The ␥-proteobacterium Francisella tularensis is one of the most infectious human pathogens, and the highly virulent organism F. tularensis subsp. tularensis (type A) and less virulent organism F. tularensis subsp. holarctica (type B) are most commonly associated with significant disease in humans and animals. Here we report the complete genome sequence and annotation for a low-passage type B strain (OSU18) isolated from a dead beaver found near Red Rock, Okla., in 1978. A comparison of the F. tularensis subsp. holarctica sequence with that of F. tularensis subsp. tularensis strain Schu4 (P. Larsson et al., Nat. Genet. 37:153-159, 2005) highlighted genetic differences that may underlie different pathogenicity phenotypes and the evolutionary relationship between type A and type B strains. Despite extensive DNA sequence identity, the most significant difference between type A and type B isolates is the striking amount of genomic rearrangement that exists between the strains. All but two rearrangements can be attributed to homologous recombination occurring between two prominent insertion elements, ISFtu1 and ISFtu2. Numerous pseudogenes have been found in the genomes and are likely contributors to the difference in virulence between the strains. In contrast, no rearrangements have been observed between the OSU18 genome and the genome of the type B live vaccine strain (LVS), and only 448 polymorphisms have been found within non-transposase-coding sequences whose homologs are intact in OSU18. Nonconservative differences between the two strains likely include the LVS attenuating mutation(s).

Background Bacillus spores are notoriously resistant to unfavorable conditions such as UV radiation, γ-radiation, H2O2, desiccation, chemical disinfection, or starvation. Bacillus pumilus SAFR-032 survives standard decontamination procedures of the Jet Propulsion Lab spacecraft assembly facility, and both spores and vegetative cells of this strain exhibit elevated resistance to UV radiation and H2O2 compared to other Bacillus species.Principal FindingsThe genome of B. pumilus SAFR-032 was sequenced and annotated. Lists of genes relevant to DNA repair and the oxidative stress response were generated and compared to B. subtilis and B. licheniformis. Differences in conservation of genes, gene order, and protein sequences are highlighted because they potentially explain the extreme resistance phenotype of B. pumilus. The B. pumilus genome includes genes not found in B. subtilis or B. licheniformis and conserved genes with sequence divergence, but paradoxically lacks several genes that function in UV or H2O2 resistance in other Bacillus species.SignificanceThis study identifies several candidate genes for further research into UV and H2O2 resistance. These findings will help explain the resistance of B. pumilus and are applicable to understanding sterilization survival strategies of microbes.

The draft genome sequence of Mannheimia haemolytica A1, the causative agent of bovine respiratory disease complex (BRDC), is presented. Strain ATCC BAA-410, isolated from the lung of a calf with BRDC, was the DNA source. The annotated genome includes 2,839 coding sequences, 1,966 of which were assigned a function and 436 of which are unique to M. haemolytica. Through genome annotation many features of interest were identified, including bacteriophages and genes related to virulence, natural competence, and transcriptional regulation. In addition to previously described virulence factors, M. haemolytica encodes adhesins, including the filamentous hemagglutinin FhaB and two trimeric autotransporter adhesins. Two dual-function immunoglobulin-protease/adhesins are also present, as is a third immunoglobulin protease. Genes related to iron acquisition and drug resistance were identified and are likely important for survival in the host and virulence. Analysis of the genome indicates that M. haemolytica is naturally competent, as genes for natural competence and DNA uptake signal sequences (USS) are present. Comparison of competence loci and USS in other species in the family Pasteurellaceae indicates that M. haemolytica, Actinobacillus pleuropneumoniae, and Haemophilus ducreyi form a lineage distinct from other Pasteurellaceae. This observation was supported by a phylogenetic analysis using sequences of predicted housekeeping genes.Mannheimia haemolytica serotype A1 is the principle bacterial pathogen associated with bovine respiratory disease complex, also known as bovine shipping fever (25, 31). M. haemolytica resides in the upper respiratory tracts of healthy ruminants, although in immunocompromised animals, such as those with a preexisting viral infection, M. haemolytica can descend into the lungs, leading to pneumonia. The mortality and morbidity associated with this disease cause substantial losses to the cattle industry (25, 31). Hence, much research on M. haemolytica is directed at understanding its virulence and designing vaccines to protect cattle (31).M. haemolytica is a member of the family Pasteurellaceae, which is classified among the ␥-proteobacteria and includes human and animal pathogens of the genera Mannheimia, Pasteurella, Haemophilus, Actinobacillus, and Histophilus (31). M. haemolytica (formerly Pasteurella haemolytica) is classified in the genus Mannheimia based upon 16S rRNA sequence phylogeny and DNA-DNA hybridizations (3). The family Pasteurellaceae includes several members whose genomes have been sequenced: Haemophilus influenzae, Pasteurella multocida, Mannheimia succiniciproducens, Actinobacillus pleuropneumoniae, Histophilus somni, Haemophilus ducreyi, and Actinobacillus actinomycetemcomitans.The primary virulence factor of M. haemolytica is considered the leukotoxin. It is a calcium-dependent toxin that is a member of the RTX family of toxins. Cytolytic at low concentrations and apoptotic at high concentrations, the leukotoxin provokes an inflammatory response that can lead to intense ed...

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