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PLoS One. 2014 Apr 21;9(4):e95726. doi: 10.1371/journal.pone.0095726. eCollection 2014.

The lung microbiome of Ugandan HIV-infected pneumonia patients is compositionally and functionally distinct from that of San Franciscan patients.

Author information

1
Division of Gastroenterology, University of California San Francisco, San Francisco, California, United States of America.
2
Division of Gastroenterology, University of California San Francisco, San Francisco, California, United States of America; School of Public Health, University of California Berkeley, Berkeley, California, United States of America.
3
HIV/AIDS Division, University of California San Francisco, San Francisco, California, United States of America.
4
Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, United States of America.
5
Department of Medicine, Mulago Hospital, Makerere University, Kampala, Uganda.
6
Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America.
7
HIV/AIDS Division, University of California San Francisco, San Francisco, California, United States of America; Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, United States of America.

Abstract

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.

PMID:
24752365
PMCID:
PMC3994144
DOI:
10.1371/journal.pone.0095726
[Indexed for MEDLINE]
Free PMC Article
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