Advertisement

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

  • Shiying Li
    Affiliations
    Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, 74# Linjiang Road, Chongqing 400010, China
    Search for articles by this author
  • Jin Tong
    Affiliations
    Department of Respiratory Medicine, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
    Search for articles by this author
  • Yi Liu
    Affiliations
    Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, 74# Linjiang Road, Chongqing 400010, China
    Search for articles by this author
  • Wei Shen
    Affiliations
    Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, 74# Linjiang Road, Chongqing 400010, China
    Search for articles by this author
  • Peng Hu
    Correspondence
    Corresponding author.
    Affiliations
    Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, 74# Linjiang Road, Chongqing 400010, China
    Search for articles by this author
Published:August 28, 2022DOI:https://doi.org/10.1016/j.jinf.2022.08.022
      We have read with great interest the study published in this journal by Peng et al.,
      • Peng J.M.
      • Du B.
      • Qin H.Y.
      • et al.
      Metagenomic next-generation sequencing for the diagnosis of suspected pneumonia in immunocompromised patients.
      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,
      • 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.
      RNA and DNA viruses,
      • Miao Q.
      • Ma Y.
      • Wang Q.
      • et al.
      Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice.
      yeast and molds,
      • Wilson M.R.
      • O'Donovan B.D.
      • Gelfand J.M.
      • et al.
      Chronic meningitis investigated via metagenomic next-generation sequencing.
      mycobacteria and parasites.
      • Miao Q.
      • Ma Y.
      • Wang Q.
      • et al.
      Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice.
      mNGS is of high value in detecting novel, rare and atypical pathogens, or the treated patients.
      • Wilson M.R.
      • Naccache S.N.
      • Samayoa E.
      • et al.
      Actionable diagnosis of neuroleptospirosis by next-generation sequencing.
      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.
      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'

      Subscribe:

      Subscribe to Journal of Infection
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Institutional Access: Sign in to ScienceDirect

      References

        • 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
        • 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)
        • 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
        • 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
        • 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
        • Uematsu H.
        • Hashimoto H.
        • Iwamoto T.
        • et al.
        Impact of guideline-concordant microbiological testing on outcomes of pneumonia.
        Int J Qual Health Care. 2014; 26: 100-107
        • Weber D.J.
        • Sickbert-Bennett E.E.
        • Brown V.
        • et al.
        Comparison of hospitalwide surveillance and targeted intensive care unit surveillance of healthcare-associated infections.
        Infect Control Hosp Epidemiol. 2007; 28: 1361-1366
        • Beovic B.
        • Bonac B.
        • Kese D.
        • et al.
        Aetiology and clinical presentation of mild community-acquired bacterial pneumonia.
        Eur J Clin Microbiol Infect Dis. 2003; 22: 584-591