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Value of Biofire Filmarray Pneumonia Panel in Evaluating Secondary Infection in Critically Ill Patients with Coronavirus Disease 2019
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摘要:
目的 探讨Biofire Filmarry下呼吸道试剂盒(pneumonia panel, PN)在危重症COVID-19继发感染患者中的应用效果。 方法 回顾性分析2020年2月至4月武汉同济医院中法新区ICU危重症COVID-19患者的临床资料。经支气管镜获取患者肺泡灌洗液后分别送检Biofire Filmarray PN/普通培养，比较两种方法的检测结果，并计算其一致率。 结果 共21例符合纳入标准的危重症COVID-19患者入选本研究，送检下呼吸道标本54份，包括Biofire Filmarray PN组21例患者33份(61.1%)标本、普通培养组14例患者21份(38.9%)标本，其中19对(共38份)为两种方法“背靠背”送检。Biofire Filmarray PN组结果回报时间约为1 h，20例患者32份(97.0%)阳性标本，检出病原体74例次，其中鲍曼不动杆菌复合体29例次(39.2%)，铜绿假单胞菌21例次(28.4%)，肺炎克雷伯菌16例次(21.6%)，大肠杆菌5例次(6.8%)，阴沟肠杆菌、流感嗜血杆菌及呼吸道合胞病毒各1例次(1.4%)。普通培养组结果回报时间约为3 d，11例患者16份(76.2%)阳性标本，检出病原体19例次，其中为铜绿假单胞菌8例次(42.1%)，鲍曼不动杆菌6例次(31.6%)，嗜麦芽窄食单胞菌4例次(21.1%)，粘金黄杆菌1例次(5.3%)。19对“背靠背”送检标本中，Biofire Filmarray PN组和普通培养组结果吻合者为15对，一致率为78.9%。 结论 危重症COVID-19患者易继发感染，病原体以鲍曼不动杆菌复合体、铜绿假单胞菌多见。Biofire Filmarray PN可用于此类患者的下呼吸道病原学诊断，具有回报速度快的优势，但其灵敏度需大样本研究进一步验证。 Abstract:Objective To explore the application value of Biofire Filmarry pneumonia panel (PN) in detection of secondary and concomitant pathogen among critically ill patients with coronavirus disease 2019(COVID-19). Methods We consecutively included and analyzed the clinical data of critically ill patients with COVID-19 transferred to the ICU from February to April 2020 in the Sino-French Campus of Wuhan Tongji Hospital. Samples of Bronchoalveolar lavage fluid obtained by bedside bronchoscopy were sent for Biofire Filmarray PN and standard culture concomitantly. We compared the results of two methods and evaluated their concordance. Results In total, 21 critically ill patients with COVID-19 were included and 54 samples were tested, including 33 (61.1%) Biofire Filmarray PN tests (21 patients) and 21 (38.9%) standard cultures (14 patients), in which 19 pairs (38 samples) underwent both tests simultaneously. In Biofire Filmarray PN group, the turnaround time was about 1 hour. There were 74 positive results in 32 samples (97.0%) from 20 patients, including 29 cases(39.2%) of Acinetobacter baumannii complex, 21 cases (28.4%) of Pseudomonas aeruginosa, 16 cases (21.6%)of Klebsiella pneumoniae, 5 cases (6.8%) of Escherichia coli, 1 case (1.4%)each of Enterobacter cloacae, Haemophilus influenzae, and respiratory syncytial virus. In the standard culture group, the turnaround time was about 3 days. 19 positive results returned in 16 (76.2%) samples from 11 patients, including 8 cases (42.1%) of Pseudomonas aeruginosa, 6 cases (31.6%) of Acinetobacter baumannii, 4 cases (21.1%) of Stenotrophomonas malt and 1 case (5.3%) of Myxobacterium. Among the 19 pairs of "back-to-back" specimens, 15 pairs were concordant, and the agreement ratio was 78.9%. Conclusions Acinetobacter baumannii and Pseudomonas aeruginosa may be the common pathogens of secondary or concomitant infection in critically ill patients with COVID-19. Biofire Filmarray PN is a rapid diagnostic test and has application value in such patients; its sensitivity and accuracy require further investigation with larger sample sizes. 作者贡献：范俊平、肖盟负责撰写并修改论文；徐英春、王京岚负责研究设计，修改论文；陈雨、张栋负责Biofire Filmarray PN的检测和数据整理；赵静、杨燕丽、孙雪峰、夏鹏参与标本采集、送检和临床信息整理；赵颖、柯帆航参与伦理申请和部分文稿撰写。利益冲突 无范俊平、肖盟对本文同等贡献 -
表 1 Biofire Filmarray下呼吸道试剂盒检测靶标分类
类别 种属 细菌(半定量)* 钙不动杆菌-鲍曼不动杆菌复合体
阴沟肠杆菌复合体
大肠杆菌
嗜血杆菌流感
产气克雷伯菌
产酸克雷伯菌
肺炎克雷伯菌
卡他莫拉菌
变形杆菌属
铜绿假单胞菌
粘质沙雷氏菌
金黄色葡萄球菌
无乳链球菌
肺炎链球菌
化脓性链球菌病毒(定性) 甲型流感
乙型流感
腺病毒
冠状病毒
副流感病毒
呼吸道合胞病毒
人鼻病毒/肠病毒
人间质肺病毒
MERS冠状病毒非典型细菌(定性) 嗜肺军团菌
肺炎支原体
肺炎衣原体抗生素耐药基因 CTX-M#
KPC#
NDM#
OXA-48-like?
VIM#
IMP*
mecA/mecC和MREJ·*以104/105/106/≥107拷贝/mL的形式报告；#同时检测到钙不动杆菌-鲍曼不动杆菌复合体、阴沟肠杆菌复合体、大肠杆菌、产气克雷伯菌、产酸克雷伯菌、肺炎克雷伯菌、变形杆菌属、铜绿假单胞菌或粘质沙雷氏菌时报告；†同时检测到阴沟肠杆菌复合体、大肠杆菌、产气克雷伯菌、产酸克雷伯菌、肺炎克雷伯菌、变形杆菌属或粘质沙雷氏菌时报告；&同时检测到金黄色葡萄球菌时报告；MERS：中东呼吸综合征 
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表 2 Biofire Filmarray PN组下呼吸道标本病原体回报结果半定量分析(n)
病原体* ≥107
拷贝数/mL106
拷贝数/mL105
拷贝数/mL104
拷贝数/mL鲍曼不动杆菌复合体 15 6 3 5 铜绿假单胞菌 10 5 6 0 肺炎克雷伯菌 1 5 4 6 大肠杆菌 2 2 0 1 阴沟肠杆菌 0 0 1 0 流感嗜血杆菌 0 0 0 1 *另检出呼吸道合胞病毒1例次；Biofire Filmarray PN：Biofire Filmarray下呼吸道试剂盒
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表 3 普通培养组下呼吸道标本病原体回报结果半定量分析(n)
病原体 +++ ++ + 嗜麦芽窄食单胞菌 2 2 0 粘金黄杆菌 1 0 0 铜绿假单胞菌 3 5 0 鲍曼不动杆菌 4 1 1
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表 4 Biofire Filmarray PN组和普通培养组结果一致性评价
序号 Biofire Filmarray PN组 普通培养组 病原体吻合性 回报结果 拷贝数/mL 回报结果 菌量 1 铜绿假单胞菌 ≥107 铜绿假单胞菌 +++ 一致 2 鲍曼不动杆菌 106 鲍曼不动杆菌 +++ 一致 3 铜绿假单胞菌 ≥107 铜绿假单胞菌 ++ 一致 4 呼吸道合胞病毒 - 阴性 - 一致 5 大肠杆菌 ≥107 嗜麦芽窄食单胞菌 ++ 不一致 6 铜绿假单胞菌 106 铜绿假单胞菌 ++ 一致 7 阴性 - 阴性 - 一致 8 铜绿假单胞菌 ≥107 阴性 - 不一致 9 鲍曼不动杆菌 ≥107 阴性 - 不一致 10 鲍曼不动杆菌 ≥107 鲍曼不动杆菌 ++ 一致 11 铜绿假单胞菌 106 阴性 - 不一致 12 铜绿假单胞菌 ≥107 铜绿假单胞菌 ++ 一致 13 铜绿假单胞菌 ≥107 铜绿假单胞菌 +++ 一致 14 鲍曼不动杆菌 ≥107 鲍曼不动杆菌 +++ 一致 粘金黄杆菌 +++ 15 鲍曼不动杆菌 ≥107 鲍曼不动杆菌 + 一致 铜绿假单胞菌 16 铜绿假单胞菌 ≥107 铜绿假单胞菌 +++ 一致 17 铜绿假单胞菌 ≥107 铜绿假单胞菌 ++ 一致 18 铜绿假单胞菌 106 铜绿假单胞菌 ++ 一致 19 鲍曼不动杆菌 ≥107 鲍曼不动杆菌 +++ 一致 嗜麦芽窄食单胞菌 +++ Biofire Filmarray PN：同表 2
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