The relationship between nasopharyngeal, oropharyngeal and sputum microbiota in patients with Chronic Obstructive Pulmonary Disease

<bold>Introduction:</bold> Disordered lower respiratory tract microbiota composition and diversity correlates with disease severity in COPD patients. Sputum and particularly bronchioalveolar lavage samples can cause discomfort and be resource-intensive to collect. Not all patients are able to expectorate spontaneously. Upper airway swabs could provide an alternative to monitor the microbiota in COPD. <bold>Methods:</bold> 537 sets of sputum samples, nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from patients with moderate to severe COPD (FEV₁/FVC ratio <0.7) enrolled from multiple centres across the UK. DNA was extracted and sequenced with 16S rRNA gene sequencing. Reads were analysed using a DADA2 taxonomic inference pipeline and the Silva 138.1 database. Composition and diversity analysis was conducted in R. <bold>Results:</bold> The sputa and OP swabs microbiotas were both dominated by <italic>Streptococcus</italic>. NP swabs showed heterogenous microbiota with <italic>Corynebacterium</italic>, <italic>Staphylococcus</italic> and <italic>Dolosigranulum</italic> being seen in similar proportions. NP swabs had a high proportion of taxa unclassified at the Kingdom level, compared to OP swabs and sputa (Kruskal–Wallis, p<0.01). No difference in evenness (Chao1, p=0.42) and richness (Simpson, p=0.85) was seen between OP swabs and sputa. Differences between NP swabs and sputa were statistically significant (Chao1, p<0.01. Simpson, p<0.01). Microbiota composition abundances positively correlated between sample types from the same patient (Sputa-NP: 0.315 (Spearman's rank), Sputa-OP: 0.728 (Spearman's rank)). <bold>Conclusion:</bold> OP swab composition and diversity are strongly correlated with the sputum microbiota.