LeptoDB: an integrated database of genomics and proteomics resource of Leptospira.

Shruti Beriwal,Priyanka Sharma,Vibhisha Vaghasia,Prabhakar D Pandit,Subhash Soni,Shivarudrappa B Bhairappanavar,Zuber M Saiyed,Afzal Ansari,Kumari Snehkant Lata,Nikhil Padhiyar,Deven Bhatt,Jayashankar Das

doi:10.1093/database/bay057

Shruti Beriwal, Priyanka Sharma + Show 10 more

Open Access

https://doi.org/10.1093/database/bay057

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Abstract

Leptospirosis is a potentially fatal zoo-anthroponosis caused by pathogenic species of Leptospira belonging to the family of Leptospiraceae, with a worldwide distribution and effect, in terms of its burden and risk to human health. The ‘LeptoDB’ is a single window dedicated architecture (5 948 311 entries), modeled using heterogeneous data as a core resource for global Leptospira species. LeptoDB facilitates well-structured knowledge of genomics, proteomics and therapeutic aspects with more than 500 assemblies including 17 complete and 496 draft genomes encoding 1.7 million proteins for 23 Leptospira species with more than 250 serovars comprising pathogenic, intermediate and saprophytic strains. Also, it seeks to be a dynamic compendium for therapeutically essential components such as epitope, primers, CRISPR/Cas9 and putative drug targets. Integration of JBrowse provides elaborated locus centric description of sequence or contig. Jmol for structural visualization of protein structures, MUSCLE for interactive multiple sequence alignment annotation and analysis. The data on genomic islands will definitely provide an understanding of virulence and pathogenicity. Phylogenetics analysis integrated suggests the evolutionary division of strains. Easily accessible on a public web server, we anticipate wide use of this metadata on Leptospira for the development of potential therapeutics.Database URL: http://leptonet.org.in

Highlights

Leptospirosis is an emerging potentially fatal zooanthroponosis with a worldwide occurrence spanning developing as well as developed countries [1,2,3]
A methodical approach is applied for building LeptoDB wherein wide range of information, interesting findings and analysis has been amalgamated
As on 5 March 2018, genomic data of 513 Leptospira serovars with distribution of pathogenic (94%), saprophytic (3.5%) and intermediate (2.5%) implies data on pathogenic strains dominates the database proposing the emergence of genome level studies to evade and manage the disease

Summary

Introduction

Leptospirosis is an emerging potentially fatal zooanthroponosis with a worldwide occurrence spanning developing as well as developed countries [1,2,3]. This disease is caused by pathogenic Leptospira species belonging to family Leptospiraceae. 1.03 million cases are reported globally with 60 000 deaths with highest morbidity in the resource poor settings and where no routine surveillance is performed [4]. Real time surveillance reports of 787 global alerts for Leptospirosis by healthmap (http://www.healthmap.org/en/) between 2007 and 2013 suggested its epidemic potential [5]

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