Frontiers in Cellular and Infection Microbiology (May 2020)

Metagenomic Diagnosis for a Culture-Negative Sample From a Patient With Severe Pneumonia by Nanopore and Next-Generation Sequencing

  • Kaiying Wang,
  • Kaiying Wang,
  • Kaiying Wang,
  • Peihan Li,
  • Peihan Li,
  • Yanfeng Lin,
  • Yanfeng Lin,
  • Hongbin Chen,
  • Lang Yang,
  • Lang Yang,
  • Jinhui Li,
  • Tingyan Zhang,
  • Tingyan Zhang,
  • Qichao Chen,
  • Zhonghong Li,
  • Zhonghong Li,
  • Xinying Du,
  • Yusen Zhou,
  • Peng Li,
  • Hui Wang,
  • Hongbin Song

DOI
https://doi.org/10.3389/fcimb.2020.00182
Journal volume & issue
Vol. 10

Abstract

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Rapid and accurate etiologic diagnosis accelerates targeted antimicrobial therapy. Metagenomic analysis has played a critical role in pathogen identification. In this study, we leveraged the advantages of both the MinION and BGISEQ-500 platforms to make a bacteriologic diagnosis from a culture-negative lung tissue sample from an immunocompromised patient with severe pneumonia. Real-time nanopore sequencing rapidly identified Klebsiella pneumoniae by an 823 bp specific sequence within 1 min. Genomic analysis further identified blaSHV-12, blaKPC-2, blaTEM-1, blaCTX-M-65, and other resistance genes. The same sample was further sequenced on the BGISEQ-500 platform, which presented consistent results regarding the most top dominant pathogens and provided additional information of resistance genes. Revised antibiotic treatment was followed by the patient's clinical recovery. Though sample preparation and the interpretation of final results still need to be improved further, metagenomic sequencing contributes to the accurate diagnosis of culture-negative infections and facilitates the rational antibiotic therapy.

Keywords