Clinical performance of metagenomic next-generation sequencing for the rapid diagnosis of talaromycosis in HIV-infected patients.

Background: Talaromycosis is an invasive endemic mycosis caused by the dimorphic fungus Talaromyces marneffei (T. marneffei, TM). It mainly affects immunodeficient patients, especially HIV-infected individuals, which causes significant morbidity and mortality. Culture-based diagnosis takes a long turnaround time with low sensitivity, leading to treatment delay. In this study, we aimed to evaluate the performance of Metagenomic Next-Generation Sequencing (mNGS) for the rapid diagnosis of talaromycosis in HIV-infected patients. Methods: Retrospectively analysis was conducted in HIV-infected cases at Changsha First Hospital (China) from January 2021 to March 2022. Patients who underwent routine microbiological examination and mNGS testing in parallel were enrolled. The clinical final diagnosis was used as a reference standard, and cases were classified into the TM group (60 cases) and the non-TM group (148 cases). The clinical performances of mNGS were compared with culture and serum Galactomannan (GM). The mixed infections detected by mNGS were analyzed. The impact of mNGS detection on treatment was also investigated. Results: The sensitivity of mNGS test reached 98.3% (95% CI, 89.8-99.9), which was significantly higher than culture (66.7% [95% CI, 53.2-77.9], P < 0.001) and serum GM (83.3% [95% CI, 71.0-91.2], P < 0.05). The specificity of 98.6% (95% CI, 94.7-99.7) was similar to culture (100.0% [95% CI, 96.8-100.0], P = 0.156), and superior to serum GM (91.9% [95% CI, 85.9-95.5], P < 0.05). In bronchoalveolar lavage fluid (BALF) samples, the positive rate of mNGS was 97.6%, which was significantly higher than culture (28.6%, P <0.001). mNGS has excellent performance in the identification of mixed infection in TM group patients. Cytomegalovirus, Epstein-Barr virus and Pneumocystis jirovecii were the most common concurrent pathogens. In summary, 60.0% (36/60) patients were added or adjusted to antimicrobial therapy after mNGS test. Conclusion: mNGS is a powerful technique with high specificity and sensitivity for the rapid diagnosis of talaromycosis. mNGS of BALF samples may be a good option for early identification of T. marneffei in HIV-infected individuals with manifestations of infection. Moreover, mNGS shows excellent performance in mixed infection, which benefits timely treatment and potential mortality reduction.

[Association between the ALK Gene Status and the Efficacy of First-line 
Pemetrexed Chemotherapy in Patients with Advanced Lung Adenocarcinoma].

BACKGROUND: Anaplastic lymphoma kinase (ALK) is one of the major driver genes of non-small cell lung cancer (NSCLC). Several studies have shown that the efficacy of pemetrexed in ALK-positive lung cancer is controversial. The aim of this study is to explore the efficacy of pemetrexed-based chemotherapy in patients with ALK-positive and negative lung adenocarcinoma. METHODS: The clinical data of 98 cases of epidermal growth factor receptor (EGFR), kirsten rat sarcoma viral oncogene (KRAS), V-rafmurine sarcoma viral oncogene homolog B1 (BRAF)-negative patients with advanced lung adenocarcinoma patients who diagnosed by histopathology from January 2015 to April 2016 in the First Affiliated Hospital of Zhengzhou University were collected. The relationships between ALK gene status, clinical characteristics and response and progression-free survival (PFS) were analyzed. RESULTS: All of the 98 patients' ALK status were determined. ALK gene fracture fusion occured in 34 cases (34.7%), no fracture fusion in 64 cases (65.3%). All patients underwent first-line pemetrexed and platinum-based chemotherapy, the objective response rate (ORR) was 21.4% and the disease control rate (DCR) was 84.7%. The ORR and DCR of patients with ALK fracture fusion were higher than those without fracture fusion (41.2% vs 10.9%, χ2=23.389, P<0.001; 91.2% vs 81.3%, χ2=4.153, P=0.042), the difference was statistically significant. ALK gene status was not related to age, gender, smoking history and clinical stage. The median PFS of ALK-positive lung adenocarcinoma was 7.1 months (95%CI: 6.1-8.1) and negative was 4.7 months (95%CI: 3.818-5.582), and the difference was statistically significant (χ2=13.269, P<0.001). Cox multivariate analysis indicates that PFS of pemetrexed combined with platinum chemotherapy was independent of gender, age, smoking, staging and platinum. ALK gene fracture fusion is an independent factor affecting PFS (HR=0.392, 95%CI: 0.243-0.634, P<0.001). CONCLUSIONS: ALK-positive lung adenocarcinoma patients with first-line pemetrexed-based chemotherapy have greater clinical benefit than ALK-negative patients.