Exploration of high-throughput sequencing method in severe pneumonia pathogens detection / 中华检验医学杂志

ABSTRACT

Objective To establish the pipeline and evaluate the feasibility of high-throughput sequencing method used in the detection of severe pneumonia pathogens.Methods Clinical control study was used.Bronchi alveolar lavage fluids (BALF) samples from 76 patients with severe pneumonia (treatment group) and 18 patients with tracheal malacia (control group) and without clinical detected pathogens were collected during March 2015 to December 2016 in Shenzhen Children′s Hospital.The pathogens in the samples were detected using clinical tests and high-throughput sequencing respectively.The results of high-throughput sequencing were confirmed by real-time quantitative PCR and the high-throughput sequencing method used in the detection of severe pneumonia pathogens was evaluated.The χ2 test was used to analyze the correlation of detection rate between the high-throughput sequencing group and the non high-throughput sequencing group.Results The pipeline and method of high-throughput sequencing used in the severe pneumonia pathogens detection was established.The pipeline included sample collection, DNA extraction, library construction, sequencing, and bioinformatic analysis.In 76 cases of patients with severe pneumonia, the results of high-throughput sequencing in 66 cases of bronchoalveolar lavage fluid specimens were positive.The sensitivity was 86.84%, which was significantly higher than the total sensitivity of traditional clinical detection methods including bacterial culture, immunofluorescence and quantitative PCR(68.42%,52/76),χ2=7.426,P<0.001.A total of 13 pathogens were detected in 66 positive samples of high-throughput sequencing, including Mycoplasma pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae and adenovirus, etc.Nine kinds of pathogens were detected in these samples through non-high-throughput sequencing.In the experimental group, the results obtained by clinical test and high-throughput (80.26%) were entirely consistent in 61 samples and not completely consistent in 15 samples (19.74%) specimens.These inconsistent results were mainly concentrated in the detection of adenovirus, Streptococcus pneumoniae and Haemophilus influenzae through high-throughput sequencing, whereas clinical cultures and immunofluorescence methods were not able to detect these pathogens.PCR validation showed that there was no significant difference between the results of high-throughput sequencing and the PCR tests (χ2=0.517,P=0.472), and the difference between the results of high-throughput sequencing and traditional clinical detection methods was statistically significant (χ2=11.671,P<0.001).Conclusion The method for the detection of severe pneumonia pathogens based on high-throughput sequencing is highly sensitive and can detect unknown pathogens, which is superior to those used in traditional clinical detection.