This retrospective study evaluated the clinical relevance of mNGS for the investigation of co-infection in a cohort of 36 HIV-infected patients. In our study, we compared detection by mNGS and traditional detection methods and found mNGS to be advantageous in three aspects. Firstly, in general, mNGS showed a higher diagnostic efficiency of infectious disease than culture and smear, although the number of samples is varied. Secondly, in BALF, blood and CSF sample types, we found a remarkably higher sensitivity in detection by mNGS vs culture compared in a pairwise manner. More importantly, mNGS is noted for its superior feasibility in detecting virus, fungus, parasite and MTB in general. Also, mNGS has proved to be a better choice when detecting those special microbes such as Coxiella burnetii. In addition, we have identified that a considerable percentage of infection diagnoses were confirmed and modified according to mNGS.
The positivity rate of mNGS was consistent with the expectation, which have reported a
variety of sensitivities from 36% [17] to 100% [18]. And interestingly, our results indicated that in recognizing common bacteria (excluding MTB), the sensitivity of mNGS is not superior to that of culture, which is consistent with a previous report that, comparing the results obtained by mNGS, a majority (74%) of bacterial pathogen is identified by standard culture in bacterium-associated pneumonia [19]. Therefore, we concluded that unlike other microbes like virus, fungus and parasite, mNGS might not have the significant advantage in identifying common bacteria. Although mNGS (3000 Ren Min Bi [RMB]) cost more than any other regular methodology, the low rate of positivity, long time consuming and lack of accuracy making pathogen screening of traditional techniques less cost-effective. In conclusion, mNGS could emerge as a promising technology for precision diagnosis and tailored therapy for HIV-infected patients with suspected infection.
For HIV-affected persons, a low CD4 + T-cell count exposes them to a higher risk of opportunistic infections and even worse, multiple infections may co-exist. However, conventional diagnostic assays lack breadth of detection and sensitivity, therefore unable to discover multiple infections, which make it ineffective in microbiological diagnosis. For example, 90–95% of blood cultures remain negative in immunocompromised patients suspected of infection, even in the cases where bacterial or fungal sepsis is likely, negative results are recorded for 50% of the blood samples [20]. A better microbiological test is urgently needed to break this situation. mNGS, with its non-targeted identification of microbes, through deep sequencing of biological samples, data mining, and identification of pathogen sequences in the absence of a priori assumption, constitutes a paradigm shift in microbiological [21, 22], which might contribute greatly to HIV-infected patients with suspected infection. To our knowledge, this is the first study to evaluate the contributions of mNGS in microbial testing in a cohort of HIV-infected patients.
Our research also has its limitations. As a small-scale cohort retrospective study of 36 patients, different samples from the same patient, including BALF, blood and CSF were treated as independent samples. Among these 36 patients, some of them have been hospitalized for several times due to different infectious diseases and each hospitalization was counted as an independent individual. Nevertheless, we believe that varied infectious diseases lead to different condition of patients, making each hospitalization analyzed independently practicable and having minimal disturbance to the final judgment. More prospective studies of mNGS testing with broader samples in real-life clinical practice remain to be documented. For HIV-infected patients with suspected infection, a vast amount of sequence data from a single clinical sample makes interpretation complicated. Can we refer to the conventional standardization? Whether the positive pathogen is causative pathogen or not. Whether treatment is needed. The added value of mNGS in clinical managements of these patients will have to be evaluated, and additional work to associate typologies of microbiota with patient status needed to be further studied. The progressive awareness of physicians to the patients’ benefit will certainly help mNGS to become standard in the practice of conducting microbiological diagnosis in HIV-affected patients.