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

Abstract

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.

Metagenomic Next-Generation Sequencing for Pathogenic Diagnosis and Antibiotic Management of Severe Community-Acquired Pneumonia in Immunocompromised Adults

“…The excessive antibiotic use can lead to resistance and medical resources waste (Webb et al, 2015;Metlay et al, 2019;Ramirez et al, 2020). Zhang et al (2020) found in of immunosuppressed patients with acute respiratory distress syndrome (ARDS) caused by severe pneumonia, the detection of mNGS can significantly shorten the ICU stay, the ventilation time and reduce the ICU cost. The distinct advantage of NGS may can help clinicians more comprehensive evaluation of empiric antimicrobial therapy and make effective adjustments for immunocompromised SCAP patients.…”

“…The BALF specimens were divided into aliquots and subjected to conventional microbiological test as well as mNGS test in a pairwise manner. Some specimens were sent to the Vision Medical Co., Ltd. (China) for the mNGS analysis, performing nucleic acid extraction, library construction, high-throughput sequencing, bioinformatics analysis, and pathogen data interpretation according to previous studies ( Li et al., 2020 ; Zhang et al., 2020 ). The other specimens were sent to our microbiological laboratory using conventional methods for microbiological analysis, including bacterial/fungal smear and culture, Pneumocystis jirovecii (PC) smear (Grocott methenamine staining), acid-fast stain and real-time PCR including cytomegalovirus (CMV), influenza virus, respiratory syncytial virus, Legionella, Mycoplasma and Chlamydia spp .…”

Exploring the Clinical Utility of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infection

“…Their results and ours both indicate that the combination of mNGS and conventional test contributes to the diagnostic ratio of the mixed pulmonary infection. Prior studies have shown that mNGS was significantly better at the identification of coinfections than conventional tests like serological antibody, PCR, or culture [ 16 , 18 , 19 ].…”

Sixteen cases of severe pneumonia caused by Chlamydia psittaci in South China investigated via metagenomic next-generation sequencing

“…But most of the time simply relying on traditional diagnostic methods may lead to a misdiagnosis and delay of the treatment. NGS does not target a specific pathogen, but high-throughput sequencing of nucleic acid is directly performed in samples [24]. NGS is a kind of culture-independent methods, based on removal of human genes, followed by amplification and sequencing of microbial communities, typically through 16S rRNA genes for bacteria, or whole genome.…”