Application of targeted next-generation sequencing to identify pathogens in the bronchoalveolar lavage fluid of adults with pulmonary infections

Abstract

Background Targeted next-generation sequencing (tNGS) has emerged as an efficient diagnostic method for pathogens identification. herein, we aimed to evaluate its performance in pathogen detection in bronchoalveolar lavage fluid (BALF). Methods BALF samples were obtained from 262 adult patients with pulmonary infection and were detected by tNGS, microbial culture, Xpert® MTB/RIF assay, and Aspergillus galactomannan (GM) test. Results In total, 47 potential pathogens were identified in the BALF samples by tNGS, including 21 bacteria, 13 viruses, 11 fungi, 1 parasite, and 1 mycoplasma. The bacterial detection rates of tNGS and ordinary bacterial culture were 74.0% (194/262) and 28.2% (74/262), respectively. The rates of negative, positive, and total consistent and the kappa value between tNGS and bacterial culture were 30.8%, 86.4%, 46.4%, and 0.116, respectively. The positive rate of fungal identification by tNGS was slightly higher than that of fungal culture (31.7% (83/262) and 22.9% (60/262), respectively). The rates of positive, negative, and total consistent and the kappa value between tNGS and fungal culture were 68.9%, 79.1%, 76.7%, and 0.424, respectively. Among the 42 patients with suspected tuberculosis infection, 23 patients showed positive results on both tNGS and Xpert® MTB/RIF assay. The rates of positive, negative, and total consistent and the kappa value between tNGS and pert® MTB/RIF assay were 100.0%, 68.4%, 85.7%, and 0.704, respectively. Finally, the sensitivity and specificity of tNGS versus the GM test were 57.1% and 90.6% versus 71.4% and 82.7%, respectively, when the fungal culture was used as the gold standard for detecting Aspergillus. Additionally, the sensitivity and specificity of tNGS increased to 86.2% and 98.7%, whereas the sensitivity of the GM test decreased to 69.0% when clinically diagnosed Aspergillus infection was used as a reference standard. The read counts of Aspergillus detected by tNGS and the optical density of the GM test were not significantly correlated. Conclusions tNGS is a promising method for detecting pathogens in BALF with a notably higher positive detection rate and a higher sensitivity and/or specificity compared with those of the conventional test.