Whole genome sequencing and de novo assembly of three virulent Indian isolates of Leptospira

• Published in: Infection, genetics and evolution genetics and evolution, 2020-11, Vol.85, p.104579, Article 104579
• Main Authors: Lata, Kumari Snehkant, Vaghasia, Vibhisha, Bhairappanavar, Shivarudrappa B., Kumar, Swapnil, Ayachit, Garima, Patel, Saumya, Das, Jayashankar
• Format: Article
• Language: English
• Subjects: Bioinformatics; Genome; Infectious disease; Leptospira interrogans, santarosai, kirshneri; Leptospirosis
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2020.104579

Leptospirosis is a re-emerging bacterial zoonosis caused by pathogenic Leptospira, with a worldwide distribution and becoming a major public health concern. Prophylaxis of this disease is difficult due to several factors such as non-specific variable clinical manifestation, presence of a large number of serovar, species and asymptomatic reservoir hosts, lack of proper diagnostics and vaccines. Despite its global importance and severity of the disease, knowledge about the molecular mechanism of pathogenesis and evolution of pathogenic species of Leptospira remains limited. In this study, we sequenced and analyzed three highly pathogenic species of Indian isolates of Leptospira (interrogans, santarosai, and kirschneri). Additionally, we identified some virulence-related and CRISPR-Cas genes. The virulent analysis showed 232 potential virulence factors encoding proteins in L. interrogans strain Salinem and L. santarosai strain M-4 genome. While the genome of L. kirschneri strain Wumalasena was predicted to encode 198 virulence factor proteins. The variant calling analysis revealed 1151, 19,786, and 22,996 single nucleotide polymorphisms (SNPs) for L. interrogans strain Salinem, L. kirschneri strain Wumalasena and L. santarosai strain M-4, respectively, with a maximum of 5315 missense and 12,221 synonymous mutations for L. santarosai strain M-4. The structural analyses of genomes indicated potential evidence of inversions and structural rearrangment in all three genomes. The availability of these genome sequences and in silico analysis of Leptospira will provide a basis for a deeper understanding of their molecular diversity and pathogenesis mechanism, and further pave a way towards proper management of the disease. •Genomic features of three pathogenic Leptospira species of Indian isolates were characterized by whole genome sequencing.•Prophage, CRISPR-Cas and virulence factor analyses were performed.•Phylogenetic and genomic structural variation analysis were achieved by comparative analysis.•Genomic data of these pathogenic Indian isolates will ameliorate the knowledge of diversity and pathogenicity of Leptospira.