Value of metagenomic next-generation sequencing to the pathogen detection after tracheoesophageal fistula airway stenting
Objective To observe the detection results of pathogens by bronchoalveolar lavage fluid(BALF)metagenomic next-generation sequencing(mNGS),protected specimen brush(PSB)mNGS,BALF culture and PSB culture in pneumonia patients after tracheoesophageal fistula airway stenting,and to investigate the value of mNGS to the pathogen diagnosis.Methods Forty-eight patients with pneumonia after tracheoesophageal fistula airway stenting in Emergency General Hospital from August 2020 to August 2021 underwent bronchoscopy before anti-infection treatment to collect BALF and PSB samples.mNGS and pathogen culture were conducted.Additionally,sputum specimens were collected for pathogen culture.The positive rates of pathogens were compared among five methods.The type and distribution of pathogen of five methods were analyzed.The number of main pathogen sequences detected by BALF mNGS was compared with that of PSB mNGS.Results There was no significant difference in the positive rate of pathogen by BALF mNGS(95.83％)compared with that by PSB mNGS(95.83％)(x2＜0.001,P＞0.999),and in the positive rate of pathogen by BALF culture(37.50％),PSB culture(33.33％)and sputum culture(33.33％)(x2=0.170,P＞0.999).The positive rates of pathogens by BALF culture,PSB culture and sputum culture were lower than those by BALF mNGS and PSB mNGS(P＜0.05).BALF mNGS identified 51 pathogens,in which 36 bacteria(70.59％)with 132 strains were detected,mainly including 22 strains of Corynebacterium striatum,20 strains of Pseudomonas aeruginosa,and 16 strains of Stenotrophomonas maltophilia;5 fungi(9.80％)with 13 strains were identified,including 6 strains of Candida albicans,4 strains of Candida tropicalis,1 strain of Aspergillus flavus,1 strain of Aspergillus fumigatus,and 1 strain of Candida glabrata;10 viruses(19.61％)with 33 strains were detected,including 10 strains of human herpes virus type 4,7 strains of human herpes simplex virus type 1,and 6 strains of human herpes virus type 7.PSB mNGS identified 46 pathogens,in which 33 bacteria(71.74％)with 125 strains were detected,including 21 strains of Corynebacterium striatum,17 strains of Pseudomonas aeruginosa,and 17 strains of Stenotrophomonas maltophilia;4 fungi(8.70％)with 9 strains were identified,including 4 strains of Candida albicans,3 strains of Candida tropicalis,1 strain of Aspergillus flavus and a strain of Candida glabrata;9 viruses(19.57％)with 19 strains were detected,including 6 strains of human herpes virus type 4,3 strains of human herpes simplex virus type 1,and 3 strains of human herpes virus type 7.BALF culture identified 9 pathogens,in which 7 bacteria(77.78％)with 21 strains were detected,including 9 strains of Pseudomonas aeruginosa,4 strains of Klebsiella pneumoniae,and 2 strains of Stenotrophomonas maltophilia;2 fungi(22.22％)with 2 strains were identified,including 1 strain of Candida albicans and 1 strain of Candida tropicalis;no viruses were detected.PSB culture identified 8 pathogens,in which 7 bacteria(87.50％)with 18 strains were detected,including 8 strains of Pseudomonas aeruginosa,3 strains of Klebsiella pneumoniae,and 2 strains of Stenotrophomonas maltophilia;1 fungus(12.50％)with 1 strain was identified as Candida tropicalis;no viruses were detected.Sputum culture identified 7 pathogens,in which 5 bacteria(71.43％)with 15 strains were detected including 8 strains of Pseudomonas aeruginosa,3 strains of Klebsiella pneumoniae,and 2 strains of Staphylococcus aureus;2 fungi(28.57％)with 5 strains were identified,including 4 strains of Candida albicans and 1 strain of Candida tropicalis;no viruses were detected.The sequences of Corynebacterium striatum,Pseudomonas aeruginosa and Stenotrophomonas maltophilia showed no significant differences between BALF mNGS[5.5×104(6.4×103,2.3×105),2.4×103(4.3 × 102,2.1×104),5.5 × 102(2.5 × 102,6.3×103)]and PSB mNGS[9.1 × 104(1.1 × 104,1.3 × 105),4.4 × 103(3.2 × 102,4.3×104),5.5 × 102(9.3 × 10,4.1 × 103)](P＞0.05).Conclusions After tracheoesophageal fistula airway stenting in patients with pneumonia,the positive rate of pathogens by BALF mNGS is similar to that by PSB mNGS,both of which are significantly higher than that by conventional culture methods.The detected pathogens by BALF mNGS and PSB mNGS are mainly Corynebacterium striatum,Pseudomonas aeruginosa,Stenotrophomonas maltophilia,Candida albicans,Candida tropicalis,and human herpes virus type 4,contributing to guiding the precise therapy.
NETL
NSTL
万方数据
维普
