The bacteriology of pleural infection (TORPIDS): an exploratory metagenomics analysis through next generation sequencing.
The bacteriology of pleural infection (TORPIDS): an exploratory metagenomics analysis through next generation sequencing.
复制标题
DOI：
10.1016/s2666-5247(21)00327-x
复制
发表时间：
2022-04
期刊：
影响因子：
--
通讯作者：
Rahman NM
中科院分区：
文献类型：
--
作者：
Kanellakis NI;Wrightson JM;Gerry S;Ilott N;Corcoran JP;Bedawi EO;Asciak R;Nezhentsev A;Sundaralingam A;Hallifax RJ;Economides GM;Bland LR;Daly E;Yao X;Maskell NA;Miller RF;Crook DW;Hinks TSC;Dong T;Psallidas I;Rahman NM
胸膜感染是一种常见病、多发病、病死率高的严重疾病。胸膜感染细菌学的知识仍然不完整，因为基于培养的病原体检测方法灵敏度不足，并且偏向于选定的微生物。我们设计了一项研究，旨在发现和调查胸膜感染的总微生物组，并评估细菌模式与患者1年生存率之间的相关性。我们评估了来自PILOT研究的243份胸膜液样本，PILOT研究是一项前瞻性观察性胸膜感染研究，采用16 S rRNA下一代测序。使用来自非感染性原因所致胸腔积液患者的20份胸腔液样品和10份PCR级水样品作为对照。使用DADA 2管道进行下游分析。我们应用多变量考克斯回归分析来研究细菌类型和胸膜感染患者1年生存率之间的关系。胸膜感染主要是多种微生物（192/243 [79%]），在单一微生物和多种微生物疾病以及社区获得性和医院获得性感染中观察到不同的细菌频率。混合厌氧菌和其他革兰氏阴性菌占主导地位的社区获得性多微生物感染，而肺炎链球菌流行的单一微生物的情况下。厌氧菌的存在（风险比0.46，95% CI 0.24 - 0.86，p= 0.015）或咽峡炎链球菌组的细菌（0.43，0.19 - 0.97，p= 0.043）与更好的患者生存率相关，而金黄色葡萄球菌的优势（5·80，2·37-14·21，p<0·0001）或优势（3·97，1·20-13·08，p=0·024）与较低的存活率相关。此外，肠杆菌科的优势与较高的死亡风险相关（2·26，1·03-4·93，p=0·041）。胸膜感染主要是多种微生物感染，这解释了大多数人需要广谱抗生素的原因。与金黄色葡萄球菌和肠杆菌科相关的高死亡率感染有利于更积极的，具有更窄谱的抗生素策略。英国医学研究理事会、国家卫生研究院牛津生物医学研究中心、威康信托基金会、牛津郡卫生服务研究委员会、中国医学科学院和约翰·费尔基金会。
Pleural infection is a common and severe disease with high morbidity and mortality worldwide. The knowledge of pleural infection bacteriology remains incomplete, as pathogen detection methods based on culture have insufficient sensitivity and are biased to selected microbes. We designed a study with the aim to discover and investigate the total microbiome of pleural infection and assess the correlation between bacterial patterns and 1-year survival of patients. We assessed 243 pleural fluid samples from the PILOT study, a prospective observational study on pleural infection, with 16S rRNA next generation sequencing. 20 pleural fluid samples from patients with pleural effusion due to a non-infectious cause and ten PCR-grade water samples were used as controls. Downstream analysis was done with the DADA2 pipeline. We applied multivariate Cox regression analyses to investigate the association between bacterial patterns and 1-year survival of patients with pleural infection. Pleural infection was predominately polymicrobial (192 [79%] of 243 samples), with diverse bacterial frequencies observed in monomicrobial and polymicrobial disease and in both community-acquired and hospital-acquired infection. Mixed anaerobes and other Gram-negative bacteria predominated in community-acquired polymicrobial infection whereas Streptococcus pneumoniae prevailed in monomicrobial cases. The presence of anaerobes (hazard ratio 0·46, 95% CI 0·24–0·86, p=0·015) or bacteria of the Streptococcus anginosus group (0·43, 0·19–0·97, p=0·043) was associated with better patient survival, whereas the presence (5·80, 2·37–14·21, p<0·0001) or dominance (3·97, 1·20–13·08, p=0·024) of Staphylococcus aureus was linked with lower survival. Moreover, dominance of Enterobacteriaceae was associated with higher risk of death (2·26, 1·03–4·93, p=0·041). Pleural infection is a predominantly polymicrobial infection, explaining the requirement for broad spectrum antibiotic cover in most individuals. High mortality infection associated with S aureus and Enterobacteriaceae favours more aggressive, with a narrower spectrum, antibiotic strategies. UK Medical Research Council, National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust, Oxfordshire Health Services Research Committee, Chinese Academy of Medical Sciences, and John Fell Fund.