Targeted next-generation sequencing to enhance detection and genomic characterization of Mycobacterium tuberculosis and high-impact bacterial pathogens among HIV-infected adults with sepsis in Uganda

项目摘要 在过去的二十年里，播散性结核分枝杆菌(MTB)的发病率越来越高 被认为是感染HIV的脓毒症患者发生致命血流感染的主要原因 给全世界的结核病(TB)/艾滋病毒环境造成负担。在这些情况下，估计#年结核分枝杆菌菌血症的患病率 感染艾滋病毒的成年人出现败血症的比例高达40%，死亡率接近50%。尽管很高 结核分枝杆菌菌血症及相关药物的患病率和死亡率、及时准确诊断 耐药性仍然具有挑战性，通常在尸检后被诊断出来。需要新的诊断策略来 加快对合并结核杆菌菌血症和其他严重血流的危重病人的识别和治疗 高负担结核病/艾滋病毒环境中的感染。这项研究的总体目标是提高快速分子检测 结核分枝杆菌和其他高影响细菌病原体在HIV感染的成人脓毒症中的应用 创新的、高度敏感的下一代测序方法。我们建议利用一种新的积极的- 核酸浓缩高通量测序平台(BacCapSeq)检测结核分枝杆菌 菌血症和耐药微生物，在试验台上进行优化，并在嵌套病例对照研究中试验 乌干达的艾滋病毒相关败血症。具体地说，我们将评估BacCapSeq和Emerging， 近点诊断法(Xpert MTB/RIF Ultra)用于检测和表征结核分枝杆菌菌血症 使用来自预期HIV感染成人队列的生物库样本和MTB耐药性 乌干达的败血症(目标1)；以及确定和表征高度优先的、具有抗生素耐药性的细菌病原体 在乌干达，未感染结核杆菌的艾滋病毒感染者与败血症有关(目标2)。在……结束时 这项工作我们将解决严重艾滋病毒/结核病的关键诊断差距，同时提供 与脓毒症相关的病原菌和抗菌素耐药性的基因组特征解析 世界各地感染艾滋病毒的青少年和成年人经常死亡。

Project Summary Over the past two decades, disseminated Mycobacterium tuberculosis (MTB) has been increasingly recognized as the leading cause of fatal bloodstream infection in HIV-infected patients with sepsis in high- burden tuberculosis (TB)/HIV settings worldwide. In these settings, estimated prevalence of MTB bacteremia in HIV-infected adults presenting with sepsis is as high as 40% with mortality approaching 50%. Despite high prevalence and mortality, timely and accurate diagnosis of MTB bacteremia and concomitant TB drug resistance remains challenging and is often diagnosed post-mortem. Novel diagnostic strategies are needed to expedite identification and treatment of critically ill patients with MTB bacteremia and other severe bloodstream infections in high-burden TB/HIV settings. The overall goal of this study is to enhance rapid molecular detection of MTB and other high-impact bacterial pathogens among HIV-infected adults with sepsis through use of an innovative, highly sensitive next-generation sequencing approach. We propose to utilize a novel positive- selection nucleic acid enrichment and high-throughput sequencing platform (BacCapSeq) to detect MTB bacteremia and drug-resistant organisms, optimized at the bench and trialed in a nested case control study of HIV-associated sepsis in Uganda. Specifically, we will evaluate the performance of BacCapSeq and emerging, near-point-of-care diagnostics (Xpert MTB/RIF Ultra) for the detection and characterization of MTB bacteremia and MTB drug resistance using biobanked samples from a prospective cohort of HIV-infected adults with sepsis in Uganda (Aim 1); and identify and characterize high-priority, antibiotic-resistant bacterial pathogens associated with sepsis in HIV-infected patients without MTB infection in Uganda (Aim 2). At the conclusion of this work we will have addressed critical diagnostic gaps for severe HIV/TB disease while providing high- resolution genomic characterization of pathogens and antimicrobial resistance associated with sepsis, a frequent pathway to death for HIV-infected adolescents and adults worldwide.