of variable-number tandem-repeat loci in Leptospira interrogans sensu stricto. J Clin Microbiol 43(2):539–545
3. Slack AT, Dohnt MF, Symonds ML, Smythe
LD (2005) Development of a multiple-locus
variable number of tandem repeat analysis
(MLVA) for Leptospira interrogans and its
application to Leptospira interrogans serovar
Australis isolates from Far North Queensland,
Australia. Ann Clin Microbiol Antimicrob 4:10
4. Ahmed N, Devi SM, Valverde M d l A,
Vijayachari P, Machang’u RS, Ellis WA et al
(2006) Multilocus sequence typing method
for identification and genotypic classification
of pathogenic Leptospira species. Ann Clin
Microbiol Antimicrob 5:28
5. Guglielmini J, Bourhy P, Schiettekatte O,
Zinini F, Brisse S, Picardeau M (2019)
Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and
global surveillance. PLoS Negl Trop Dis 13(4):
e0007374
6. Vincent AT, Schiettekatte O, Goarant C, Neela
VK, Bernet E, Thibeaux R et al (2019) Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of
genomics. PLoS Negl Trop Dis 13(5):
e0007270
7. Jolley KA, Maiden MC (2010) BIGSdb: scalable analysis of bacterial genome variation at
the population level. BMC Bioinformatics 11
(1):595
8. Letunic I, Bork P (2016) Interactive tree of life
(iTOL) v3: an online tool for the display and
annotation of phylogenetic and other trees.
Nucleic Acids Res 44(W1):W242–W245
9. Zhou Z, Alikhan NF, Sergeant MJ,
Luhmann N, Vaz C, Francisco AP et al
(2018) GrapeTree: visualization of core genomic relationships among 100,000 bacterial
pathogens. Genome Res 28(9):1395–1404
10. Saitou N, Nei M (1987) The neighbor-joining
method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425
11. Fukami K, Tateno Y (1989) On the maximum
likelihood method for estimating molecular
trees: uniqueness of the likelihood point. J
Mol Evol 28(5):460–464
12. Casanovas-Massana A, Hamond C, Santos LA,
de Oliveira D, Hacker KP, Balassiano I et al
(2019) Leptospira yasudae sp. nov. and Leptospira stimsonii sp. nov., two new species of the
pathogenic group isolated from environmental
sources. Int J Syst Evol Microbiol. https://doi.
org/10.1099/ijsem.0.003480
13. Nally JE, Bayles DO, Hurley D, Fanning S,
McMahon BJ, Arent Z (2016) Complete
genome sequence of Leptospira alstonii serovar
Room22 strain GWTS #1. Genome Announc 4
(6):e01230-16
14. Yoon SH, Ha SM, Lim J, Kwon S, Chun J
(2017) A large-scale evaluation of algorithms
to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110(10):1281–1286
15. Thibeaux R, Girault D, Bierque E, Soupe ´-Gilbert M-E, Rettinger A, Douye `re A et al
(2018) Biodiversity of environmental Leptospira: improving identification and revisiting
the diagnosis. Front Microbiol 9:816
cgMLST Scheme for Leptospira
21
3. Slack AT, Dohnt MF, Symonds ML, Smythe
LD (2005) Development of a multiple-locus
variable number of tandem repeat analysis
(MLVA) for Leptospira interrogans and its
application to Leptospira interrogans serovar
Australis isolates from Far North Queensland,
Australia. Ann Clin Microbiol Antimicrob 4:10
4. Ahmed N, Devi SM, Valverde M d l A,
Vijayachari P, Machang’u RS, Ellis WA et al
(2006) Multilocus sequence typing method
for identification and genotypic classification
of pathogenic Leptospira species. Ann Clin
Microbiol Antimicrob 5:28
5. Guglielmini J, Bourhy P, Schiettekatte O,
Zinini F, Brisse S, Picardeau M (2019)
Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and
global surveillance. PLoS Negl Trop Dis 13(4):
e0007374
6. Vincent AT, Schiettekatte O, Goarant C, Neela
VK, Bernet E, Thibeaux R et al (2019) Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of
genomics. PLoS Negl Trop Dis 13(5):
e0007270
7. Jolley KA, Maiden MC (2010) BIGSdb: scalable analysis of bacterial genome variation at
the population level. BMC Bioinformatics 11
(1):595
8. Letunic I, Bork P (2016) Interactive tree of life
(iTOL) v3: an online tool for the display and
annotation of phylogenetic and other trees.
Nucleic Acids Res 44(W1):W242–W245
9. Zhou Z, Alikhan NF, Sergeant MJ,
Luhmann N, Vaz C, Francisco AP et al
(2018) GrapeTree: visualization of core genomic relationships among 100,000 bacterial
pathogens. Genome Res 28(9):1395–1404
10. Saitou N, Nei M (1987) The neighbor-joining
method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425
11. Fukami K, Tateno Y (1989) On the maximum
likelihood method for estimating molecular
trees: uniqueness of the likelihood point. J
Mol Evol 28(5):460–464
12. Casanovas-Massana A, Hamond C, Santos LA,
de Oliveira D, Hacker KP, Balassiano I et al
(2019) Leptospira yasudae sp. nov. and Leptospira stimsonii sp. nov., two new species of the
pathogenic group isolated from environmental
sources. Int J Syst Evol Microbiol. https://doi.
org/10.1099/ijsem.0.003480
13. Nally JE, Bayles DO, Hurley D, Fanning S,
McMahon BJ, Arent Z (2016) Complete
genome sequence of Leptospira alstonii serovar
Room22 strain GWTS #1. Genome Announc 4
(6):e01230-16
14. Yoon SH, Ha SM, Lim J, Kwon S, Chun J
(2017) A large-scale evaluation of algorithms
to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110(10):1281–1286
15. Thibeaux R, Girault D, Bierque E, Soupe ´-Gilbert M-E, Rettinger A, Douye `re A et al
(2018) Biodiversity of environmental Leptospira: improving identification and revisiting
the diagnosis. Front Microbiol 9:816
cgMLST Scheme for Leptospira
21