Metagenomic Next-Generation Sequencing for the Diagnosis of Suspected Opportunistic Infections in People Living with HIV

Abstract

The diagnosis of suspected opportunistic infections in HIV patients is challenging due to the wide range of potential causes. This study used mNGS to analyse specimens of suspected opportunistic infections in HIV patients from a single centre to explore this method's applicability as a diagnostic tool compared to that of CMTs. Methods: We retrospectively investigated 46 suspected opportunistic infections in people living with HIV(PLWH) Hospitalized at Hangzhou Xixi hospital from January 2020 to August 2021. In total, we collected 49 samples (3 patients provided 2 samples) and sent them out for mNGS. Results: mNGS had a better detection rate for fungi and nontuberculous mycobacteria than that of CMTs. Specifically, the diagnostic detection rate of fungi (11 vs 19, P<0.05) and nontuberculous mycobacteria (1 vs 6, p<0.05) was significantly higher; there was no difference in detection rate for other pathogens (bacteria, Mycobacterium tuberculosis, or viruses). The sensitivity of mNGS was 90.91%, 50%, 0%, 100%, and 100% for detecting fungi, bacteria, Mycobacterium tuberculosis, nontuberculous mycobacteria, and viruses, respectively; the corresponding specificities were 74.29%, 97.73%, 86.36%, 86.67%, and 91.11%. Conclusion: mNGS technology provides an alternative and promising method of identifying suspected opportunistic infections in PLWH. Thus, the best diagnosis strategy may be using a combination of mNGS and CMTs.

Pathogen Diagnosis Value of Nanopore Sequencing in Severe Hospital-Acquired Pneumonia Patients

“…Due to the lack of criteria for the interpretation of mNGS results, we used the developed criteria from previous study. 18 The infectious bacteria (excluding mycobacteria), fungi, and parasites were considered positive if they met any of the following standards of the mNGS/ONT sequencing: (i) if mNGS/ONT detected the same pathogen as culture with the number of unique reads from a single species exceeded 50; (ii) if the unique reads of pathogen less than 50, the diagnosis of infection can still be made based on the clinical manifestations; (iii) mycobacterium tuberculosis: at least one read was identified to a species, and TB was considered positive; (iv) if mNGS/ONT detected the pathogen with the number of unique reads exceeded 50 while culture missed this pathogen, it was considered potential pathogenic microbe.…”