Pub Date : 2021-05-01DOI: 10.1164/AJRCCM-CONFERENCE.2021.203.1_MEETINGABSTRACTS.A1220
C. Barnett, I. Sulaiman, J. Tsay, Benjamin G. Wu, K. Krolikowski, Yonghua Li, R. Postelnicu, J. Carpenito, S. Rafeq, J. Clemente, L. Angel, V. Mukherjee, D. Pradhan, S. Brosnahan, A. Lubinsky, S. Yeung, G. Jour, G. Shen, M. Chung, K. Khanna, E. Ghedin, L. Segal
RATIONALE:Secondary infections with bacterial pathogens are thought to be responsible for poor outcomes in the 1918 Spanish and H1N1 pandemics. We postulate that poor prognosis in patients with SARS-CoV2 may be associated with uncontrollable viral replication, co-infection with a secondary pathogen, and over exuberant host immune response. We seek to evaluate whether there is an association between distinct features of the lower airway microbiota and poor clinical outcome in patients with SARS-CoV2. METHODS:We collected lower airway samples in 148 patients from NYU admitted between 3/10/2020 and 5/10/2020 with severe respiratory failure requiring mechanical ventilation and that underwent bronchoscopy for airway clearance and/or tracheostomy. Clinical outcome was defined as dead vs alive. DNA was isolated in parallel using zymoBIOMICS™ DNA/RNA Miniprep Kit (Cat: R2002) as per manufacturer's instructions. The V4 region of the 16S rRNA gene marker was sequenced using Illumina MiSeq. Sequences were analyzed using the Quantitative Insights into Microbial Ecology (QIIME version 1.9.1) pipeline. Total bacterial load was evaluated in lower airway samples using digital droplet PCR targeting the 16S rRNA gene. RESULTS:Of the 148 patients included, 114 survived (77%) and 34 (23%) died. Among those with poor clinical outcome, there was a non-statistically significant trend towards higher age and BMI. Patients who died more commonly had chronic kidney disease and prior cerebrovascular accidents, and more often required dialysis. There was no statistically significant difference in the rate of positive bacterial respiratory or blood cultures among those that survived vs. those that died (75 vs. 73% and 43 vs 38%, respectively). Topographical analysis of the 16S RNA microbiome shows compositional differences between the upper and lower airways based on β diversity comparisons. When comparing across clinical outcomes, the α diversity was lower in the dead group but there was no statistically significant difference in overall community composition (β diversity). Taxonomic differential enrichment analysis using DESeq analysis showed that oral commensals were enriched in the group that survived. Patients that died had a higher bacterial load in their lower airways than those who survived. CONCLUSION:Using samples obtained via bronchoscopy we identified lower airway microbiota signatures associated with mortality among critical patients infected with SARS-CoV2. Taxonomic signals identified as associated with poor prognosis did not reveal bacterial taxa commonly classified as respiratory pathogens. This data is not supportive of the hypothesis that secondary untreated bacterial co-infections are responsible for increased mortality in patients with severe SARS-CoV-2.
理由:细菌性病原体的继发性感染被认为是导致1918年西班牙流感和H1N1流感大流行的不良后果的原因。我们推测，SARS-CoV2患者预后不良可能与病毒复制不可控、与继发病原体共感染以及宿主免疫反应过度有关。我们试图评估下气道微生物群的不同特征与SARS-CoV2患者的不良临床结局之间是否存在关联。方法:我们收集了2020年10月3日至2020年10月5日期间入院的148名需要机械通气的严重呼吸衰竭患者的下气道样本，这些患者接受了支气管镜检查以清除气道和/或气管造口术。临床结果定义为死亡vs存活。按照制造商的说明，使用zymoBIOMICS™DNA/RNA迷你试剂盒(Cat: R2002)平行分离DNA。采用Illumina MiSeq对16S rRNA基因标记的V4区进行测序。序列分析使用Quantitative Insights into Microbial Ecology (QIIME version 1.9.1)管道。采用针对16S rRNA基因的数字液滴PCR方法评估下气道样本中的细菌总负荷。结果:纳入的148例患者中，114例(77%)存活，34例(23%)死亡。在临床结果较差的患者中，年龄和BMI升高的趋势无统计学意义。死亡的患者通常患有慢性肾脏疾病和既往脑血管事故，并且更经常需要透析。存活患者与死亡患者的呼吸道细菌或血液培养阳性率无统计学差异(分别为75%对73%和43%对38%)。16S RNA微生物组的地形分析显示基于β多样性比较的上、下气道的组成差异。当比较临床结果时，死亡组的α多样性较低，但总体群落组成(β多样性)无统计学差异。利用DESeq分析进行分类差异富集分析，发现存活组口腔共生体富集。死亡患者的下呼吸道细菌负荷高于存活患者。结论:通过支气管镜检查获得的样本，我们确定了与SARS-CoV2感染危重患者死亡率相关的下气道微生物群特征。与不良预后相关的分类信号没有显示通常归类为呼吸道病原体的细菌分类群。这一数据不支持继发性未经治疗的细菌合并感染导致严重SARS-CoV-2患者死亡率增加的假设。
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Pub Date : 2021-05-01DOI: 10.1164/AJRCCM-CONFERENCE.2021.203.1_MEETINGABSTRACTS.A1221
Fransiskus Xaverius Ivan, M. M. Aogáin, N. M. Ali, T. Poh, P. Y. Tiew, M. I. Setyawati, D. Bello, P. Demokritou, K. Ng, S. H. Chotirmall
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