Targeted next generation sequencing is comparable with metagenomic next generation sequencing in adults with pneumonia for pathogenic microorganism detection

We have read with great interest the study published in this journal by Peng et al., 1 Peng J.M. Du B. Qin H.Y. et al. Metagenomic next-generation sequencing for the diagnosis of suspected pneumonia in immunocompromised patients. J Infect. 2021; 82: 22-27 Abstract Full Text Full Text PDF PubMed Scopus (30) Google Scholar comparing the potential of metagenomic next-generation sequencing (mNGS) with that of comprehensive conventional microbiological tests (CMTs) as a front-line diagnostic in immunocompromised patients with suspected pneumonia. mNGS has markedly improved the efficiency of pneumonia's etiological diagnosis. Pathogens can be identified by mNGS include bacteria, 2 Ivy M.I. Thoendel M.J. Jeraldo P.R. et al. Direct detection and identification of prosthetic joint infection pathogens in synovial fluid by metagenomic shotgunsequencing. J Clin Microbiol. 2018; 56 (pii:e00402-18) Crossref PubMed Scopus (82) Google Scholar RNA and DNA viruses, 3 Miao Q. Ma Y. Wang Q. et al. Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice. Clin Infect Dis. 2018; 67: S231-S240 Crossref PubMed Scopus (262) Google Scholar yeast and molds, 4 Wilson M.R. O'Donovan B.D. Gelfand J.M. et al. Chronic meningitis investigated via metagenomic next-generation sequencing. JAMA Neurol. 2018; 75: 947-955 Crossref PubMed Scopus (153) Google Scholar mycobacteria and parasites. 3 Miao Q. Ma Y. Wang Q. et al. Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice. Clin Infect Dis. 2018; 67: S231-S240 Crossref PubMed Scopus (262) Google Scholar mNGS is of high value in detecting novel, rare and atypical pathogens, or the treated patients. 5 Wilson M.R. Naccache S.N. Samayoa E. et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med. 2014; 370: 2408-2417 Crossref PubMed Scopus (528) Google Scholar However, mNGS was expensive and greatly influenced by human genes, and it is not possible to conduct DNA and RNA dual process detection at the same time. Herein, we adopted a more rapid and economic technology, target next-generation sequencing (tNGS), to achieve an early diagnosis of respiratory infection, whose target detection were of only 153 pathogens (Supplementary Table 1) but covered for more than 95% of the respiratory infection.