Oral and airway microbiota in HIV-infected pneumonia patients

Abstract

Despite the increased frequency of recurrent pneumonia in HIV-infected patients and recent studies linking the airway bacterial community (microbiota) to acute and chronic respiratory infection, little is known of the oral and airway microbiota that exist in these individuals and their propensity to harbor pathogens despite antimicrobial treatment for acute pneumonia. This pilot study compared paired samples of the oral and airway microbiota from 15 hospitalized HIV-infected patients receiving antimicrobial treatment for acute pneumonia. Total DNA was extracted, bacterial burden was assessed by quantitative PCR, and amplified 16S rRNA was profiled for microbiome composition using a phylogenetic microarray (16S rRNA PhyloChip). Though the bacterial burden of the airway was significantly lower than that of the oral cavity, microbiota in both niches were comparably diverse. However, oral and airway microbiota exhibited niche specificity. Oral microbiota were characterized by significantly increased relative abundance of multiple species associated with the mouth, including members of the Bacteroides, Firmicutes, and TM7 phyla, while airway microbiota were primarily characterized by a relative expansion of the Proteobacteria. Twenty-two taxa were detected in both niches, including Streptococcus bovis and Chryseobacterium species, pathogens associated with HIV-infected populations. In addition, we compared the airway microbiota of five of these patients to those of five non-HIV-infected pneumonia patients from a previous study. Compared to the control population, HIV-infected patients exhibited relative increased abundance of a large number of phylogenetically distinct taxa, which included several known or suspected pathogenic organisms, suggesting that recurrent pneumonia in HIV-infected populations may be related to the presence of these species.

Fig 1

Bacterial community richness (number of taxa detected) in paired oral and airway samples of HIV-infected patients with pneumonia.

Fig 2

Comparison of oral and airway microbiota of HIV-infected patients with pneumonia. (A) Hierarchical cluster analysis of oral (O) and airway (A) samples. Samples from patients receiving ART are indicated with an asterisk. (B) Taxa exhibiting significant (P < 0.05) changes in relative mean fluorescence intensity values between oral and airway samples. The background is colored based on phylum; specific Proteobacteria classes are indicated.

Fig 3

Comparison of airway microbiota detected in HIV-infected and non-HIV-infected patients with pneumonia. (A) Venn diagram depicting the number of taxa shared (light gray) and the numbers exclusive to HIV-infected (white) and non-HIV-infected (gray) patients. (B) Taxa exhibiting significant (P < 0.05) changes in relative mean fluorescence intensity values between HIV-infected and non-HIV-infected airway samples. The background is colored based on phylum (only phyla possessing at least three taxa are labeled).