**1. Introduction**

Cystic fibrosis (CF) is an autosomal recessive disease which basis on a dysfunctional cystic fibrosis transmembrane conductance regulator (CFTR) protein [1]. It is an inherited chronic disease that remains a common cause of morbidity and mortality in affected patients [2]. Also, it is a monogenic autosomal recessive condition affecting approximately 1 in 3000 of the Caucasian population and involves multiple organs, predominantly the lungs, gastrointestinal tract, pancreas, and liver [3].

Mutations in CFTR gene are resulted in defective mucociliary clearance leading to the production of thick and sticky bronchial mucus. This mucus facilitates the entrapment of viruses, bacteria, and fungal spores and acts as a suitable environment for growth of these microorganisms [4]. High morbidity and mortality rates are secondary to recurrent respiratory infections, which, when associated with this obstructive lung disease, lead to respiratory insufficiency [5]. Complex microorganisms and microbial communities can be identified in the distal airways in a

variety of respiratory diseases, including CF [6]. Chronic infection is the defined characteristics of CF airway disease. Conditions within the airways of patients living with CF are conducive to colonization by a variety of opportunistic bacterial, viral, and fungal pathogens [7].

Also, bacterial strains that colonize the respiratory tract include *Haemophilus influenzae*, *Staphylococcus aureus*, *Pseudomonas aeruginosa* [8], and *Burkholderia cepacia*; these have been recorded as the main common CF pathogens. Traditionally, *Pseudomonas aeruginosa* has been regarded as the main pathogen in CF, and chronic infections have been linked to disease morbidity and mortality [9]. Little attention has been paid to the role of *Aspergillus* sp. and other filamentous fungi in CF. It has become more apparent, however, that *Aspergillus* sp. may play an important role in chronic lung disease in CF [10]. This chapter discusses the complications of microorganisms in patients with cystic fibrosis, including bacterial, fungal, and viral pathogens and their effects on this disease leading to an increased risk of mortality.
