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

靶向下一代测序可增强乌干达感染艾滋病毒的脓毒症成人中结核分枝杆菌和高影响细菌病原体的检测和基因组特征

• 批准号: 10116263
• 负责人: Max O'Donnell
• 金额: $ 28.25万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-03-01 至 2024-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10116263
• 关键词: Address; Adopted; Adult; Affect; Africa; Africa South of the Sahara; Antimicrobial Resistance; Applications Grants; Autopsy; Bacteremia; Bacteria; Bacterial Antibiotic Resistance; Biological Assay; Blood; Blood specimen; Caring; Cessation of life; Characteristics; Clinical; Clinical Data; Clinical Research; Collaborations; Country; Critical Illness; DNA; Data; Detection; Diagnosis; Diagnostic; Disease; Drug resistance; Drug resistance in tuberculosis; Etiology; Genomics; Goals; HIV; HIV Infections; HIV-infected adolescents; HIV/TB; High Prevalence; High-Throughput Nucleotide Sequencing; Human; Immunity; In Vitro; Incidence; Infection; Laboratories; Medicine; Methods; Molecular; Morbidity - disease rate; Mycobacterium tuberculosis; Nested Case-Control Study; Nucleic Acids; Organism; Pathogenicity; Pathway interactions; Patients; Performance; Population; Prevalence; Prospective Studies; Prospective cohort; Reaction; Reference Standards; Research Institute; Resistance; Resolution; Resources; Reverse Transcriptase Polymerase Chain Reaction; Rifampicin resistance; Role; Sampling; Scientist; Sensitivity and Specificity; Sepsis; Sputum; Testing; Time; Translational Research; Tuberculosis; Uganda; Universities; Virus; Work; accurate diagnosis; biobank; case control; college; design; detection limit; detection sensitivity; diagnostic accuracy; diagnostic platform; drug resistant pathogen; emerging pathogen; experimental study; genomic biomarker; improved; innovation; molecular diagnostics; mortality; next generation; next generation sequencing; non-tuberculosis mycobacteria; novel; novel diagnostics; pathogen; pathogenic bacteria; peripheral blood; point-of-care diagnostics; priority pathogen; resistance gene; septic patients; sequencing platform; tuberculosis diagnostics; tuberculosis drugs

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.

项目摘要 在过去的二十年中，分散结核分枝杆菌（MTB）越来越多 被认为是艾滋病毒感染的败血症患者高 - 负担结核病（TB）/HIV环境。在这些情况下，MTB菌血症中估计的患病率 患有败血症的艾滋病毒感染的成年人高达40％，死亡率接近50％。尽管很高 患病率和死亡率，及时，准确诊断MTB菌血症和伴随的结核病药物 阻力仍然具有挑战性，并且经常被诊断出验证后。需要新颖的诊断策略 快速鉴定和治疗患有MTB菌血症和其他严重血液的重症患者 高负TB/HIV设置中的感染。这项研究的总体目标是增强快速分子检测 通过使用 创新的，高度敏感的下一代测序方法。我们建议利用一种新颖的积极 - 选择核酸富集和高通量测序平台（Baccapseq）以检测MTB 菌血症和抗药性生物，在长凳上进行了优化，并在嵌套的病例对照研究中进行了试验 乌干达与艾滋病毒相关的败血症。具体而言，我们将评估Baccapseq和新兴的性能， 用于检测和表征MTB菌血症的近点诊断（XPERT MTB/RIF ULTRA） 使用来自HIV感染的成年人的前瞻性队列的生物群样本和MTB耐药性 乌干达的败血症（目标1）；并识别和表征高优先性，抗生素耐药性细菌病原体 乌干达没有MTB感染的HIV感染患者与败血症有关（AIM 2）。结束 这项工作我们将解决严重的HIV/TB疾病的关键诊断差距，同时提供高 与败血症相关的病原体和抗菌抗性的分辨率基因组表征 全世界的HIV感染青少年和成年人的频繁死亡途径。