Epidemiology, population structure, and pathogenesis of opportunistic respiratory tract colonising bacteria

[eng] The bacterial colonisation of the respiratory tract is critical for health as it establishes a symbiotic relationship between the bacterial community and the host. Haemophilus influenzae and Staphylococcus aureus are two opportunistic microorganisms that usually colonise the respiratory tract, and while their interaction is usually asymptomatic, in some cases colonisation is the first step before the development of severe infections. From a microbiological perspective, the goals of this thesis focus on studying the epidemiology, the population structure, and the pathogenesis of these microorganisms, since changes in some of these factors may influence the development of serious diseases. We provided an update on H. influenzae disease at the Hospital Universitari de Bellvitge between 2014 and 2019, and compared its evolution to a previous period, 2008 and 2013. The overall incidence of H. influenzae disease was 2.07 cases per 100,000 population, and remained constant between the two periods. During the second period (2014-2019), the rate of ampicillin resistance increased from 10% to 17.6%, mainly due to the production of β-lactamase TEM-1. Non-typeable H. influenzae (NTHi) strains were the leading cause of invasive H. influenzae disease in both study periods (84.3% and 85.3%, respectively). NTHi population was genetically heterogeneous, and its classification into six clades (I-VI) based on the presence and absence of 17 accessory genes showed that most of them were clustered in clade V. Strains from clade V and grouped the most frequent NTHi STs (ST3, ST103, ST160), and were associated with the production of β-lactamase TEM-1. On the other hand, capsulated strains were uncommon in invasive disease, with serotype f being the most prevalent (8.8%). We analysed the population structure and the pangenome of capsulated strains, paying especial attention to serotype f, which is rising among cases of invasive disease in Europe. Capsulated genomes belonged to a small number of clonal complexes (CCs) associated ...