-generation sequencing for Rickettsia and Coxiella burnetii diagnosis

Rapid diagnosis of Aspergillus fumigatus endocarditis using mNGS assay: A case report and review of the literature

Fungal endocarditis is caused mainly by Candida albicans and Aspergillus spp. and was first reported in the 1950s. Natural-valve endocarditis caused by Aspergillus is relatively uncommon. In this case, a 56-year-old male patient was admitted to the hospital on account of a cough accompanied by chills and fever and ineffective self-medication. Infective endocarditis was initially suspected based on echocardiography (indicating right atrial growth) and clinical manifestations. However, routine pathogen detections were always negative. The patient's condition was identified as Aspergillus fumigatus endocarditis (AFE) and was treated with targeted therapy, considering the detection of significant AFE sequences in the blood through metagenomic next-generation sequencing (mNGS). On this basis, the paper further summarizes the clinical manifestations, diagnosis, treatments, and outcomes of AFE endocarditis cases reported in recent years, aiming to provide a reference to better understand this rare infective disease and guide medical practitioners in choosing the right diagnostic and therapeutic strategy.

Applicability of Bronchoalveolar Lavage Fluid and Plasma Metagenomic Next-Generation Sequencing Assays in the Diagnosis of Pneumonia

Background

Metagenomic next-generation sequencing (mNGS) provides innovative solutions for predicting complex infections. A comprehensive understanding of its strengths and limitations in real-world clinical settings is necessary to ensure that it is not overused or misinterpreted.

Methods

Two hundred nine cases with suspected pneumonia were recruited to compare the capabilities of 2 available mNGS assays (bronchoalveolar lavage fluid [BALF] mNGS and plasma mNGS) to identify pneumonia-associated DNA/RNA pathogens and predict antibiotic resistance.

Results

Compared to clinical diagnosis, BALF mNGS demonstrated a high positive percent agreement (95.3%) but a low negative percent agreement (63.1%). Plasma mNGS revealed a low proportion of true negatives (30%) in predicting pulmonary infection. BALF mNGS independently diagnosed 65.6% (61/93) of coinfections and had a remarkable advantage in detecting caustic, rare, or atypical pathogens. Pathogens susceptible to invasive infection or bloodstream transmission, such as Aspergillus spp, Rhizopus spp, Chlamydia psittaci, and human herpesviruses, are prone to be detected by plasma mNGS. BALF mNGS tests provided a positive impact on the diagnosis and treatment of 128 (61.2%) patients. Plasma mNGS, on the other hand, turned out to be more suitable for diagnosing patients who received mechanical ventilation, developed severe pneumonia, or developed sepsis (all P < .01). BALF mNGS was able to identify resistance genes that matched the phenotypic resistance of 69.4% (25/36) of multidrug-resistant pathogens.

Conclusions

Our data reveal new insights into the advantages and disadvantages of 2 different sequencing modalities in pathogen identification and antibiotic resistance prediction for patients with suspected pneumonia.

Diagnostic Performance of Metagenomic Next-Generation Sequencing in Central Nervous System Cryptococcosis Using Cerebrospinal Fluid

Purpose

Metagenomic next-generation sequencing (mNGS) has been widely used to diagnose infectious diseases. However, there are few studies on its diagnostic performance in the central nervous system (CNS) cryptococcosis. This study examined the diagnostic efficacy of mNGS in identifying Cryptococcus spp. in cerebrospinal fluid (CSF) samples.

Patients and Methods

From March 2021 to March 2023, 290 patients with suspected CNS infection were recruited from the First Affiliated Hospital, School of Medicine, Zhejiang University, and 74 patients were ultimately included in the study. Lastly, 22 patients with CNS cryptococcosis were included. Of these patients, 25 CSF samples were enrolled. The diagnostic performance of conventional assays [including India ink, cryptococcal antigen (CrAg) testing, and culture] and mNGS was evaluated for CNS cryptococcosis.

Results

In the 25 samples collected, the coincidence rates of mNGS with India ink, CrAg, and culture were 64.0% (16/25), 80.0% (20/25), and 80.0% (20/25), respectively. Without antifungal drug exposure, the coincidence rates were increased to 66.7% (10/15), 100.0% (15/15), and 93.3% (14/15), respectively. The coincidence rates after antifungal therapy were all decreased to 60.0% (6/10), 50.0% (5/10), and 60.0% (6/10), respectively. Moreover, in the 25 samples, the sensitivity of mNGS reached 80.0%, and of India ink, CrAg testing, and culture were 68.0, 100.0, and 60.0%, respectively. The mNGS showed an excellent positive rate (100.0%) in the 15 samples collected without antifungal drug exposure, which was significantly higher than the antifungal drug-exposed group (n = 10) (50.0%) (P = 0.005). The reads of Cryptococcus spp. before antifungal therapy were significantly higher than after it (median, 25,915 vs 2, P = 0.008).

Conclusion

mNGS is an effective tool for diagnosing CNS cryptococcosis using CSF; however, its sensitivity decreases considerably in patients who have been effectively treated with antifungal drugs.

Clinical metagenomics-challenges and future prospects

Infections lacking precise diagnosis are often caused by a rare or uncharacterized pathogen, a combination of pathogens, or a known pathogen carrying undocumented or newly acquired genes. Despite medical advances in infectious disease diagnostics, many patients still experience mortality or long-term consequences due to undiagnosed or misdiagnosed infections. Thus, there is a need for an exhaustive and universal diagnostic strategy to reduce the fraction of undocumented infections. Compared to conventional diagnostics, metagenomic next-generation sequencing (mNGS) is a promising, culture-independent sequencing technology that is sensitive to detecting rare, novel, and unexpected pathogens with no preconception. Despite the fact that several studies and case reports have identified the effectiveness of mNGS in improving clinical diagnosis, there are obvious shortcomings in terms of sensitivity, specificity, costs, standardization of bioinformatic pipelines, and interpretation of findings that limit the integration of mNGS into clinical practice. Therefore, physicians must understand the potential benefits and drawbacks of mNGS when applying it to clinical practice. In this review, we will examine the current accomplishments, efficacy, and restrictions of mNGS in relation to conventional diagnostic methods. Furthermore, we will suggest potential approaches to enhance mNGS to its maximum capacity as a clinical diagnostic tool for identifying severe infections.

Diagnosis of Non-Tuberculous Mycobacterial Pulmonary Disease by Metagenomic Next-Generation Sequencing on Bronchoalveolar Lavage Fluid

Purpose

Metagenomic next-generation sequencing (mNGS) has been extensively used in the diagnosis of infectious diseases but has rarely been applied in non-tuberculous mycobacterial pulmonary disease (NTMPD). This study analyzed the diagnostic performance of mNGS in bronchoalveolar lavage fluid (BALF) samples to identify non-tuberculous mycobacteria (NTM).

Patients and Methods

A total of 231 patients with suspected NTMPD were recruited from the First Affiliated Hospital, School of Medicine, Zhejiang University, from March 2021 to October 2022. A total of 118 cases were ultimately included. Of these patients, 61 cases were enrolled in the NTMPD group, 23 cases were enrolled in the suspected-NTMPD group, and 34 cases were enrolled in the non-NTMPD group. The diagnostic performance of traditional culture, acid-fast staining (AFS), and mNGS for NTMPD was assessed.

Results

Patients in the NTMPD group had a higher proportion of bronchiectasis (P=0.007). Among mNGS-positive samples in the NTMPD group, a significantly higher reads number of NTM was observed in AFS-positive patients [61.50 (22.00, 395.00) vs 15.50 (6.00, 36.25), P=0.008]. Meanwhile, mNGS demonstrated a sensitivity of 90.2%, which was far superior to AFS (42.0%) and culture (77.0%) (P<0.001). The specificity of mNGS in detecting NTM was 100%, which was the same as that of traditional culture. The area under the receiver operating characteristic curve of mNGS was 0.951 (95% CI 0.906-0.996), which was higher than that of culture (0.885 [95% CI 0.818-0.953]) and AFS (0.686 [95% CI 0.562-0.810]). In addition to NTM, other pulmonary pathogens were also found by mNGS.

Conclusion

mNGS using BALF samples is a rapid and effective diagnostic tool for NTMPD, and mNGS is recommended for patients with suspected NMTPD or NTM coinfected pneumonia.