4 Notes
1. Platforms usually provide some quality control measures and
follow protocols for filtering sequencing artifacts.
2. Leptospira strains have genomes that are 3.8–4.6 Mb in size
with 35–45% GC content.
3. It is important to perform whole-genome sequencing from a
clonal culture to avoid comparing mixed genomes. Isolation
from an individual colony on an agar plate is, therefore, recommended to recover clonal Leptospira cultures [15].
4. A simulation of the effect of missing data (uncalled cgMLST
alleles) on the clustering results showed that cluster assignment
is robust even with high amounts of missing data (affecting up
to 400 loci out of 545) [5], indicating that even incomplete
genomes should be typeable by cgMLST.
Table 1
(continued)
Species
Isolate
BIGSdb
id
Phylogenetic
group
Country
Source
L. perdikensis
201702692
585
S1
Malaysia
Environment
L. ellinghausenii
201800220
632
S1
Japan
Environment
L. terpstrae
ATCC
700639
634
S1
China
Environment
L. montravelensis
201800279
658
S1
New
Caledonia
Environment
L. bourretii
201800280
659
S1
New
Caledonia
Environment
L. noumeaensis
201800287
666
S1
New
Caledonia
Environment
L. kanakyensis
201800292
670
S1
New
Caledonia
Environment
L. ilyithenensis
201400974
2
S2
Algeria
Environment
L. ognonensis
201702476
580
S2
France
Environment
L. kobayashii
E30
587
S2
Japan
Environment
L. ryugenii
YH101
588
S2
Japan
Environment
L. idonii
201300427
630
S2
Japan
Environment
a
L. yasudae and L. stimsonii [12] are presented here as L. dzianensis and L. putramalaysiae [6]
b
L. tipperaryensis was originatelly described as L. alstonii [13] and later on reclassified as a new species and named
L. tipperaryensis [6]
18
Linda Grillova ´ and Mathieu Picardeau