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. 2022 Sep 8:12:987692.
doi: 10.3389/fcimb.2022.987692. eCollection 2022.

Rapid diagnosis of Talaromyces marneffei infection by metagenomic next-generation sequencing technology in a Chinese cohort of inborn errors of immunity

Lipin Liu  1 , Bijun Sun  1 , Wenjing Ying  1 , Danru Liu  1 , Ying Wang  1 , Jinqiao Sun  1 , Wenjie Wang  1 , Mi Yang  1 , Xiaoying Hui  1 , Qinhua Zhou  1 , Jia Hou  1 , Xiaochuan Wang  1
Affiliations

Rapid diagnosis of Talaromyces marneffei infection by metagenomic next-generation sequencing technology in a Chinese cohort of inborn errors of immunity

Lipin Liu et al. Front Cell Infect Microbiol. .

Abstract

Talaromyces marneffei (T. marneffei) is an opportunistic pathogen. Patients with inborn errors of immunity (IEI) have been increasingly diagnosed with T. marneffei in recent years. The disseminated infection of T. marneffei can be life-threatening without timely and effective antifungal therapy. Rapid and accurate pathogenic microbiological diagnosis is particularly critical for these patients. A total of 505 patients with IEI were admitted to our hospital between January 2019 and June 2022, among whom T. marneffei was detected in 6 patients by metagenomic next-generation sequencing (mNGS), and their clinical and immunological characteristics were summarized. We performed a systematic literature review on T. marneffei infections with published immunodeficiency-related gene mutations. All patients in our cohort were confirmed to have genetic mutations in IL12RB1, IFNGR1, STAT1, STAT3, and CD40LG. T. marneffei was detected in both the blood and lymph nodes of P1 with IL12RB1 mutations, and the clinical manifestations were serious and included recurrent fever, weight loss, severe anemia, splenomegaly and lymphadenopathy, all requiring long-term antifungal therapy. These six patients received antifungal treatment, which relieved symptoms and improved imaging findings. Five patients survived, while one patient died of sepsis after hematopoietic stem cell transplantation. The application of mNGS methods for pathogen detection in IEI patients and comparison with traditional diagnosis methods were investigated. Traditional diagnostic methods and mNGS tests were performed simultaneously in 232 patients with IEI. Compared to the traditional methods, the sensitivity and specificity of mNGS in diagnosing T. marneffei infection were 100% and 98.7%, respectively. The reporting time for T. marneffei detection was approximately 26 hours by mNGS, 3-14 days by culture, and 6-11 days by histopathology. T. marneffei infection was first reported in IEI patients with IL12RB1 gene mutation, which expanded the IEI lineage susceptible to T. marneffei. For IEI patients with T. marneffei infection, we highlight the application of mNGS in pathogenic detection. mNGS is recommended as a front-line diagnostic test for rapidly identifying pathogens in complex and severe infections.

Keywords: IL12RB1 mutation; T-cell-mediated immunity; Talaromyces marneffei; inborn errors of immunity; intrinsic and innate immunodeficiencies; metagenomic next-generation sequencing.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Gene distribution of patients with T. marneffei infection in IEIs. Gene distribution in our cohort (A). Gene distribution in previously reported cases (B).
Figure 2
Figure 2
The expression of IL12RB1 (CD212) and IFNGR1 (CD119) protein in P1-P3. IL12RB1 protein was not expressed in P1 and P2. IFNGR1 protein was not expressed in P3.
Figure 3
Figure 3
Histopathological staining and mNGS results in P1 and P5. Lymph node enlargement of the right axilla was seen in P1 (A). Confirmation of T. marneffei-specific amplification from lymph node tissue by mNGS showed 108,380 unique sequence reads of T. marneffei, accounting for 18.93% of the genome coverage (B). Granulomatous inflammation observed during histopathological examination of the cervical lymph node (C). PAS staining of the cervical lymph node revealed fungal spores (arrows) (magnification × 400) (D). A large number of neutrophil infiltrates were observed in the histopathological examination of abdominal lymph nodes of P5, and a patchy distribution of tissue cells was observed. Fungal spore-like substances were scattered or clustered in some tissue cells (magnification × 400) (E). PAS staining of the abdominal lymph node tissues revealed fungal spores (arrows) (magnification × 400) (F).
Figure 4
Figure 4
Dynamic changes in imaging examinations of patients during follow-up. Imaging examination of P1 revealed that the axillary and mediastinal lymph nodes were enlarged (A.1). After oral itraconazole and anti-tuberculous therapy for nearly 2 months, chest CT re-examination showed that the axillary and mediastinal lymph nodes were still enlarged (A.2). A lymph node biopsy was performed on April 19, 2022, and mNGS indicated high reads of T. marneffei. Antifungal therapy was adjusted to amphotericin B for 2 weeks, followed by oral itraconazole. One month later, the imaging examination suggested that the lymph nodes were smaller than before (A.3). Chest CT of P3 suggested pneumonia and partial consolidation of the left lung with slight pleural effusion in the acute phase (B.1), and the patient received oral itraconazole antifungal combined with anti-tuberculosis therapy. Chest CT re-examination revealed significant improvement in the lungs after 3 months (B.2) and 8 months (B.3). Abdominal CT of P5 indicated hepatosplenomegaly and multiple abnormal lesions at the beginning (C.1). He received intravenous voriconazole treatment for 25 days and then oral voriconazole. The multiple abnormal lesions improved after treatment for 2 weeks (C.2) and 3.5 months (C.3).
Figure 5
Figure 5
Distribution of sample types with T. marneffei positivity. In our cohort, T. marneffei was detected in 15 samples using different methods, including mNGS (n=10), culture (n=3), and histopathological staining (n=2). In the previous cohort, T. marneffei was mainly detected by cultures (n=36) and histopathological staining (n=4), and only two patients were detected by mNGS (n=2).
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