Case report: Metagenomic next-generation sequencing for the diagnosis of rare Nocardia aobensis infection in a patient with immune thrombocytopenia

Abstract

Background: Nocardiosis poses a diagnostic challenge due to its rarity in clinical practice, non-specific clinical symptoms and imaging features, and the limitations of traditional detection methods. Nocardia aobensis (N. aobensis) is rarely detected in clinical samples. Metagenomic next-generation sequencing (mNGS) offers significant advantages over traditional methods for rapid and accurate diagnosis of infectious diseases, especially for rare pathogens.

Case presentation: A 52-year-old woman with a history of immune thrombocytopenia for over 2 years was hospitalized for recurrent fever and cough lasting for 10 days. Her initial diagnosis on admission was community-acquired pneumonia, based on chest computed tomography findings of lung inflammation lesion. Empirical treatment with moxifloxacin and trimethoprim-sulfamethoxazole (TMP-SMZ) was initiated. However, her condition failed to improve significantly even after 1 week of treatment. Bronchoalveolar lavage fluid (BALF) subjected to mNGS revealed the presence of N. aobensis, resulting in a diagnosis of pulmonary nocardiosis caused by N. aobensis. This diagnosis was also supported by Sanger sequencing of the BALF. After adjusting the antibiotic regimen to include TMP-SMZ in combination with imipenem, the patient's condition significantly improved. She was finally discharged with instructions to continue oral treatment with TMP-SMZ and linezolid for 6 months. The patient's first follow-up 1 month after discharge showed good treatment outcomes but with obvious side effects of the drugs. Consequently, the antibiotic regimen was changed to doxycycline, and the patient continued to improve.

Conclusion: We report the first detailed case of pulmonary nocardiosis caused by N. aobensis diagnosed by mNGS. mNGS could be an effective method that facilitates early diagnosis and timely decision-making for the treatment of nocardiosis, especially in cases that involve rare pathogens.

Keywords: Nocardia aobensis; case report; diagnosis; metagenomic next-generation sequencing; nocardiosis.

Figure 1

Timeline of the hospitalization and treatment course.

Figure 2

Chest computed tomography image. (A) At admission; (B) on Day 7; (C) on Day 18; (D) at follow-up 1 month after discharge; and (E) at follow-up 4 months after discharge.

Figure 3

Diagnostic tests on bronchoalveolar lavage fluid. (A) Metagenomic next-generation sequencing of the BALF reported 9,806 reads of Nocardia aobensis, with a genome coverage of 7.09%. (B) Weak acid-fast staining of BALF showed positive result (×1,000).