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Expression of the marA, soxS, acrB and ramA genes related to the AcrAB/TolC efflux pump in Salmonella entérica strains with and without quinolone resistance-determining regions gyrA gene mutations

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The

Brazilian

Journal

of

INFECTIOUS

DISEASES

w w w . e l s e v i e r . c o m / l o c a t e / b j i d

Original

article

Expression

of

the

marA,

soxS,

acrB

and

ramA

genes

related

to

the

AcrAB/TolC

efflux

pump

in

Salmonella

enterica

strains

with

and

without

quinolone

resistance-determining

regions

gyrA

gene

mutations

Rafaela

Gomes

Ferrari

a,∗

,

Antonio

Galiana

b

,

Rosa

Cremades

b

,

Juan

Carlos

Rodríguez

b

,

Marciane

Magnani

a

,

Maria

Cristina

Bronharo

Tognim

c

,

Tereza

C.R.M.

Oliveira

a

,

Gloria

Royo

b

aAgriculturalSciencesCenter,DepartmentofFoodScienceandTechnology,UniversidadeEstadualdeLondrina,Londrina,PR,Brazil bMicrobiologyDepartment,UniversityGeneralHospitalofElche,UniversidadMiguelHernándezdeElche,Elche,Spain

cDepartmentofBasicHealthScience,UniversidadeEstadualdeMaringá,Maringá,PR,Brazil

a

r

t

i

c

l

e

i

n

f

o

Articlehistory:

Received11April2012

Accepted13September2012

Availableonline28February2013

Keywords: Salmonellasp. Fluoroquinolone Effluxpump Antibioticresistance

a

b

s

t

r

a

c

t

Several studieshave been conducted in recentyears to elucidate the structure,

func-tionandsignificanceofAcrB,MarA,SoxSandRamAinSalmonellaenterica.Inthisstudy,

therelativequantificationofacrB,soxS,marAandramAgenesexpressionwasevaluated

in 14 strainsofS. enterica,with or without accompanying mutationsinthe quinolone

resistance-determiningregionsofthegyrAgene,thatwereexposedtociprofloxacin

dur-ingtheexponentialgrowthphase.Thepresenceofciprofloxacinduringthelogphaseof

bacterialgrowthactivatedthegenesmarA,soxS,ramAandacrBinallS.entericastrains

ana-lyzedinthisstudy.ThehighestexpressionlevelsforacrBwereobservedinstrainswith

gyrA mutation,andmarA showedthe highestexpressioninthe strainswithout

muta-tion.Considering onlythestrainswithciprofloxacinminimuminhibitoryconcentration

values<0.125␮g/mL (sensitivetociprofloxacin),themostexpressed geneinthestrains

both withandwithoutmutationswasacrB.Inthestrainswithciprofloxacin minimum

inhibitoryconcentrationvalues≥0.125␮g/mL(lowsusceptibility),withandwithout

muta-tionsingyrA,themostexpressedgenewasmarA.Inthisstudy,weobservedthatstrains

resistant tonalidixicacidmayexpressgenesassociatedwiththeeffluxpumpandthe

expressionoftheAcrAB-TolCpumpgenesseemstooccurindependentlyofmutationsin

gyrA.

©2013 ElsevierEditoraLtda.Allrightsreserved.

Correspondingauthorat:CentrodeCiênciasAgrárias,DepartamentodeCiênciaeTecnologiadeAlimentos,UniversidadeEstadualde

Londrina,Av.CelsoGarciaCids/n,Londrina,PR,Brazil.

E-mailaddress:rafaelaferrari@yahoo.com.br(R.G.Ferrari).

1413-8670/$–seefrontmatter©2013 ElsevierEditoraLtda.Allrightsreserved.

(2)

Introduction

The resistance of Salmonella enterica to quinolones is

usu-allymediatedbymutationsintopoisomerasegenes.However,

the presence of plasmids and active efflux pumpscan be

determinantfactorsindecreasedantibioticsusceptibilityand

increasedresistance.1

Effluxpumpsactinresponsetobacterialstressandthe

expressionof pumps reducesthe accumulationof organic

compoundsorantimicrobialagentswithinthecellandcan

alsobecausedbychromosomalmutations,resultingin

mul-tiple antibiotic resistance (MAR).2 According to Baucheron

etal.,3effluxpumpsplayanimportantroleinresistance,

espe-ciallywhenfluoroquinolonesareinvolved.

The AcrB efflux pump belongs to the

resistance-nodulation-cell division (RND) superfamily and acts in

associationwithtwotypesofproteins:theoutermembrane

channel (TolC)and a periplasmic ‘adaptor’ protein(AcrA).4

Regulators belonging to the AraC/Xyls family of

transcrip-tional activators,5 i.e. marA,6 soxRS,7 rob,8 and ramA9 have

beenfoundtoactivateacrABtranscriptionbybindingtothe

marboxsequencecharacterizedinitspromoter.10

TheMarAand SoxS proteinscanactivate acrAB

expres-sion. The marRAB operon isresponsible for producing the

MarAtranscriptional activator protein,6 which canbe

syn-thesizedinresponsetothe presenceofantibioticsandcan

resultinthemulti-drugresistancephenotype(MDR).Inturn,

thesoxRSoperonisactivatedinresponsetooxidativestress,

withtheSoxSproteinsubsequentlyactingastranscriptional

activator.11 TheoverexpressionofsoxRSalsocontributesto

increasedantibioticresistanceinGram-negativebacteria.

TheproductoftheramRgeneregulatesthegeneramA,12

whichproducestheproteinRamA.RamAishomologous to

MarAandSoxS.13BacteriaoverexpressingramAmayexhibit

theMDRphenotypebyinducingexpressionofacrABandtolC.9

S.entericastrainswiththetolCgeneexperimentallydeleted

show anincreased susceptibility toantimicrobial agents.14

Similarly,strainsofS.entericashowedhighersusceptibilityto

ciprofloxacinwhenramAwasinactivated.15

Althoughseveralstudieshavebeen conductedinrecent

yearstoelucidatethestructure,functionandsignificanceof

AcrB,MarA,SoxSandRamA,16–18theirregulationinS.

enter-icaisnotfully understood.In thisstudy,the expressionof

acrB,soxS,marAandramAwasevaluatedinfourteenstrains ofS.enterica,withorwithoutaccompanyingmutationsinthe

quinoloneresistance-determiningregions(QRDR)ofthegyrA

gene,thatwereexposedtociprofloxacinduringthe

exponen-tialgrowthphase.

Materials

and

methods

Strains

We analyzed 14 strains of S. enterica that are resistant to

nalidixic acid (NAL). These strains were divided into two

groups:sevenstrainswithout mutationintheQRDRregion

ofthegenesgyrA,gyrB,parCandparEandsevenstrainswith

mutationsin the QRDRof gyrA,but withno mutations in

theQRDRofothergenes.Amongthestrainswithmutations

inthe gyrAQRDR,onewaspositive forthe qnrB19plasmid

gene. Theciprofloxacin minimum inhibitory concentration

(CipMIC)ofeachstrainwasdeterminedusingE-testgradient

strips(ABBiodisk,Solna,Sweden).OncetheCipMIChadbeen

determined, each strainwas cultivated induplicatefor2h

inMueller-Hintonbroth(MHB)andciprofloxacinwasadded

tooneofthetwoculturesataconcentrationcorresponding

tohalfofthecorrespondentlyCipMICofeachstrain.19After

30minofexposuretotheantibioticat37◦C,theculturewas

centrifugedforsubsequentRNAextraction.

RNAisolation

RNAisolationwasperformedaccordingtoChomczynskiand

Sacchi20bytheguanidinium-thiocyanate–phenol–chloroform

method, with some modifications. After centrifugation at

14,000×gfor10min,thesupernatantwasdiscarded,200␮L

of lysis solution was added and the samples were

incu-batedfor1hat37◦C.Afterthistime, 50␮Lof1%SDS was

added. Aftervortex agitation,25␮Lof2MNaCl and200␮L

phenol:chloroformweremixedintothematerial;whichwas

placedonicefor10min.Thematerialwasthencentrifuged

at 14,000×g for 20min at 4◦C, and the supernatant was

recovered.Anequalvolumeofisopropanolwasaddedtothe

supernatant;mixturewasincubatedat−70◦Cfor2handthen

centrifuged at14,000×g for11minat4◦C.Afterthe

super-natantwasdiscarded,thepelletwasdriedunderairfluxand

thenvortexedin750␮Lof75%ethanol.Anewcentrifugation

wasconductedat14,000×gfor11minat4◦C;thesupernatant

wasdiscarded;thepelletwasdriedfor1handresuspendedin

30␮Lofnuclease-freewater(InvitrogenTM).TheRNAsamples

were treatedwithRQ1 DNase(AmbionAM 1906),following

themanufacturer’s instructions.RNApurityand

concentra-tionwasmeasuredusingtheNanodropND-1000.

Reversetranscriptase(RT)

RT reactionswereconductedasdescribedbyChicoetal.,21

using1␮goftotalRNA,90ngofrandomhexamers(QIAGEN®)

and 0.5mMdNTPs (InvitrogenTM).Prior tocDNA synthesis,

denaturationwasperformedfor5minat65◦C.Afterthisstep,

200UofMMLVreversetranscriptase(InvitrogenTM),10mMof

DTT (InvitrogenTM),and 20unitsofRNaseinhibitor (RNase

OUT,Invitrogen)wereaddedtoeachreactiontoafinal

vol-ume of20␮L.Thereactionconditionswere 10minat25◦C,

15minat42◦Cand5minat99◦C.

Relativequantificationofgeneexpression

After obtaining the cDNA, quantitative real-time reverse

transcriptase PCR(qRT-PCR) wasperformed using the7500

Real-Time PCR System, SDS software version 1.4 (Applied

Biosystems). The reactions were performed in a final

vol-ume of20␮L,containing300nM ofeach primer,100nMof

each probe (Table 1), 2␮L ofcDNA and 1× TaqMan®

uni-versal master mix (Applied Biosystems). Standard curves

wereconstructedtocalculatethegene-specificPCRefficiency

from10-foldseriesdilutionofthemixedcDNAtemplatefor

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Table1–TaqMan®primersandprobes.Sequencesof

primersandprobesusedforqRT-PCR(quantitative real-timereversetranscriptasePCR)reactions,designed withthehelpofthePrimerExpressTM2.0software

(AppliedBiosystems).

Primersandprobesa Primerssequences53

16s-F CGTGTTGTGAAATGTTGGGTTAA

16s-R CCGCTGGCAACAAAGGATAA

probe16s TCCCGCAACGAGCGCAACC

acrB-F TGAAGACCAGGGCGTATTCCT acrB-R TTTTTGCGTGCGCTCTTG

probeacrB ACAATGGTCCAGCTCCCCGCG

soxS-F CGGAATACACGCGAGAAGGT soxS-R GAGCGCCCGATTTTTGATATC

probesoxS TGCTGCGATACATAGCCCAGGTCCA

marA-F GACCCGGACGTTCAAAAACTAT marA-R TCGCCATGCATATTGGTGAT

probemarA TGATGTGCCGCCACACAAATACCG

ramA-F CCAGAAGGTGTATGATATTTGTCTCAAG ramA-R GGTTGAACGTGCGGGTAAA

proberamA TTGATTCGCAGCAAACCTTTACGCG

a Probe used: 6-carboxyfluorescein (FAM); quencher used: 6-carboxytetramethylrhodamine(TAMRA).

calculated using the formula E=[10(−1/S)]1, where E

rep-resentsthe calculated efficiency, and Sis the slope ofthe

standardcurve.22 Tocheckallprimers specificity,real-time

PCRwas performed on cDNA and productswere analyzed

byelectrophoresison2%agarosegelandethidiumbromide

staining.NegativeqRT-PCRcontrolwithnotemplateswas

per-formedforeachprimerpair.22

Statisticalanalysis

TheresultswereanalyzedusingSPSS18.0software.The

geo-metric means (GM) of the CipMICs were calculated using

thefollowing



n y1y2y2···ynformula:whereyrepresentsthe

individualCipMICofeachstrain,andnrepresentsthetotal

numberofCipMICvalues.23

Results

Thepresenceofciprofloxacinduringthelogphaseof

bacte-rialgrowthactivatedatleastoneofthefourgenestestedin

allS.entericastrainsanalyzedinthis study.Theexpression

levelsofthegenesmarA,soxSandramAwerehigherinthe

strainswithoutamutationingyrA,gyrB,parAorparCthanfor

strainswithmutations.However,thehighestexpressionlevels

foracrBwereobservedinstrainswithgyrAmutation(Fig.1).

The GM value for the four pump genes evaluated in

Salmonellastrainswithoutmutationswas2.70,andforstrains

withamutationingyrAitwas2.13.Amongthestrainsmutated

ingyrA,strain209-2showedhigherexpressionofthegenes

analyzed,witha5.99GM.Incontrast,thestrainwithout

muta-tioningyrAwiththehighestlevelsofgeneexpressionwas

238-2,witha15.38GM(Table2).

Afterassessingthelevelofexpressionforeachgeneinthe

strainswithoutmutation,marAshowedthehighest

expres-sion(GM=6.93),followedbysoxS(GM=2.72),acrB(GM=2.38)

andramA(GM=1.16).InthestrainswithmutationsingyrA,

the gene marA also showed higher levels of gene

expres-sion (GM=3.41) but was followed by acrB (GM=3.25), soxS

(GM=1.77)andramA(GM=1.05).

Considering only the strains with CipMIC

val-ues<0.125␮g/mL (sensitive to ciprofloxacin), the most

expressedgeneinthestrainsbothwithandwithout

muta-tionswasacrB.Inthethreemutatedstrains,theGMforthis

genewas9.28,andinthestrainwithoutmutationthelevelof

expressionofacrBwas11.8(Table2).

InthestrainswithCipMICvalues≥0.125␮g/mL(low

sus-ceptibility), withand without mutationsin gyrA,the most

expressedgenewasmarA.Forthefourmutatedstrains,marA

expressionrangedfrom0.98to11.96,andtheGMwas3.36.

In contrast,forthesixstrains withoutmutation, themarA

expressionlevelrangedfrom1.29to122,withaGMof6.62.

AmongthefourstrainswithgyrAmutationsandreduced

susceptibility to ciprofloxacin,strain 288-2, serovar

Heidel-berg,andstrain300-2,serovarEnteritidis,scarcelyexpressed

thepumpgenestested.Ontheotherhand,S.Enteritidisstrain

209-2,despiteaGMof5.99,presentedaCipMICvaluefour

timeslowerthanS.Enteritidisstrain216-2,whichshoweda

GMof1.66(Table2).

Fourofthesixstrainswithoutmutationsandreduced

sus-ceptibilitytociprofloxacinshowedsignificant expressionof

theeffluxpumpgenesevaluated,withGMvaluesbetween4.25

and15.26.Incontrast,strain232-2,withnomutationingyrA

andthelowestlevelofgeneexpressionlinkedtothepump

(GM=0.23),presentedaCipMICvalueof0.5␮g/mL.Strain

297-2,serovarCorvallis,positivefortheqnrB19plasmidgene,also

presentednoexpressionofanyofthefourgenesstudiedthat

arelinkedtothepumpcomplex(GM=0.65).

Discussion

There are reports that AcrAB pump expression in

Escherichia coli can increase the MIC for ciprofloxacin and

norfloxacin uptofive times.24 In thisstudy,all the strains

evaluated showed expression of at least one gene related

to effluxpumpsinthe presenceofciprofloxacin.However,

the expression ofthese genes and their relationship with

reducedsusceptibilitytociprofloxacinwashighlydivergent,

independentofmutationsingyrA.TheS.Enteritidisstrains

250-2,229-2and213-2,withmutationsingyrAandexpression

of atleast 3 genes linked to the pump, presentedCipMIC

valuesoflessthan0.125␮g/mL.

However, other S. Enteritidis strains (209-2, 300-2 and

216-2),withgyrAmutationsandbothwithandwithout

expres-sionofthe genesstudied,showedreducedsusceptibilityto

ciprofloxacin.

Baucheronetal.3 havereportedareductionofupto

64-foldinCipMICvaluesafterinhibitionoftheAcrABoperonin

strainsofS.Typhimurium,withorwithoutmutationsingyrA.

Morgan-Linnelletal.25alsofailedtocorrelateAcrAB

expres-sionandthepresenceofmutationsintopoisomerasegenes

withtheMICforfluoroquinolones.Theincreaseinthelevels

ofAcrABexpressiondidnotalwaysincreasetheMICs,

(4)

Fig.1–DistributionoftheexpressionlevelsofthemarA,soxS,ramAandacrBgenesstudiedinrelationtoCipMIC(␮g/mL)

andgyrAgenemutations.WT,wild-typestrain;CIP,ciprofloxacin.

values.Furthermore,theexpressionoftheeffluxpumpwas

reportedasbeingresponsibleonlyforbaselineresistance.26

Inthisstudy,strainsofS.EnteritidiswithoutQRDR

muta-tionsinthe genesgyrA,gyrB,parCorparEshowedreduced

susceptibilitytociprofloxacin.Theexpressionofgenes

asso-ciatedwiththe effluxpumpseemstohaveinfluenced this

reduction.Strains121-1,135-2,91-1and238-2ofS.Enteritidis

showedaGMof4.94,4.25,5.25and15.26,respectively.Inthis

Table2–DistributionofthemutationsobservedinQRDRofthegyrAgeneinSalmonellastrainsofdifferentserovarswith thecorrespondingminimalinhibitoryconcentrationforciprofloxacin(CipMIC)andgeometricmean(GM)data.

Straina Serotype CipMIC(␮g/mL) Mutation Levelofexpressioninthepresenceofciprofloxacin

soxS db marA db acrB db ramA db GMc

250-2 Enteriditis 0.0156 Ser83-Tyr 1.39 0.11 7.26 0.51 7.67 0.38 2.46 0.26 3.71 229-2 Enteriditis 0.0156 Asp87-Asn 1.88 0.14 2.60 0.47 4.70 0.07 19.43 0.78 4.60 213-2 Enteriditis 0.0156 Asp87-Asn 0.40 0.30 2.26 0.20 22.16 0.16 9.78 0.33 3.74 209-2 Enteriditis 0.1250 Ser83-Tyr 9.65 0.13 11.96 0.30 37.27 0.54 0.30 0.85 5.99 300-2 Enteriditis 0.2500 Ser83-Phe 1.99 0.61 3.16 0.10 0.00 0.00 0.00 0.00 0.50 288-2 Heidelberg 0.5000 Ser83-Tyr 2.71 0.46 0.98 1.30 0.59 0.79 0.00 0.00 0.63 216-2 Enteriditis 0.5000 Ser83-Tyr 1.00 0.11 3.43 0.16 2.20 0.27 1.01 0.70 1.66 238-2 Enteriditis 0.2500 wt 42.2 0.29 9.65 0.40 3.43 0.22 38.85 0.19 15.26 121-1 Enteriditis 0.3800 wt 4.66 0.31 2.82 0.72 7.89 0.40 5.74 0.46 4.94 135-2 Enteriditis 0.3800 wt 2.90 0.45 122 0.20 9.19 0.24 0.00 0.00 4.25 91-1 Enteriditis 0.1250 wt 6.96 0.96 8.50 0.43 1.56 0.14 8.22 0.43 5.25 119-2 Enteriditis 0.0470 wt 2.27 0.18 9.19 0.38 11.80 0.36 1.25 0.30 4.19 232-2 Enteriditis 0.5000 wt 0.16 0.68 1.29 0.39 0.00 0.00 0.13 1.25 0.23 297-2d Corvallis 0.5000 wt 0.79 0.33 2.31 0.13 0.97 0.19 0.00 0.00 0.65

wt,strainwithoutmutationsingyrA,gyrB,parCandparE. a AllstrainswereresistanttoNAL.

b Typicaldeviation.

c Geometricmeanofthefourgenes. d StrainpositiveforqnrB19.

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group,itisimportanttonotethatstrain135-2presentedmarA

expressionof122,andstrain238-2ofS.Enteritidisincreased

expressionofboththesoxSandramAgenesaswellasmarA

(Table2).

TheexpressionofmarAisinduced byanumberof

sub-stances,including quinolones.27 ThemarA gene isable to

mediatedrugresistancebydecreasingexpressionoftheOmpF

porinandcausingoverexpressionoftheAcrBeffluxpump.6,16

StudieswithE. colireportedMICvaluesforofloxacinup to

eightfoldhigherinstrainswithoverexpressionofthe marA

gene,in comparisontostrains that onlyhad mutationsin

gyrA.12,28,29Kernetal.30observedthattherateofsuccessful

treatmentofE. coliwithfluoroquinolones was significantly

lower in strains that expressed marA. In clinical isolates,

increasedlevels ofAcrABpumpgeneexpressionmayarise

duetochangesinmarAortobactericidalprotectiongenerated

bytheregulatorsofthisgene.ThefactthatthemarAgeneis

associatedwiththemarRABoperonactivatorsuggestsitsuse

(marA)asatargetforstudiesonstrategiesagainstmicrobial

resistance.25

ThesoxSgenewasthemostexpressed,aftermarA,inthe

non-mutatedstrainsanalyzedinthisstudy.Thisgeneisthe

transcription activatorthat positively regulatesthe

expres-sionofmorethan20genesrelatedtotheincreasedsynthesis

ofproteinsassociatedwiththeAcrAB-TolCeffluxpump.31–33

TheSoxRSregulatorysystemprotectscellsagainstoxidative

stressgeneratedbyvariousantimicrobials.32TheS.Enteritidis

strain238-2,withoutmutationsingyrA,showedexpression

ofthesoxSgeneandreducedsusceptibilitytociprofloxacin.

Kehrenbergetal.34observedaneightfoldincreaseinthe

Cip-MICvaluesofS.VirchowstrainswhensoxSwasexpressedbut

norelationshipwiththepresenceofgyrAmutations.

Theexpressionofeffluxpumpgeneswaspracticallyzero

fortheHeidelbergserovarstrain(GM=0.63),whichshowedthe

highestCipMICamongallthestrainsanalyzedinthisstudy.

Itsuggeststhatthisreductioninsusceptibilityisduetothe

intrinsicresistancecommonlyobservedinthisserovar.35

TheCorvallisserovarpresentedaCipMICof0.5␮g/mL,but

nomutationintheQRDRregionofthetopoisomerasegenes

thatcorrelateswiththelowexpressionlevelsforthestudied

genesrelatedtoeffluxpumps.However,thereduced

suscep-tibilitytociprofloxacinobservedmayrelatetothepresence

oftheqnrB19plasmidgene. AccordingtoLi,36 theqnrgene

facilitatestheselectionofchromosomalmutationsrelatedto

quinoloneresistanceinS.entericabysignificantlyincreasing

thelevelsatwhichmutantscanbeselected.

The 232-2 S. Enteritidis strain presented a CipMIC of

0.5␮g/mLanddidnotexpressanyofthestudiedgeneslinked

totheeffluxpump.Itispossiblethatalternativemechanisms

ofgeneregulation,suchasacrR,thatareindependentof

mar-sox-robwereresponsibleforcontrollingtheexpressionofAcrB inS.enterica.37Mutationsingenescontrollingthe

transcrip-tionorexpressionofothergenes,suchasacrD,acrAortolC15

mayalsobeinvolved,inadditiontotheAcrEFeffluxpreviously

describedinS.enterica.38,39

Another possibility for the reduced susceptibility to

ciprofloxacin observed in strain 232-2 could be mutations

ingyrAoutside the QRDRregion.Capooret al.40 have

sug-gested anincreaseto the regionalboundariesthat include

theQRDRofthegyrAgenebecausemutationsassociatedwith

resistancetoquinoloneswere observedbeyondthe current

domain.

In this study,weobserved thatstrains resistant toNAL

may express genes associated with the efflux pump as a

formofprimaryresistancetothisdrug.Thismechanismmay

perform a pre-selectionfor less sensitive strains, with the

subsequentemergenceofmutatedandresistantstrains.One

possiblemechanism toincrease thelife ofquinolonesand

fluoroquinoloneswouldbethedevelopmentofinhibitorsof

theAcrAB-TolCsystem,whichcouldminimizetheselection

ofstrainsresistanttoNAL.TheexpressionoftheAcrAB-TolC

pumpgenesseemstooccurindependentlyofmutationsin

gyrA,becausestrainswithoutmutationsintheQRDRregions

ofthetopoisomerasegenesevaluatedinthisstudypresented

higher expression of the genes associated with the efflux

pumps.However,theresultsindicatetheneedforadditional

studiestobetterunderstandthecomplexinterplaybetween

theexpressionandregulationofeffluxpumpgenesandother

mechanismsofresistancetoquinolonesinS.enterica.

Conflict

of

interest

Allauthorsdeclaretohavenoconflictofinterest.

Acknowledgements

WewouldliketoacknowledgeCNPqandCapesforfinancial

supportintheformofPhDscholarshipsawardedtoRFand

MM.

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