h tt p : / / w w w . b j m i c r o b i o l . c o m . b r /
Medical
Microbiology
The
role
of
gyrA
and
parC
mutations
in
fluoroquinolones-resistant
Pseudomonas
aeruginosa
isolates
from
Iran
Roghayeh
Nouri
a,b,c,
Mohammad
Ahangarzadeh
Rezaee
a,b,∗,
Alka
Hasani
a,b,
Mohammad
Aghazadeh
b,
Mohammad
Asgharzadeh
daTabrizUniversityofMedicalSciences,InfectiousandTropicalDiseasesResearchCenter,Tabriz,Iran bTabrizUniversityofMedicalSciences,FacultyofMedicine,DepartmentofMicrobiology,Tabriz,Iran cTabrizUniversityofMedicalSciences,StudentResearchCommittee,Tabriz,Iran
dTabrizUniversityofMedicalSciences,BiotechnologyResearchCenter,Tabriz,Iran
a
r
t
i
c
l
e
i
n
f
o
Articlehistory:
Received15July2015 Accepted25March2016 Availableonline26July2016 AssociateEditor:AfonsoLuísBarth
Keywords: Pseudomonasaeruginosa Fluoroquinoloneresistance gyrA parC
a
b
s
t
r
a
c
t
Theaimofthisstudywastoexaminemutationsinthequinolone-resistance-determining region(QRDR)ofgyrAandparCgenesinPseudomonasaeruginosaisolates.Atotal of100 clinicalP.aeruginosaisolateswerecollectedfromdifferentuniversity-affiliatedhospitals inTabriz,Iran.Minimuminhibitoryconcentrations(MICs)ofciprofloxacinandlevofloxacin wereevaluatedbyagardilutionassay.DNAsequencesoftheQRDRofgyrAandparCwere determinedbythedideoxychainterminationmethod.Ofthetotal100isolates,64were resistanttociprofloxacin.NoaminoacidalterationsweredetectedingyrAorparCgenesof theciprofloxacinsusceptibleorciprofloxacinintermediateisolates.Thr-83→Ile substitu-tioningyrAwasfoundinall64ciprofloxacinresistantisolates.Forty-four(68.75%)ofthem hadadditionalsubstitutioninparC.Acorrelationwasfoundbetweenthenumberofthe aminoacidalterationsintheQRDRofgyrAandparCandthelevelofciprofloxacinand levo-floxacinresistanceoftheP.aeruginosaisolates.Ala-88→ProalterationinparCwasgenerally foundinhighlevelciprofloxacinresistantisolates,whichweresuggestedtoberesponsible forfluoroquinoloneresistance.ThesefindingsshowedthatinP.aeruginosa,gyrAwasthe primarytargetforfluoroquinoloneandadditionalmutationinparCledtohighlyresistant isolates.
©2016SociedadeBrasileiradeMicrobiologia.PublishedbyElsevierEditoraLtda.Thisis anopenaccessarticleundertheCCBY-NC-NDlicense(http://creativecommons.org/
licenses/by-nc-nd/4.0/).
∗ Correspondingauthorat:InfectiousandTropicalDiseasesResearchCenter,TabrizUniversityofMedicalSciences,Tabriz,Iran. E-mail:rezaee@tbzmed.ac.ir(M.AhangarzadehRezaee).
http://dx.doi.org/10.1016/j.bjm.2016.07.016
1517-8382/©2016SociedadeBrasileiradeMicrobiologia.PublishedbyElsevierEditoraLtda.ThisisanopenaccessarticleundertheCC BY-NC-NDlicense(http://creativecommons.org/licenses/by-nc-nd/4.0/).
Introduction
Pseudomonas aeruginosa is an important opportunistic pathogen1–3causinglife-threateninginfections,especiallyin
immunocompromisedpatients.4–6Oftentheseinfectionsare
difficulttotreatduetotheintrinsicresistanceofthespecies7
aswell as its remarkable abilitytoacquire resistanceto a wide range of antimicrobial agents.8 Fluoroquinolones are
the only accessible antibiotics for effective oral treatment of infections caused by this organism.9 Among
fluoro-quinolones,ciprofloxacinandlevofloxacinarewidelyusedin thetreatmentofP.aeruginosainfections.10
Fluoroquinolones act by inhibiting the action of tar-getenzymes,DNA gyraseand topoisomerase IV,with both enzymesplayingaprincipal roleinDNAreplication.11DNA
gyraseandtopoisomeraseIVare heterotetramericenzymes thatarecomposedoftwosubunitsencodedbythegyrA,gyrB
andparC, parE,respectively.12 ThegyrAand gyrBgenesare
homologstoparCandparE,respectively.13Themechanismsof
fluoroquinoloneresistanceinP.aeruginosaincludemutations inthe DNA gyrase and topoisomerase IV,14,15
overexpress-ion ofefflux pump system and the innate impermeability ofthemembrane.16 Alterations intheso-called
quinolone-resistance-determining region (QRDR) within DNA gyrase andtopoisomeraseIVarethemajormechanismsfor fluoro-quinoloneresistanceinP.aeruginosa.17–20
Moreover,isolateswith mutationsin QRDRofgyrA and
parCshowthehighestlevelsoffluoroquinoloneresistance.21
AlthoughaminoacidalterationsinthegyrBandparEgenes havebeendescribed,but thefrequencyofthesemutations islow, withonly acomplementary role influoroquinolone resistance.18,21
SeveralstudiesfromIranhavereportedthehighprevalence ofMDRstrainsamongIranianhospitalsandstrainsisolated from hospitalized patients; especially, burn patients have showhighlevelresistancetomostavailableantibiotics.22,23
Theprevalence of mutationsin DNA gyrase and topoi-somerase IV has not been well studied in Iran. This is
the largest analysis of the QRDR of gyrA and parC in the clinical isolates ofP. aeruginosafrom Iran.The aimof this studywastoexaminethemutationsingyrAandparCgenes and characterize their correlation with ciprofloxacin and levofloxacin resistance, as well as the evaluation of their effectonciprofloxacinandlevofloxacinMinimuminhibitory concentrations(MICs)amongtheclinicalisolatesofP. aerugin-osa.
Materials
and
methods
Bacterialisolates
Inaprospectivestudy,atotalof100non-repetitiveclinical isolates of P. aeruginosa were collected, between December 2013,andJuly2014,fromfourEducational-HealthCare Cen-tersofTabrizUniversityofMedicalSciencesinNorthwestIran. Thebacterialisolateswererecoveredfromdifferentclinical specimenssuchasurine(29%),wounddischarge(25%), tra-chealaspirates(21%),blood(8%)andotherclinicalspecimens
(Table1).Allisolateswereidentifiedbystandardconventional
biochemicaltests.24
Antimicrobialsusceptibilitytesting
Antimicrobialsusceptibilitytoticarcillin(75g), piperacillin-tazobactam(100/10g),ceftazidime(30g),cefepime(30g), aztreonam (30g), imipenem (10g), meropenem (10g), gentamicin (10g), amikacin (30g), ciprofloxacin (5g), levofloxacin (5g) and ofloxacin(5g) (Mast,UK) was per-formed by employing the standard disk diffusion method. MICsofciprofloxacinandlevofloxacin(Sigma-Aldrich)were determined by the standard agar dilution assay. The results of disk diffusion assay as well as MIC were inter-preted according to the clinical and laboratory standard institute (CLSI) guidelines.25 Pseudomonas aeruginosa ATCC
27853 was used as the control strain for susceptibility testing.
Table1–DistributionofPseudomonasaeruginosaisolatesbythesiteofisolationandhospitalorigin.
Sourceofisolates Hospitalorigin Totalno.ofisolates
ImamReza Sina Koodakan ShahidMadani
Trachealaspirate 7 4 6 4 21 Wounddischarge 7 8 4 6 25 Urine 7 6 9 7 29 Blood 1 4 1 2 8 Throatculture 1 0 3 0 4 Catheter 0 0 2 2 4 Sputum 0 1 1 0 2 Bronchialwashing 0 0 0 2 2
Pleuralfluidculture 1 0 0 0 1
Urethraldischarge 1 0 0 0 1
Peritonealfluid 1 0 0 0 1
Eardischarge 0 1 0 0 1
Stool 1 0 0 0 1
Table2–AminoacidalterationsingyrAandparCinciprofloxacinresistantisolatesofPseudomonasaeruginosa.
Groups No.ofisolates ReplacementinQRDR
GyrAatposition ParCatposition
83 87 87 88
PAO1 Thr(ACC) Asp(GAC) Ser(TCG) Ala(GCC)
I 20 Ile(ATC) – – –
II 8 Ile(ATC) – – Pro(CCC)
III 31 Ile(ATC) – Leu(TTG) –
IV 5 Ile(ATC) Asn(AAC) Leu(TTG) –
PCRamplificationandDNAsequencing
Chromosomal DNA from the isolates of P. aeruginosa was extracted by DNA extraction kit (Yekta Tajhiz Azma, Iran) accordingtothemanufacturer’sinstructions.ThePCR reac-tion was performed in a 50Lmixture containing 1.5mM MgCl2,0.5pmolofeachprimer,0.2mMdNTPs(YektaTajhiz Azma,Iran),1UofPfuDNApolymerase(YektaTajhizAzma, Iran),1XPfuDNApolymerasebufferand10–100ngofthe tem-plateDNA.
The amplification of gyrA and parC genes was carried outusingthepolymerasechainreactionandspecificprimer sets as described previously.26 Purified PCR products were
sequenced using the Applied Biosystems 3730/3730xl DNA analyzerssequencing(ABI)system,(BioneerCo.,Korea). Statisticalanalysis
Categoricalvariableswere comparedbytheChi-squaretest orFisher’sexacttestusingSPSS16.0statisticalsoftware(SPSS Inc.,Chicago,IL).Astatisticallysignificantdifferencewas con-sideredasaP-value<0.05.
Results
Antimicrobialsusceptibilitytesting
Ofthe100P.aeruginosaclinicalisolatestestedfor antimicro-bialsusceptibility,71ofthemwerefoundtoshowmultidrug resistance(MDR).MDRwasdefinedasresistancetothreeor moreunrelatedantibiotics.27 Thehighestrateofresistance
was observed against ticarcillin (84%) and ofloxacin (82%). Moreover,thehighestsusceptibilityratewasobtainedagainst ceftazidime(45%),followedbygentamicin(44%).Ofthetotal isolates, 64 (64%) were resistant, 2 (2%) were intermediate and34(34%)wereobservedtobesusceptibletociprofloxacin. Moreover,63%ofisolateswereresistant,1%were intermedi-ate,and36%weresusceptibletolevofloxacin.
DNAsequencesanalysis
DNAsequencesofallP.aeruginosaisolateswerecomparedwith thecorrespondingsequencesofP.aeruginosaPAO1(Accession: NC002516.2GI:110645304).Asidefromciprofloxacin suscep-tible,levofloxacinsusceptibleandciprofloxacinintermediate isolateswhichhadnoaminoacidalterationsintheirgyrAor
parCgenes,theaminoacidalterationswererecognizedingyrA
andparCQRDRof64ciprofloxacinresistant,63levofloxacin
resistantand1levofloxacinintermediateisolates,asdescribed
inTable2.Thetotalmutationsfoundintheseisolateswere
classified into4distinct groupsaccordingtothe patternof aminoacidalteration.GroupI:isolatescontainedsingle muta-tion Thr-83→ Ile ingyrA.Group II: isolatescontainedone mutationThr-83→IleingyrAandonemutationAla-88→Pro inparC.GroupIII:IsolatescontainedonemutationThr-83→ IleingyrAandonemutationSer-87→LeuinparC.GroupIV: isolatescontainedtwomutationsThr-83→IleandAsp-87→ AsningyrAandonemutationSer-87→LeuinparC.
DNAsequencesofQRDRgyrAshowedThr-83→Ile substi-tutionforall64ciprofloxacinresistantisolates.Of64isolates, 20(31.25%)hadamutation(Thr-83→Ile)ingyrAalone(group I). Adoublemutationin gyrA (Thr-83→ Ile and Asp-87→ Asn)wasdetectedin5of64isolates.Aminoacidalteration intheQRDRparCwasobservedin44(68.75%)of64isolates. AlloftheseisolatespossessedadditionalmutationsingyrA.
NodoublemutationsinparCwerefound.TheSer-87→Leu substitutionwasfoundin31(48.4%)of64isolates.Moreover, thesubstitutionofProforAla-88wasobservedin8(12.5%)of 64isolates.
CorrelationbetweenfluoroquinolonesMICandQRDRs mutations
TheMICvaluesofciprofloxacinandlevofloxacinfor64 resis-tant isolates and their correlation with different types of mutations in gyrA and parC genes are shown in Table 3. Asshown, ciprofloxacinMICforisolateswithasinglegyrA
substitution(Thr-83 →Ile)rangedfrom4–64g/mLandfor levofloxacin, the 4–32g/mL range was observed. Isolates with a single gyrA (Thr-83 → Ile) substitution and a sin-gle parC substitution (Ala-88 → Pro or Ser-87 → Leu) had ciprofloxacinMICsrangingfrom8to128or16to256g/mL andlevofloxacinMICsvariedfrom8to64or8to256g/mL. Moreover,the isolateswithdouble gyrAsubstitutions (Thr-83 →IleandAsp-87→Asn)and asingleparCsubstitution (Ser-87→Leu)hadciprofloxacinandlevofloxacinMICs ran-gingfrom32to256g/mL.Ourresultsshowedthatthetwo concurrentmutationsin gyrAand parC geneswere associ-atedwithahigherlevelofciprofloxacinandlevofloxacinMICs, ascomparedtoasinglemutationingyrA.(Geometricmean MICs ofciprofloxacin,29.34(group2) and 32(group3) ver-sus16.56(group1)g/mL,p<0.05;geometricmeanMICsof levofloxacin,24.67(group2)and28.6 (group3) versus14.42 (group 1)g/mLp<0.05). Moreover,three concurrent muta-tionsingyrAandparCgeneswere associatedwithahigher levelofciprofloxacinandlevofloxacinMICs,ascomparedto
Table3–CorrelationofmutationsingyrAandparCgenesandMICsdistributionofciprofloxacinandlevofloxacin.
Group No.ofisolates Antimicrobial agents
No.ofisolateswithMICs(g/mL)
0.5 1 2 4 8 16 32 64 128 256 I 20 Ciprofloxacin 2 2 10 5 1 GyrA(83) Levofloxacin 1 4 12 3 II 8 Ciprofloxacin 1 1 5 1
GyrA(83),ParC(88) Levofloxacin 1 3 2 2
III
31 Ciprofloxacin 12 11 5 2 1
GyrA(83),ParC(87) Levofloxacin 4 8 12 4 2 1
IV
5 Ciprofloxacin 2 1 1 1
GyrA(83and87),ParC(87) Levofloxacin 2 1 2
twoconcurrentmutationsingyrAandparCgenes(Geometric meanMICsofciprofloxacin,73.5(group4)versus29.3(group 2)g/mL, and 32 (group 3)g/mL p<0.05; geometric mean MICsoflevofloxacin,64(group4)versus24.6 (group2)and 28.61(group3)g/mLp<0.05)orsinglemutationingyrA. (Geo-metricmeanMICsofciprofloxacin,73.51(group4)versus16.56 (group1)g/mL,p<0.05;geometricmeanMICsoflevofloxacin, 64(group4)versus14.42(group1)g/mLp<0.05).
Discussion
Fluoroquinolonessuchasciprofloxacinandlevofloxacinare animportantclassofantibioticsforthetreatmentofP. aeru-ginosa infections.26 However, P. aeruginosa rapidly becomes
resistanttothesedrugsduringantibiotictherapy.15The
princi-plemechanismoffluoroquinolonesresistanceinP.aeruginosa
involvesmutationsinthegenesofDNAgyraseand topoiso-meraseIV.18
In the present study, the alteration of Thr-83 to Ile in
gyrA was found inall ciprofloxacin and levofloxacin resis-tant P. aeruginosa isolates.Moreover, a doubleconcomitant mutation in gyrA (Thr-83 → Ile and Asp-87 → Asn) was observed in five ciprofloxacin and levofloxacin resistant isolates.More noteworthy,theMIC valuesoftested fluoro-quinolonesamong theseisolates were significantly higher. However,noaminoacidchangewasdetectedinciprofloxacin susceptible,levofloxacinsusceptibleandciprofloxacin inter-mediate isolates. So Thr-83 → Ile was shown to be the chief mechanism of fluoroquinolones resistance. This was consistentwiththe resultsofother studies.26,28–30
Further-more, the amino acid sequences analysis in the QRDR of
parCshowedthatmorethanhalfofciprofloxacin and levo-floxacinresistantisolateshadanalterationinparCandthe Ser-87→Leusubstitutionwasthepredominantaminoacid change (48.4%). Lee et al.18 and Mouneimne et al.16 have
previously reported this amino acid change in 35.9% and 25%oftheciprofloxacinresistantisolates,respectively.Also, another alteration in parC, Ala-88→ Pro substitution, was highlyfrequentinourisolates,incomparisontotheresults ofAkasakaet al.,17 and Sekiguchiet al.31 They foundthis
aminoacidchangeonlyinoneofallstudiedisolates.More importantly,thissubstitutionwasobservedgenerallyamong high level ciprofloxacin resistant isolates suggested to be responsibleforfluoroquinoloneresistance.However,wedid
notdetectaminoacidalterationatpositionsPro-83,Gly-85,31
Glu-91andLeu-9517inparC,asreportedintheprevious
stud-ies.
Based on the analysis of sequencing results, all of the isolates with parC mutationhad one or two mutationsin
gyrA.Thisobservation confirmedthat theDNA gyrasewas the primary target for fluoroquinolone resistance in the clinical isolatesof P. aeruginosa.However, isolatesthat had doublemutationingyrAand parChad higherciprofloxacin and levofloxacin MICs than those with a single mutation ingyrA,therebysuggestingthatalterationinparCoccurred after gyrA, leading to higher level fluoroquinolone resis-tance in P. aeruginosa. Moreover, the addition of a second
gyrA alteration to gyrA and parC mutations had a signif-icant effect on ciprofloxacin and levofloxacin MICs. Our resultssuggestedthattherecouldbeacorrelationbetween the number of gyrA and parC alterations and the level of fluoroquinolone resistance. This has been reported by Lee et al.18 for the clinical isolates of P. aeruginosa.
Dif-ferences in the MICs of ciprofloxacin and levofloxacin for isolates had a single alteration in QRDR of gyrA with or without an alteration in QRDR of parC, revealing that other resistance factors were involved in fluoroquinolone resistance. Mechanisms such as overexpression of efflux pumps(MexAB-OprM32,33 MexCD-OprJ,28 MexEF-OprN21 and
MexXY-OprM34) and mutation in gyrB and parE have been
describedforfluoroquinoloneresistanceinP.aeruginosa.17,18
However, the impact of these mechanisms on MICs of ciprofloxacinandlevofloxacincanbeclarifiedbyfurther stud-ies.
Toconclude, mechanisms other thanmutationsin gyrA
and parC (such as activeeffluxpumps, alterations ingyrB, parE orinnate impermeabilityofthe membrane)may con-tributetotheleveloffluoroquinoloneresistanceintheclinical isolatesofP. aeruginosa, but asingleaminoacid alteration, Thr-83→Ile,ingyrA,issufficienttocauseclinicallyimportant levels of resistance to fluoroquinolones, and the simul-taneous presence of mutation in parC (Ser-87 → Leu or Ala-88 → Pro) mediates significantly higher level fluoro-quinoloneresistance.
Finally,ourresultsrevealedthatthemutationsingyrAand
parCwerethemainmechanismoffluoroquinoloneresistance amongtheclinicalisolatesofP.aeruginosainTabriz,Iran.To thebestofourknowledge,thisstudyisthelargestanalysisof
theQRDRofgyrAandparCintheclinicalisolatesofP. aerugin-osafromIran.
Conflicts
of
interest
Theauthorsdeclarenoconflictsofinterest.
Acknowledgment
ThisworkwasfullysupportedbyInfectiousandTropical Dis-easesResearchCenter(grantNo.93-02),TabrizUniversityof MedicalSciences.Itisalsoareportorginiatingfromadatabase developedforthe thesisoffirst author registered in Infec-tiousandTropicalDiseasesResearchCenter,TabrizUniversity ofMedicalSciences,Tabriz,Iran.TheauthorsalsothankDr. HosseinSamadiKafilforhiskindhelpinanalyzing sequenc-ingresults,andMrs.MaryamRasoliandMr.JaberKamranfor collectingtheclinicalisolates.
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