Towards unravelling the genome of Avibacterium paragallinarum
Avibacterium paragallinarum is an avian pathogen and has the ability to cause vast economical losses. This bacterium forms part of the Pasteurellaceae family and factors contributing to pathogenicity, immunogenicity and serotyping are not clearly understood. One of the main questions that were addressed in this study was the identification of genetic tools are that is responsible for the NAD+- independence ability of this organism. NAD+ recycling genes were implicated for this bacterium and Av. paragallinarum seem to follow the recycling pathway as set out for the Pasteurellaceae family. Still the question regarding NAD+- independence remains unanswered as no complete pathway could be implicated for this trait. Furthermore, no plasmid(s) could be isolated that conferred this trait and no complete NAD+ synthesis pathway could be implicated. Only two genes were identified to form part of a NAD+-independent pathway which indicated that Av. paragallinarum may use genetic tools for NAD+-independence as set out for bacteria in general and not as the rest of the Pasteurellaceae family members. Plasmid isolation studies revealed only the plasmid p250 identical to the established plasmid p250 for Av. paragallinarum. Literature reports on two other native plasmids namely pYMH5 and pA14, however, these two plasmids could not be detected in any of the strains used in this study during plasmid screens. This study confirms and illustrates the integration of plasmid p250 within the genome of Av. paragallinarum by different serovars. In order to study this bacterium on a genomic level a whole genome sequencing project was launched. This project experienced vast amount of difficulties regarding the assembly of a complete genome for Av. paragallinarum. This bacterium contains numerous repeated regions within its genome which, with current sequencing technology, prevent the genome assembly into a single chromosome. A complete assembled genome can only be achieved when longer read lengths are available in high-throughput sequencing technologies and will thus enable clarification regarding the repeated regions. A pseudo-assembled molecule was sent to the JCVI for genome annotation. Annotated data revealed that Av. paragallinarum contains a high degree of complexity regarding its cell envelope which may shed light on pathogenicity and immunogenicity problems endured. This bacterium contains numerous mobile and extrachromosomal elements which contribute to the inability to close the genome of Av. paragallinarum. Nine site-specific integrases and 10 transposases were identified. These tools could allow for a high degree of genetic diversity within the Av. paragallinarum specie. Alongside these tools two putative prophages was identified for Av. paragallinarum. One prophage resembles the Mu-like prophages and was termed ФAvpmuC-2M, the other resembles the HP2-like prophages and was termed ФAvpC-2M-HP2.