Research Article The Characteristics of Ubiquitous and Unique … · 2019. 7. 31. · Research Article The Characteristics of Ubiquitous and Unique Leptospira Strains from the Collection

Research ArticleThe Characteristics of Ubiquitous and Unique LeptospiraStrains from the Collection of Russian Centre for Leptospirosis

Olga L. Voronina, Marina S. Kunda, Ekaterina I. Aksenova, Natalia N. Ryzhova,Andrey N. Semenov, Evgeny M. Petrov, Lubov V. Didenko, Vladimir G. Lunin,Yuliya V. Ananyina, and Alexandr L. Gintsburg

N.F. Gamaleya Institute for Epidemiology and Microbiology, Ministry of Health of Russia, Gamaleya Street 18,Moscow 123098, Russia

Correspondence should be addressed to Olga L. Voronina; [email protected]

Received 22 May 2014; Revised 29 July 2014; Accepted 5 August 2014; Published 2 September 2014

Academic Editor: Vassily Lyubetsky

Copyright © 2014 Olga L. Voronina et al. This is an open access article distributed under the Creative Commons AttributionLicense, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properlycited.

Background and Aim. Leptospira, the causal agent of leptospirosis, has been isolated from the environment, patients, and widespectrum of animals in Russia. However, the genetic diversity of Leptospira in natural and anthropurgic foci was not clearlydefined.Methods. The recent MLST scheme was used for the analysis of seven pathogenic species. 454 pyrosequencing technologywas the base of the whole genome sequencing (WGS). Results. The most wide spread and prevalent Leptospira species in Russiawere L. interrogans, L. kirschneri, and L. borgpetersenii. Five STs, common for Russian strains: 37, 17, 199, 110, and 146, wereidentified as having a longtime and ubiquitous distribution in various geographic areas. Unexpected properties were revealed for theenvironmental Leptospira strain Bairam-Ali. WGS of this strain genome suggested that it combined the features of the pathogenicand nonpathogenic strains and may be a reservoir of the natural resistance genes. Results of the comparative analysis of rrs andrpoB genes andMLST loci for different Leptospira species strains and phenotypic and serological properties of the strain Bairam-Alisuggested that it represented separate Leptospira species.Conclusions.Thus, the natural and anthropurgic foci supported ubiquitousLeptospira species and the pool of genes important for bacterial adaptivity to various conditions.

1. Introduction

Leptospira is a genus of bacteria that is encountered in allgeographical areas, except arctic and arid regions. SomeLeptospira are responsible for leptospirosis, a natural-focusdisease. According to the List of Prokaryotic names withStanding inNomenclature, theLeptospira genus has 21 species[1]. Seven of the species have been established as pathogenic:L. interrogans, L. borgpetersenii, L. kirschneri, L. noguchii,L. santarosai, L. weilii, and L. alexanderi. Two species, L.alstonii and L. kmetyi, are candidates for assignment to thepathogenic group; they are rarely isolated, and the sourcesof their isolation are not ill humans. L. alstonii was isolatedfrom a frog and L. kmetyiwas isolated from soil. Phylogeneticanalysis with 16S rRNAgene sequences showed thatL. alstoniiand L. kmetyi clustered with the pathogenic Leptospiraspecies [2, 3]. Five species, L. broomii, L. fainei, L. inadai,

L. licerasiae, and L. wolffii, are classified as intermediate, andsix species, L. biflexa, L. meyeri, L. terpstrae, L. vanthielii, L.wolbachii, and L. yanagawae, are nonpathogenic [4]. One newspecies, L. idonii, isolated from the environmental water, iscandidate for assignment to the nonpathogenic group. Thisspecies is placed within the clade of the known saprophyticspecies of the genus Leptospira on the 16S rRNA gene-basedphylogenetic analysis [5].

According to WHO guidance [6], the incidence of lep-tospirosis ranges from about 0.1–1 per 100 000 persons peryear in temperate climates to 10–100 per 100 000 in thehumid tropics. In the Russian Federation, only 0.01 casesper 100 000 were reported in 2013. During 2012-2013, 506cases were registered in Russia according to the report ofthe Federal Service for Supervision of Consumer RightsProtection and HumanWelfare (http://rospotrebnadzor.ru/).Long-term control of the multiple natural and anthropurgic

Hindawi Publishing CorporationBioMed Research InternationalVolume 2014, Article ID 649034, 15 pageshttp://dx.doi.org/10.1155/2014/649034

2 BioMed Research International

foci in the USSR has been organized with the participationof the MoH Centre for Leptospirosis, an action which maybe responsible for the decrease in incidence. During theregistration period, strains of Leptospira species were isolated,from the animals (maintenance and supplementary hosts ofthe Leptospira), human patients, and environment, and savedin the Gamaleya Institute Microbial Collection (GIMC).

Among the strains of Leptospira species in GIMC onestrain was mysterious and not closely related to any Lep-tospira, either pathogenic or saprophytic; it was namedLeptospira spp. strain Bairam-Ali. Bairam-Ali was isolatedfrom the water of a drainage canal in Turkmenia in 1971. Onthe basis of phenotypic tests, it was classified as a saprophyticspecies, although its resistance to the leptospiracidal activityof normal mammal sera and some other features made itcloser to the pathogenic leptospires. Thus, Leptospira sp.strain Bairam-Ali was used in a diagnostic systemon the basisof macroagglutination reaction. This diagnostic system wasdifferent from the original genus-specific microagglutinationtest, which requires multiple serovars of live Leptospira andinvolves a risk of infection. Strain Bairam-Ali is a naturalsubstitute for the microcapsule of synthetic polymer [7] ascarrier of antigens similar to pathogenic strains, and it is safefor humans.

Only whole genome sequence could help resolve themystery of the strain Bairam-Ali and clarify its phylogeneticposition in the Leptospira genus and relationships with thepathogenic Leptospira species.

2. Materials and Methods

2.1. Bacterial Strains. Leptospira strains were cultured bythe Russian MoH Centre for Leptospirosis laboratory at theN.F. Gamaleya Institute for Epidemiology and Microbiology,Moscow, according toWHO guidance [6]. Fifty-eight strains,including 29 reference strains and 29 isolates from varioussources and geographical regions, were analyzed. Twenty-sixreference strains were members of seven pathogenic species.By the start of this study, seven reference strains were absentfrom the LeptospiraMLST database [8].

2.2. Phenotypic and Serological Characterization of StrainBairam-Ali. Methods for differentiation of pathogenic versussaprophytic strains and for cross-agglutination-absorptionreactions were performed according to WHO guidance [6].

2.3. Scanning Electron Microscopy. Samples were prepared asdescribed in detail [9] and analyzed with dual-beam focusedion beam/scanning electronmicroscope,Quanta 200 3D (FEICompany, USA), in both high and low vacuum, mostly at5 kV electron beam acceleration [10].

2.4. DNA Isolation. DNA for PCR analysis was extractedfrom the bacterial cultures as described previously [11].Preparation of genomic DNA for the whole genome sequenc-ing was performed according to [12].

2.5. Leptospira Species Identification. The species of isolateswere identified by amplification and sequencing of therpoB gene (coding 𝛽 subunit of bacterial RNA polymerase),according to La Scola et al. [13]. Sequence data for rpoBhas been deposited in GenBank, with accession numbersKJ701730–KJ701749.

2.6. MLST. MLST for the strains of L. interrogans and L.kirschneri was performed by use of the original scheme ofThaipadungpanit et al. [14]. After publication of the modifiedMLST scheme [15], we completed earlier results by usingcaiB gene sequences. For the new isolates and strains of fiveother species, we used only themodifiedMLST scheme. Somemodifications were inserted in the published protocol. Theconditions of the amplification were modified for the glmU,pntA, and sucA genes by raising the melting temperature to50∘C. Also, the MgCl

2concentration was changed to 3.5mM

for the glmU, pntA, and sucA genes. Reference collectionstrains were used for adaptation of the method to ourlaboratory and for control of the reproducibility of the results.

2.7. PCR Products Sequencing. PCR products were sequencedaccording to the protocol of BigDye Terminator 3.1 CycleSequencing kit for the Genetic Analyzer 3130 of AppliedBiosystems/Hitachi.

2.8. Nucleotide Sequence Analysis. Thealignment of rpoB andMLST gene sequences was made by use of ClustalW2 [16].BLAST search was used for species identification; similarityof rpoB gene sequences was more than 98%.

Allele numbers for MLST genes were assigned with thehelp of website MLST Home. Allelic profiles, in the orderglmU-pntA-sucA-tpiA-pfkB-mreA-caiB, were used to assignsequence types (STs) to strains. New alleles and ST werecontrolled and submitted by the curator of Leptospira spp.MLSTdatabase [8]. All new Leptospira strainswere submittedin the Leptospira spp.MLST database under the identificationnumbers indicated in Table 1.

Relatedness between STs on the base of allelic profiles wasanalyzed by use of BURST version 1.00 [17, 18].

2.9. Nucleotide Sequence Polymorphism. BLAST searchwas used for retrieving homologues rrs (16S rRNA-coding), rpoB, and MLST gene sequences from Gen-Bank (http://www.ncbi.nlm.nih.gov/genome/browse/).For comparative sequence analysis and phylogeneticreconstruction, nucleotide sequences of 92 additionalLeptospira strains were retrieved. Seventy-five nucleotidesequences represented either complete or partial cds of rrsgene and rpoB gene, and 15 sequences represented wholegenome sequencing data and genome drafts (Table 1).Turneriella parva have been included in the analysis asan out-group taxon from Leptospiraceae, for which wholegenome sequence data are available (Table 1). Sequences ofseven concatenated MLST loci for 201 ST available at thetime of analysis were retrieved [8]. The alignments of rrs,rpoB, and MLST gene sequences and analysis nucleotidesimilarity (in %) were performed by use of ClustalW2 [16].

BioMed Research International 3

Table1:Strainsu

sedin

geno

typing

andph

ylogeneticanalysis.

Num

ber

Strain

Species

STOur

subm

issionID

orGenBa

nkaccessionnu

mber

forM

LSTgenes

rpoB

GenBa

nkaccession

number

16SrD

NAGenBa

nkaccessionnu

mber

1∗

GIM

C2029:Li130

L.alexanderi,

serogrou

pManhao,serovar

lichu

an207

337

KJ701742

2∗

GIM

C2051:V

eldratBa

taviae

46L.borgpetersenii,serogrou

pJavanica,

serovarjavanica

143

InMLSTHom

edatab

ase

KJ701733

3∗

GIM

C2052:Sari

L.borgpetersenii,serogrou

pMini,serovar

mini

142

InMLSTHom

edatab

ase

KJ701736

4GIM

C2002:101PJ


pJavanica,

serovarp

oi146

339

5GIM

C2003:29PJ


pJavanica,

serovarp

oi146

340

KJ701734

6GIM

C200

4:Yarosla

vl7


pJavanica,

serovarp

oi146

341

7GIM

C2005:1217PJ


pJavanica,

serovarjavanica

146

342

8GIM

C200

6:1622PJ


pJavanica

146

343

9GIM

C2007:5-I


pJavanica

146

344

10∗

GIM

C2049:Ca

stello

n3

L.borgpetersenii,serogroupBa

llum,serovar

caste

llonis

149

InMLSTHom

edatab

ase

KJ701737

11∗

GIM

C2050:Perepelitsin


pTarassovi,

serovartarassovi

153

InMLS

THom

edatab

ase

KJ701735

12∗

GIM

C2008:Mus

24L.borgpetersenii,serogrou

pSejro

e,serovar

saxkoebing

155

345

13∗

GIM

C204

8:Naam

L.interrogan

s,serogrou

pIcterohaem

orrhagiae,serovarn

aam

23In

MLS

THom

edatab

ase

KJ701731

14GIM

C2014:AV

4L.interrogan

s,serovarn

odata

23351

15∗

GIM

C2047:Djasim

anL.interrogan

s,serogrou

pDjasim

an,serovar

djasim

an11

InMLS

THom

edatab

ase

16∗

GIM

C204

6:RG

AL.interrogan

s,serogrou

pIcterohaem

orrhagiae,serovar

icterohaem

orrhagiae

17In

MLS

THom

edatab

ase

17GIM

C2010:Sv-19

L.interrogan

s,serogrou

pIcterohaem

orrhagiae

17347

18GIM

C2009:Rn

-2010

L.interrogan

s,serogrou

pIcterohaem

orrhagiae,serovarc

openhageni

17346

19GIM

C2011:R

n-493

L.interrogan

s,serogrou

pIcterohaem

orrhagiae,serovarc

openhageni

17348


Table1:Con

tinued.

Num

ber

Strain

Species

STOur

subm

issionID

orGenBa

nkaccessionnu

mber

forM

LSTgenes

rpoB

GenBa

nkaccession

number

16SrD

NAGenBa

nkaccessionnu

mber

20GIM

C2012:Rn

-16

L.interrogan

s,serogrou

pIcterohaem

orrhagiae,serovarc

openhageni

17349

21GIM

C2013:Rn

-77

L.interrogan

s,serogrou

pIcterohaem

orrhagiae,serovarc

openhageni

17350

22∗

GIM

C204

2:Ezh-1=

Jez

Bratislava

L.interrogan

s,serogrou

pAu

stralis,serovar

bratislava

24In

MLSTHom

edatab

ase

23∗

GIM

C2043:AkiyamiA

L.interrogan

s,serogrou

pAu

tumnalis,

serovara

utum

nalis

27In

MLS

THom

edatab

ase

24∗

GIM

C204

4:Za

noni

L.interrogan

s,serogrou

pPy

rogenes,serovar

zano

ni31

InMLSTHom

edatab

ase

KJ701732

25∗

GIM

C2045:Hebdo

madis

L.interrogan

s,serogrou

pHebdo

madis,

serovarh

ebdo

madis

36In

MLS

THom

edatab

ase

26GIM

C2015:Ka

shirsky

L.interrogan

s,serogrou

pCa

nicola,serovar

canicola

37352

27GIM

C2016:Mitron

ovL.interrogan

s,serogrou

pCa

nicola,serovar

canicola

37353

28GIM

C2017:Bu

gay

L.interrogan

s,serogrou

pCa

nicola,serovar

canicola

37354

29GIM

C2018:Sobaka

2000

L.interrogan

s,serogrou

pCa

nicola,serovar

canicola

37355

30GIM

C2019:Udalov

L.interrogan

s,serogrou

pCa

nicola,serovar

canicola

37356

31∗

GIM

C2038:Ba

llico

L.interrogan

s,serogrou

pAu

stralis,serovar

austr

alis

51In

MLS

THom

edatab

ase

32∗

GIM

C2039:3705

L.interrogan

s,serogrou

pSejro

e,serovar

woffi

58In

MLS

THom

edatab

ase

33∗

GIM

C204

0:Szwajizak

L.interrogan

s,serogrou

pMini

73In

MLS

THom

edatab

ase

34∗

GIM

C204

1:Pom

ona

L.interrogan

s,serogrou

pPo

mon

a,serovar

pomon

a140

InMLS

THom

edatab

ase

35∗

GIM

C2020:M-20R

L.interrogan

s,serogrou

pIcterohaem

orrhagiae,serovarc

openhageni

199

357

KJ701730

36GIM

C2021:A

bduloev

L.interrogan

s,serogrou

pIcterohaem

orrhagiae,serovarc

openhageni

199

358

37GIM

C2022:CL

-11

L.interrogan

s,serogrou

pIcterohaem

orrhagiae,serovarc

openhageni

199

359

38GIM

C2030:CL

-17

L.interrogan

s,serogrou

pIcterohaem

orrhagiae,serovarc

openhageni

206

336


Table1:Con

tinued.

Num

ber

Strain

Species

STOur

subm

issionID

orGenBa

nkaccessionnu

mber

forM

LSTgenes

rpoB

GenBa

nkaccession

number

16SrD

NAGenBa

nkaccessionnu

mber

39∗

GIM

C2023:Vleermuis3

868

L.kirschneri,

serogrou

pCy

nopteri,serovar

cyno

pteri

70360

40∗

GIM

C2024:MoskvaV

L.kirschneri,

serogrou

pGrip

potyph

osa,

serovarg

rippo

typh

osa

110361

41GIM

C2025:181PG

L.kirschneri,

serogrou

pGrip

potyph

osa,

serovarg

rippo

typh

osa

110362

KJ701738

42GIM

C2026:617P

GL.kirschneri,

serogrou

pGrip

potyph

osa,

serovarg

rippo

typh

osa

110363

43GIM

C2027:859P

GL.kirschneri,

serogrou

pGrip

potyph

osa,

serovarg

rippo

typh

osa

110364

44GIM

C2028:1106PG

L.kirschneri,

serogrou

pGrip

potyph

osa,

serovarg

rippo

typh

osa

110365

45∗

GIM

C2037:5621

L.kirschneri,

serogrou

pPo

mon

a,serovar

mozdo

k117

InMLS

THom

edatab

ase

46∗

GIM

C2031:H

S26R

L.kirschneri,

serogrou

pBa

taviae,serovar

djatsi

204

334

KJ701739

47∗

GIM

C2033:LSU1945

L.noguchii,serogrou

pLo

uisia

na,serovar

panama

169

InMLSTHom

edatab

ase

KJ701740

48∗

GIM

C2034:CZ

214K

L.noguchii,serogrou

pPanama,serovar

panama

171

InMLSTHom

edatab

ase

KJ701741

49∗

GIM

C2035:Celledo

niL.we

ilii,serogrou

pCelledo

ni,serovar

celledo

ni185

InMLSTHom

edatab

ase

KJ701746

50∗

GIM

C2036:Sarm

inL.

weilii,serogrou

pSarm

in,serovar

sarm

in191

InMLS

THom

edatab

ase

51∗

GIM

C2032:CZ

299U

L.santarosai,serogroup

Pomon

a,serovar

tropica

208

338

52GIM

C2001:B

airam-Ali

L.sp.,serogrou

pBa

iram-Ali,serovar

baira

m-ali

KJ676852-K

J676858

KJ701604

KJ701750

53∗

GIM

C2055:Lyme

L.inadai,serogroup

Lyme,serovarlym

eKJ

701743

54GIM

C2056:EM

JH86

L.inadai,serovar

lyme

KJ701744

55GIM

C2057:En

r88

L.inadai,serogroup

Lyme-Detroit,

serovar

lyme-detro

itKJ701745

56∗

GIM

C206

0:SaoPaulo

L.yanagawa

e,serogrou

pSemaranga,

serovarsao

paulo

KJ701747

57GIM

C2058:LT

-8L.biflexa,serovar

patoc

KJ701748

58GIM

C2059:GR

L.biflexa,serovar

andamana

KJ701749

59DSM

21527

Turneriellaparva

NC

018020

CP002959

CP002959

6080–4

12L.alsto

ni,serovar

pingchang

NZAO

HD0200

0041.1

NZAO

HD0200

0066.1

6179601

L.alsto

ni,serovar

sichu

anAY

631881


Table1:Con

tinued.

Num

ber

Strain

Species

STOur

subm

issionID

orGenBa

nkaccessionnu

mber

forM

LSTgenes

rpoB

GenBa

nkaccession

number

16SrD

NAGenBa

nkaccessionnu

mber

62L60

L.alexanderi,

serovarm

anhao3

NZAHMT0

2000

060.1

63A23

L.alexanderi,

serovarm

anzhuang

AY996803.1

64A85

L.alexanderi,

serovarm

engla

DQ991481.1

65M

6901

L.alexanderi,

serovarn

anding

AY996804

66Mus

127

L.borgpetersenii,serovarb

allum

EU747302

67Lely607


pSejro

e,serovar

hardjo

FJ154586

68L550

L.borgpetersenii,serovarh

ardjo-bo

vis

CP00

0348.1

69JB197


ardjo-bo

vis

CP00

0350

70Lely607


ardjo-bo

vis

EU747305

71Ve

ldratB

atavia46

L.borgpetersenii,serovarjavanica

AY887899.1

72M84

L.borgpetersenii,serovarsejroe

EU747311

73Perepelitsin

L.borgpetersenii,serovartarassovi

EU747307

JQ988861.1

74Whitticombi

L.borgpetersenii,serovarw

hitticombi

EU747314

75Mini-C

TGL.borgpetersenii,serovarn

odata

JQ765635.1

76Ba

llico

L.interrogan

s,serovara

ustralis

FJ154556.1

77AkiyamiA

L.interrogan

s,serovara

utum

nalis

AM050580.1

78Jez-bratislava

L.interrogan

s,serovarb

ratislava

EU747300

79Mallik

aL.interrogan

s,serovarb

ulgaric

aAY

996792.1

80Hon

dUtre

chtIV

L.interrogan

s,serovarc

anicola

FJ154561.1

81FiocruzL

1-130

L.interrogan

s,serovarc

openhageni

17AE0

16823.1

AE0

16823.1

82Djasim

anL.interrogan

s,serovard

jasim

anEU

747312

FJ154550.1

83HardjoDB3

3L.interrogan

s,serovarh

ardjo

JQ988854.1

84RG

AL.interrogan

s,serovaricteroh

aemorrhagiae

NR029361.1

85Kr

emastos

L.interrogan

s,serovark

remastos

AY461868.1

86IPAV

L.interrogan

s,serovarlai

CP001221

87LT

398

L.interrogan

s,serovarm

anilae

FJ154545.1

88Hon

dHC

L.interrogan

s,serovarm

edanesis

DQ991471.1

89Po

mon

aL.interrogan

s,serovarp

omon

aEU

747306

AY996800.1

90Salin

emL.interrogan

s,serovarp

yrogenes

FJ154552.1

91Vleermuis

L.interrogan

s,serovarschueffn

eri

EU747313

92Szwajizak

L.interrogan

s,serovarszw

ajizak

DQ991466.1

933705

L.interrogan

s,serovarw

olffi

EU747308

94Za

noni

L.interrogan

s,serovarz

anon

iDQ991473

95Ba

taviae

DB5

9L.interrogan

s,serovarn

odata

JQ988841.1


Table1:Con

tinued.

Num

ber

Strain

Species

STOur

subm

issionID

orGenBa

nkaccessionnu

mber

forM

LSTgenes

rpoB

GenBa

nkaccession

number

16SrD

NAGenBa

nkaccessionnu

mber

96Agogo

L.kirschneri,

serovara

gogo

DQ991476.1

97Ba

fani

L.kirschneri,

serovarb

afani

DQ991477.1

981051

L.kirschneri,

serovarb

imAY

996802.1

99Bu

tembo

L.kirschneri,

serovarb

utem

boQ991478.1

100

3522

CL.kirschneri,

serovarc

ynop

teri

FJ154546

.1101

MoskvaV

L.kirschneri,

serovarg

rippo

typh

osa

EU747301

102

Kambale

L.kirschneri,

serovark

ambale

AY461878.1

103

5621

L.kirschneri,

serovarp

omon

aFJ154559.1

104

Wum

alasena

L.kirschneri,

serovarratnapu

raDQ991479.1

105

Bejo-Is

o9L.km

etyi,serovar

malaysia

AHMP0

2000

003

AHMP0

2000

003

NR04

1544

.1106

Hoo

kL.noguchii,serogrou

pAu

stralis

EU349504

107

Bonito

L.noguchii,serogrou

pAu

tumnalis

EU349501

108

Caco

L.noguchii,serogrou

pAu

tumnalis

EU349498

109

Cascata

L.noguchii,serogrou

pBa

taviae

EU349502

110LSU1945

L.noguchii,serogrou

pLo

uisia

naEU

349505

111

1348U

L.noguchii,serovarc

layton

iDQ991498.1

112

1996K

L.noguchii,serovarc

ristobali

DQ991497.1

113

M7

L.noguchii,serovarh

uallaga

DQ991499.1

1141011

L.noguchii,serovarn

icaragua

EU349499

115

LSU2580

L.noguchii,serovaro

rleans

EU349500

116CZ

214K

L.noguchii,serovarp

anam

aEU

349497

NR043050.1

117DB5

7L.noguchii,serovarp

anam

aEU

349501

JQ988837.1

118HS616

L.santarosai,serovar

alexi

FJ154585.1

119Alice


alice

DQ991493.1

120

MAV

J401


arenal

AHMU0200

0055

121

LT79


bakeri

FJ154589.1

122

LT117


georgia

AY996805.1

123

CZ320


kobb

eDQ991495.1


Table1:Con

tinued.

Num

ber

Strain

Species

STOur

subm

issionID

orGenBa

nkaccessionnu

mber

forM

LSTgenes

rpoB

GenBa

nkaccession

number

16SrD

NAGenBa

nkaccessionnu

mber

124

1342


shermani

FJ154576.1

125

CZ390


weaveri

DQ991496.1

126

CBC6

13L.santarosai,serovar

nodata

ANIH

0100

0040

127

ST188


nodata

AOHA0200

0081

128

MOR0

84L.santarosai,serovar

nodata

AHON0200

0051

129

2000

030832


nodata

AFJN0200

0030

130

Celledo

niL.we

ilii,serovarc

elledo

niDQ991486.1

131

H27

L.we

ilii,serovarh

ekou

DQ991487.1

132

M39090

L.we

ilii,serovarlangati

DQ991488.1

133

WB4

6L.we

ilii,serovarsarmin

U12673.1

134

LT89-68

L.we

ilii,serovarv

ughia

FJ154590.1

135

5399

L.broomii,serovarh

urstb

ridge

AHMO0200

0008

AHMO0200

0008

AHMO0200

0008.1

136

BUT6

L.fainei,

serovarh

urstb

ridge

AKW

Z02000

010

AKW

Z02000

010

NR043049.1

137

BKID

6L.fainei,

serovarh

urstb

ridge

AY996789.1

138

10L.inadai,serovar

lyme

AHMM0200

0025

AHMM0200

0015

AHMM0200

0015.1

139

VAR010

L.licerasiae,serovarv

arillal

AHOO0200

0005

AHOO0200

0005

NR04

4310.1

140

Kho

rat-H

2L.wo

lffii,serovark

horat

AKW

X02000

020

NZAKW

X02000

004.1

141

PatocA

mes

L.biflexa,serovar

patoc

NC

010842

NC

010842

NC

010842

142

PatocP

aris

L.biflexa,serovar

patoc

NC

0106

02NC

0106

02143

CH11

L.biflexa,serovar

andamana

FJ154577.1

144

VeldratS

emarang173

L.meyeri,serovarsem

aranga

AF157089.1

145

Went5

L.meyeri,serovarh

ardjo

AKX

E01000

002

AKX

E01000

001

NZAKX

E01000

007.1

146

LT11-33

ATCC

700639

L.terpstrae,serovar

hualin

AOGW0200

0006

AOGW0200

0010

NZAO

GW0200

0008.1

147

Waz

Holland

ATCC

700522

L.vanthielii,serovarh

olland

AOGY0

2000

070

AOGY0

2000

051

NZAO

GY0

2000

072.1

148

CDC;

ATCC

43284

L.wo

lbachii,serovarc

odice

AOGZ0

2000

014

AOGZ0

2000

008

NR043046

.1149

SaoPauloAT

CC700523

L.yanagawa

e,serovarsaopaulo

AOGX0

2000

015

AOGX0

2000

024

ZAO

GX0

2000

022.1

150

Eri-1(T)D

SM26084(T)

=JCM

18486(T)

L.idonii,serogrou

pHebdo

madis

AB7

21966

∗

Ther

eference

strains

from

GIM

C.


2.10. Phylogenetic Analysis. Phylogenetic analysis of Lep-tospira species was performed based on the rrs gene fragment,rpoB gene fragment, and seven concatenated sequences ofMLST loci. Phylogenetic trees were constructed by useof neighbor-joining, maximum likelihood, and maximumparsimony methods.

Genetic distances between Leptospira genotypes wereevaluated by use of Kimura’s two-parameter model [19],which was chosen as an optimal evolution distance modelderived from model test based on the Akaike informationcriterion [20].The evolutionary history was inferred by usingthe Maximum Likelihood method based on the general timereversible model [21]. Initial tree(s) for the heuristic searchwere obtained automatically by applying neighbor-joiningand BioNJ algorithms to a matrix of pairwise distancesestimated by use of the maximum composite likelihoodapproach and then selecting the topology with superiorlog likelihood value. A discrete gamma distribution wasused to model evolutionary rate differences among sites (sixcategories (+G, parameter = 0.4818)). Maximum parsimonytrees were constructed with an algorithm implemented inMEGA version 6.0 [22]. Bootstrap analyses were performedwith 1,000 replicates.

2.11. Whole Genome Sequencing. Whole genome sequencingof Leptospira spp. strain GIMC2001:Bairam-Ali was per-formed according to the manufacturer’s guidelines (Roche)for the next generation sequencing (NGS). Two protocolswere used for a shotgun-sequencing library preparation:rapid library and pair-end library.The rapid library wasmadeaccording to the Rapid Library Preparation Method Manual(Roche).Thepair-end librarywas performed according to the3 kb protocol provided by the manufacturer to aid in scaffoldbuilding. The paired-end library insert size was from 1347 to4364 bp, with an average of 2695 bp.

Assembly was performed with 454 Sequencing SystemSoftware v.2.7 (Roche), yielding 14 scaffolds, with the largestsize being 3 342 467 bp. Gap closure was performed by use ofContig Graph result file generated by GS De Novo Assemblerprogram (Roche). For the oriC region search, Ori-Finderprogram was used [23].

2.12. Gene Annotation. The software Rapid Annotations Sub-systemsTechnology and SEED [24, 25]were used for annotat-ing the genome of Leptospira spp. strain GIMC2001:Bairam-Ali.

3. Results and Discussion

A sample of the collection (GIMC) of the Russian MoHCentre for Leptospirosis was used for the verification thespecies and strains based on the currently recommendedmolecular-genetic methods. The sample included 29 ref-erence strains and 29 isolates of Leptospira from variousgeographical regions (Table 1, ∗—marker of the referencestrains from GIMC).

The analysis of rpoB gene sequences demonstratedthat 29 reference strains belonged to seven pathogenic

species, one nonpathogenic species (L. yanagawae), andone intermediate species (L. inadai). Among 29 isolatesof Leptospira twenty-four field isolates were related to thethree pathogenic species (L. interrogans, L. borgpetersenii,and L. kirschneri). Four cultures were isolated from thecommercially available Ellinghausen-McCullough-Johnson-Harris (EMJH) medium: two isolates from this groupbelonged to the nonpathogenic species L. biflexa and theother two isolates belonged to the intermediate speciesL. inadai. Thus, the prevailing species among the isolatescollected on the territory of Russia comprised L. interrogans,L. borgpetersenii, and L. kirschneri.

The modified MLST scheme was applied to the isolatesand reference strains representing 7 pathogenic Leptospiraspecies. Twenty-four isolates of pathogenic species belongedto 8 different STs (Table 1). Five STs, common for Russianstrains of Leptospira (L. interrogans ST37, 17, and 199; L.kirschneri ST110; and L. borgpetersenii ST146), were identifiedas having a longtime and ubiquitous distribution in variousgeographic areas.

Among the strains of Leptospira species available inGIMC, one strain seemed to be mysterious and not closelyrelated to any Leptospira, either pathogenic or saprophytic, orintermediate. It was named Leptospira spp. strain Bairam-Ali,because it was isolated in 1971 in Turkmenia from the waterof a drainage canal.

3.1. Morphology of the Leptospira spp. Strain Bairam-Ali. Themorphology of the mysterious strain Bairam-Ali is typical ofthat of the Leptospira genus (Figure 1). Electron microscopydemonstrated that its cells are corkscrew-shaped with endhooks. They are thin and helical, like the cells of all knownleptospires. Also, the cells have a diameter (𝑑) of 0.12 𝜇m andlength (𝑙) from9.44 to 10.14𝜇m, like that of known leptospires(𝑑 = 0.15–0.3 𝜇m and 𝑙 = 6,00–20,00𝜇m) [26].

3.2. Phenotypic Characterization of the Leptospira spp.Strain Bairam-Ali. Physiological characteristics of Bairam-Ali, demonstrated in Table 2, suggest that strain Bairam-Alican be classified as saprophytic Leptospira.

For pathogenicity experiment, six four-week-old malegolden Syrian hamsters were inoculated subcutaneously with108 cells of strain Bairam-Ali in 1mL of PBS. No hamster diedfrom infection even at such a high bacterial dose. Leptospiracells were not detected during following bacterioscopic andbacteriological examination of the hamsters’ viscera. This isan additional evidence of saprophytic quality of Bairam-Ali.

On the other hand, Bairam-Ali was resistant to thebactericidal (leptospiracidal) activity of the normal serum ofhuman and of some other mammal animals. The most ofpathogenic Leptospira species were resistant too, whereas thesaprophytic species L. biflexa was sensitive.

3.3. Serological Characterization of the Leptospira spp. StrainBairam-Ali. The strain Bairam-Ali had no antigenic affinitywith 18 different serovars represented by reference strains. Sothe conclusion about the original serotype of Bairam-Ali was


(a) (b)

Figure 1: Dual-beam scanning electron microscopy image of 𝐿. species Bairam-Ali cells. (a) Original image; (b) with measuring the objectin the program “Scandium” (green, length 10,14𝜇m; yellow, length (diameter) 0,12 𝜇m; and green, length 9,44 𝜇m).

Table 2: Physiological characteristics of the Leptospira spp. strain Bairam-Ali.

Strain Growth at temp (∘C) of Growth in the presence of Lipase activity Hemolytic activity against sheep erythrocytes

11 30 37 8-Azaguanine 225 pg/mLBairam-Ali + + + + + −

made. The serovar of Bairam-Ali was named bairam-ali. Itformed the separated serogroup Bairam-Ali.

3.4. The Whole Genome Sequence Analysis. The wholegenome sequence could help to resolve the mystery of thestrain Bairam-Ali and clarify its phylogenetic position in theLeptospira genus.

According to the NGS data the whole Bairam-Ali genomeis 4,4Mb, with GC % 34,74 and two chromosomes. The firstchromosome is 4 059 463 bp and the second is 325 649 bp.Plasmid, typical of nonpathogenic Leptospira species, wasabsent from the Bairam-Ali genome. On the base of genomesize and GC content, demonstrated in Table 3, Bairam-Ali ismore similar to the pathogenic species L. interrogans and L.noguchii.

Based on rpoB gene sequence, we established thatBairam-Ali is more similar to pathogenic strain L. interrogansFiocruz-L1-130 (but the level of similarity is only 70.00%).However, by sequence of rDNA genes it is similar to non-pathogenic strains: for gene rrs, coding 16S rRNA, L. meyeriwas most closely related (92.74%); for gene rrl, coding 23SrDNA, L. biflexa was more similar (95.00% fragment 1 and93.00% fragment 2). Sequences of rDNA genes of Bairam-Ali were deposited inGenBank, accession numbers KJ701750,KJ701751, and KJ701752.

These data suggest dual phenotypic characteristics of thestrain Bairam-Ali. In spite of having differences from bothpathogenic and nonpathogenic species, many of the func-tional categories that are involved in essential housekeepingfunctions are represented in its core gene [27, 28].Thus, basicgroups of proteins involved in cell metabolism, survival, envi-ronmental adaptability, and potential pathogenic factors were

Table 3: Comparison L. spp. Bairam-Ali strain genome characteris-tics with most closely related Leptospira species.

Leptospira strain or species Genome size, Mbp GC%L-BA∗ 4,4 34,7L. interrogans 4,56 ± 0,32 35,22 ± 0,27L. noguchii 4,76 ± 0,16 35,63 ± 0,27L. terpstrae 4,09 38,2L. meyeri 4,15 38,05L. vanthielii 4,23 38,9L. biflexa 3,95 38,9∗

𝐿-BA: Leptospira spp. Bairam-Ali.

present. Enzyme complexes participating in implementationof genetic information, in particular inDNA replication, wereidentified in strain Bairam-Ali: chromosomal replication ini-tiator protein DNA, single-stranded DNA-binding protein;all subunits of DNA polymerase III, DNA polymerase I, andDNA polymerase IV; DNA gyrase; ligase; and helicase [29].Also, the large groups of enzymes that take part in DNAreparation [29], for example, excinuclease ABC subunits A–C and exodeoxyribonuclease (III, V, and VII), and proteinsof postreplicative mismatch repair system (Mutator S andMutator L) were present. Archaeal DNA polymerase I genewas detected in the Bairam-Ali genome; this gene is amemberof Family B and bacterial DNA polymerase II. The samegene was present in nonpathogenic strain L. biflexa Patocgenome but not in pathogenic L. interrogans Fiocruz-L1-130and L. borgpetersenii Hardjo-bovis-L550 genomes [27, 30].The sequences of DNA metabolome have been deposited inGenBank, with accession numbers KJ701710–KJ701729.


According to Bourret et al. [31], enteric bacteria usuallyhave about 50 genes coding for structural and functionalproteins involved in motility. Motility is a distinctive featureof Leptospira; forty-seven different proteins provide bacteriallocomotion [32]. In the Bairam-Ali genome, the genes forproteins of the basic parts of periplasmic flagella weredetected: basal-body (Flg B–D, FlgF, and FlgG), hook (FlgE,FlgK, FlgL, FliE, FliD, and fliK), and four copies of FlaA(sheath protein of filament).The genes for proteins of flagellarrings L (FlgH), MS (FliF), and P (FlgI); biosynthesis protein(FlhA, FlhB (2), FlhF, FliL, and Fli Q-S); motors (MotB (3),MotA (2), FliG (3), FliM, and FliN); flagellar assembly factor(FliW and FliH), cell division (BolA (2), FtsA, FtsH (2), FtsI,FtsK, FtsW, and FtsZ), and gliding motility (GldF and GldG)proteins also were registered. Strain Bairam-Ali was foundto have more than ten genes for the regulation of flagellumgenes transcription and for signal transduction to flagellamotor. Sequences of the flagellum genes have been depositedin GenBank, accession numbers KJ701653–KJ701709.

It should be noted that the important structural element,that is, numerous groups of predicted lipoproteins (Lip),which may be either surface-exposed or located in theperiplasm, is present in both saprophytic and pathogenicLeptospira species. In the strain Bairam-Ali genome, as in thegenome of nonpathogenic species L. biflexa [27], genes ororthologs of themajor lipoproteins LipL32 and LipL41, whichare important immunodominant antigens in pathogenicLeptospira species [33, 34], were not identified. Nevertheless,in the genome of Bairam-Ali, we detected six genes of LipL45(GenBank accession numbers KJ701647–KJ701652), whichare processed to a peripheral membrane associated with theouter membrane complex. According to Matsunaga et al.[35] expression of P31, derived from the carboxy terminusof LipL45, is upregulated in stationary phase cultures; thusit may have a membrane-stabilizing function. Also, in a ham-ster model infected with pathogenic L. kirschneri, antibodiesto LipL45 [35] were produced, suggesting its involvement inpathogenesis.

Further analysis of the genome of Bairam-Ali revealedthe presence of genes for more than 40 different classesof proteins, ensuring its natural resistance to a wide rangeof antibiotics (𝛽-lactams, tetracyclines, glycopeptides (van-comycin), and polymyxin); efflux system and resistance toheavy metals (Czc A–C and arsenical-resistance proteins);and possible abortive infection phage-resistance protein.The broad resistance characteristics of strain Bairam-Ali areconsistent with it being a natural reservoir for storage andpossible transmission of these properties to other free-livingLeptospira species. Sequences of the resistome genes and theirproteins have been deposited inGenBank, accession numbersKJ701605–KJ701646.

3.5. Sequence Polymorphism. To determine the place ofthe original strain Bairam-Ali in the Leptospira genus, weundertook phylogenetic analysis of the Leptospira groupswith different pathogenicity.

Based on performed alignments, the percentnucleotide similarities of rrs, rpoB, and MLST gene

sequences of analyzed Leptospira genotypes weredetermined; see Supplementary Material available onlineat http://dx.doi.org/10.1155/2014/649034 (S1, S2, and S3).According to the obtained data, aligned sequences of 16SrRNA-coding rrs gene were 1305 bp, aligned sequences ofgene rpoBwere 493 bp, and aligned sequences of sevenMLSTtags (glmU-pntA-sucA-tpiA-pfkB-mreA-caiB) were 3105 bp.

Among the investigated Leptospira sequences, gene rpoBshowed the highest variability, reaching 40.61%. 16S rRNA-coding gene was more conservative, and general sequencevariability of the rrs gene across all strains and species reached11.52%. Sequence variability of seven MLST tags reached34.88%.

Detectable intraspecific sequence polymorphism forstudied loci also was different. Intraspecific differencesdetected by rrs were less than 1%. Intraspecific differencesdetected bymost polymorphic rpoB genes ranged from 0.61%(L. kirschneri) to 11.63% (L. borgpetersenii), with, in somecases, overlapping of intraspecific and interspecific values (S1,S2, and S3).

Notably, the intraspecific differences detected by sevenMLST tags resolved all of the Leptospira genotypes andmatched 3% accepted threshold values for prokaryote speciesdivergence [36, 37]. The exception was L. weilii; interspeciesdifferences of L. weilii strains revealed by seven MLST tagsreached 5.77% (S1, S2, and S3).

Despite the differences in resolution ability of studiedloci, all of them confirmed the unique nature of Leptospiraspp. strain Bairam-Ali. rrs, rpoB, and MLST tags obtainedfor Bairam-Ali had low similarity with other sequences.Maximum similarity of Bairam-Ali MLST tags (69.7%) wasdetected for L. interrogans (Table 3). At the same time,related levels of sequence similarity also characterized non-pathogenicand pathogenic Leptospira species (67.29–68.95%)and intermediate and pathogenic Leptospira species (70.0–72.8%). Sequence similarity in pairs of Bairam-Ali, to inter-mediate Leptospira species, to nonpathogenic Leptospiraspecies, and to pathogenic Leptospira species, was 65.8–67.31%, 67.6–69.18%, and 66.27–69.7%, respectively. The levelof sequence similarity between Bairam-Ali and Turneriellaparva was the lowest (55.3%), which is evidence of Bairam-Ali belonging to the genus Leptospira.

3.6. Leptospira Phylogeny and L. spp. Bairam-Ali Locationin the Leptospira Genus. The most prominent phylogeneticinformation was obtained through concatenated sequencesof seven MLST tags. All genotypes were divided into threespecies groups: pathogenic, nonpathogenic, and intermedi-ate. T. parva formed a distinct basal out-group branch.

The genetic diversity of pathogenic Leptospira reached0.159 (MLST data), 0.006 (rrs data), and 0.121 (rpoB data).The most variable species were L. borgpetersenii (0.086 rpoB)and L. noguchii (0.069). Despite the fact that L. interroganswas themost representative species in the analysis (120MLSTgenotypes), intraspecies genetic diversity for L. interroganswas only 0.002 (Figure 2).

The genetic diversity of nonpathogenic Leptospira wassimilar to that of the pathogenic Leptospira species and


L aleL intL borL kir

L nogL san

PATHINT

NON-PATH

PATH-INTINT-NON-PATH

L BA-L-aleL BA-L intL BA-L borL-BA-L kir

L BA-L nogL BA-L sanL BA-PATH

L BA-INTLBA-NON-PATH

LBA-TURPA

0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 5 5.5 6 6.5 7

0.344 4.532 6.757

0.104 0.727 1.800

0.121 0.803 1.886

0.121 1.232 1.635

0.125 0.821 1.690

0.117 0.830 1.811

0.121 0.827 1.737

0.121 0.819 1.589

0.120 0.856 1.385

0.124 0.807 1.707

0.157 0.845 2.509

0.047 0.873 0.691

0.133 1.208 2.063

0.0072 0.0633 0.1395

0.013 0.167 0.188

0.006 0.159 0.121

0.0004 0.0011 0.0684

0 0.0069 0.0356

0.0002 0.0023 0.0042

0.0008 0.0014 0.0865

0 0.002 0.043

0.002 0.081

L BA-L nogL-BA-L kirL BA-L borL BA-L intL BA-L-ale

INT-NON-PATHPATH-INT

PATH-NON-NON-PATH

INTPATHL sanL nogL kirL borL intL ale

Species or groupname

Genesrrs rpoB

LBA-TURPALBA-NON-PATH

L BA-INTL BA-PATHL BA-L san

7, 00E − 04

rpoBMLST

MLST

rrs (16SrDNA)

PATH-NON-. . .

Figure 2: The number of base substitutions per site from averaging over all sequence pairs within each group is shown. Analyses wereconducted using the Kimura 2-parameter model.

reached 0.063 (MLST data), 0.007 (rrs data), and 0.139 (rpoBdata).

Interestingly, the intermediate group Leptospira hadbroader genetic diversity than did the nonpathogenic orpathogenic Leptospira (0.167, MLST data; 0.013, rrs data; and0.188 rpoB data) (Figure 2).

In pathogenic group accessions of each species, excludingL. weilii, clearly distinct phylogenetic clusters, with highbootstrap supporting values, were present.In some data sets,significant subdivision of L. weilii genotypes, combined witha close relationship between L. weilii and L. alexanderi, wasfound. Possible polyphyletic nature of L. weilii has beendescribed previously, particularly in the highly divergent tpiAlocus [15]. According to our data, excluding from analysisglmU and pfkB loci, L. weilii and L. alexanderi genotypesfall into two different but closely related subclusters. Thisdifferentiation was found also with rrs gene phylogeny (S4).

Three species in the pathogenic group, L. interrogans,L. kirschneri, and L. noguchii, formed one close geneticsubgroup (BI = 99%, bootstrap index). The strains of thesespecies are often the cause of the human leptospirosis. Fourspecies, L. weilii, L. alexanderi, L. borgpetersenii, and L.santarosai, formed another phylogenetic subgroup (BI =98%) (Figure 3). The strains of these species are usuallyisolated in natural foci. The candidate pathogenic species,L. alstoni and L. kmetyi, fell in the common big clusterof pathogenic Leptospira species. On the MLST tree, L.alstoni formed a sister clade to the L. weilii/L. alexanderi/L.borgpetersenii/L. santarosai group of pathogenic Leptospiraspecies (BI = 70%), whereas L. kmetyi formed a basal branch

(BI = 99) (Figure 3). The levels of genetic similarity of L.alstoni and L. kmetyi to pathogenic Leptospira species (0.913and 0.926) were much higher than to nonpathogenic (0.13and 0.09) or intermediate species (0.58 and 0.54). Our dataconfirm the results of previous characterization for L. alstonion the base of 16SrDNA gene and for L. kmetyi on the base of16SrDNA, gyrB, and rpoB genes analysis [2, 3].

The single Leptospira spp. strain, Bairam-Ali, formeda separate distinct branch on dendrogram, with geneticdistances comparable to those of distantly related species ofdifferent Leptospira groups. For example, differences betweenpathogenic and nonpathogenic, pathogenic and intermedi-ate, and intermediate and nonpathogenic groups were 1.208,0.873, and 0.845, respectively (Figure 2), whereas the differ-ences between Leptospira spp. Bairam-Ali and pathogenic,intermediate, and nonpathogenic species were 1.232, 0.803,and 0.727, respectively; this result points to significant dif-ferences between Bairam-Ali and other Leptospira species,a result that is consistent with whole genome sequencingdata.

It should be noted that the comparative studies of dif-ferent Leptospira groups based on the rrs gene variability,which added to the analysis the newly described saprophyticL. idonii strain Eri-1T [5] and recently approved 16S rDNAsequences of leptospires from the Peruvian Amazon, pre-viously termed “clade C” [38, 39], did not change separatephylogenetic position of Leptospira spp.strain Bairam-Ali.

Thus, according to our results the Leptospira strainBairam-Ali forms a separate phylogenetic branch of theLeptospira genus and cannot be attributed to any group of


ST19

9 L

int tni

L602TS ST

17 L

int

ST99

L in

t

58

ST13

4 L

int

ST20

0 L

int

ST12

L in

tST

29 L

int

ST49

L in

tST

74 L

int

ST76

L in

tST

75 L

int

ST10

7 L in

tST

14 L

int

ST43

L in

tST

44 L

int

ST13

L in

tST

88 L

int

ST8 L

int

ST19

L in

tST

30 L

int

ST51

L int

ST55

L int

ST13

7 L in

tST

5 L in

tST

98 L

intST

128 L

int

ST1 L

int

ST6 L

int

ST16

L int

ST34

L int

ST112

L int

ST4 L

int

ST11 L

int

ST56 L

int

ST81 L

int

ST54 L

int

ST21 L

int

ST73 L

int

ST84 L

int

ST48 L

int

ST83 L i

nt

ST77 L in

t

ST86 L in

t

ST132 L in

t

ST78 L int

ST85 L int

ST22 L int

ST32 L int

ST105 L int

ST23 L int

ST109 L int

54ST201 L int

ST47 L int

ST72 L int

ST202 L intST80 L intST119 L intST140 L intST138 L intST90 L intST95 L intST27 L intST60 L intST37 L intST36 L intST39 L intST96 L intST120 L intST50 L intST31 L intST45 L intST111 L intST87 L intST41 L intST42 L intST108 L int

ST89 L intST130 L int




ST129 L int

ST203 L int

ST24 L int

ST25 L int

ST198 L int

ST20 L int

ST2 L int

ST10 L int

ST79 L int

ST58 L int

ST82 L int

ST97 L int

ST28 L int

ST102 L int

ST139 L int

ST59 L int

ST61 L int

ST15 L int

ST101 L int

ST46 L int

ST9 L int

ST133 L int

ST91 L int

ST3 L int

ST113 L int51

ST93 L int

ST131 L int


tni

L7

TStn

iL

29TS

ST57

L in

t60

ST52

L in

tST

53 L

int

69

99

ST68

L k

ir

ST71

L k

ir

ST11

6 L

kir

ST12

5 L

kir

69

ST62

L k

ir

ST12

4 L

kir

ST67

L k

ir

52

ST12

1 L

kir

ST63

L k

ir

ST70

L k

ir

63

ST64

L ki

r

ST12

6 L ki

r

ST20

4 L ki

r

ST66

L ki

r

58

ST12

3 L ki

r

ST65

L kir

ST13

6 L ki

r

ST69

L kir

ST11

0 L ki

r

ST11

5 L ki

r

ST11

7 L ki

r

ST12

2 L ki

r

ST12

7 L ki

r

ST14

1 L ki

r

51 91

95

57

ST16

7 L no

g

ST163

L no

g

ST169

L nog

ST168

L nog

ST164

L nog

ST170

L nog

78

ST166

L nog

ST165

L nog

ST171 L

nog

92 78 88

99

ST195 L

wei

ST189 L

wei96

ST194 L

weiST182 L

weiST190 L

weiST187 L w

ei86

98ST183 L

weiST188 L

weiST184 L w

ei58 55

ST186 L weiS

T193 L wei

70ST196 L wei

ST191 L wei 91

ST192 L wei

ST185 L wei 9

998

ST207 L aleST161 L aleST162 L aleST160 L aleST159 L aleST158 L ale 61

5893

93

78

ST156 L borST152 L bor

55

ST153 L bor

ST151 L bor

ST150 L bor

ST142 L bor

ST144 L bor

ST143 L bor

ST148 L bor

ST197 L bor

ST149 L bor

ST157 L bor

ST145 L bor

ST146 L bor

ST147 L bor

ST155 L bor

ST154 L bor

99

95

ST172 L san

ST178 L san

ST180 L san

ST177 L san

ST173 L san

82

ST179 L san

64

ST208 L san

ST181 L san

ST175 L san

70

ST176 L san

ST174 L san

70

5699

98

L als Sichuan

L als Pingchang

99

70

L kme Malaysia

99

INT L lic Varillal

INT L wlf Khorat

INT fai Hurstbridge

INT bro Hurstbridge

INT L ind Lyme

8999

94

93

NON-PATH bif Ames

NON-PATH bif Paris99

NON-PATH yan Saopaulo

NON-PATH m

ey Hardjo

NON-PATH ter Hualin

NON-PATH

van Holland

NO

N-PATH

wlb Codice94

6572

99

51

LBATU

RPA

Figure 3: Phylogenetic tree of Leptospira species based on concatenated sequences of seven MLST loci.

pathogenic, intermediate, or saprophytic Leptospira, illustrat-ing its uniqueness.

In conclusion, we found that the natural and anthropurgicfoci supported ubiquitous pathogenic, intermediate, andnonpathogenic Leptospira species. They have circulated for along time, interacting with maintenance and supplementaryanimal hosts. The relationships between the different Lep-tospira strains provide for horizontal gene transfer and createin the bacterial population the pool of genes important foradaptivity to various conditions. Modern molecular geneticmethods are suitable for investigation of Leptospira andcontrol of the pathogenic species, which are the causal agentof leptospirosis. Also, the taxonomic position of the newstrains with unexpected properties can be founded on thebase of these methods. Further investigation of the geneticdiversity in the natural and anthropurgic foci is required forthe identification of the Leptospira genotypes, control of the

strain’s transmission, and better understanding of the originand evolution of the Leptospira species.

Abbreviations

L int: L. interrogansL kir: L. kirschneriL nog: L. noguchiiL wei: L. weiliiL ale: L. alexanderiL bor: L. borgpeterseniiL san: L. santarosaiL als: L. alstoniL kme: L. kmetyiL lic: L. licerasiae


L wlf: L. wolffiifai: L. faineibro: L. broomiiL ind: L. inadaibif: L. biflexayan: L. yanagawaemey: L. meyeriter: L. terpstraevan: L. vanthieliiwlb: L. wolbachiiLBA: L. species Bairam-AliTURPA: Turneriella parvaINT: Intermediate speciesNON-PATH: Nonpathogenic species.

Conflict of Interests

The authors declare that there is no conflict of interestsregarding the publication of this paper.

References

[1] The List of Prokaryotic names with Standing in Nomenclature,Site founded by: J. P. Euzéby, http://www.bacterio.net/.

[2] L. Smythe, B. Adler, R. A. Hartskeerl, R. L. Galloway, C.Y. Turenne, and P. N. Levett, “Classification of Leptospiragenomospecies 1, 3, 4 and 5 as Leptospira alstonii sp. nov.,Leptospira vanthielii sp. nov., Leptospira terpstrae sp. nov. andLeptospira yanagawae sp. nov., respectively,” International Jour-nal of Systematic and Evolutionary Microbiology, vol. 63, no. 5,pp. 1859–1862, 2013.

[3] A. T. Slack, S. Khairani-Bejo, M. L. Symonds et al., “Leptospirakmetyi sp. nov., isolated from an environmental source inMalaysia,” International Journal of Systematic and EvolutionaryMicrobiology, vol. 59, no. 4, pp. 705–708, 2009.

[4] G. M. Cerqueira and M. Picardeau, “A century of Leptospirastrain typing,” Infection, Genetics and Evolution, vol. 9, no. 5, pp.760–768, 2009.

[5] M. Saito, S. Y. Villanueva, Y. Kawamura et al., “Leptospira idoniisp. nov., isolated from environmental water,” InternationalJournal of Systematic and Evolutionary Microbiology, vol. 63,part 7, pp. 2457–2462, 2013.

[6] Human Leptospirosis: Guidance for Diagnosis, Surveillanceand Control, World Health Organization, Geneva,Switzerland, 2003, http://www.who.int/csr/don/en/WHO CDSCDS CSR EPH 2002.23.pdf.

[7] Y. Arimitsu, E. Kmety, Y. Ananyina et al., “Evaluation ofthe one-point microcapsule agglutination test for diagnosis ofleptospirosis,” Bulletin of theWorld Health Organization, vol. 72,no. 3, pp. 395–399, 1994.

[8] Leptospira MLST database which is located at ImperialCollege London and is funded by the Wellcome Trust,http://leptospira.mlst.net/.

[9] L. V. Didenko, G. A. Avtandilov, N. V. Shevlyagina et al., “Biode-struction of polyurethane by Staphylococcus aureus (an inves-tigation by SEM, TEM and FIB),” in Current Microscopy Contri-butions to Advances in Science and Technology, A.Méndez-Vilas,Ed., vol. 1, pp. 323–334, Formatex Research Center, Badajoz,Spain, 2012.

[10] M. Milani, D. Drobne, and F. Tatti, Atlas of FIB/SEM in SoftMaterials and Life Sciences, Aracne, Rome, Italy, 2006.

[11] O. L. Voronina, M. Y. Chernukha, I. A. Shaginyan et al.,“Characterization of genotypes for Burkholderia cepacia com-plex strains isolated from patients in hospitals of the Russianfederation,”Molecular Genetics, Microbiology and Virology, vol.28, no. 2, pp. 64–73, 2013.

[12] K. Wilson, “Unit 2.4. Preparation of genomic DNA frombacteria,” in Current Protocols in Molecular Biology, John Wileyand Sons, New York, NY, USA, 2001.

[13] B. La Scola, G. Baranton, A. Khamis, and D. Raoult, “PartialrpoB gene sequencing for identification of Leptospira species,”FEMS Microbiology Letters, vol. 263, no. 2, pp. 142–147, 2006.

[14] J. Thaipadungpanit, V. Wuthiekanun, W. Chierakul et al., “Adominant clone of Leptospira interrogans associated with anoutbreak of human leptospirosis in Thailand,” PLoS NeglectedTropical Diseases, vol. 1, no. 1, article e56, 2007.

[15] S. Boonsilp, J. Thaipadungpanit, P. Amornchai et al., “A Sin-gle Multilocus Sequence Typing (MLST) scheme for sevenpathogenic Leptospira species,” PLoS Neglected Tropical Dis-eases, vol. 7, no. 1, Article ID e1954, 2013.

[16] The Main Site EMBL-EBI, European Bioinformatics Institute,http://www.ebi.ac.uk/Tools/msa/clustalw2.

[17] E. J. Feil, E. C. Holmes, D. E. Bessen et al., “Recombinationwithin natural populations of pathogenic bacteria: short-termempirical estimates and long-term phylogenetic consequences,”Proceedings of the National Academy of Sciences of the UnitedStates of America, vol. 98, no. 1, pp. 182–187, 2001.

[18] K. A. Jolley, E. J. Feil, M. S. Chan, and M. C. J. Maiden,“Sequence type analysis and recombinational tests (START),”Bioinformatics, vol. 17, no. 12, pp. 1230–1231, 2002.

[19] M. Kimura, “A simple method for estimating evolutionary ratesof base substitutions through comparative studies of nucleotidesequences,” Journal ofMolecular Evolution, vol. 16, no. 2, pp. 111–120, 1980.

[20] D. Posada andK. A. Crandall, “MODELTEST: testing themodelof DNA substitution,” Bioinformatics, vol. 14, no. 9, pp. 817–818,1998.

[21] M. Nei and S. Kumar, Molecular Evolution and Phylogenetics,Oxford University Press, New York, NY, USA, 2000.

[22] K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar,“MEGA6: Molecular Evolutionary Genetics Analysis version6.0,”Molecular Biology and Evolution, vol. 30, no. 12, pp. 2725–2729, 2013.

[23] F. Gao and C.-T. Zhang, “Ori-finder: a web-based systemfor finding oriCs in unannotated bacterial genomes,” BMCBioinformatics, vol. 9, article 79, 2008.

[24] R. K. Aziz, D. Bartels, A. Best et al., “The RAST Server: rapidannotations using subsystems technology,” BMCGenomics, vol.9, article 75, 2008.

[25] R. Overbeek, T. Begley, R. M. Butler et al., “The subsystemsapproach to genome annotation and its use in the project toannotate 1000 genomes,” Nucleic Acids Research, vol. 33, pp.5691–5702, 2005.

[26] M. Picardeau, “Diagnosis and epidemiology of leptospirosis,”Médecine et Maladies Infectieuses, vol. 43, no. 1, pp. 1–9, 2013.

[27] M. Picardeau, D. M. Bulach, C. Bouchier et al., “Genomesequence of the saprophyte Leptospira biflexa provides insightsinto the evolution of Leptospira and the pathogenesis of lep-tospirosis,” PLoS ONE, vol. 3, no. 2, Article ID e1607, 2008.

[28] S.-X. Ren, G. Fu, X.-G. Jiangk et al., “Unique physiological andpathogenic features of Leptospira interrogans revealed bywhole-genome sequencing,” Nature, vol. 422, no. 6934, pp. 888–893,2003.


[29] M. Singer and P. Berg, Genes & Genomes: A Changing Perspec-tive, University Science Books, 1991.

[30] A. L. T. O. Nascimento, A. I. Ko, E. A. L. Martins et al., “Com-parative genomics of two Leptospira interrogans serovars revealsnovel insights into physiology and pathogenesis,” Journal ofBacteriology, vol. 186, no. 7, pp. 2164–2172, 2004.

[31] R. B. Bourret, N. W. Charon, A. M. Stock, and A. H. West,“Bright lights, abundant operons—fluorescence and genomictechnologies advance studies of bacterial locomotion and sig-nal transduction: review of the BLAST meeting, Cuernavaca,Mexico, 14 to 19 January 2001,” Journal of Bacteriology, vol. 184,no. 1, pp. 1–17, 2002.

[32] C. Li, C. W. Wolgemuth, M. Marko, D. G. Morgan, and N. W.Charon, “Genetic analysis of spirochete flagellin proteins andtheir involvement in motility, filament assembly, and flagellarmorphology,” Journal of Bacteriology, vol. 190, no. 16, pp. 5607–5615, 2008.

[33] A. L. T. O. Nascimento, S. Verjovski-Almeida,M. A. van Sluys etal., “Genome features of Leptospira interrogans serovar Copen-hageni,” Brazilian Journal of Medical and Biological Research,vol. 37, no. 4, pp. 459–478, 2004.

[34] P. A. Cullen, S. J. Cordwell, D. M. Bulach, D. A. Haake, andB. Adler, “Global analysis of outer membrane proteins fromLeptospira interrogans serovar Lai,” Infection and Immunity, vol.70, no. 5, pp. 2311–2318, 2002.

[35] J. Matsunaga, T. A. Young, J. K. Barnett, D. Barnett, C. A. Bolin,andD.A.Haake, “Novel 45-kilodalton leptospiral protein that isprocessed to a 31-kilodalton growth-phase-regulated peripheralmembrane protein,” Infection and Immunity, vol. 70, no. 1, pp.323–334, 2002.

[36] E. Stackebrandt and J. Ebers, “Taxonomic parameters revisited:tarnished gold standards,”Microbiology Today, vol. 33, pp. 152–155, 2006.

[37] P.Vandamme andP.Dawyndt, “Classification and identificationof the Burkholderia cepacia complex: past, present and future,”Systematic and Applied Microbiology, vol. 34, no. 2, pp. 87–95,2011.

[38] C. A. Ganoza, M. A. Matthias, D. Collins-Richards et al.,“Determining risk for severe leptospirosis bymolecular analysisof environmental surface waters for pathogenic Leptospira,”PLoS Medicine, vol. 3, no. 8, article e308, 2006.

[39] J. S. Lehmann, M. A. Matthias, J. M. Vinetz, and D. E. Fouts,“Leptospiral pathogenomics,” Pathogens, vol. 3, no. 2, pp. 280–308, 2014.

Submit your manuscripts athttp://www.hindawi.com

Hindawi Publishing Corporationhttp://www.hindawi.com Volume 2014

Anatomy Research International

PeptidesInternational Journal of


Hindawi Publishing Corporation http://www.hindawi.com

International Journal of

Volume 2014

Zoology


Molecular Biology International

GenomicsInternational Journal of


The Scientific World JournalHindawi Publishing Corporation http://www.hindawi.com Volume 2014


BioinformaticsAdvances in

Marine BiologyJournal of



Signal TransductionJournal of


BioMed Research International

Evolutionary BiologyInternational Journal of



Biochemistry Research International

ArchaeaHindawi Publishing Corporationhttp://www.hindawi.com Volume 2014


Genetics Research International


Advances in

Virolog y

Hindawi Publishing Corporationhttp://www.hindawi.com

Nucleic AcidsJournal of

Volume 2014

Stem CellsInternational



Enzyme Research


International Journal of

Microbiology

Documents

Research Article The Characteristics of Ubiquitous and Unique … · 2019. 7. 31. · Research Article The Characteristics of Ubiquitous and Unique Leptospira Strains from the Collection