Evidence map›Paper›PMID 35544096›Full record

Observational studyThe Lancet. Microbe2022

Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study.

Natasha Spottiswoode, Joshua D Bloomstein, Saharai Caldera, Abdul Sessolo, Kathryn McCauley, Patrick Byanyima, Josephine Zawedde, Katrina Kalantar, Sylvia Kaswabuli, Rachel L Rutishauser and 12 more

Open access · goldAbstract readObservational Study
PubMed Full text at PMC Publisher
In one paragraph

Observational study in The Lancet. Microbe, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed, 1 pooled it
2.2field-weighted citation impact, top 12% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed, 1 synthesis or guideline pooled it, 14 citations in OpenAlex.

  1. Pooled it
  2. Article
  3. Observational
  4. Article
  5. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

22 authors at 5 institutions in 2 countries.

Natasha SpottiswoodeDepartment of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA.
Joshua D BloomsteinDepartment of Medicine, University of California Davis School of Medicine, Sacramento, CA, USA.
Saharai CalderaDivision of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
Abdul SessoloInfectious Disease Platform, Makerere University, Kampala, Uganda.
Kathryn McCauleyDivision of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA.
Patrick ByanyimaInfectious Disease Platform, Makerere University, Kampala, Uganda.
Josephine ZaweddeInfectious Disease Platform, Makerere University, Kampala, Uganda.
Katrina KalantarChan Zuckerberg Initiative, Redwood City, CA, USA.
Sylvia KaswabuliInfectious Disease Platform, Makerere University, Kampala, Uganda.
Rachel L RutishauserDepartment of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA.
Monica K LiengDepartment of Medicine, University of California Davis School of Medicine, Sacramento, CA, USA.
J Lucian DavisDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health and Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA.
Julia MooreDivision of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA.
Amanda JanDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health and Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA.
Shoko IwaiDivision of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA.
Meera ShenoyDivision of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA.
Ingvar SanyuInfectious Disease Platform, Makerere University, Kampala, Uganda.
Joseph L DeRisiDepartment of Biochemistry, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
Susan V LynchDivision of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA.
William WorodriaInfectious Disease Platform, Makerere University, Kampala, Uganda.
Laurence HuangDivision of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA.
Charles R LangelierDepartment of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA. Electronic address: chaz.langelier@ucsf.edu.
University of California, San Francisco · USMakerere University · UGChan Zuckerberg Initiative (United States) · USUniversity of California, Davis · USYale University · US

Funding

Inflammation, Aging, Microbes, Obstructive Lung Disease and Diffusion Abnormalities (I AM OLD-DA) Study - Diversity SupplementR01HL128156 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HUANG, LAURENCE, HUNT, PETER W · 2015 to 2024
$7.1M
Microbial Pathogenesis and Host DefenseT32AI060537 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Joanne N. Engel · 2004 to 2026
$6.5M
International HIV-associated Opportunistic Pneumonias (IHOP) StudyR01HL090335 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HUANG, LAURENCE · 2007 to 2011
$4.0M
Lung Microbiome in Cohorts of HIV-Infected Persons (Lung MicroCHIP) StudyU01HL098964 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HUANG, LAURENCE · 2009 to 2013
$3.9M
Integrated Analysis of Microbial and Genomic data in Obstructive Lung Disease (I AM GOLD) StudyR01HL143998 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHRISTENSON, STEPHANIE A, HUANG, LAURENCE · 2019 to 2022
$3.2M
Patient-Oriented Research and Mentoring in PneumocystisK24HL087713 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HUANG, LAURENCE · 2006 to 2018
$1.8M
Integrated Host/Microbe (IHM) Metagenomics of the Lower Airway to Diagnose PediatricRespiratory Infections, Identify Etiologic Pathogens, and Predict OutcomesR01AI182308 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Charles Langelier, Peter Michael Mourani · 2025 to 2026
$1.6M
NHLBI NIH HHS R01 HL090335NHLBI NIH HHS R01 HL128156NIAID NIH HHS R01 AI182308NIAID NIH HHS T32 AI060537
6 · The paper itself

Abstract

backgroundPneumonia 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.

methodsWe 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.

findingsWe 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.

interpretationWe 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.

fundingUS National Institutes of Health, Chan Zuckerberg Biohub.

Indexed as

COVID-19HIV InfectionsPneumoniaAdolescentAdultCross-Sectional StudiesHumansSARS-CoV-2UgandaUnited States

Identifiers

PMID35544096
PMCPMC12193104
OpenAlexW4220886591

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.