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Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications pp 49–82Cite as

Application of Genomics to Understand the Pathogenic Microbial Diversity

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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.

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Authors and Affiliations

  1. Division of Molecular Microbiology, Institute of Life Sciences, Bhubaneswar, Odisha, India

    Jhasketan Badhai, Sushanta Deb & Subrata K. Das

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  1. Jhasketan Badhai
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  2. Sushanta Deb
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Correspondence to Subrata K. Das .

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  1. Division of Biological Sciences & Engineering, Netaji Subhas University of Technology, New Delhi, Delhi, India

    Tulasi Satyanarayana

  2. Department of Biotechnology, Barkatullah University, Bhopal, Madhya Pradesh, India

    Bhavdish Narain Johri

  3. Division of Molecular Microbiology, Institute of Life Sciences, Bhubaneswar, Odisha, India

    Subrata Kumar Das

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Badhai, J., Deb, S., Das, S.K. (2019). Application of Genomics to Understand the Pathogenic Microbial Diversity. In: Satyanarayana, T., Johri, B., Das, S. (eds) Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications. Springer, Singapore. https://doi.org/10.1007/978-981-13-8315-1_3

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