Primary and secondary outcomes.

Introduction Infection causes a vast burden of disease, with significant mortality, morbidity and costs to health-care systems. However, identifying the pathogen causative infection can be challenging, resulting in high use of broad-spectrum antibiotics, much of which may be inappropriate. Novel metagenomic methods have potential to rapidly identify pathogens, however their clinical utility for many infections is currently unclear. Outcome from infection is also impacted by the effectiveness of immune responses, which can be impaired by age, co-morbidity and the infection itself. The aims of this study are twofold: To compare diversity of organisms identified and time-to-result using metagenomic methods versus traditional culture -based techniques, to explore the potential clinical role of metagenomic approaches to pathogen identification in a range of infections. To characterise the ex vivo function of immune cells from patients with acute infection, exploring host and pathogen-specific factors which may affect immune function and overall outcomes. Methods This is a prospective observational study of patients with acute infection. Patients with symptoms suggestive of an acute infection will be recruited, and blood and bodily fluid relevant to the site of infection collected (for example, sputum and naso-oropharyngeal swabs for respiratory tract infections, or urine for a suspected urinary tract infection). Metagenomic analysis of samples will be compared to traditional microbiology, alongside the antimicrobials received. Blood and respiratory samples such as bronchoalveolar lavage will be used to isolate immune cells and interrogate immune cell function. Where possible, similar samples will be collected from matched participants without a suspected infection to determine the impact of infection on both microbiome and immune cell function.前言 感染性疾病可造成沉重的疾病负担，伴随高死亡率、高发病率，并给医疗体系带来巨额成本支出。然而，精准识别引发感染的病原体颇具挑战，这会导致广谱抗生素的大量使用，其中多数可能并不合理。新型宏基因组（metagenomic）检测技术具备快速识别病原体的潜力，但目前其在多数感染性疾病中的临床应用价值尚不明确。感染的转归还会受到免疫应答有效性的影响，而年龄、合并症以及感染本身均可削弱免疫应答功能。本研究旨在达成双重目标： 其一，对比宏基因组检测技术与传统培养技术在检出微生物多样性及检测耗时上的差异，探究宏基因组方法在多类感染性病原体识别中的潜在临床应用价值； 其二，分析急性感染患者体内免疫细胞的体外（ex vivo）功能，探索可能影响免疫功能及整体转归的宿主与病原体特异性因素。 方法 本研究为一项针对急性感染患者的前瞻性观察性研究。将招募出现急性感染相关症状的患者，并采集感染部位对应的血液及体液样本：例如呼吸道感染患者留取痰液与鼻咽拭子，疑似尿路感染患者留取尿液样本。将对样本开展宏基因组分析，并与传统微生物学检测结果、患者所用抗菌药物情况进行对比分析。将采集血液及呼吸道样本（如支气管肺泡灌洗液（bronchoalveolar lavage））以分离免疫细胞并分析其功能。在条件允许的情况下，还将从匹配的无感染疑似人群中采集同类样本，以明确感染对微生物组及免疫细胞功能的影响。