Antimicrobial resistance (AMR) refers to the ability of microorganisms like bacteria, viruses, fungi and parasites to resist the effects of antimicrobial drugs (such as antibiotics) which are widely used as treatment. AMR poses an escalating global health threat, contributing to difficult-to-treat infections associated with increased disease spread, disability and death, as well as a substantial economic burden.

In chronic lung diseases, such as bronchiectasis, Cystic fibrosis or chronic obstructive lung disease (COPD), there is a higher risk of AMR due to the exposure to frequent or prolonged courses of antibiotics to treat recurrent lung infections and exacerbations (flares of the disease), to reduce lung inflammation or to control chronic infection within the lung with suppression of colonising microbes.

Most data on AMR in chronic lung diseases derive from analysing pre-existing routinely collected health data collected on a national basis which is often incomplete. Hence a prospective study is crucial to better understand and address AMR in chronic lung diseases. Prospective studies follow patients forward in time, collecting data on outcomes and allowing researcher to observe the natural history of AMR development, monitor trends and evaluate interventions.

This multicentre prospective study, as part of the European Respiratory Society (ERS) Clinical Research Collaboration on Antimicrobial Resistance in Lung Disease (CRC - AMR Lung), aims to investigate the patterns of AMR in chronic lung diseases through a fully anonymous registry alongside a prospective sub-cohort study tracking individuals with chronic lung disease and known colonisation with high-priority AMR pathogens (microorganisms). This study will enable analysis of prevalence and burden of AMR within chronic lung disease alongside understand the genetic drivers of resistance, the link between the microbial genotype and antimicrobial resistance and how transmission of resistance occurs in 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.

Patients will be recruited from hospital chronic lung disease clinics.

Researchers can apply to the ERS CRC for anonymised data access