Application of metagenomic next-generation sequencing in the diagnosis of pulmonary invasive fungal disease

Abstract

BackgroundMetagenomic next-generation sequencing (mNGS) is increasingly being used to detect pathogens directly from clinical specimens. However, the optimal application of mNGS and subsequent result interpretation can be challenging. In addition, studies reporting the use of mNGS for the diagnosis of invasive fungal infections (IFIs) are rare.ObjectiveWe critically evaluated the performance of mNGS in the diagnosis of pulmonary IFIs, by conducting a multicenter retrospective analysis. The methodological strengths of mNGS were recognized, and diagnostic cutoffs were determined.MethodsA total of 310 patients with suspected pulmonary IFIs were included in this study. Conventional microbiological tests (CMTs) and mNGS were performed in parallel on the same set of samples. Receiver operating characteristic (ROC) curves were used to evaluate the performance of the logarithm of reads per kilobase per million mapped reads [lg(RPKM)], and read counts were used to predict true-positive pathogens.ResultThe majority of the selected patients (86.5%) were immunocompromised. Twenty species of fungi were detected by mNGS, which was more than was achieved with standard culture methods. Peripheral blood lymphocyte and monocyte counts, as well as serum albumin levels, were significantly negatively correlated with fungal infection. In contrast, C-reactive protein and procalcitonin levels showed a significant positive correlation with fungal infection. ROC curves showed that mNGS [and especially lg(RPKM)] was superior to CMTs in its diagnostic performance. The area under the ROC curve value obtained for lg(RPKM) in the bronchoalveolar lavage fluid of patients with suspected pulmonary IFIs, used to predict true-positive pathogens, was 0.967, and the cutoff value calculated from the Youden index was −5.44.ConclusionsIn this study, we have evaluated the performance of mNGS-specific indicators that can identify pathogens in patients with IFIs more accurately and rapidly than CMTs, which will have important clinical implications.

Metagenomic Next-Generation Sequencing Assists in the Diagnosis of Mediastinal Aspergillus fumigatus Abscess in an Immunocompetent Patient: A Case Report and Literature Review

“…According to one report, the sensitivity rate of GM serum samples identifying aspergillosis was 65.71%, and the specificity rate was 78.12%. 8 BAL-GM is a sensitive and specific test for the diagnosis of invasive aspergillosis. 9 The efficiency of BAL-GM for diagnosing aspergillosis was relatively high in one study, with 60–100% sensitivity and 68–100% specificity.…”

Metagenomic Next-Generation Sequencing for Diagnostically Challenging Mucormycosis in Patients with Hematological Malignancies

“…It is less affected by the use of antibiotics and autoimmune status of patient. 15 At present, many studies have explored the significance [16][17][18][19] Our previous research found that mNGS seems to be more meaningful for the diagnosis of fungal infection. 20 Because mucormycosis is rare, the diagnostic value of mNGS is only reported in cases.…”

“…But these manifestations are nonspecific. The median time from symptom appearance to suspected IFD was 4 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19).…”

Building a nomogram plot based on the nanopore targeted sequencing for predicting urinary tract pathogens and differentiating from colonizing bacteria

“…There is no doubt that urine culture is still an independent factor in determining the pathogenic organism but not the most important with positive results scoring approximately 20 in the nomogram, even negligible in certain cases, while NTS score was apparently higher and dominant. Multi-study results consistent with clinical experience showed that culture methods always seem to lag, and the positive rate would be influenced by potential applications of empirical antibiotics therapy (Wang et al, 2022). Gupta suggested that the role of urine culture is to retrospectively confirm and emphasized the definition of "contaminants" and the threshold of bacteriuria required for the diagnosis needed to be re-discussed (Gupta et al, 2017).…”