Chapter 19
Identification and Characterization of Mycobacterial
Species Using Whole-Genome Sequences
Marco A. Riojas, Andrew M. Frank, Samuel R. Greenfield, Stephen P. King,
Conor J. Meehan, Michael Strong, Alice R. Wattam, and
Manzour Hernando Hazbo ´ n
Abstract
Whole-genome sequencing (WGS) has shown immense value in enabling identification and characterization of bacterial taxa. This is particularly true for mycobacteria, where culture-based characterization
becomes delayed by the inherently slow growth rate of these organisms. This chapter reviews the general
techniques behind WGS and their optimization, existing techniques for species-level identification and the
advantages of WGS for this purpose, and a variety of useful tools for the genomic characterization of
mycobacterial strains.
Key words Whole-genome sequence, DNA, Sequencing, ANI, dDDH, Species identification,
Mycobacteria
1 Introduction
Whole-genome sequencing (WGS) has proven to be an extremely
valuable tool for understanding the natural world around us. From
the first DNA genome to be sequenced (φX174: 5375 bp) [1] to
the Human Genome Project (Homo sapiens: 2.85 Gbp) [2–4] to
the largest genome sequenced to date (axolotl: 32 Gbp) [5], WGS
has allowed us to peer into the very instructions that encode life and
yielded valuable insights into how it functions.
The rapidly declining cost of WGS [6] has driven an explosion
in the number of sequencing projects and the amount of sequence
data available. As of December 2019, The National Center for
Biotechnology Information (NCBI) housed over 1.12 billion
whole-genome sequences, totaling 6.28 Â 10
12 bases [7].
Due to their smaller and simpler genomes, WGS has been
particularly useful in the identification and characterization of
microorganisms such as bacteria and viruses. One of the areas that
Tanya Parish and Anuradha Kumar (eds.), Mycobacteria Protocols, Methods in Molecular Biology, vol. 2314,
https://doi.org/10.1007/978-1-0716-1460-0_19, © Springer Science+Business Media, LLC, part of Springer Nature 2021
399
Identification and Characterization of Mycobacterial
Species Using Whole-Genome Sequences
Marco A. Riojas, Andrew M. Frank, Samuel R. Greenfield, Stephen P. King,
Conor J. Meehan, Michael Strong, Alice R. Wattam, and
Manzour Hernando Hazbo ´ n
Abstract
Whole-genome sequencing (WGS) has shown immense value in enabling identification and characterization of bacterial taxa. This is particularly true for mycobacteria, where culture-based characterization
becomes delayed by the inherently slow growth rate of these organisms. This chapter reviews the general
techniques behind WGS and their optimization, existing techniques for species-level identification and the
advantages of WGS for this purpose, and a variety of useful tools for the genomic characterization of
mycobacterial strains.
Key words Whole-genome sequence, DNA, Sequencing, ANI, dDDH, Species identification,
Mycobacteria
1 Introduction
Whole-genome sequencing (WGS) has proven to be an extremely
valuable tool for understanding the natural world around us. From
the first DNA genome to be sequenced (φX174: 5375 bp) [1] to
the Human Genome Project (Homo sapiens: 2.85 Gbp) [2–4] to
the largest genome sequenced to date (axolotl: 32 Gbp) [5], WGS
has allowed us to peer into the very instructions that encode life and
yielded valuable insights into how it functions.
The rapidly declining cost of WGS [6] has driven an explosion
in the number of sequencing projects and the amount of sequence
data available. As of December 2019, The National Center for
Biotechnology Information (NCBI) housed over 1.12 billion
whole-genome sequences, totaling 6.28 Â 10
12 bases [7].
Due to their smaller and simpler genomes, WGS has been
particularly useful in the identification and characterization of
microorganisms such as bacteria and viruses. One of the areas that
Tanya Parish and Anuradha Kumar (eds.), Mycobacteria Protocols, Methods in Molecular Biology, vol. 2314,
https://doi.org/10.1007/978-1-0716-1460-0_19, © Springer Science+Business Media, LLC, part of Springer Nature 2021
399