About

The ESKAPE pathogens are the group of pathogens that are the leading cause of nosocomial infections throughout the world. The ESKAPE acronym stands for Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species. Understanding the resistance and virulence mechanisms of these bacteria is crucial to combat public health challenges. AMR (Antimicrobial Resistance) is considered to be the biggest threat to public health as it continues to evolve and disseminate beyond geographical boundaries and across three components of “One Health” viz., Human health, Animal health, and environmental health. This dynamic dashboard presents information on resistomes, virulomes, and mobilomes in the genome of ESKAPE pathogens sequenced worldwide and submitted to the public database. The primary sources for the genome and the associated metadata are collected from the NCBI Pathogen detection website and analyzed by ABRicate for the mass screening of genomes to mine AMR, virulence, and mobile genetic elements.

With recent advances in quick and cost-effective DNA sequencing technologies, a huge amount of bacterial genomic data is being generated from different continents and deposited in public repositories. These data would provide the best opportunity to gather the individuating traits of a pathogen. This project is aimed to analyze the percentage of AMR-associated genes, virulence genes, and mobile genetic elements among the draft genomes of ESKAPE pathogens retrieved from a public database. Further the project is also aimed at comparing the genes detected with respective genome metadata, performing spatiotemporal analysis, and developing future trends prediction models. In this project, scientists from across the globe with microbial and biomedical backgrounds collaborated together to perform a global genome analysis of ESKAPE pathogens and develop a platform to display the global spatiotemporal trends in resistomes, virulomes, and mobilomes. The current project includes retrieval of draft genome datasets and associated metadata from the NCBI pathogens database, performing the search of resistomes, virulomes, and mobilome genetic elements, and representation of results using suitable statistical tools. The dashboard is a user-friendly web interface that allows users to access the ESKAPE genome data and run analysis based on various parameters such as isolate collection year, geographical location of isolate, and source of isolation. The dashboard offers outputs that could be used for species-specific profiling or comparative analysis among ESKAPE pathogens.

1. Data Source:
   • Genome data were retrieved from NCBI Pathogens (https://www.ncbi.nlm.nih.gov/pathogens)
   • Reference databases for ABRicate:

   Antibiotic resistance gene – CARD database
   Virulence genes – VFDB database
   Mobile genetic elements – Plasmidfinder

2. Methodology:
   • The draft genome data retrieved from NCBI pathogens were subjected to AMR genes, virulence genes, and mobile genetic elements detection using ABRicate.
   • The results were curated and combined with genome metadata in Microsoft excel sheets and used for dashboard analysis.
   • The detailed methodology followed is provided in the link given below.

• Organizations:
  1. Nitte University Centre for Science Education & Research, Nitte (DU), Mangaluru, Karnataka, 575018, India AMR Insights B.V., Keizersgracht 482, 1017 EG Amsterdam, Netherlands
  2. SRM University-AP, Neerukonda, Mangalagiri Mandal, Guntur District, Andhra Pradesh - 522 240, India
  3. AMR Insights B.V., Keizersgracht 482, 1017 EG Amsterdam, Netherlands

• Co-ordinating team:
  1. Maarten B.M. van Dongen
  2. Jayaseelan Murugaiyan
  3. Ballamoole Krishna Kumar
  4. Kattapuni Suresh Prithvisagar
  5. Kivumbi Mark Tefero
  6. Tilocca Bruno
  7. Mohsin Mashkoor
  8. Ekwanzala Mutshiene Deogratias
  9. Saranya Adukkadukkam
  10. Zhao Jinxin
  11. Fatoba Dorcas