Bioinformatics analysis of bacterial pathogens from East African camels Comparative genomics of Streptococcus agalactiae and Staphylococcus aureus

The camel is the most valuable livestock species in arid and semi-arid regions in the Greater Horn of Africa. Streptococcus agalactiae and Staphylococcus aureus are important pathogens for a wide range of hosts including camels, cattle and humans. Streptococcus agalactiae has been reported to cause infections of the skin, the respiratory tract, the mammary gland and the vaginal tract in camels. Staphylococcus aureus has been isolated from the nasal cavity, wound infections and mastitis from camels. Both pathogens account for decline in health and productivity of camels, hence causing economic losses to the inhabitants of arid and semi arid lands. To define candidate virulence traits in these bacteria, we compared the genomes of S. agalactiae and S. aureus. We sequenced and completely assembled the genomes of two S. agalactiae isolates ILRI005 and ILRI112 from abscessed case camels and an S. aureus isolate ILRI_Eymole1/1 from the nasal swab of camel in Kenya. To perform comparative analysis, we also sequenced and assembled an S. agalactiae isolate 09mas018883 from subclinical mastitis case cattle in Sweden. Mapping assembly, de novo assembly and post-assembly genome finishing were performed to obtain completely assembled genomes. Comparative genomics approach was applied to explore the genetic heterogeneity, core genome construction and protein repertoire comparison of these novel genomes, and to highlight potential virulence factors that could have contributed to the pathogenicity of these isolates in their hosts. Newly sequenced camel S. agalactiae genomes were compared with human and cattle S. agalactiae genomes. This comparison revealed that the two camel isolates were genetically close to each other but relatively distinct from other isolates, while cattle isolate 09mas018883 was genetically closer to the human isolates. Large proportion of the isolate-specific genes of the camel S. agalactiae isolates was clustered in putative phage insertions and genomic islands suggesting the lateral transfer of these putative phages. The two camel S. agalactiae isolates shared a novel potential virulent locus, the CRISPR2 (Cluster Regularly Interspaced Palindromic Repeats) locus. The two cattle S. agalactiae isolates and three human S. agalactiae isolates contained similar putative phage insertions. Important potential pathogenic factors found in all S. agalactiae isolates were CRISPR1 locus, cyl locus, capsular polysaccharide locus and pilus islands. Phylogenetic analysis of novel camel S. aureus genome of strain type ST30 and previously sequenced human S. aureus genomes of type Clonal Complex 30 (CC30) revealed that camel S. aureus isolate is genetically distinct from human S. aureus isolates of the same sequence type. Important features were also identified such as genes encoding bacterial adhesins and secretory proteins. The availability of genomic sequences of S. agalactiae and S. aureus from camels, their detailed bioinformatics analysis and identified potential virulence factors will foster the development of control measures such as molecular diagnostic assays and vaccines for control of S. agalactiae and S. aureus infections in camels. This will ensure improvement in health and productivity of camels.