bioRxiv2024
In Colombia, pathogenic knowledge of endemic Leptospira species is limited. Leptospira santarosai serogroup Autumnalis serovar Alice Strain JET was isolated from a patient from Uraba Antioquia, so it is necessary to know more about its genomic components and pathogenomics. A comparative analysis of the bacterial genome was carried out by computational biology. Complete information for analysis was obtained fromhttps://www.ncbi.nlm.nih.gov/from where the complete genome sequences of 67 species of the genus Leptospira spp were accessed. The genome of the Colombian strain consists of a major chromosome (chromosome I) and the minor chromosome (chromosome II), which add up to a total of 4.13 Mb. The chromosomes have a G+C percentage of 41.6% three genes for ribosomal RNA distributed 1 for the 23s subunit, 1 for the 16s subunit and 1 for the 5s subunit, 6 for other types of RNA and 37 transfer RNA genes. Two chromosomal pseudomolecules were inferred for the Colombian strain, assigning proteins 3,796 and 318 to chromosomes I and II respectively. Genomic identity analysis resulted in a nucleotide identity of 92.95% and a high degree of synteny between chromosomes. 53 and 68 exclusive proteins were identified for serovar Shermani and the Colombian strain respectively. Of the 68 proteins, most are hypothetical, however, nine transposases, two integrases and one membrane protein were identified. The Colombian strain shares orthologous proteins with members of the different subgroups of species that range between 3,286-2,600 with pathogenic species, 2,416-2,296 intermediate species and 1,972-1,864 saprophytic species and 40.98% of the proteins present in the genome of The Colombian strain has a high percentage of identity with the proteins of the main pathogenic species L. interrogans (80-100% similarity), which demonstrates a strong genetic relationship between the Colombian strain and the pathogenic subgroup. For the Colombian strain, it was found to contain CRISPR/Cas repeats and 9 families of class 1, type I and subtype IA and IE were located where each of these subtypes contained 8 cas genes; In addition, 25 proteins were found involved in the de novo biosynthesis of vitamin B12. In the Colombian strain, three species of different phage structures were found that could facilitate infection and subsequent colonization in the host. Therefore, the objective is to describe the structural and functional genomic composition of L. santarosai serovar Alice. The genomic characteristics evidenced are basic in the knowledge of the bacterial mechanisms, the evolutionary, phylogenetic and pathogenic analysis of Leptospira spp that affects the population of Colombian endemic areas.