We cannot identify any clear gene or constellation of genes that might account
for greater UUR virulence in some situations; although we do note a difference in the genes whose products are associated with resistance to H2O2, a known microbial pathogenicity factor. The widely different clinical outcomes of ureaplasmal infection could be the result of the presence or absence of potential pathogenicity factors in the colonizing ureaplasma strain. Alternatively, it may be more likely that the different clinical outcomes are either all or in part the result of patient to patient differences in terms of autoimmunity and microbiome. Future studies of ureaplasma biology should concentrate on the development of molecular tools for the generation of ureaplasma gene knock-out mutants for example, in order to study genes potentially involved in pathogenicity. The SAHA HDAC concentration sequenced Selleckchem Bleomycin genomes can aid in the development of such tools, by identifying transposons, integrated phage genomes, and genes involved in horizontal gene transfer. To aid the identification of potential pathogenicity factors, the large collection of clinical isolates should be explored for presence/absence of candidate genes. Considering the selleck chemical low cost of sequencing nowadays, the genomes of isolates from
patients with different conditions should be sequenced and their comparison should further aid the identification of genes involved in differential pathogenicity. Methods Sequencing methods for ATCC and 4 clinical isolates Ureaplasmas were grown in 10B medium and phenol chloroform extracted as described previously [25]. We randomly fragmented through shearing the purified genomic DNA from the 14 ATCC type strains and generated 1–2 kbp and 4–6 kbp fragment libraries. Using Sanger
chemistry and ABI 3730 DNA sequencers, each serovar was sequenced to 8-12X redundancy. In order to obtain data to complete the genome sequence of Serovar 2, the Sanger data were supplemented with 454 BCKDHA pyrrosequencing (Roche) data. We sequenced the 4 clinical isolates only using 454 chemistry. Genome sequences produced with Sanger chemistry were assembled using the Celera Assembler. The 454 data were assembled using the Newbler Software Package for de novo genome assembly. Annotation All 14 ureaplasma strains were annotated using the JCVI Prokaryotic Annotation Pipeline followed by manual quality checks and manual curration to enhance the quality of annotation before being submitted to NCBI. Annotation was done on various levels, the individual protein level, the pathways and the multiple genome comparisons. The annotation pipeline has two distinct modules: one for structural annotation and the other for functional annotation. The structural annotation module predicts an extensive range of genomic features in the genome.