Clinical application of nanopore sequencing in detecting bacterial infections in lower respiratory tract / 中华检验医学杂志

ABSTRACT

Objective:To establish the method for detecting lower respiratory infections (LRIs) bacterialpathogens using nanopore sequencing, and evaluate the feasibility of this method.Methods:Bronchoalveolar lavage fluid (BALF) samples from 33 patients with LRIs who visited the Department of Respiratory and Critical Care Medicine of Beijing Hospital from July 2019 to September 2020 were collected.Nanopore 16S amplicon sequencing were performed on these samples. In order to evaluate the clinical value of the nanopore sequencing, χ 2 test was used to analyze the pathogen differences between the detection rate and pathogen types results found with using the nanopore 16S sequencing and the results found with bacterial culture. Results:The process and method of nanopore sequencing used in the detection of the LRIs pathogens were established. The pathogen detection rate of the 16S sequencing was higher than that of the traditional bacterial culture (75.8% [25/33], 45.5% [15/33], χ2=5.140, P<0.05). From the 25 positive samples found with nanopore 16S sequencing, 16 pathogens were detected, including Haemophilus parainfluenzae, Haemophilus influenzae, Streptococcus pneumoniae, Streptomonas maltophilia, Acinetobacter baumannii, and Acinetobacter junii, Staphylococcus aureus, Klebsiella pneumoniae, Enterococcus faecalis, Enterococcus gallinarum, Corynebacterium striatum, Mycobacterium paraintracellulare, Serratia marcescens, Achromobacter insuavis, Citrobacter murliniae and Mycoplasma pneumoniae. More than 6 pathogens were tested in clinical culture, including Haemophilus parainfluenzae, Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, Klebsiella pneumoniae and Streptomonas maltophilia (χ2=7.949, P<0.05). 16S sequencing aligned to species level sequences accounted for 80.0 (60.0, 86.0)% of the genus level. The results obtained by using16S sequencing and bacterial culture were consistent in 11 (33.3%) samples. Conclusions:Nanopore 16S amplicon sequencing can quickly identify pathogenic bacteria from BALF in LRIs patients. Nanopore 16S amplicon sequencing has a high detection rate, it can detect more pathogens than traditional bacterial culture, and it can also identify most bacteria to the species level. This technology is a very promising platform with broad application prospects.