Upper and lower respiratory tract microbiota in CF and non-CF BX Michael J Cox National Heart and Lung Institute, Imperial College London

Acknowledgements ECFS Bill Cookson and Miriam Moffatt –Ghazala Mirza, Kenny Wong, Paul Cardenas and Phil Molyneux –Molecular Genetics and Genomics Section Diana Bilton, Jane Davies and Michael Loebinger –Andy Jones –CSLD Microbiology Group –Royal Brompton and Harefield NHS Foundation Trust Funding MOSAIC Consortium, Novartis, Asmarli Foundation, Wellcome Trust

1.Microbial ecology and techniques 2.Respiratory tract microbiota 3.CF exacerbation study 4.Non CF BX study 5.Summary

Only two questions… Who’s there? What are they doing?

16S rRNA Ribosomal Subunit

A census-taker once tried to test me… Address Ethnicity Who you live with Who moves in and out of the neighbourhood Can guess at what you do for a living Don’t know hobbies, what you had for breakfast etc.

1.Microbial ecology and techniques 2.Respiratory tract microbiota 3.CF exacerbation study 4.Non CF BX study 5.Summary

Lower respiratory tract canonically considered sterile Not true, illogical, but hard to prove

What are we actually sampling? Nasopharyngeal swab Nasopharyngeal aspirate Saliva Throat swab Cough swab Endotracheal aspirate Expectorated sputum Induced sputum Bronchoalveolar Lavage Lung brush Biopsy Section Whole lung What a respiratory microbial ecologist wants What a respiratory microbial ecologist doesn’t want Common proxies for “Lower Respiratory Tract”

Figure 2. Percentage distribution of common phyla and genera at different airway levels (nose, OP and LUL), subdivided into the seven most frequent genera (Croynebacterium, Prevotella, Staphylococcus, Streptococcus, Veilonella, Haemophilus and Neisseria) found in the samples. Hilty M, Burke C, Pedro H, Cardenas P, et al. (2010) Disordered Microbial Communities in Asthmatic Airways. PLoS ONE 5(1): e8578. doi: /journal.pone

Exacting sampling to take attempt to exclude influence of upper on lower respiratory tract Concluded that there is continuity of the upper and lower respiratory tract microbial communities They did find a small number of organisms unique to the LRT – so not entirely continuous – strongly interacting metacommunities

Healthy lungs not sterile, transiently colonised Emmigration Clearance Immigration Deposition and growth

Emmigration Clearance Immigration Deposition and growth CF and Non CF BX lungs colonised

1.Microbial ecology and techniques 2.Respiratory tract microbiota 3.CF exacerbation study 4.Non CF BX study 5.Summary

Studies CF Exacerbation Study –Dr Andy Jones, Dr Diana Bilton, Dr Jane C Davies 24 Subjects Exacerbation –5 sputum samples (admission before ABX, 7, 10, 14 and final clinical stable sample ~30 days) Must have had P. aeruginosa isolation Comprehensive additional data from the main study including –Hypermutator characterisation –Quorum sensing molecules –Detailed clinical information

Pseudomonas most common, but not exclusively so, despite isolation being inclusion criterion. It is possible to discriminate individual subjects by their community composition

Individual communities Treatment has the greatest effect on microbial community – exacerbation and stable, not sig different

1.Microbial ecology and techniques 2.Respiratory tract microbiota 3.CF exacerbation study 4.Non CF BX 5.Summary

Studies CF Exacerbation Study –Dr Andy Jones, Dr Diana Bilton, Dr Jane C Davies 24 Subjects Exacerbation –5 sputum samples (admission before ABX, 7, 10, 14 and final clinical stable sample ~30 days) Must have had P. aeruginosa isolation Comprehensive additional data from the main study including –Hypermutator characterisation –Quorum sensing molecules –Detailed clinical information Non CF Bronchiectasis –Dr Michael Loebinger 76 Patients 7 sputum samples (monthly) – clinical stability –Additional samples if exacerbation Multiple aetiologies –Idiopathic, post-infective, ABPA etc. Comprehensive clinical database 16S rRNA sequencing on all

Mark Rothko Nice colours – but what does it mean?!

1.Microbial ecology and techniques 2.Respiratory tract microbiota 3.CF exacerbation study 4.Non CF BX 5.Summary

Summary Upper and lower respiratory tract microbial communities in communication and current evidence is that they can be similar CF and non CF BX communities –Stable over time –Individual –Responsive to treatment –Responsive to changes in clinical state In order to understand community effect and response of exacerbation: –need to include the whole microbiota (viruses, phage, fungi etc.) –In situ function

Other talks by the team Nick Simmonds – Sex –Symposium 6 – Outcome determinants – just after this Imogen Felton – Exophiala –Symposium 18 – Grand Rounds – 8:30 Friday Diana Bilton –Symposium 30 – The young adult – 9:00 Sat –Plenary – Delivering quality care in CF – 11:00 Sat Things that I’ll definitely be going to! Symposium 8 –Translating Bacterial Genomics to CF Care Workshop 8 –Microbial Communities: relationships and disease Symposium 14 –Fungi in CF Symposium 20 –The pulmonary and intestinal microbiome in CF Workshop 17 –Novel anti-microbial therapies Workshop 22 –Host-pathogen interactions