Emerging cystic fibrosis pathogens and the microbiome.

Cystic fibrosis (CF) respiratory infection is characterised by the presence of typical human bacterial pathogens such as Pseudomonas aeruginosa, Haemophilus influenzae and Staphylococcus aureus. Less typical pathogens such as Burkholderia, Stenotrophomonas, Achromobacter, Pandorea and Ralstonia have emerged as problematic infections which are largely unique to people with CF. Using molecular methods, two groups of anaerobic bacteria Prevotella species and the Streptococcus milleri group have also recently been shown to be highly prevalent in CF sputum. Collectively, the diversity of microorganisms present in respiratory specimens has been designated the CF microbiome. The challenges posed by emerging CF pathogens and a microbiome-based view of CF infection are discussed in terms of their impact on clinical outcome, diagnosis and therapy.