基于宏基因组二代测序技术的840例疑似肺部感染患者下呼吸道微生物特征分析

Microbial profile analysis of lower respiratory tract in 840 patients with suspected pulmonary infection based on metagenomic next-generation sequencing technology

目的利用宏基因组二代测序(metagenomic next-generation sequencing,mNGS)技术分析肺部感染患者下呼吸道微生物特征,提高临床对于肺部感染患者病原学特征的认识。方法纳入在2020年8月—2021年10月期间,四川大学华西医院应用mNGS技术检测肺泡灌洗液微生物特征的840例疑似肺部感染患者,回顾性分析所有患者的下呼吸道微生物特征。结果共纳入840例患者,743例检出微生物阳性,其中细菌感染比例最高,占35.13%(261/743);细菌中鲍曼不动杆菌比例最高,占18.98%(141/743),其次是肺炎链球菌(14.13%、105/743),肺炎克雷伯菌(13.46%、100/743),屎肠球菌(12.11%、90/743)和结核分枝杆菌复合群(11.98%、89/743)。其中平均序列数最高的是鲍曼不动杆菌(2607.48)。另外,也检出了一些特殊的病原体,如检出9例鹦鹉热衣原体。真菌感染主要为白色念珠菌(12.38%、92/743),耶氏肺孢子菌(9.02%、67/743)和烟曲霉(7.40%、55/743),其中耶氏肺孢子菌的平均序列数较高(141.86)。另外,也检出了一些特殊的病原体,如检出1例马尔尼菲篮状菌。病毒感染主要为人类β疱疹病毒5型(17.90%、133/743),人类γ疱疹病毒4型(17.36%、129/743),人类β疱疹病毒7型(16.15%、120/743)和人类α疱疹病毒1型(13.59%、101/743),其中平均序列数最高的是人类α疱疹病毒1型(367.27)。寄生虫感染最少,只检出2例多房棘球绦虫,2例广州管圆线虫,2例屋尘螨和1例粉尘螨,以合并细菌和病毒感染为主。共有407例患者检出混合型感染,其中以病毒和细菌混合型感染最多(22.61%、168/743)。不同季节的微生物分布也存在一定的特征。秋冬季检出频数最多的是细菌(鲍曼不动杆菌),春夏季检出频数最多的是病毒(人类γ疱疹病毒4型)。结论肺部感染患者的下呼吸道微生物中,革兰阴性菌以鲍曼不动杆菌和肺炎克雷伯菌为主,革兰阳性菌以肺炎链球菌,屎肠球菌和结核分枝杆菌复合群为主;真菌以白色念珠菌,耶氏肺孢子菌和烟曲霉为主;病毒以人类β疱疹病毒5型,人类γ疱疹病毒4型和人类β疱疹病毒7型为主;寄生虫感染很少,无明显特征;合并感染以细菌感染和细菌病毒混合感染为主;秋冬季和春夏季的微生物特征不同;另外,需要注意特殊的致病微生物,例如鹦鹉热衣原体和马尔尼菲篮状菌等。提示临床医生这些特征可以作为肺部感染病因诊断的参考与依据。

Objective By using metagenomic next-generation sequencing(mNGS),we aimed to analyze the microbes characteristics of lower respiratory tract of patients with pulmonary infection,so as to improve the further understanding of clinical etiological characteristics of patients with pulmonary infection.Methods A total of 840 patients with suspected pulmonary infection were enrolled from August 2020 to October 2021 in West China Hospital of Sichuan University.mNGS was used to detect the microbiome of bronchoalveolar lavage fluid of all patients,and the microbial characteristics of lower respiratory tract of all patients were retrospectively analyzed.Results A total of 840 patients were enrolled,of which 743 were positive for microbiome,with bacterial infection accounting for 35.13%(261/743).Acinetobacter baumannii accounted for 18.98%(141/743),followed by Strep tococcus pneumoniae(14.13%,105/743),Klebsiella pneumoniae(13.46%,100/743),Enterococcus faecium(12.11%,90/743)and Mycobacterium tuberculosis complex(11.98%,89/743).Acinetobacter baumannii had the highest average reads(2607.48).In addition,some specific pathogens were detected,such as 9 cases of Chlamydia psittaci.The main fungal infections were Candida albicans(12.38%,92/743),Pneumocystis jirovecii(9.02%,67/743)and Aspergillus fumigatus(7.40%,55/743),among which the average reads of Pneumocystis jirovecii was higher(141.86)than Candida albicans and Aspergillus fumigatus.In addition,some special pathogens were also detected,such as a case of Talaromyces marneffei.The main viral infections included humanβherpevirus 5(17.90%,133/743),human y herpevirus 4(17.36%,129/743),humanβherpevirus 7(16.15%,120/743)and humanαherpevirus 1(13.59%,101/743),among which the average reads of human herpesvirus type1(367.27)was the highest.Parasitic infection was least,with only 2 cases of Echinococcus multilocularis,2 cases of Angiostrongylus 2 cases of Dermatophagoides pteronyssinus and 1 case of Dermatophagoides farinae,which were mainly infected with bacteria and viruses.In addition,a total of 407 patients were diagnosed with mixed infection,of which virus and bacteria mixed infection was the most(22.61%,168/743).The distribution of microorganisms in different seasons also has certain characteristics.For example,bacteria(Acinetobacter baumannii)were most frequently detected in autumn and winter,while viruses(human gamma-herpesvirus type 4)were most frequently detected in spring and summer.Conclusions In the lower respiratory tract of patients with pulmonary infection,the main gram-negative bacteria are Acinetobacter baumannii and Klebsiella pneumoniae,while the main gram-positive bacteria are Streptococcus pneumoniae,Enterococcus faecium and Mycobacterium tuberculosis complex;the main fungi are Candida albicans,Pneumocystis jirovecii and Aspergillus fumigatus;the main viruses are humanβherpevirus 5,human y herpevirus 4 and humanβherpevirus 7.However,parasites are rarely detected and have no obvious characteristics.Bacterial infection and bacterial virus mixed infection are the main co-infections;the microbial characteristics of autumn and winter are different from those of spring and summer.In addition,attention should be paid to special pathogenic microorganisms,such as Chlamydia psittaci and Talaromyces marneffei.These characteristics could be used as reference and basis for the pathogenic diagnosis of pulmonary infection.