Oropharyngeal microbiome of a college population following a meningococcal disease outbreak

Abstract

Asymptomatic oropharyngeal carriage of Neisseria meningitidis peaks in adolescence and young adulthood. Following a meningococcal disease outbreak at a U.S. college, we profiled the oropharyngeal microbiomes of 158 students to identify associations between bacterial community composition and meningococcal carriage or risk factors for carriage, including male gender, smoking, and frequent social mixing. Metagenomic shotgun sequencing identified 268 bacterial taxa at the genus or species level, with Streptococcus, Veillonella, and Rothia species being most abundant. Microbiome composition showed weak associations with meningococcal carriage and risk factors for carriage. N. meningitidis abundance was positively correlated with that of Fusobacterium nucleatum, consistent with hypothesized propionic acid cross-feeding. Additional species had positive abundance correlations with N. meningitidis, including Aggregatibacter aphrophilus, Campylobacter rectus, Catonella morbi, Haemophilus haemolyticus, and Parvimonas micra. N. meningitidis abundance was negatively correlated with unidentified Veillonella species. Several of these species are commonly found in dental plaque, while N. meningitidis is primarily found in the pharynx, suggesting that ecological interactions extend throughout the oral cavity. Although risk factors for meningococcal carriage do not strongly impact most bacterial species in the oropharynx, variation in the upper respiratory tract microbiome may create conditions that are more or less favorable for N. meningitidis carriage.

Figure 1

Bacterial species composition of 158 oropharyngeal swabs, clustered by species composition. (A) Abundance of each genus that accounts for over 10% of any swab. Average abundance is in parentheses in legend. (B) Heatmap showing the 100 most common bacterial taxa. Cells are color coded on a logarithmic scale to show the proportional abundance of each species (row) in each swab (column). In both panels, swabs are clustered according to average Bray-Curtis distances of their taxonomic profiles, represented by the dendrogram on the top. Taxa in panel B are clustered according to the Bray-Curtis distance of their abundance in each swab, shown by the dendrogram on the left. Colored portions of the dendrogram indicate groups for which distances are <70% of the maximum distance. Neisseria meningitidis is emphasized with bold font.

Figure 2

Abundance of dominant species among 158 oropharyngeal swabs. Curves show number of swabs in which each species was found at the given abundance; the y-intercept is equal to the number of swabs in which the species was identified. The twenty species shown have an abundance greater than 10% in one or more specimens, and a mean abundance greater than 1% overall (shown in parentheses in legend).