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Application of Genomics to Understand the Pathogenic Microbial Diversity

  • Jhasketan Badhai
  • Sushanta Deb
  • Subrata K. DasEmail author
Chapter

Abstract

Conventional bacteriological, biochemical, and molecular methods used in diagnostic laboratories for identification of pathogens are laborious, time-consuming, and expensive. Moreover, it provides limited information which is not sufficient to evaluate the disease outbreak and epidemiological investigations. Due to drastic reduction in sequencing cost concomitant with an increase in the sequence quality, whole genome sequencing of prokaryotes based on NGS is economically feasible as a routine tool for clinical diagnostics and surveillance of pathogens. Availability of comprehensive biological information databases and advanced bioinformatics tools for analysis of pan-genomes, single nucleotide polymorphisms, virulence factors, antibiotic resistance, recombination, and lateral or horizontal gene transfer events have greatly facilitated the identification of emerging pathogenic strains, understanding their population dynamics, genomic plasticity, virulence and pathogenicity, and epidemiology. Genomics studies have greatly enriched our knowledge of various genetic events that have shaped pathogenic bacterial genomes and guided their evolution, such as mutations, insertions, deletions, duplications, inversions, transpositions, and recombination. Whole genome analyses of the classical mammalian Bordetella spp., Vibrio cholerae, and Salmonella enterica have revealed important features of their virulence and pathogenicity, as well as their evolution as successful human pathogens. Gene inactivation, polymorphism, accumulation of IS elements, and genome decay have guided the evolution of the classical Bordetella spp. as separate host-restricted pathogens, while the acquisition of pathogenicity islands by HGT mechanisms has the greatest impact on the evolution, virulence, and pathogenicity of Vibrio cholerae and Salmonella enterica.

Keywords

Genomics Pan-genome SNPs Virulence factors Antibiotic resistance Pathogenicity Recombination Horizontal gene transfer PAIs Bordetella Vibrio Salmonella 

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Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Jhasketan Badhai
    • 1
  • Sushanta Deb
    • 1
  • Subrata K. Das
    • 1
    Email author
  1. 1.Division of Molecular MicrobiologyInstitute of Life SciencesBhubaneswarIndia

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