Spottiswoode Natasha, Bloomstein Joshua D, Caldera Saharai, Sessolo Abdul, McCauley Kathryn, Byanyima Patrick, Zawedde Josephine, Kalantar Katrina, Kaswabuli Sylvia, Rutishauser Rachel L, Lieng Monica K, Davis J Lucian, Moore Julia, Jan Amanda, Iwai Shoko, Shenoy Meera, Sanyu Ingvar, DeRisi Joseph L, Lynch Susan V, Worodria William, Huang Laurence, Langelier Charles R
Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA.
Department of Medicine, University of California Davis School of Medicine, Sacramento, CA, USA.
Lancet Microbe. 2022 May;3(5):e357-e365. doi: 10.1016/S2666-5247(21)00357-8. Epub 2022 Mar 25.
Pneumonia is a leading cause of death worldwide and is a major health-care challenge in people living with HIV. Despite this, the causes of pneumonia in this population remain poorly understood. We aimed to assess the feasibility of metatranscriptomics for epidemiological surveillance of pneumonia in patients with HIV in Uganda.
We performed a retrospective observational study in patients with HIV who were admitted to Mulago Hospital, Kampala, Uganda between Oct 1, 2009, and Dec 31, 2011. Inclusion criteria were age 18 years or older, HIV-positivity, and clinically diagnosed pneumonia. Exclusion criteria were contraindication to bronchoscopy or an existing diagnosis of tuberculosis. Bronchoalveolar lavage fluid was collected within 72 h of admission and a combination of RNA sequencing and Mycobacterium tuberculosis culture plus PCR were performed. The primary outcome was detection of an established or possible respiratory pathogen in the total study population.
We consecutively enrolled 217 patients during the study period. A potential microbial cause for pneumonia was identified in 211 (97%) patients. At least one microorganism of established respiratory pathogenicity was identified in 113 (52%) patients, and a microbe of possible pathogenicity was identified in an additional 98 (45%). M tuberculosis was the most commonly identified established pathogen (35 [16%] patients; in whom bacterial or viral co-infections were identified in 13 [37%]). Streptococcus mitis, although not previously reported as a cause of pneumonia in patients with HIV, was the most commonly identified bacterial organism (37 [17%] patients). Haemophilus influenzae was the most commonly identified established bacterial pathogen (20 [9%] patients). Pneumocystis jirovecii was only identified in patients with a CD4 count of less than 200 cells per mL.
We show the feasibility of using metatranscriptomics for epidemiologic surveillance of pneumonia by describing the spectrum of respiratory pathogens in adults with HIV in Uganda. Applying these methods to a contemporary cohort could enable broad assessment of changes in pneumonia aetiology following the emergence of SARS-CoV-2.
US National Institutes of Health, Chan Zuckerberg Biohub.
肺炎是全球主要死因，也是艾滋病毒感染者面临的一项重大医疗保健挑战。尽管如此，这一人群中肺炎的病因仍知之甚少。我们旨在评估宏转录组学用于乌干达艾滋病毒患者肺炎流行病学监测的可行性。
我们对2009年10月1日至2011年12月31日期间入住乌干达坎帕拉穆拉戈医院的艾滋病毒患者进行了一项回顾性观察研究。纳入标准为年龄18岁及以上、艾滋病毒呈阳性且临床诊断为肺炎。排除标准为支气管镜检查禁忌证或现患结核病诊断。在入院72小时内收集支气管肺泡灌洗液，并进行RNA测序与结核分枝杆菌培养加PCR检测。主要结局是在整个研究人群中检测到已确诊或可能的呼吸道病原体。
在研究期间，我们连续纳入了217例患者。211例（97%）患者中确定了肺炎的潜在微生物病因。113例（52%）患者中至少鉴定出一种已确定具有呼吸道致病性的微生物，另有98例（45%）患者鉴定出一种可能具有致病性的微生物。结核分枝杆菌是最常鉴定出的已确诊病原体（35例[16%]患者；其中13例[37%]患者存在细菌或病毒合并感染）。缓症链球菌虽然此前未被报告为艾滋病毒患者肺炎的病因，但却是最常鉴定出的细菌（37例[17%]患者）。流感嗜血杆菌是最常鉴定出的已确诊细菌病原体（20例[9%]患者）。耶氏肺孢子菌仅在CD4细胞计数低于每毫升200个细胞的患者中鉴定出。
我们通过描述乌干达艾滋病毒感染成人呼吸道病原体谱，展示了使用宏转录组学进行肺炎流行病学监测的可行性。将这些方法应用于当代队列研究，能够广泛评估新型冠状病毒出现后肺炎病因的变化。
美国国立卫生研究院、陈·扎克伯格生物中心。
