Comparative genomic analysis between the Haemophilus influenzae biogroup aegyptius Brazilian purpuric fever invasive strain F3031 and the Haemophilus influenzae biogroup aegyptius non-invasive strain F1947

by McGillivary, Glen.

Comparative Genomic Analysis Between the Haemophilus influenzae biogroup aegyptius Brazilian Purpuric Fever Invasive Strain F3031 and the Haemophilus influenzae biogroup aegyptius Non-invasive Strain F1947 By Glen McGillivary Haemophilus influenzae biogroup aegyptius (H. aegyptius) strain F3031 is the causative agent of Brazilian purpuric fever (BPF), a serious hemorrhagic disease of humans. The H. aegyptius strain F1947 is an isolate that was taken from a Brazilian child who acquired conjunctivitis but did not develop BPF. A genome subtraction procedure was utilized to isolate DNA specific to the F3031 strain and several subtracted clones were found to have no or poorly described homologs in GenBank, some translated products were similar to proteins in other bacteria, and some had similarity to phage-related proteins. One of the subtracted fragments had sequence similarity to IgA1 proteases and this fragment was found to localize to the region of the sequenced F3031 iga1 gene which would encode the proposed active site. The protease from the F3031 strain cleaved IgA1 with a different specificity than its cognate protease in the F1947 strain. Eight of the other F3031-specific subtracted fragments were found to be part of a genomic island that is not found in the F1947 strain. This 34,387-bp genomic island contains 44 predicted ORFs and is almost perfectly conserved in several other bacterial strains. The association of genomic island-like sequences in more pathogenic bacterial strains suggests that genomic island-like sequences have a role in virulence and the proximity of transposon, inverted repeat, and nutrient transport gene remnants in multiple organisms suggests that the island has been involved in the evolution of other species. The F3031 and F1947 strains contain similar but distinct plasmids which act as markers for defining BPF and non-BPF H. aegyptius strains, respectively. The resident plasmids pF3031 and pF1947 were sequenced and were found to encode 34 ORFs of which only three have similar sequences to other known Haemophilus sequences. A majority of the ORFs in both plasmids seem dedicated to expressing proteins involved in conjugation although the conditions for conjugation were not found. The two plasmids were shown to differ in several ways of which the most important was a truncation in a gene encoding the conjugation protein TraL in the pF1947 plasmid. Comparative Genomic Analysis Between the Haemophilus influenzae biogroup aegyptius Brazilian Purpuric Fever Invasive Strain F3031 and the Haemophilus influenzae biogroup aegyptius Non-invasive Strain F1947 A Dissertation Submitted to the Faculty of Miami University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Microbiology By Glen McGillivary Miami University Oxford, OH 2004 Dissertation Director: Luis A. Actis, Ph.D.