The lung microbiome of Ugandan HIV-infected pneumonia patients is compositionally and functionally distinct from that of San Franciscan patients
Open accessAbstract
Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome was significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population.
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These features of bacterial pneumonia correlate tightly with multiple indices of host inflammation, including alveolar neutrophilia and high alveolar concentrations of catecholamines and TNF-α.
“These features correlate tightly with multiple indices of host inflammation, including alveolar neutrophilia93 and high alveolar concentrations of catecholamines50 and TNF-α.”
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- Authors
- Iwai, S., Huang, D., Fong, S., Jarlsberg, L. G., Worodria, W., Yoo, S., Cattamanchi, A., Davis, J. L., Kaswabuli, S., Segal, M., Huang, L., & Lynch, S. V.
- Affiliations
- University of California, San Francisco (US)
- Mulago Hospital (UG)
- Corresponding author
- Lynch, Susan V.
- ORCID
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-04-21
- Volume
- 9
- Issue
- 4
- Pages
- e95726
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3994144
- OpenAlex
- W2006001174
- Cited by
- 58
- References
- 26
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 3 · 2022: 4 · 2021: 2 · 2020: 6 · 2019: 7 · 2018: 8 · 2017: 5 · 2016: 6 · 2015: 10 · 2014: 3
- FWCI
- 3.28
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Funders
- National Institutes of Health
- National Heart, Lung, and Blood Institute (HL098964, K24HL087713, HL090335-02S109, HL087713, U01HL098964, R01HL090335)
- National Institute of Allergy and Infectious Diseases (U01AI075410, AI075410)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Epidemiology › Pneumonia and Respiratory Infections
- Life Sciences › Immunology and Microbiology › Microbiology › Microbial infections and disease research
- Keywords
- lung microbiome, HIV infection, pneumonia, lower airway microbiota, Pseudomonas aeruginosa, Lachnospiraceae, sulfur-reducing bacteria, TNF-α, MMP-9, bacterial load, 16S rRNA gene profiling, Ugandan patients, cross-population comparison, secretion systems
- MeSH terms
- Adult, Aged, Aged, 80 and over, Female, Humans, Lung, Male, Middle Aged, Pneumonia, Pseudomonas aeruginosa, San Francisco, Uganda, HIV Infections, Young Adult, Microbiota
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