Microbial Genomics and Pathogen Discovery*

Jennifer K. Spinler; Peera Hemarajata; James Versalovic

doi:10.1128/9781555817381.ch16

Chapter 16 : Microbial Genomics and Pathogen Discovery*

Authors: Jennifer K. Spinler, Peera Hemarajata, James Versalovic

Content Type: Reference

Publication Year: 2015

Category: Clinical Microbiology

Book DOI: 10.1128/9781555817381

Chapter DOI: 10.1128/9781555817381.ch16

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Microbial Genomics and Pathogen Discovery*, Page 1 of 2

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Abstract:

In recent years, our understanding of microbial diversity has grown tremendously as many previously unidentified bacterial, archaeal, and viral species have been discovered and sequenced. In the era of the human microbiome and metagenomics (chapter 15), large-scale DNA sequencing projects and advances in bioinformatics have yielded abundant data regarding human-associated microbes. As human microbiology rapidly expands beyond its past framework of cultured pathogens in the medical microbiology laboratory, opportunities for detection and identification of novel human pathogens associated with infectious diseases abound. In this chapter, we focus on specific or defined sets of pathogens associated with human infections, in contrast to microbial components of disease and microbial ecology. We begin with an overview of historical methodologies, followed by a brief description of the evolution of nucleic acid sequencing technologies. Finally, we describe how microarrays, nucleic acid sequencing technologies, and mass spectrometry are profoundly reshaping strategies aimed at pathogen discovery and identification.

Citation: Spinler J, Hemarajata P, Versalovic J. 2015. Microbial Genomics and Pathogen Discovery*, p 238-251. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch16

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Microbial Genomics and Pathogen Discovery*

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FIGURE 1

A timeline depicting major landmarks in medical microbiology and molecular microbiology that have enhanced pathogen discovery. doi:10.1128/9781555817381.ch16.f1

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10.1128/9781555817381/9781555817381.ch16.f1.gif

FIGURE 1

A timeline depicting major landmarks in medical microbiology and molecular microbiology that have enhanced pathogen discovery. doi:10.1128/9781555817381.ch16.f1

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FIGURE 2

A proposed workflow for bacterial, WGS-based molecular diagnostics. This workflow uses benchtop sequencing for data generation and implements cloud storage for central data storage and remote data processing. Double-headed arrows indicate constant updating of the central data repository and reference database. Reprinted from reference 128 with permission of Nature Publishing Group. doi:10.1128/9781555817381.ch16.f2

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FIGURE 2

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FIGURE 3

Phylogenetic analysis and genome assembly of Bradyrhizobium enterica, a novel organism associated with cord colitis. Assembly of the B. enterica genome included unmappable reads generated from WGS of samples from patients with cord colitis. (A) Multisequence alignment of 400 core protein-coding genes was used to generate a rooted phylogenetic tree showing the predicted evolutionary relationships between B. enterica and related species. (B) Genomic comparison of B. enterica to Bradyrhizobium japonicum. Dark blue lines on the inner circle depict genes present in the genome of B. enterica that are absent in the genome of B. japonicum. The outer circle depicts amino acid sequence identity of each B. enterica predicted protein to its closest homologue in B. japonicum. The middle circle is a representation of the contig assembly, with the borders of each contig (dark green) outlined in light green. Reprinted from reference 19 with permission of Massachusetts Medical Society. doi:10.1128/9781555817381.ch16.f3

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FIGURE 3

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Tables

Microbial Genomics and Pathogen Discovery*

/content/10.1128/9781555817381.mcm11.ch16.ch16.tab001

TABLE 1

Novel viruses discovered by Sanger sequencing methods

TABLE 1

Novel viruses discovered by Sanger sequencing methods

/content/10.1128/9781555817381.mcm11.ch16.ch16.tab002

TABLE 2

Novel viruses discovered by NGS methods

TABLE 2

Novel viruses discovered by NGS methods