Next-generation sequencing technology for detecting pulmonary fungal infection in bronchoalveolar lavage fluid of a patient with dermatomyositis: a case report and literature review

BMC Infect Dis. 2020 Aug 17;20(1):608. doi: 10.1186/s12879-020-05341-8.


Background: Invasive fungal pneumonia is a severe infectious disease with high mortality in immunocompromised patients. However, the clinical diagnosis of the pathogen(s) remains difficult since microbiological evidence is difficult to acquire.

Case presentation: Here, we report a case of pulmonary fungal infection detected by next-generation sequencing (NGS) of bronchoalveolar lavage fluid (BALF) in a 61-year-old male with corticosteroid-treated dermatomyositis. Cytomegalovirus and influenza A virus infections were confirmed by nucleic acid detection and treated with antiviral medicine. The patient had been diagnosed with severe pneumonia and treated with empiric broad-spectrum antibacterial and antifungal drugs before bronchoscopy was performed. The patient responded poorly to those empiric treatments. Three fungi were found by NGS in the BALF, namely, Pneumocystis jirovecii, Aspergillus fumigatus and Rhizopus oryzae. After adjusting the patient's treatment plan according to the NGS results, he improved significantly.

Conclusions: This case highlights the combined application of NGS and traditional tests in the clinical diagnosis of pulmonary invasive fungal disease. NGS is proposed as an important adjunctive diagnostic approach for identifying uncommon pathogens.

Keywords: Bronchoalveolar lavage fluid; Next-generation sequencing; Pneumonia.

Publication types

  • Case Reports

MeSH terms

  • Antifungal Agents / therapeutic use
  • Aspergillus fumigatus / genetics
  • Aspergillus fumigatus / isolation & purification
  • Bronchoalveolar Lavage Fluid / microbiology*
  • DNA, Fungal / chemistry
  • DNA, Fungal / metabolism
  • Dermatomyositis / complications
  • Dermatomyositis / diagnosis*
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Lung / diagnostic imaging
  • Lung Diseases, Fungal / diagnosis*
  • Lung Diseases, Fungal / drug therapy
  • Lung Diseases, Fungal / microbiology
  • Male
  • Middle Aged
  • Pneumocystis carinii / genetics
  • Pneumocystis carinii / isolation & purification
  • Rhizopus / genetics
  • Rhizopus / isolation & purification
  • Tomography, X-Ray Computed


  • Antifungal Agents
  • DNA, Fungal