Epidemiology of Anaerobic Bacteria in Cystic Fibrosis Patients: Descriptive and Non-interventional Study

Recently, the respiratory microbiota characterisation of a Cystic Fibrosis (CF) patients' cohort has highlighted the potential role of anaerobes, and specially species belonging to the genus Porphyromonas, in the first P. aeruginosa colonization.

The aim of this project is to describe the bacterial anaerobic population in the respiratory microbiota of a CF cohort. At the end of this study, an inventory of the anaerobic microbiota in CF respiratory samples will be establish in relation to the patients' pulmonary function and P. aeruginosa colonization status in order to speculate about the pulmonary anaerobes roles, still unknown.

The innovative aspect of the ANA-MUCO study is the use of a specific sample kit designed for the study which allows preserving anaerobic bacteria in sputum according to the recommendations of the International Human Microbiome Standards (IHMS). Extended-culture and molecular approaches will be performed to identify and describe the anaerobic bacteria which could be involved in the pulmonary homeostasis in CF respiratory samples.

Cystic Fibrosis (CF) is a lethal genetic disease whose prognostic depends on the patients' respiratory impairment. Indeed, the airways microbial chronic colonization, particularly to Pseudomonas aeruginosa, leads to infectious exacerbations and to noteworthy respiratory function impairment and represents the main cause of morbidity and mortality. Nowadays, antibiotherapy is the main therapeutic solution to thwart bacterial development and to slow respiratory function degradation. However, during the disease progression, this therapeutical approach is limited by the bacteria accommodation and antibiotic resistance development.

Thanks to the development of high-throughput sequencing methods, the respiratory microbiota of CF patients has been mainly described and points the way to new therapeutic approaches. It has been establish that, i) from an early age, the respiratory microbiota of CF children is modified in comparison with the healthy children one, ii) bacterial diversity decrease progressively throughout the disease evolution, iii) anaerobes represent an important part of the healthy and CF respiratory microbiota. Thus pulmonary microbiota composition could be a better disease progression indicator than the only detection of P. aeruginosa in CF respiratory samples. Furthermore, the respiratory microbiota could influence the pathogenesis through direct interactions between micro-organism/micro-organism or micro-organism/host. Recently, thanks to the respiratory microbiota characterisation of a CF patients' cohort (MUCOBIOME study, 2012-2015), the potential role of anaerobes (and particularly species belonging to the genus Porphyromonas) in the first P. aeruginosa colonization has been highlighted. Indeed, the respiratory microbiota study of 34 CF patients has revealed that if patients are deprived or lowly colonized by Porphyromonas spp., the relative risk of P. aeruginosa colonization is 3.7 fold higher. Conversely, the relative abundance's increase of Porphyromonas spp. in CF patients receiving Ivacaftor treatment is correlated with the respiratory function improvement. Thus, in addition to be used as biomarker, the investigators speculate on the fact that some strict anaerobic species, such as Porphyromonas spp., could act as CF pathogens (like P. aeruginosa) competitors and limit their setting up in the airways.

The investigators see here the necessity of complementary studies in order to better characterise anaerobic bacteria in the airways. The aim of the ANA-MUCO study is to identify and describe anaerobic bacteria in sputum of a CF patients' cohort, to characterise the antibiotic resistance profiles of the anaerobic species isolated, to study the anaerobes repartition within the CF population and to evaluate the interactions between anaerobes and CF pathogens (P. aeruginosa, S. aureus, H. influenzae, ...). In order to be the most exhaustive as possible in the anaerobes description, the innovative aspect of this study is the conception and the use of a specific sample kit which preserves anaerobic conditions in sputum according to the recommendations of the International Human Microbiome Standards (IHMS). Then, extended-culture and molecular approaches will be performed to identify the anaerobic bacteria which could be involved in the pulmonary homeostasis in CF respiratory samples.

Eligibility Criteria:
Inclusion Criteria:

* Patients with a confirmed diagnosis of Cystic Fibrosis regardless of CFTR genotype
* Persons affiliated to the social security system
* Minor or major patients able to expectorate spontaneously or after induction
* Consent signed by the patient or the holder of parental authority for the children

Exclusion Criteria:

* Persons deprived of liberty, persons under guardianship or curatorship, persons in emergency situations
* Persons non affiliated to a social security system or not entitled
* Pulmonary transplant patients
* Refusal to participate to the study