Stuck in the past – testing polymicrobial lung infections in cystic fibrosis


Molecular-based techniques uncover the shocking inadequacy of the limited culture-based approach of routine CF (cystic fibrosis) lung infection testing and the danger of current antibiotic treatment targets.

The dangers of current testing

The routine testing of polymicrobial lung infections in cystic fibrosis patients remains unchanged for the past 100 years. Current testing is culture-based and relies on the idea that specific species, such as Pseudomonas aeruginosa, are the main pathogens and should be the treatment target, ignoring the microbiota as a whole. This classical aerobic culture-based method of testing relies on the presence or absence of a species and not the abundance of a species. This is based on Koch’s postulates and the pathogenesis concept of ‘one microbe, one disease.’

Despite the knowledge we have today that CF lung infections are polymicrobial [1], testing and therefore antibiotic treatments remain insufficient. The danger of this stagnant methodology is that patients suffering with recurring infections worsen throughout their lifetimes, with chronic use of antibiotics that decrease the microbial diversity in the lungs, allowing more resistant species to thrive.

Furthermore, treatment needs to focus on the infection community and its interactions as a whole. The complex lung microbiota of the CF patient needs to be understood in much more depth so that antibiotic treatment can target the species driving infection. Aside from vital microbiomic research, the next step forward is to update routine testing from culture-based to molecular sequencing.

The CF lung microbiome

Chronic lung infections are the main cause of death in individuals with cystic fibrosis. These infections result in the chronic use of antibiotics. Routine screening for lung infections in CF patients focuses on the abundance of a few bacterial species including, P. aeruginosa, Haemophilus influenzae, Staphylococcus aureus, Burkholderia cepacia complex and Achromobacter xylosoxidans. However, CF lung infections are comprised of a complex infection microbiota ranging from aerobic to strictly anaerobic species. This microbiota includes the standard species that are routinely tested for and many other species, including those with presently unknown functions.

In addition to this, the way in which these species interact with one another and with the host is little understood. Microbiomic research is crucial to understanding these chronic infections.  At present, little is known about how these microbes interact and therefore treatment is limited and lacks efficacy.

The CF lung microbiota consists of core taxa, the most abundant and persistent species such as P. aeruginosa and S. aureus. The rest of the microbiota is composed of satellite taxa, the rarer and less prevalent species such as the Privatella species. The core taxa account for the majority of relative abundance but the satellite taxa account for the majority of the diversity within the microbiota.

Intensive antibiotic therapies are used to control CF lung infections. The current treatment targets are a few of the core species ignoring how the microbial community is affected as a whole.

Research published in The Journal of Cystic Fibrosis found that antibiotic treatment targeting P. aeruginosa can actually increase the abundance of the species whilst reducing numbers of non-pseudomonal species [2]. P. aeruginosa is highly tolerant of antibiotics due to virulence factors such as the secretion of an exopolysaccharide matrix and its ability to grow as a biofilm. P. aeruginosa is also highly adaptable and therefore capable of developing more resistance with the repeated exposure to antibiotics. Subsequent research is required, investigating the functionality of the core and satellite species as a microbiota, as opposed to individual species acting in isolation. Further knowledge would enable antibiotics to be used more effectively.

Microbiota diversity and lung function

Research carried out at Manchester Metropolitan University (Manchester, UK), published in Microbiome, investigated the relationship between microbial diversity and lung function in CF using 16S rRNA gene targeted amplicon sequencing. This method is a targeted next generation technique using PCR technology to analyze a variety of genes at once. It is an effective and highly sensitive method for dealing with large amounts of information such as that of the lung microbiome.

Amplicon sequencing reveals much more than simply the presence or absence of a microbe. Using this method the abundance of a species can be measured. The research discovered that as lung function decreases, microbiota diversity decreases too [3]. This could be viewed as an ecological pattern of CF microbiota. Exploring and understanding these patterns within the lung microbiota is key to understanding the pathology and in advancing testing methods and subsequent treatments.

Microbiota diversity and antibiotics

As microbial diversity decreases, there is an increase in the dominance of core taxa such as P. aeruginosa. Antibiotic treatment targeted at P. aeruginosa further decreases diversity allowing P. aeruginosa to dominate, it is evident that the way in which chronic lung infections are treated in CF patients needs to evolve.

In the study at Manchester Metropolitan University, antibiotic exposure explained the variation in microbiota composition. The more abundant core taxa are resistant to antibiotic treatment and the rarer satellite taxa are resilient to antibiotic treatment. Therefore when CF patients undergo antibiotic therapy (instigating selective pressure within the microbiota) there is a reduction in the satellite taxa abundance, allowing core taxa to increase in abundance and dominate, hence the reduction in diversity.

In summary, the chronic use of antibiotics reduces satellite taxa abundance allowing core taxa such as P. aeruginosa to flourish, dominating in patients with the most reduced lung function.

The bigger picture

This study highlights the need for a change in testing methods along with the findings that several known taxa were in fact more important species than previously thought. B. cepacia complex, H. influenzae, S. maltophilia and A. xylosoxidan were found to be greater in prevalence with the use of a molecular-based method, B. cepacia complex and S. maltophilia were found to be core taxa. Additionally, it was discovered that A. xylosoxidans did not dominate when lung function was reduced and was in fact a satellite taxa, with perhaps less pathological importance than perceived in classical routine testing. These observations are examples of what useful information can be obtained with modern molecular-based testing that is missed when using limited techniques.

Moreover, the research observed that genera Prevotella, Porphyromonas and Veillonella were increasingly dominant in the microbiota of patients with better lung function. This brings up the question as to whether increasing the abundance of specific species, rather than reducing with antibiotics, could be a future potential treatment.

The microbiomic research to date has begun to delve into the complex microbial communities in CF lung infections. Despite the need for more research into the microbiota of the CF-affected lung to enable the understanding of the pathology, it is time for a change in the way CF lung infections are tested.

Improve testing, improve treatment

Microbiomic research has made it evident that a molecular-based approach divulges a more detailed view of what is happening within the lung microbiota. Thus shedding light on potential treatment targets and what to be aware of when prescribing antibiotic treatment for these lung infections.

Testing a patient’s microbiota diversity and dominance coupled with lung function measures could be used as indicators of disease state. To improve testing, microbiota sampling should be a new and much needed addition to routine testing. Antibiotics are an important and crucial weapon in fighting chronic lung infections in CF, but by ignoring the bigger picture they could be doing more harm than good.


The opinions expressed in this interview are those of the interviewee and do not necessarily reflect the views of Infectious Diseases Hub or Future Science Group.


1) O’Toole GA. Cystic fibrosis airway microbiome: overturning the old, opening the way for the new. J Bacteriol. 200:e00561-17,doi:10.1128/JB.00561-17 (2017).

2) Daniels TMV, Rogers GB, Stressmann FA et al. Impact of antibiotic treatment for pulmonary exacerbations on bacterial diversity in cystic fibrosis. J. Cystic Fibrosis. 12(1), 22-28 (2013).

3) Cuthbertson L, Walker AW, Oliver AE et al. Lung function and microbiota diversity in cystic fibrosis. Microbiome. 8, 45 (2020).



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