Diagnosis of Legionnaires’ Disease Assisted by Next-Generation Sequencing in a Patient with COVID-19

Abstract

Coinfection in COVID-19 patients is associated with worsening outcome. Among patients with COVID-19, Legionella pneumophila, a common cause of pneumonia, has been reported as a co-occurring respiratory infection. A nonspecific clinical presentation, however, makes an early diagnosis difficult. Bronchoalveolar lavage fluid was collected from a patient suffering from COVID-19 and presenting with pneumonia and sent for metagenomic analysis. Differential abundance analysis was carried out by comparing each taxon reads per million between the bronchoalveolar lavage fluid sample and the negative control. Two replicates of metagenomic sequencing were conducted on bronchoalveolar lavage fluid samples. Within each replicated sequencing, one negative control was sequenced for comparison of taxon abundance in the BALF sample. In both replicates, Legionella pneumophila was the only taxon with significantly higher abundance when compared with the negative control. PCR of the bronchoalveolar further confirmed the presence of L. pneumophila. Several studies have estimated that the incidence of Legionnaires’ disease co-infection in patients with COVID-19 infection is approximately 0% to 1.5%. There are some common characteristics of COVID-19 and co-infection with Legionnaires’ disease, making it difficult to diagnose bacterial infection early. The diagnosis of these cases is important due to the different treatments used. Current diagnostic tests for Legionnaires’ disease include conventional culture, urinary antigen for L. pneumophila serogroup 1, polymerase chain reaction, direct fluorescent antibody stain, and paired serology. The current study demonstrated that metagenomics is a promising approach that facilitated the diagnosis of Legionnaires’ disease.

Keywords:

• Legionnaires’ disease
• COVID-19
• co-infection
• next-generation sequencing

Abbreviations

COVID-19, Coronavirus disease, SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; PCR, polymerase chain reaction; BALF, bronchoalveolar lavage fluid; MGI, MGIEasy FS DNA Library Prep Kit; DNBs, DNA nanoballs; RefSeq, reference genomes; RPM, Reads per Million; LMAP, loop-mediated isothermal amplification.

Data Sharing Statement

All data generated or analyzed during this study are included in this published article and its Supplementary Document.

Ethics Approval and Informed Consent

This study was approved by the Institutional Review Board of Taichung Veterans General Hospital (CE20261A).

Consent for Publication

Written informed consent was obtained from the patient for publication of this article and any accompanying images.

Author Contributions

CHT, PYL, and YTH conceived and designed the study. PHH, CHT, PYL, YTH, and CWL contributed to comprehensive research and sample collection. PHH, PYL, YTH, and CWL wrote the paper. PHH, PYL, YTH, and CWL participated in manuscript editing. All authors made a significant contribution to the work reported, whether that is in the conception, study design, execution, acquisition of data, analysis and interpretation, or in all these areas; took part in drafting, revising or critically reviewing the article; gave final approval of the version to be published; have agreed on the journal to which the article has been submitted; and agree to be accountable for all aspects of the work.

Disclosure

The authors report no conflicts of interest in this work.

Additional information

Funding

YTH was supported in part by Taiwan’s Ministry of Science and Technology (109-2221-E-194 −038 -MY3). PYL was supported in part by Taiwan’s Ministry of Science and Technology (110-2314-B-075A-011), Taichung Veterans General Hospital (TCVGH-1113901D, TCVGH-1113901C).