epidemiology and general biology of Leptospira spp. First, cgMLST
can be applied to pathogenic (sub-clade P1), intermediate
(sub-clade P2), and saprophytic isolates (sub-clades S1 and S2)
and, thus, has a potential to elucidate the role of intermediates,
which is a group of strains of unclear pathogenicity from the clinical
perspective phylogenetically related to pathogens. cgMLST has a
high discrimination power resulting in the identification of species,
clades, clonal groups (CGs), sequencing types (STs), and most
probable serogroups. This would allow tracking of Leptospira
strains and could help, for example, the detection of new genotypes
and length of time for which a given genotype persists. The widespread use of this cgMLST scheme should enable the identification
of such relationships at the global level and over time. The Leptospira cgMLST database (https://bigsdb.pasteur.fr/leptospira/) is a
publicly available web-based database hosted at the Institut Pasteur.
At present, the database contains data from 1007 Leptospira strains
(08/28/2019).
The Bacterial Isolate Genome Sequence Database (BIGSdb)
platform was initially developed by Jolley and Maiden [7] for
automatic ST and CG assignments, for determination of new
alleles, for storage of sample metadata, for identification of new
associations between genotypes and metadata using various tools,
and for user-friendly visualization of molecular typing data using
breakdown options and external plug-ins such as Interactive Tree of
Life (iTOL) [8] and GrapeTree [9]. This chapter presents some
examples of how the WGS data can be used in BIGSdb for userfriendly visualization of phylogenic relationships among STs of
Leptospira.
2 Materials
2.1 Genome
Requirements
For submission, the treated WGS data are needed (i.e., low Phred
score base, trimming, exogenous oligonucleotide clipping,
sequencing error correction, and read coverage homogenization)
(see Note 1). Draft genomes with 50Â minimum coverage and a
minimum N50 of 10,000 nt are required (see Notes 2–4).
2.2 Information
on Isolates
Relevant information of isolates such as isolate identification
name/number, country of origin, biological source of sample,
year of isolation, serogroup and serovar, etc. are required.
2.3 Hardware/
Software
Requirements
The BIGSdb is an online database. As such, users do not need to
install a particular software.
12
Linda Grillova ´ and Mathieu Picardeau
can be applied to pathogenic (sub-clade P1), intermediate
(sub-clade P2), and saprophytic isolates (sub-clades S1 and S2)
and, thus, has a potential to elucidate the role of intermediates,
which is a group of strains of unclear pathogenicity from the clinical
perspective phylogenetically related to pathogens. cgMLST has a
high discrimination power resulting in the identification of species,
clades, clonal groups (CGs), sequencing types (STs), and most
probable serogroups. This would allow tracking of Leptospira
strains and could help, for example, the detection of new genotypes
and length of time for which a given genotype persists. The widespread use of this cgMLST scheme should enable the identification
of such relationships at the global level and over time. The Leptospira cgMLST database (https://bigsdb.pasteur.fr/leptospira/) is a
publicly available web-based database hosted at the Institut Pasteur.
At present, the database contains data from 1007 Leptospira strains
(08/28/2019).
The Bacterial Isolate Genome Sequence Database (BIGSdb)
platform was initially developed by Jolley and Maiden [7] for
automatic ST and CG assignments, for determination of new
alleles, for storage of sample metadata, for identification of new
associations between genotypes and metadata using various tools,
and for user-friendly visualization of molecular typing data using
breakdown options and external plug-ins such as Interactive Tree of
Life (iTOL) [8] and GrapeTree [9]. This chapter presents some
examples of how the WGS data can be used in BIGSdb for userfriendly visualization of phylogenic relationships among STs of
Leptospira.
2 Materials
2.1 Genome
Requirements
For submission, the treated WGS data are needed (i.e., low Phred
score base, trimming, exogenous oligonucleotide clipping,
sequencing error correction, and read coverage homogenization)
(see Note 1). Draft genomes with 50Â minimum coverage and a
minimum N50 of 10,000 nt are required (see Notes 2–4).
2.2 Information
on Isolates
Relevant information of isolates such as isolate identification
name/number, country of origin, biological source of sample,
year of isolation, serogroup and serovar, etc. are required.
2.3 Hardware/
Software
Requirements
The BIGSdb is an online database. As such, users do not need to
install a particular software.
12
Linda Grillova ´ and Mathieu Picardeau