Chapter 2
Core Genome Multi-locus Sequence Typing Analyses
of Leptospira spp. Using the Bacterial Isolate Genome
Sequence Database
Linda Grillova ´ and Mathieu Picardeau
Abstract
With the advent of whole-genome sequencing (WGS), comparative analysis has led to the use of core
genome MLST (cgMLST) schemes for the high-resolution reproducible typing of bacterial isolates. In
cgMLST, hundreds of loci are used for gene-by-gene comparisons of assembled genomes for studying the
genetic diversity of clinically important pathogens. Combination of the cgMLST data and metadata of the
isolates is useful for epidemiological investigations.
Here we present a cgMLST scheme for the high-resolution typing of isolates from the whole Leptospira
genus, enabling identification at the level of species, clades, clonal groups, and sequence types. We show
several examples how the cgMLST Leptospira database, which is a publicly available web-based database,
can be used for the analyses of WGS data of Leptospira isolates. This effort was undertaken in order to
facilitate international collaborations and support the global surveillance of leptospirosis.
Key words Genome, Core genome multi-locus sequence typing, Bacterial Isolate Genome Sequence
Database (BIGSdb)
1 Introduction
Molecular typing of bacterial isolates is a powerful tool for surveillance and epidemiology of diseases. Discrimination of genetic variants and characterization of the predominant Leptospira strains in
the environment, patients, or animal populations are essential for
identifying sources of infection and developing evidence-based
infection control and prevention strategies. Different molecular
typing schemes are currently available for pathogenic Leptospira
[1–4], but a harmonized typing tool needs to be established not
only for pathogenic species but also for the whole genus. A core
genome multi-locus sequence typing (cgMLST; based on 545 core
genes) was recently designed based on high-quality genome
sequences representing all known Leptospira species [5, 6]. This
scheme can significantly increase our understanding of the
Nobuo Koizumi and Mathieu Picardeau (eds.), Leptospira spp.: Methods and Protocols, Methods in Molecular Biology, vol. 2134,
https://doi.org/10.1007/978-1-0716-0459-5_2, © Springer Science+Business Media, LLC, part of Springer Nature 2020
11
Core Genome Multi-locus Sequence Typing Analyses
of Leptospira spp. Using the Bacterial Isolate Genome
Sequence Database
Linda Grillova ´ and Mathieu Picardeau
Abstract
With the advent of whole-genome sequencing (WGS), comparative analysis has led to the use of core
genome MLST (cgMLST) schemes for the high-resolution reproducible typing of bacterial isolates. In
cgMLST, hundreds of loci are used for gene-by-gene comparisons of assembled genomes for studying the
genetic diversity of clinically important pathogens. Combination of the cgMLST data and metadata of the
isolates is useful for epidemiological investigations.
Here we present a cgMLST scheme for the high-resolution typing of isolates from the whole Leptospira
genus, enabling identification at the level of species, clades, clonal groups, and sequence types. We show
several examples how the cgMLST Leptospira database, which is a publicly available web-based database,
can be used for the analyses of WGS data of Leptospira isolates. This effort was undertaken in order to
facilitate international collaborations and support the global surveillance of leptospirosis.
Key words Genome, Core genome multi-locus sequence typing, Bacterial Isolate Genome Sequence
Database (BIGSdb)
1 Introduction
Molecular typing of bacterial isolates is a powerful tool for surveillance and epidemiology of diseases. Discrimination of genetic variants and characterization of the predominant Leptospira strains in
the environment, patients, or animal populations are essential for
identifying sources of infection and developing evidence-based
infection control and prevention strategies. Different molecular
typing schemes are currently available for pathogenic Leptospira
[1–4], but a harmonized typing tool needs to be established not
only for pathogenic species but also for the whole genus. A core
genome multi-locus sequence typing (cgMLST; based on 545 core
genes) was recently designed based on high-quality genome
sequences representing all known Leptospira species [5, 6]. This
scheme can significantly increase our understanding of the
Nobuo Koizumi and Mathieu Picardeau (eds.), Leptospira spp.: Methods and Protocols, Methods in Molecular Biology, vol. 2134,
https://doi.org/10.1007/978-1-0716-0459-5_2, © Springer Science+Business Media, LLC, part of Springer Nature 2020
11