The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with infectious diseases

The value of metagenomic next-generation sequencing in the diagnosis of fever of unknown origin

Fever of unknown origin (FUO) caused by infection is a disease state characterized by complex pathogens and remains a diagnostic dilemma. Metagenomic next-generation sequencing (mNGS) technology is a promising diagnostic tool for identifying pathogenic microbes of FUO caused by infection. Little is known about the clinical impact of mNGS in the etiological diagnosis of FUO. This study focuses on the value of mNGS in the etiologic diagnosis of FUO by diagnostic performance, further clarifying the value of mNGS in clinical management. In a single-centre retrospective cohort study, 263 FUO patients who underwent both mNGS and culture at the First Affiliated Hospital of Nanchang University were enrolled from December 2020 to February 2023. The sensitivity and specificity of culture and mNGS were analyzed based on the final clinical diagnosis as the gold standard to assess the diagnostic value of mNGS in FUO cases. Among the 263 patients, 69.96%(184/263) cases were diagnosed as infectious diseases, of which lower respiratory tract infections were the most common, accounting for 53.26%(98/184). 30.04%(79/263) cases had a diagnosis of non-infectious disease. From these cases, mNGS identified 150 true-positive cases, 21 false-positive cases, 58 true-negative cases, and 34 false-negative cases. The sensitivity of mNGS in infection diagnosis was much higher than that of culture [81.52%(150/184) vs. 47.28%(87/184)], but the specificity was the opposite[73.42%(58/79) vs. 84.81%(67/79)]. mNGS had a receiver operating characteristic (ROC) curve of 0.775 for infectious disease, which was significantly higher than that of culture (0.661, P < 0.05). mNGS detection revealed that bacteria were the most commonly identified potential pathogens. The top causative pathogens identified were Acinetobacter baumannii. Of the 263 patients with FUO, clinical management of 48.67% (128/263) patients was positively affected by mNGS, and 51.33% (135/263) patients were not affected by mNGS(P = 0.1074). To sum up, infectious diseases are the principal cause of FUO. mNGS could significantly improve the detected pathogen spectrum of FUO caused by infection. However, the FUO disease spectrum is relatively broad, including a large number of non-infectious diseases. Therefore, Further investigation is warranted into the specific clinical scenarios for which mNGS may offer the greatest clinical diagnostic value.

Evaluation of Different Sampling Methods Combined with Metagenomic Next-Generation Sequencing of Respiratory Specimens in Etiological Diagnosis of Patients with Severe Pneumonia

Objective

To evaluate the value of respiratory specimens collected via different sampling methods combined with metagenomic next-generation sequencing (mNGS) in the etiological diagnosis of severe pneumonia.

Methods

A total of 117 patients with severe pneumonia between 2019 and 2024 were included in this study, with 60 patients undergoing endotracheal aspiration (ETA) and 57 undergoing bronchoalveolar lavage (BAL), respectively. Patient records were retrospectively reviewed. Both ETA and BAL samples were tested using mNGS and conventional microbiological tests (CMT) to compare the detection rates, microbial profiles and their effects on clinical outcomes.

Results

The positive rates of mNGS for ETA and BAL samples were 96.7% and 80.7%, respectively, which were higher than CMT. A total of 39 pathogenic microorganisms were detected, of which Klebsiella pneumoniae, Candida albicans and herpes simplex virus-4 (HSV-4), and cytomegalovirus (CMV) were the most commonly detected as bacteria, fungi and viruses, respectively. The percentages of Pseudomonas aeruginosa (30.0% vs 12.3%, p = 0.019) and Stenotrophomonas maltophilia (25.0% vs 8.8%, p = 0.020) were significantly higher in the ETA group compared to the BALF group. The detection rate of three or more microorganisms was notably higher in the ETA group. No significant differences existed in antibiotics adjustment between the groups. The ETA group experienced a higher frequency of continuous renal replacement therapy (CRRT), mechanical ventilation and complications. There was no significant difference in the hospital length of stay, duration of mechanical ventilation and mortality between both groups.

Conclusion

Respiratory specimens collected by different sampling methods yield different microbial findings. ETA and BAL combined with mNGS play a role in guiding the pathogenetic diagnosis of patients with severe pneumonia. However, it is recommended that their sampling methods be determined by clinical symptoms and patient conditions.

Utility of Metagenomic Next-Generation Sequencing for Diagnosis of Infectious Diseases in Critically Ill Immunocompromised Pediatric Patients

Purpose

Infections cause high rates of illness and death in children worldwide. However, studies on the clinical value of metagenomic next-generation sequencing (mNGS) for immunocompromised children are still limited.

Patients and Methods

From June 2021 to December 2023, 119 samples were collected at Pediatric Intensive Care Unit (PICU) of a single-center pediatric hospital and classified into two groups based on their immune states. We compared the diagnostic performance of mNGS and conventional microbiological test (CMT) for pathogen identification, and assessed the clinical impacts of mNGS.

Results

Among the 119 samples, 48 (40.34%) belonged to the immunocompromised children. mNGS had a higher positivity rate than CMT (76.47% vs 55.46%, P = 0.0006). The positive percent agreement (PPA) of mNGS for immunocompromised children was higher compared to immunocompetent children (95.24% vs 77.78%). The most common pathogens for immunocompromised patients were gram-negative bacteria and herpesvirus. However, immunocompetent children showed a higher detection rate for gram-positive bacteria and respiratory viruses. Furthermore, the proportions of the positive impact of mNGS results were significantly higher in immunocompromised patients compared to immunocompetent patients for both diagnosis (91.67% vs 57.75%) and treatment (95.83% vs 64.79%) (P < 0.0001). Immunocompromised state, length of hospital stays, times stay in ICU, Pediatric Risk of Mortality (PRISM) score, neutrophil percentage (NEUT%) and the ratio of arterial oxygen partial pressure to fractional inspired oxygen (PaO2/FiO2) were considered independent factors for poor prognosis in critically ill pediatric patients.

Conclusion

In patients from PICU, mNGS had a greater clinical significance in immunocompromised children compared to immunocompetent children. mNGS technology is an important auxiliary method for achieving accurate diagnosis and treatment of critically ill pediatric patients.

A case of chronic wounds caused by Sporothrix schenckii infection was rapidly detected by metagenomic next generation sequencing

The dimorphic fungus Sporothrix schenckii is widely distributed in soil, vegetation, and decaying organic matter, and can cause sporotrichosis when the patient's skin trauma was exposed to contaminated material with Sporothrix spp. The cases of Sporothrix schenckii infection in chronic wounds are rarely reported. Here we reported a 53-year-old male construction worker who was admitted to our hospital on July 9, 2022, without underlying disease presented with a painless subcutaneous hard nodule on his right calf, which later ulcerated and oozed, with an enlarged wound and no fever during the course of the disease. His procalcitonin, C-reactive protein, erythrocyte sedimentation rate increased, and necrotic histopathology suggested chronic granulomatous inflammation. Then his necrotic tissue and pus were sent for metagenomic next generation sequencing(mNGS), the result reported Sporothrix schenckii after 43 hours, which was consistent with the result of culture after 18 days. mNGS might be more useful and valuable in diseases such as sporotrichosis where it is difficult to see the yeast cells in the tissues.