Cystic fibrosis (CF) is a complex, heterogeneous, multi-organ disorder caused by defects in the CF transmembrane conductance regulator (CFTR) gene. The gene encodes an ion channel that is physiologically involved in the transport of chloride and bicarbonate and is expressed on the apical epithelial cell surfaces throughout the body [1]. CFTR gene defects result in various degrees of ion channel dysfunction, thus ultimately affecting the secretory function of many organs [2]. CF is the most common autosomal recessive life-shortening condition of Caucasians; although its incidence varies significantly, it is estimated that it occurs between 1:3000 and 1:6000 live births, which equates to 1:28 and 1:40 carrier rates, respectively [3].

In the lungs, reduced chloride excretion and unrestricted sodium absorption at the airway epithelial surface result in the overproduction of thick and viscid mucus that affects airway clearance, leading to small airways plugging, irreversible structural and functional defects, and eventually, respiratory failure [4]. Repeated bacterial respiratory infections are the hallmark of the disease [4]; these lead to a domino sequence of persistent lower airway inflammation that accelerates tissue damage and accounts for the majority of the disease-related morbidity and mortality [5]. Common CF pathogens are comprised mainly of Staphylococcus aureus and Pseudomonas aeruginosa; later, as the disease progresses, many patients are infected with more uncommon and difficult-to-treat microorganisms, such as Burkholderia cepacia. Several complications can occur in parallel with the progression of the disease, including liver dysfunction, pancreatic exocrine insufficiency (expressed as malnutrition and failure to thrive in the pediatric population), CF-related diabetes, male infertility, nasal polyposis, intestine obstruction, bronchiectasis, and others [2,6,7].

In individuals with CF, microbial communities colonize the airways shortly after birth, while peripheral lung colonization and chronic inflammation occur later [8]. In contrast to respiratory infections in non-CF patients, these have the tendency to be persistent and involve phenotypic alterations of the infecting organisms [9]. Throughout life, patients with CF are repeatedly treated with antibiotics, especially during the exacerbations of the disease. Antibiotic administration together with novel therapeutic interventions, such as mutation-specific modulator therapies, have substantially expanded life expectancy because the latter relies mainly upon the progression of pulmonary complications [5]. However, accumulating evidence suggests the available therapeutic strategies are frequently inadequate to completely eradicate the involved pathogens [8], while standard dosing schemes may result in sub-therapeutic antibiotic levels, thus increasing the risk of treatment failure and most importantly, augmenting the appearance of antimicrobial resistance (AMR) [10]; the widespread alternating use of ‘suppressive’ and ‘curative’ antibiotic schemes increases the risk of AMR even further [11].

Notwithstanding, the evaluation of AMR is demanding; conventional laboratory antibiotic susceptibility-testing techniques rely on the interpretation of planktonic cultures, which are not entirely representative of the lung (micro) environment [12]. Indeed, the administration of an antibiotic to which a pathogen is resistant in vitro does not steadily prejudge a poor clinical result and vice versa [13]. This is an existing concern in individuals with chronic Pseudomonas aeruginosa and other non-fermenting Gram-negative rod (NFGR) infections [14]. Evidence has also demonstrated pathogens in CF patients commonly form biofilms, which renders them more resistant to a large spectrum of antibiotics [15]. Additionally, features linked to modified pharmacokinetics and pulmonary parenchyma penetration make the dosing of antibiotics in CF even more challenging [16].

2. Antibiotic Susceptibility and Biofilm Formation