An Observational Study Into Antimicrobial Resistance in Patients With a Chronic Lung Disease

Pathway 1:

Prospective data collection will occur twice a year over a two-week period capturing attendees to chronic lung disease clinics in that period. No participant identifiable information will be recorded with a e-CRF capturing baseline demographics, medical history, clinical characteristics, treatment regimens, and microbiological findings and inputted into a secure online Redcap database. The end of the last 2 week period will be defined as the end of the study for pathway 1.

Pathway 2:

Clinical Visits and Sampling:

(i) Baseline visit All eligible individuals will undergo screening when clinically stable including clinical history/ examination, respiratory function testing (spirometry) and a severity assessment with the use of validated questionnaires (COPD assessment test (CAT), Bronchiectasis Health Questionnaire (BHQ)). Clinical information including microbiology cultures, the underlying lung disease and other medical conditions and medication history will be obtained from medical records. Microbiological isolates from clinical sputum sampling will be stored for further genomic analysis.

At the first study visit the following biological samples will be taken to address the study objectives:

• sputum
• nasal samples (Nasopharyngeal swab, synthetic absorptive matrix (SAM) sampling to sample nasal lining fluid and nasal brushings)
• Exhaled breath
• Venous blood (40mls)
• Stool (remote stool sampling (performed at home and posted in) using secure bespoke collection kits)

(ii) Exacerbation monitoring and sampling: Participants that develop symptoms of acute viral infection or acute exacerbation will have the following sampling and clinical assessment as detailed above.

• Early exacerbation sampling (<48hrs of increased symptoms) (REMOTE STUDY VISIT from home)
• Remote nasopharyngeal swab and sputum sampling with bespoke collection kits
• Mid-exacerbation sampling (within 5 days of increased symptoms) (IN PERSON VISIT)
• clinical assessment, spirometry, validated questionnaires (as per baseline)
• sputum
• nasal samples (Nasopharyngeal swab, SAM and nasal brushings)
• Exhaled breath
• Venous (40mls)
• Stool (remote stool sampling using bespoke collection kits)

(iii) Stable longitudinal assessment: All participants will undergo further clinical visits similar to baseline at 6 monthly intervals over a 2 year period (as detailed above).

(iiii) At 6 monthly intervals throughout the 2 year period, air and surface swab samples will be taken from hospital high-traffic areas such as inpatient ward and outpatient clinic settings for analysis of presence of hospital environmental AMR reservoirs.

Inclusion criteria

• Presence of an underlying chronic lung disease (e.g. Bronchiectasis, COPD) stratified by colonisation status:

• Pseudomonas sp (n=30)
• Klebsiella sp (n=20)
• Haemophilus sp (n=20)
• E-coli sp (n=20)
• Stenotrophomonas sp (n=20)
• Staphylococcus sp (n=20)
• Other chronic colonisation (n=20)
• Not colonised with any bacterial pathogen (n=20)

Exclusion criteria

• Inability to provide informed consent
• Pregnancy
• Medical instability preventing ability to attend for regular study visits at baseline.