In vitro reconstitution of the polymicrobial community associated with cystic fibrosis airway infections

Project background

Patients with chronic respiratory diseases, such as asthma and cystic fibrosis (CF), are predisposed to microbial colonisation of the airways. Although these respiratory diseases are not caused by microbial infections, repeated infections can exacerbate the condition. It is now understood that the range of bacteria colonising patient airways extends beyond specialised respiratory pathogens and includes a wider range of taxa. Infections associated with chronic respiratory diseases are largely polymicrobial yet animal models are predominantly infected with one or two pathogens only.

Why we funded it

This PhD Studentship aims to replace the need for animal models in the study of polymicrobial infections by establishing an in vitro model to represent the polymicrobial community in the airways of CF patients. 

The most widely-used bronchopulmonary infection model involves introducing bacteria into the lower respiratory tract either via direct injection or surgery. Most of the current procedures modelling respiratory infection are classified as moderate or severe under the Animals (Scientific Procedures) Act 1986. With the developed in vitro model Dr Welch estimates that approximately 10% of current animal models relating to respiratory infection can be replaced.

Research methods

Bioreactor culture conditions will be established to allow the propagation of a stable polymicrobial community representative of the lung community in chronically-infected CF patients. Various growth conditions will be tested to establish a steady-state composition similar to that seen in CF patient sputa. The ability to sub-culture and lyophilise samples without impairing steady-state composition will also be explored. This will allow for the development of a bank of lyophilised stocks enabling reconstitution of a range of polymicrobial communities. The cultured polymicrobial communities will also be challenged with antibiotics to establish their response and whether steady-state compositions alter in response to clinically relevant treatments.   

Each year in the UK, around 160,000 people are diagnosed with asthma, 110,000 with chronic obstructive pulmonary disorder (COPD), 10,000 with bronchiectasis and 300 with cystic fibrosis (CF). These are all respiratory diseases in which the patient's condition becomes worsened by persistent bacterial infections. Over the years, researchers have tried to recapitulate these infections in animal models, and in doing so, they have focussed almost exclusively on infecting the animals (usually mice or rats) with just one species of respiratory pathogen at a time. However, many bacteria are not easily cultured, and over the last decade 16S rDNA sequencing technologies have revealed that many of these chronic respiratory infections are in fact, polymicrobial. Remarkably though, and in spite of these revelations, there have been little or no efforts to try and reconstitute such multi-species communities in the laboratory. The main aim of the current studentship is to rectify this by developing an in vitro system that enables the propagation and maintenance of a stable polymicrobial community derived from the CF lung environment. Animal models of polymicrobial respiratory infections are beginning to appear, and it becoming increasingly apparent that we will see more of these over the next decade. Therefore, we have a window of opportunity in which to develop and disseminate a competing alternative in vitro system that will reduce reliance on these animal models. However, we also want to go further by showing that our model system can reveal novel biology. For example, how does the polymicrobial community respond to antibiotic challenge? What happens if we
introduce a new species or a mutant variant of an existing species? How does the community architecture change over time? Because the in vitro model can be experimentally manipulated and perturbed in ways that are just not possible in living mammals, such questions become experimentally tractable.