Distribution characteristics of pathogens in patients with community-acquired pneumonia were detected by metagenomic sequencing
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摘要: 目的 利用宏基因组二代测序(mNGS)检测社区获得性肺炎(CAP)患者的感染病原体，分析其分布特征，为此类患者初始经验性抗感染策略的制定提供依据。方法 分析2020年7月-2022年2月我院呼吸内科、ICU收治的CAP患者痰液及支气管肺泡灌洗液的mNGS结果，归纳此类患者的病原体种类特征。结果 共纳入45例患者，mNGS检出阳性患者44例，细菌检出率最高(33/45，73.33%)，其次为病毒(22/45，48.89%)、非典型病原体(12/45，26.67%)、真菌(6/45，13.33%)及分枝杆菌(2/45，4.44%)。入选患者中，CAP 20例(CAP组)，重症社区获得性肺炎(SCAP)25例(SCAP组)，两组患者呈现出与总体情况相似的病原学分布特征。结论 利用mNGS技术检测到CAP患者非典型病原体占比有增高趋势，特别是SCAP患者，在初始经验性选择抗生素时应考虑覆盖G-、G+细菌及非典型病原体。Abstract: Objective Detect infectious pathogens in patients with community-acquired pneumonia(CAP) by metagenomic sequencing (mNGS), and to analyze their distribution characteristics, so as to provide evidence for the development of initial empirical anti-infection strategies for these patients.Methods mNGS results of sputum and bronchoalveolar lavage fluid from patients with CAP admitted to the Department of Respiratory Medicine and ICU of Daxing Hospital, Capital Medical University from July 2020 to February 2022 were analyzed, and the pathogen characteristics of these patients were summarized.Results A total of 45 patients were included in the study, of which 44 were positive for mNGS, with the highest bacterial detection rate(33/45, 73.33%). The second was virus(22/45, 48.89%), atypical pathogen(12/45, 26.67%), fungus(6/45, 13.33%) and mycobacterium(2/45, 4.44%). There were 20 cases of CAP and 25 cases of severe community-acquired pneumonia(SCAP). The etiological distribution characteristics of the two groups were similar to the general situation.Conclusion The proportion of atypical pathogens in patients with CAP was increased by mNGS technique, especially in patients with SCAP. The coverage of G-, G+ bacteria and atypical pathogens should be considered in the initial empiric antibiotic selection.
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表 1 两组患者mNGS检测出菌株数及占比
例(%) 类型 CAP组(20例) SCAP组(25例) 合计(45例) 细菌 肺炎克雷伯菌 1(5.00) 10(40.00) 11(24.44) 金黄色葡萄球菌 2(10.00) 6(24.00) 8(17.78) 肺炎链球菌 2(10.00) 4(16.00) 6(13.33) 流感嗜血杆菌 3(15.00) 3(12.00) 6(13.33) 屎肠球菌 0 3(12.00) 3(6.67) 惠尔普养障体 1(5.00) 3(12.00) 4(8.89) 铜绿假单鲍菌 3(15.00) 2(8.00) 5(11.11) 鲍曼不动杆菌 1(5.00) 2(8.00) 3(6.67) 嗜麦芽窄食假单鲍菌 0 2(8.00) 2(4.44) 粪肠球菌 0 2(8.00) 2(4.44) 成团泛菌 0 1(4.00) 1(2.22) 医院不动杆菌 0 1(4.00) 1(2.22) 大肠埃希菌 0 1(4.00) 1(2.22) 乳明串珠菌 0 1(4.00) 1(2.22) 纹带棒状杆菌 0 1(4.00) 1(2.22) 非典型病原体 嗜肺军团菌 0 5(20.00) 5(11.11) 鹦鹉热衣原体 5(25.00) 2(8.00) 7(15.56) 病毒 EBV 8(40.00) 6(24.00) 14(31.11) HSV1 3(15.00) 5(2.000) 8(17.78) HHV7 1(5.00) 4(16.00) 5(11.11) CMV 1(5.00) 3(12.00) 4(8.89) HHV6 0 3(12.00) 3(6.67) TTV 1(5.00) 0 1(2.22) 真菌 卡氏肺孢子菌 1(5) 2(8) 3(6.67) 黄曲霉 1(5) 1(4) 2(4.44) 黑曲霉 1(5) 0 1(2.22) 烟曲霉 1(5) 0 1(2.22) 特殊菌 结核分枝杆菌 0 1(4) 1(2.22) 蟾蜍分枝杆菌 1(5) 0 1(2.22) 菌株总数/株 37 74 111 
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表 2 CAP组及SCAP组混合感染情况
例 感染类型 CAP组 SCAP组 合计 细菌+病毒 4 9 13 细菌+真菌+病毒 0 3 3 细菌+衣原体 1 2 3 衣原体+病毒 1 0 1 真菌+病毒 2 0 2 合计/例(%) 8(40.00) 14(56.00) 22(48.89)
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