Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in critically ill patients

Abstract

The purpose of this study was to assess the value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) for the diagnosis of severe respiratory diseases based on interpretation of sequencing results. BALF samples were harvested and used for mNGS as well as microbiological detection. Infectious bacteria or fungi were defined according to relative abundance and number of unique reads. We performed mNGS on 35 BALF samples from 32 patients. The positive rate reached 100% in the mNGS analysis of nine immunocompromised patients. Compared with the culture method, mNGS had a diagnostic sensitivity of 88.89% and a specificity of 74.07% with an agreement rate of 77.78% between these two methods. Compared with the smear method and PCR, mNGS had a diagnostic sensitivity of 77.78% and a specificity of 70.00%. In 13 cases, detection results were positive by mNGS but negative by culture/smear and PCR. The mNGS findings in 11/32 (34.4%) cases led to changes in treatment strategies. Linear regression analysis showed that diversity was significantly correlated with interval between disease onset and sampling. Dynamic changes in reads could indirectly reflect therapeutic effectiveness. BALF mNGS improves sensitivity of pathogen detection and provides guidance in clinical practice. Potential pathogens can be identified based on relative abundance and number of unique reads.

<p>Metagenomic Next-Generation Sequencing in Diagnosis of a Case of <em>Pneumocystis jirovecii</em> Pneumonia in a Kidney Transplant Recipient and Literature Review</p>

“…To date, there have been 5 reports on successful use of mNGS to diagnose pulmonary infections involving P. jirovecii (Table 2). [14][15][16][17][18] While the sample size is small (1 to 13 specimens each), these studies involve the use of different types of specimens (BALF, sputum, lung biopsy and blood) and different NGS platforms. The numbers of sequence reads for P. jirovecii are highly variable (2 to 303,572) among studies though all are less than the P. jirovecii reads identified from our case (1,665,693).…”

“…This method has been successfully used as a diagnostic tool for various infectious diseases including PCP. [14][15][16][17] Its application to diagnose PCP in renal transplant recipients has been attempted in one study, 18 and its value awaits further evaluation. Here we report a case of PCP diagnosed by mNGS following negative results in multiple conventional diagnostic tests.…”

Epidemiological and clinical characteristics analysis of COVID-19 in the surrounding areas of Wuhan, Hubei Province in 2020

“…In addition, 19.2 % of patients needed multiple throat swabs to obtain Q-PCR positive results, suggesting that the sensitivity of the throat swab test is limited. For patients with high clinical suspicion, multiple sampling or combined sputum and alveolar lavage fluid might help to decrease the false negative rate [18]. Imaging is often reveals multiple patchy and ground-glass shadows in the lungs, which is common in the subpleural or peripheral regions of the lungs, whereas only one lesion occurred mostly in the early phase [19].…”

Early diagnosis and appropriate respiratory support for Mycoplasma pneumoniae pneumonia associated acute respiratory distress syndrome in young and adult patients: a case series from two centers

“…In recent years, rapid diagnostic methods have been developed, allowing for early diagnosis of M. pneumoniae pneumonia. Detection of M. pneumoniae using fluorescence-quantatitive PCR in respiratory samples [19,[21][22][23][24] and metagenomic next-generation sequencing (mNGS) has increased [25]; these methods are especially useful for early detection of rare, atypical, and slow-growing microbes. Case reports have also described using new forms of respiratory support for M. pneumoniae pneumonia induced ARDS, such as highflow nasal cannula (HFNC) [26], non-invasive ventilation (NIV) [27] and veno-venous extracorporeal membrane oxygenation (ECMO) [18,24,28].…”