Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing

Qi, Chao; Hountras, Peter; Pickens, Chiagozie I; Walter, James M.; Kruser, Jacqueline M.; Singer, Benjamin D.; Seed, Patrick; Green, Stefan J.; Wunderink, Richard G.

doi:10.1099/jmm.0.000968

Cited by 27 publications

(20 citation statements)

References 32 publications

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“…Thirdly, the positive rate of mNGS detection of specific pathogens (22.2%) was higher than that of culture (0%, P = 0.001) and antibody plus PCR (2.2%, P = 0.007). This conclusion was consistent with a previous study by Qi et al (2019) in that the positive of mNGS was much higher than that of culture, and rare pathogens could be detected. In addition, we analyzed the consistency between mNGS and culture, 31.1% of identified pathogens in the NGS group were consistent, 15.6% were partially consistent, and 53.3% were completely inconsistent.…”

Section: Discussionsupporting

confidence: 93%

Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study

Zhang

Chen

et al. 2020

PeerJ

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Background Metagenome next-generation sequencing (mNGS) is a valuable diagnostic tool that can be used for the identification of early pathogens of acute respiratory distress syndrome (ARDS) in severe pneumonia. Little is known about the use of this technology in clinical application and the evaluation of the prognostic value of ARDS. Methods We performed a retrospective cohort study of patients with ARDS caused by severe pneumonia. Samples were collected from patients in the intensive care unit (ICU) of Jiangmen Central Hospital from January 2018 to August 2019. The no-next generation sequencing (NGS) group was composed of patients given conventional microbiological tests to examine sputum, blood, or bronchoalveolar lavage fluid. The NGS group was composed of patients tested using mNGS and conventional microbiological tests. We evaluated the etiological diagnostic effect and clinical prognostic value of mNGS in patients with ARDS caused by severe pneumonia. Results The overall positive rate (91.1%) detected by the mNGS method was significantly higher than that of the culture method (62.2%, P = 0.001), and antibody plus polymerase chain reaction (28.9%, P < 0.001). Following adjustment of the treatment plan based on microbial testing results, the Acute Physiology and Chronic Health Evaluation-II (APACHE II) score of the NGS group was lower than that of the no-NGS group 7 days after treatment (P < 0.05). The 28-day mortality rate of the NGS group was significantly lower than that of the no-NGS group (P < 0.05). Longer ICU stay, higher APACHE II score and sequential organ failure assessment score were risk factors for the death of ARDS, and adjusting the medication regimen based on mNGS results was a protective factor. The detection of mNGS can significantly shorten the ICU stay of immunosuppressed patients (P < 0.01), shorten the ventilation time (P < 0.01), and reduce the ICU hospitalization cost (P < 0.05). Conclusions Metagenome next-generation sequencing is a valuable tool to determine the etiological value of ARDS caused by severe pneumonia to improve diagnostic accuracy and prognosis for this disease. For immunosuppressed patients, mNGS technology can be used in the early stage to provide more diagnostic evidence and guide medications.

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Section: Discussionsupporting

confidence: 93%

Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study

Zhang

Chen

et al. 2020

PeerJ

View full text Add to dashboard Cite

show abstract

“…Thirdly, the positive rate of mNGS detection of specific pathogens (22.2%) was higher than that of culture (0%, P = 0.001)) and antibody plus PCR (2.2%, P = 0.007). This conclusion was consistent with a previous study by Qi et al (Qi et al 2019) in that the positive of mNGS was much higher than that of culture, and rare pathogens could be detected. In addition, we analyzed the consistency between mNGS and culture, 31.1% of identified pathogens in the NGS group were consistent, 15.6% were partially consistent, and 53.3% were completely inconsistent.…”

Section: Discussionsupporting

confidence: 93%

Peer Review #1 of "Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study (v0.1)"

2020

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Background. Metagenome Next-Generation Sequencing (mNGS) is a valuable diagnostic tool that can be used for the identification of early pathogens of acute respiratory distress syndrome (ARDS) in severe pneumonia. Little is known about the use of this technology in clinical application and the evaluation of the prognostic value of ARDS. Methods. We performed a retrospective cohort study of patients with ARDS caused by severe pneumonia. Samples were collected from patients in the intensive care unit (ICU) of Jiangmen Central Hospital from January 2018 to August 2019. The no-NGS group was composed of patients given conventional microbiological tests to examine sputum, blood, or bronchoalveolar lavage fluid (BALF). The NGS group was composed of patients tested using mNGS and conventional microbiological tests. We evaluated the etiological diagnostic effect and clinical prognostic value of mNGS in patients with ARDS caused by severe pneumonia. Results. The overall positive rate (91.1%) detected by the mNGS method was significantly higher than that of the culture method (62.2%, P = 0.001), and antibody plus polymerase chain reaction (PCR) (28.9%, P < 0.001). Following adjustment of the treatment plan based on microbial testing results, the Acute Physiology and Chronic Health Evaluation-II (APACHE II) score of the NGS group was lower than that of the no-NGS group 7 d after treatment (P < 0.05). The 28-day mortality rate of the NGS group was significantly lower than that of the no-NGS group (P < 0.05). Longer ICU stay, higher APACHE II score and Sequential Organ Failure Assessment (SOFA) score were risk factors for the death of ARDS, and adjusting the medication regimen based on mNGS results was

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“…Previous studies have shown great concordance between mNGS and conventional microbiologic testing [ 6 , 13 , 14 , 29 , 30 ] and suggested mNGS might lead to better clinical prognosis than conventional testing in severe pneumonia in intensive care unit [ 13 ]. Our study also showed BALF mNGS had good concordance with culture results (sensitivity = 81.3%, specificity = 76.9%), while there were also some inconsistencies between blood mNGS and BALF mNGS as well as between conventional tests and mNGS.…”

Section: Discussionmentioning

confidence: 99%

Blood and Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumonia

Ding

Cheng

et al. 2020

Canadian Journal of Infectious Diseases and Medical Microbiolog

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Background. Metagenomic next-generation sequencing (mNGS) has made a revolution in the mode of pathogen identification. We decided to explore the diagnostic value of blood and bronchoalveolar lavage fluid (BALF) as mNGS samples in pneumonia. Methods. We retrospectively reviewed 467 mNGS results and assessed the diagnostic performance of paired blood and BALF mNGS in 39 patients with pneumonia. Results. For bacteria and fungi, 16 patients had culture-confirmed pathogen diagnosis, while 13 patients were culture-negative. BALF mNGS was more sensitive than blood mNGS (81.3% vs. 25.0%, p=0.003), and the specificity in BALF and blood mNGS was not statistically significant different (76.9% vs. 84.6%, p=0.317). For 10 patients without culture test, treatments were changed in 2 patients. For viruses, Epstein-Barr virus was positive in blood mNGS in 9 patients. Human adenovirus was detected in both BALF and blood mNGS in 3 patients. Conclusion. Our study suggests that BALF mNGS is more sensitive than blood mNGS in detecting bacteria and fungi, but blood also has advantages to identify the pathogens of pneumonia, especially for some viruses.

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Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing

Cited by 27 publications

References 32 publications

Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study

Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study

Peer Review #1 of "Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study (v0.1)"

Blood and Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumonia

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