Metagenomic next-generation sequencing for identifying pathogens in patients with rheumatic diseases and diffuse pulmonary lesions: A retrospective diagnostic study

Jiang, Juan; Yang, Wei; Wu, Yanhao; Peng, Wenzhong; Zhang, Wenjuan; Pan, Pinhua; Li, Yisha; Li, Yuanyuan

doi:10.3389/fcimb.2022.963611

Cited by 5 publications

(11 citation statements)

References 32 publications

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“…The study found that only 12.7% of patients suffered from chest tightness and shortness of breath. The proportion was significantly lower than in other studies ( 1 , 7 ). Different diagnostic classifications of dyspnea and treatment approaches may explain this.…”

Section: Discussioncontrasting

confidence: 83%

“…Several imaging characteristics, such as consolidation of the chest with a bronchogram obtained via chest CT, have been reported ( 19 ). Most patients have bilateral, middle-lower lobe, or multilobar lesions, usually presenting as consolidation, and have pleural effusions ( 7 ). Moreover, bilateral lung consolidation and numerous lobe infiltration were observed primarily in severe cases.…”

Section: Discussionmentioning

confidence: 99%

“…It is consistent with the previous reports that the leukocyte increase is not noticeable ( 4 ), the neutrophil ratio and NLR increase, the lymphocyte ratio decreases, the PCT increases, the transaminase increases, the creatinine and urea nitrogen increases, and the hypoproteinemia increases, etc. ( 1 , 7 ). However, in our study, further binomial logistic regression analysis and ROC curve analysis showed that both the increase of neutrophil ratio and NLR were risk factors of the severe group, with ORs of 10.057 and 9.750 respectively, both statistically significant, and AUCs of both were over 0.8, both also statistically significant.…”

Section: Discussionmentioning

confidence: 99%

“…The research discovered that nearly all patients had had close contact with birds or poultry ( 16 ). Several reports showed that most patients had a history of poultry contact ( 7 , 15 ). Among 116 patients studied, only 18 (15.5%) had a history of exposure ( 1 ).…”

Section: Discussionmentioning

confidence: 99%

“…In contrast to traditional microbial culture methods, mNGS detects pathogens within 3 days ( 24 ). More evidence suggests that mNGS is an effective tool for diagnosing C. psittaci pneumonia ( 7 , 25 ). But for some patients, mNGS testing is unaffordable due to its high cost.…”

Section: Discussionmentioning

confidence: 99%

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Chlamydia psittaci pneumonia in Wuxi, China: retrospective analysis of 55 cases and predictors of severe disease

Gao,

Wu,

et al. 2023

Front. Med.

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PurposeMore and more patients with community-acquired pneumonia have been detected with Chlamydia psittaci (C. psittaci) infected using metagenomic next-generation sequencing (mNGS). Previously, this was unheard of, and several patients presented with severe pneumonia and even required ECMO. We aimed to clarify the clinical characteristics of C. psittaci pneumonia and find out if there are any possible predictors of severe C. psittaci pneumonia.MethodsIn this retrospective study, we included all confirmed cases of C. psittaci pneumonia in Wuxi. Epidemiological, clinical, and radiological features, as well as laboratory data, were collected and analyzed.ResultsWe enrolled 55 patients with C. psittaci pneumonia, with 30 (54.5%) having a history of exposure to birds or their internal organs. 50 (90.9%) patients were diagnosed by mNGS. Patients with C. psittaci pneumonia had many complications, among which, that deserve sufficient attention from clinicians were vascular embolic events (3, 5.5%). High fever was the most common clinical manifestation (41, 74.5%). The majority of patients had a significant increase in neutrophils ratio, neutrophils to lymphocytes ratio (NLR), rapid c-reactive protein, creatine kinase (CK), and lactate dehydrogenase (LDH), as well as a decrease in lymphocytes ratio, albumin, serum sodium, serum potassium, and serum phosphorus. Chest computed tomography scans revealed unilateral pneumonia (70.9%), consolidation (87.3%), air bronchogram (76.4%), and ground-glass opacity (69.1%). The neutrophil ratio, NLR, LDH, and CK were all factors that could identify severe pneumonia. Both AUCs exceeded 0.8; the respective 95% CIs were 0.715–0.944, 0.710–0.963, 0.677–0.937, and 0.718–0.950; all p < 0.05 (0.01, 0.001, 0.007, 0.007 respectively). The ORs were 10.057, 9.750, 10.057, and 9.667, respectively; the 95% CIs were 2.643–38.276, 2.339–40.649, and 2.643–38.276, respectively; all p-values were less than 0.05 (0.001, 0.002, 0.001, 0.001 respectively).ConclusionC. psittaci pneumonia is a very complex disease that changes all the time. Some patients showed severe pneumonia. Patients will have a poor prognosis if they are not treated promptly and effectively. We discovered that many clinical indicators were typical. Meanwhile, significant increases in neutrophil ratio, NLR, LDH, and CK predicted severe pneumonia. Timely detection of mNGS provided substantial help for clinical diagnosis and early treatment.

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Section: Discussioncontrasting

confidence: 83%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Chlamydia psittaci pneumonia in Wuxi, China: retrospective analysis of 55 cases and predictors of severe disease

Gao,

Wu,

et al. 2023

Front. Med.

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Diagnosis and treatment of a patient with pulmonary infection caused by Emergomyces Orientalis : a case report

Jiang,

Tian,

Zhang

et al. 2024

Future Microbiology

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Emergomycosis is a dimorphic fungal disease that is typically disseminated and fatal among immunocompromised individuals. In the case report, we presented a patient with intermittent fever, night sweats, coughing and phlegm. Chest computed tomography revealed multiple soft-tissue nodules in both lungs. Routine pathological and microbiological tests did not confirm the diagnosis. Therefore, we conducted pathogen detection using metagenomic next-generation sequencing in bronchoalveolar lavage fluid and identified the pulmonary infection caused by Emergomyces orientalis ( Es. orientalis ). During the antifungal treatment, the patient experienced renal function damage, and we have attempted various antifungal drugs for treatment. Finally, the patient’s condition was brought under control. Therefore, the metagenomic next-generation sequencing pathogen detection was essential.

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Combination of transbronchial cryobiopsy based clinic-radiologic-pathologic strategy and metagenomic next-generation sequencing for differential diagnosis of rapidly progressive diffuse parenchymal lung diseases

Sun

Chen

Liu

et al. 2023

Front. Cell. Infect. Microbiol.

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BackgroundThe complicated spectrum of rapidly progressive diffused parenchymal lung diseases (RP-DPLD) creates obstacles to the precise diagnosis and treatment. We evaluated the differential diagnostic value of transbronchial cryobiopsy (TBCB) based clinic-radiologic-pathologic (CRP) strategy combined with bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) in RP-DPLD patients.MethodsRP-DPLD patients who underwent the diagnostic strategy of TBCB-based CRP combined with BALF mNGS at Shanghai East Hospital from May 2020 to Oct 2022 were retrospectively analyzed. Clinical characteristics were summarized, including demographic data, high-resolution computed tomography (HRCT) findings, histopathology of TBCB and microbiological results. Diagnostic value of the combined strategy, as well as the sensitivity, specificity, and positive detection rates of mNGS were evaluated.ResultsA total of 115 RP-DPLD patients were enrolled, with a mean age of 64.4 years old and a male proportion of 54.8%. The pulmonary imaging findings in most patients were complex and diverse, with all patients showing bilateral lung diffuse lesions in HRCT, and progressively aggravated imaging changes within one month. After combining TBCB-based CRP strategy with mNGS, all participants received a corresponding diagnosis with 100% diagnostic yield. In these patients, 58.3% (67/115) were diagnosed with noninfectious RP-DPLD and 41.7% (48/115) with infection-related RP-DPLD. There were 86.1% of cases with known etiology according to the DPLD classification. BALF mNGS and traditional pathogen detection methods were performed in all patients, the positive detection rates were 50.4% (58/115) and 32.2% (37/115), respectively. Meanwhile, the mNGS showed significantly higher sensitivity and negative predictive value than the traditional pathogen detection methods for the diagnosis of infection-related RP-DPLD (100% vs 60.4% (p<0.001), 100% vs 75.6% (p<0.001), respectively). Among noninfectious RP-DPLD patients, the true negative rate of mNGS was 85.1% (57/67). All patients had their treatment regimen modified and the 30-day mortality was 7.0%.ConclusionThe novel strategy of TBCB-based CRP combined with mNGS provided dependable and sufficient evidence for the diagnosis, meanwhile further improved the accuracy of RP-DPLD treatment, as well as the prognosis of patients. Our results highlight the significant value of combined strategy in determining whether the RP-DPLD patients were infection associated or not.

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Metagenomic next-generation sequencing for identifying pathogens in patients with rheumatic diseases and diffuse pulmonary lesions: A retrospective diagnostic study

Cited by 5 publications

References 32 publications

Chlamydia psittaci pneumonia in Wuxi, China: retrospective analysis of 55 cases and predictors of severe disease

Chlamydia psittaci pneumonia in Wuxi, China: retrospective analysis of 55 cases and predictors of severe disease

Diagnosis and treatment of a patient with pulmonary infection caused by Emergomyces Orientalis : a case report

Combination of transbronchial cryobiopsy based clinic-radiologic-pathologic strategy and metagenomic next-generation sequencing for differential diagnosis of rapidly progressive diffuse parenchymal lung diseases

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