Comparative genomics and genetic diversity of Moraxella associated with infectious bovine keratoconjunctivitis: insights into pathogenicity and taxonomy

Abstract

Infectious bovine keratoconjunctivitis (IBK) is a widespread ocular disease in cattle, characterized by high morbidity and significant economic impact due to reduced weight gain, production losses, and costs associated with management and treatment. Classically, its etiology has been attributed to Moraxella bovis; however, advances in molecular approaches have broadened our understanding of the microbial diversity associated with the disease, revealing multiple Moraxella species in cattle. In this context, this thesis aimed to investigate the diversity, phenotypic and genomic characterization, as well as the taxonomic and evolutionary relationships of Moraxella spp. isolated from cattle with clinical signs of IBK in Brazil. The work was structured into four chapters: the first reports the first identification of Moraxella oculi associated with IBK outbreaks in the country; the second presents the phenotypic and genotypic characterization and proposes a novel species, Moraxella tarda; the third addresses the comparative analysis of eight isolates representing different species and genotypes within the genus, based on whole-genome data; and the fourth discusses the taxonomic and evolutionary implications of the findings, with emphasis on the relationship between Moraxella bovoculi and Moraxella ovis. Taken together, the results expand the number of Moraxella species described in association with cattle in Brazil and highlight intra- and interspecific diversity within the genus. Comparative genomic analyses based on complete genomes revealed patterns of conservation and variability in genes associated with surface proteins, adhesion, secretion systems, and host interaction, highlighting potential mechanisms involved in bacterial adaptation. In addition, genomic islands were identified, showing signatures consistent with horizontal gene transfer and suggesting a role in the acquisition of adaptive traits. Furthermore, the integration of genomic and comparative evidence supports the need for taxonomic reassessment within the M. bovoculi–M. ovis complex, indicating close phylogenomic relationships and possible inconsistencies in current species delimitation. These findings reinforce the importance of genome-based approaches for accurate identification and classification of Moraxella spp. in cattle. Overall, this work advances the understanding of the diversity, evolution, and genomic organization of Moraxella associated with cattle and provides insights to support improved diagnostic tools, epidemiological surveillance, and more effective control strategies for IBK in bovine production systems.