Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients

Abstract

Chronic rhinosinusitis (CRS) is a common and potentially debilitating disease characterized by inflammation of the sinus mucosa for longer than 12 weeks. Bacterial colonization of the sinuses and its role in the pathogenesis of this disease is an ongoing area of research. Recent advances in culture-independent molecular techniques for bacterial identification have the potential to provide a more accurate and complete assessment of the sinus microbiome, however there is little concordance in results between studies, possibly due to differences in the sampling location and techniques. This study aimed to determine whether the microbial communities from one sinus could be considered representative of all sinuses, and examine differences between two commonly used methods for sample collection, swabs, and tissue biopsies. High-throughput DNA sequencing of the bacterial 16S rRNA gene was applied to both swab and tissue samples from multiple sinuses of 19 patients undergoing surgery for treatment of CRS. Results from swabs and tissue biopsies showed a high degree of similarity, indicating that swabbing is sufficient to recover the microbial community from the sinuses. Microbial communities from different sinuses within individual patients differed to varying degrees, demonstrating that it is possible for distinct microbiomes to exist simultaneously in different sinuses of the same patient. The sequencing results correlated well with culture-based pathogen identification conducted in parallel, although the culturing missed many species detected by sequencing. This finding has implications for future research into the sinus microbiome, which should take this heterogeneity into account by sampling patients from more than one sinus.

Keywords: 16S rRNA gene sequencing; chronic rhinosinusitis; microbiome; sinus; swabs.

Figure 1

Weighted unifrac distances between individual swab samples for each patient, as well as all intra-individual (all within patient) and inter-individual (all between patient) distances. The number of samples for each patient is shown in brackets next to the patient ID. Boxes represent second and third quartiles; whiskers represent 1.5 times the interquartile range, and all individual data points are shown beside the boxes (where more than one data point is available per patient), except for the all within and all between patient groups.

Figure 2

Bar plots showing bacterial communities from individual sinus swabs of patients with low (<0.2) or high (>0.2) median between-sinus weighted unifrac distances. Sinus locations are indicated by LE (left ethmoid), LF (left frontal), LM (left maxillary), LS (left sphenoid), RE (right ethmoid), RF (right frontal), RM (right maxillary), and RS (right sphenoid), with patient numbers indicated below. Only bacterial genera which represented at least 5% sequences in at least one sample were included.

Figure 3

Weighted unifrac distances between swab and tissue samples within patients. Distances were plotted for matched swab and tissue samples (23 pairs) for each patient separately, and all together, The number of sinuses with sequence data for both swab and tissue samples is shown in brackets next to the patient ID. Boxes represent second and third quartiles; whiskers represent 1.5 times the interquartile range, and all individual data points are shown beside the boxes (where more than one data point is available per patient).

Figure 4

Weighted unifrac distances between nostril swab samples and sinus swabs within patients. Distances are plotted for each patient separately, and all together. The number of samples compared is shown in brackets next to the patient ID. Boxes represent second and third quartiles; whiskers represent 1.5 times the interquartile range, and all individual data points are shown beside the boxes (where more than one data point is available per patient).