Microbial profiling of dental plaque from mechanically ventilated patients

Abstract

Micro-organisms isolated from the oral cavity may translocate to the lower airways during mechanical ventilation (MV) leading to ventilator-associated pneumonia (VAP). Changes within the dental plaque microbiome during MV have been documented previously, primarily using culture-based techniques. The aim of this study was to use community profiling by high throughput sequencing to comprehensively analyse suggested microbial changes within dental plaque during MV. Bacterial 16S rDNA gene sequences were obtained from 38 samples of dental plaque sampled from 13 mechanically ventilated patients and sequenced using the Illumina platform. Sequences were processed using Mothur, applying a 97% gene similarity cut-off for bacterial species level identifications. A significant 'microbial shift' occurred in the microbial community of dental plaque during MV for nine out of 13 patients. Following extubation, or removal of the endotracheal tube that facilitates ventilation, sampling revealed a decrease in the relative abundance of potential respiratory pathogens and a compositional change towards a more predominantly (in terms of abundance) oral microbiota including Prevotella spp., and streptococci. The results highlight the need to better understand microbial shifts in the oral microbiome in the development of strategies to reduce VAP, and may have implications for the development of other forms of pneumonia such as community-acquired infection.

Fig. 1

Bray–Curtis and Jaccard analyses of dental plaque samples. A red spot represents each sample; the sample number follows X. By both methods, 31 samples are seen to cluster tightly, with seven outliers identifiable.

Fig. 2

The proportion of each of the major phyla identified in dental plaque samples.

Fig. 3

A stacked bar graph representing the five most abundant organisms present in the dental plaque community at the start of mechanical ventilation for each of the 13 patients. Each patient is represented by a different colour.

Fig. 4

A stacked bar graph representing the 10 most abundant microbial species within dental plaque, at each of the four time points of MV and recovery. This bar graph allows the comparison between oral organisms and putative respiratory pathogens.

Fig. 5

Heat map indicating the level of phyla, species variation and species abundance during MV.

Fig. 6

Non-metric multidimensional scaling (NMDS) analysis of grouped dental plaque samples. (a) Scatter representations of dental plaque communities and (b) the grouping, and therefore relationship between dental plaque communities from the start of intubation and at the end of extubation. (c) Overlap of communities at all sample time points.

Fig. 7

Species-specific PCR for the detection of Pseudomonas aeruginosa from dental plaque samples in cases where Pseudomonas aeruginosa was isolated during microbial culture. A total of five dental plaque samples were positive for Pseudomonas aeruginosa. M, size marker.

Fig. 8

Stacked bar graph representing the 10 most abundant microbial species for the biofilm community time point for groups start and end. The two most abundant species within dental plaque sampled on the ward were oral organisms, Veillonella and Lactobacillus. A decrease in Escherichia coli and absence of Enterococcus species was also observed post extubation.