Evaluating the diagnostic value of using metagenomic next-generation sequencing on bronchoalveolar lavage fluid and tissue in infectious pathogens located in the peripheral lung field

Liu, Binbin; Tian, Qi; Wang, Ping; Xu, Shufeng; Tian, Yaling; Zhao, Jing; Yin, Xi‐Jun

doi:10.21037/apm-21-3474

Cited by 5 publications

(4 citation statements)

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“…The advantages of mNGS in detecting lung disease pathogens include its unbiased comprehensive profiling of microbial genomes, high throughput sequence, rapid results, and high sensitivity, even in patients previously treated with antibiotics. Additionally, BALF meets the requirements for accurate diagnosis of lung infections ( 12 ) and is feasible and accurate for patients undergoing mechanical ventilation. However, there are limitations to using mNGS, including (I) limited access to NGS platform due to technical requirement and high cost; (II) the challenge of obtaining qualified samples; (III) the potential detection of both pathogens and the airway microbiome; (IV) the need for a specific method for fungi DNA extraction when fungal infection is suspected based on clinical evidence.…”

Section: Discussionmentioning

confidence: 99%

Chlamydia psittaci causing severe pneumonia with an initial complaint of massive watery sputum: a case report

Huang,

Liu,

et al. 2024

AME Case Rep

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Background With the widespread application of metagenomic next-generation sequencing (mNGS) in pathogen detection, the reports of severe Chlamydia psittaci ( C. psittaci ) pneumonia are increasing. It is essential to determine the best management of severe C. psittaci pneumonia. Case Description This report describes a 51-year-old male patient who presented with symptoms of expectoration, relative bradycardia, and dyspnea. Lung computed tomography (CT) on day 1 (D1) showed consolidation of the left lower lobe. He was intubated and transferred to the intensive care unit (ICU). The symptoms of high fever and progressive dyspnea [the lowest level of arterial partial pressure of oxygen/fractional inspired oxygen (PaO 2 /FiO 2 ): 52 mmHg] persisted on D3. Meanwhile, he produced a large volume of golden-yellow, watery sputum, due to which endotracheal suction was repeatedly performed to maintain patency of the airway. The repeat radiography showed extensive deterioration of diffuse exudation in bilateral lobes. An early treatment with methylprednisolone was initiated on D3, after which the watery sputum decreased and turned viscous. The mNGS of the bronchoalveolar lavage fluid (BALF) identified C. psittaci on D7, and combined targeted antimicrobial therapy (azithromycin and doxycycline) was subsequently initiated. After 1 week of treatment, the patient was extubated on D14. He was transferred to the respiratory department on D17 and discharged on D25 with oral medications (azithromycin and doxycycline for 2 weeks). The repeat chest CT on D68 showed that the bilateral exudation and left lower lobe consolidation had almost disappeared, without pleural effusion. Conclusions In severe C. psittaci pneumonia, although the presentations differ, the rapid pathogen identification through BALF mNGS may facilitate the early use of effective antibiotics. Timely and comprehensive treatment is important for improving outcomes in severe C. psittaci pneumonia.

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Section: Discussionmentioning

confidence: 99%

Chlamydia psittaci causing severe pneumonia with an initial complaint of massive watery sputum: a case report

Huang,

Liu,

et al. 2024

AME Case Rep

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“…The mNGS of BALF (5) has the potential to improve pathogen identification in severe pneumonia, and it is widely used in identifying pathogens, especially in severe cases. The advantages of mNGS in the detection of lung disease pathogens include that it can provide unbiased comprehensive profiling of microbial genomes with high throughput sequence, great speed, and high sensitivity, even in patients pretreated with broad-spectrum antibiotics, as well as allowing to identify the anaerobic bacteria and viruses that are not searched for in the routine tests; moreover, it is feasible and accurate in BALF of patients under mechanical ventilation, as BALF meets the requirements for accurate diagnosis of lung infections (13). Besides BALF, lung biopsy tissues and tracheal aspirates are proved to be effective to identify pulmonary infectious pathogens (12), and the standardized quality control and data interpretation are also important to improve the accuracy of mNGS.…”

Section: Discussionmentioning

confidence: 99%

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Huang¹,

Liu²,

Gao³

et al. 2023

Ann Transl Med

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Background: With the widespread application of metagenomic next-generation sequencing (mNGS) in pathogen detection, the reports of severe Chlamydia psittaci pneumonia are increasing. It is essential to determine the best management of severe C. psittaci pneumonia.Case Description: This report describes a 51-year-old male patient who presented with symptoms of expectoration, relative bradycardia, and dyspnea. Lung computed tomography (CT) on Day 1 (D1) showed consolidation of the left lower lobe. He was intubated and transferred to the intensive care unit (ICU). The symptoms of high fever and progressive dyspnea [the lowest level of arterial partial pressure of oxygen/ fractional inspired oxygen (PaO 2 /FiO 2 ): 52 mmHg] persisted on D3. Meanwhile, he produced a large volume of golden-yellow, watery sputum, due to which endotracheal suction was repeatedly performed to maintain patency of the airway. The repeat radiography showed extensive deterioration of diffuse exudation in bilateral lobes. An early treatment with methylprednisolone was initiated on D3, after which the watery sputum decreased and turned viscous. The mNGS of the bronchoalveolar lavage fluid (BALF) identified C. psittaci on D7, and combined targeted antimicrobial therapy (azithromycin and doxycycline) was subsequently initiated. After 1 week of treatment, the patient was extubated on D14. He was transferred to the respiratory department on D17 and discharged on D25 with oral medications (azithromycin and doxycycline for 2 weeks). The repeat chest CT on D68 showed that the bilateral exudation and left lower lobe consolidation had almost disappeared, without pleural effusion.Conclusions: In severe C. psittaci pneumonia, although the presentations differ, the rapid pathogen identification through BALF mNGS may facilitate early use of effective antibiotics. Timely and integrative treatment are important for improving outcomes in severe C. psittaci pneumonia.

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“…However, the turnaround time of bacterial/fungal cultures is long (3–7 days) in conventional microbiological testing. 4 The low positive rates cannot meet the need for early pathogen diagnosis. 5 mNGS, known as a powerful, low-cost, shorter turn round-time method, has been used in pathogen diagnosis in recent years.…”

Section: Introductionmentioning

confidence: 99%

Pathogen Diagnosis Value of Nanopore Sequencing in Severe Hospital-Acquired Pneumonia Patients

Xin¹,

Ge²,

Zhang³

et al. 2023

IDR

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Background Next-generation sequencing of the metagenome (mNGS) is increasingly used in pathogen diagnosis for infectious diseases due to its short detection time. The time for Oxford Nanopore Technologies (ONT) sequencing-based etiology detection is further shortened compared with that of mNGS, but only a few studies have verified the time advantage and accuracy of ONT sequencing for etiology diagnosis. In 2022, a study confirmed that there was no significant difference in sensitivity and specificity between ONT and mNGS in suspected community-acquired pneumonia patients, which there was no clinical study verified in patients with SHAP. Methods From October 24 to November 20, 2022, 10 patients with severe hospital-acquired pneumonia (SHAP) in the Nanfang Hospital intensive care unit (ICU) were prospectively enrolled. Bronchoalveolar lavage fluid (BALF) was collected for ONT sequencing, mNGS, and traditional culture. The differences in pathogen detection time and diagnostic agreement among ONT sequencing, mNGS, traditional culture method, and clinical composite diagnosis were compared. Results Compared with mNGS and the traditional culture method, ONT sequencing had a significant advantage in pathogen detection time (9.6±0.7 h versus 24.7±2.7 h versus 132±58 h, P <0.05). The agreement rate between ONT sequencing and the clinical composite diagnosis was 73.3% (kappa value=0.737, P <0.05). Conclusion ONT sequencing has a potential advantage for rapidly identifying pathogens.

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Evaluating the diagnostic value of using metagenomic next-generation sequencing on bronchoalveolar lavage fluid and tissue in infectious pathogens located in the peripheral lung field

Cited by 5 publications

References 0 publications

Chlamydia psittaci causing severe pneumonia with an initial complaint of massive watery sputum: a case report

Chlamydia psittaci causing severe pneumonia with an initial complaint of massive watery sputum: a case report

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Pathogen Diagnosis Value of Nanopore Sequencing in Severe Hospital-Acquired Pneumonia Patients

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