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

Abstract

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.

Fig. 1

CT scan of the lung. a On the 1st day, a CT scan showed bronchitis and inflammation in the right lung lobes, the left ligule lobe and the left lower lobe. b: On the 9th day, a CT scan showed that some of the inflammation was alleviated, but inflammation in most lung lobes was worse

Fig. 2

Timeline of the patient’s clinical manifestations and treatment. a Timeline of the patient’s tests and treatment. MP, methylprednisolone; MOX, moxifloxacin; PIP-TAZ, piperacillin/tazobactam; OST, oseltamivir; VORI, voriconazole; MCFG, micafungin; GCV, ganciclovir; PCZ, posaconazole; TMP-SMX, trimethoprim/sulfamethoxazole; G test, 1,3-β-D-glucan test; GM test, galactomannan test. b Timeline of the patient’s body temperature

Fig. 3

Other microorganisms found by NGS. a Bacteria found by NGS. Megasphaera micronuciformis: 6358 reads; Megasphaera elsdenii: 4 reads; Cardiobacterium hominis: 4660 reads; Cardiobacterium valvarum: 71 reads; Leptotrichia trevisanii: 339 reads; Leptotrichia buccalis: 238 reads; others: 360412 reads. b Viruses found by NGS. Human betaherpesvirus 5: 35 reads; Human alphaherpesvirus 1: 15 reads; others: 5 reads