microbiology question and need an explanation and answer to help me learn. 1. Is this

microbiology question and need an explanation and answer to help me learn.

1. Is this paper a primary literature article (is someone who did the experiments reporting on the data) or a review paper (a scientist talking about the general state of hte field).
Hint: On the main results page after entering your search terms, Reviews will have the word “Review” next to them.
2. Based on the abstract summarize the paper in a single sentence.
3.Describe one figure or table in the paper in a way that someone who had not read the paper could understand. This will mean that you will likely have to look a bit deeply into the results and methods section to understandt he background and the context. Your description should be about two paragraphs so that someone can fully understand the idea that the authors were trying to get across.
REVIEWOpenAccessAntibioticresistance:it’sbad,butwhyisn’titworse?NicholasWaglechnerandGerardD.Wright*AbstractAntibioticnaturalproductsareancientandsoisresistance.Consequently,environmentalbacteriaharbornumerousandvariedantibioticresistanceelements.Nevertheless,despitelonghistoriesofantibioticproductionandexposure,environmentalbacteriaarenotresistanttoallknownantibiotics.Thismeansthattherearebarrierstotheacquisitionofacompleteresistancearmamentarium.Thesources,distribution,andmovementofresistancemechanismsindifferentmicrobesandbacterialpopulationsaremosaicfeaturesthatactasbarrierstoslowthismovement,thusmoderatingtheemergenceofbacterialpan-resistance.Thisishighlyrelevanttounderstandingtheemergenceofresistanceinpathogenicbacteriathatcaninformbetterantibioticmanagementpracticesandinfluencenewdrugdiscovery.TheinevitabilityofresistanceThehistoryofantibioticdrugsoverthepastsevende-cadesisoneofcyclesofdiscoveryandclinicalimple-mentation,followedinevitablybyresistance(Fig.1).Noclassesofantibioticsareexceptionstothisnarrative.Theevolutionofresistanceanditsselectionis,therefore,anintrinsiccomponentofantibiotics,makingthemquiteuniqueamongdrugs.Whileparallelsexistintheanti-cancerfield,thediversityofresistancemechanismsthatbacteriadeployinresponsetoantibioticsisun-equaledandreflectiveoftheirlongnaturalhistory.Giventhisexperience,fairquestionsincludewhatistheoriginofthisdiversity,whyisresistanceapparentlyine-vitable,andifitis,howisitdisseminatedamongbac-terialpopulations,whatbarriers(ifany)preventpan-resistance,andwhataretheultimateprospectsforthefutureofantibiotics?*Correspondence:wrightge@mcmaster.caMichaelG.DeGrooteInstituteforInfectiousDiseaseResearch,DepartmentofBiochemistryandBiomedicalSciences,McMasterUniversity,1280MainStreetWest,Hamilton,ONL8N4K1,CanadaAntibioticsandresistanceareancientThefossilrecordisconsistentwiththeriseofsinglecellorganismsapproximately3.5billionyearsago[1].Forthemostpart,thesecellsfunctionthroughacommonprimarymetabolism—carbon,nitrogen,andphosphorusacquisitionandtransformationintotheelementarycom-ponentsofcells(aminoacids,sugars,lipids),proteinandnucleicacidsynthesis,etc.—buttheyaredifferentiatedbytheirrelativeabilitiestogeneratesecondarymetabo-lites.Thesearethespecializedmoleculesproducedbymicrobesthataretheresultofnaturalselectionwithingivenenvironmentsandecosystems.Thesemetabolitesincludeabroaddiversityofcompoundssuchassidero-phoresformetalacquisition,quorumsensingmoleculesdeployedforinter-cellcommunication,andantibiotics,tonamebutafew.Thelatterhavewell-knownanti-microbialactivitybutalsoatlowerconcentrationshavepleiotropiceffectsongeneexpressionperhapsnotre-latedtotheirinhibitoryphenotypes[2].Thisactivityprofilethatchangesacrossaconcentrationgradientisafascinatingandpoorlyunderstoodfeatureofantibiotics.Molecularclockstudiesontheoriginsofthebiochem-icalmachineryrequiredforantibioticbiosynthesisisconsistentwiththeiremergenceasearlyasonebillionyearsagointhecaseofpenicillinsandresistancemustbejustasancient[3,4].Directevidenceofancientanti-bioticresistanceis,however,difficulttoobtain.AncientDNAstudiesconductedonpreservedspecimenshun-dredstothousandsofyearsoldrevealthattheportionsofmoderngenomesthatcanbecoveredbyancientse-quencereadshavechangedonlylittleincomparisontomoderncounterparts[5–7].ProspectsforobtainingDNAfrommucholderperiodsarepoorgiventhechal-lengeofpreservationofbiologicalsamples.Microbialmetagenomesequencesobtainedfrompermafrosthavebeencollectedandshowntopossesscomparableresist-ancetomodernsequences[8].Forexample,werecon-structedthecomplexvancomycinresistanceclusterfrommetagenomicDNAisolatedfrom30,000-year-oldBeringianpermafrost.Oneoftheresurrectedenzymes©Wrightetal.2017OpenAccessThisarticleisdistributedunderthetermsoftheCreativeCommonsAttribution4.0InternationalLicense(http://creativecommons.org/licenses/by/4.0/),whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedyougiveappropriatecredittotheoriginalauthor(s)andthesource,providealinktotheCreativeCommonslicense,andindicateifchangesweremade.TheCreativeCommonsPublicDomainDedicationwaiver(http://creativecommons.org/publicdomain/zero/1.0/)appliestothedatamadeavailableinthisarticle,unlessotherwisestated.WaglechnerandWrightBMCBiology (2017) 15:84 DOI10.1186/s12915-017-0423-1
demonstratedidenticalstructureandfunctiontomodernmechanismscirculatinginhospitalstoday[8].Phylogen-eticanalysesalsosupporttheemergenceofmethicillinresistanceinStaphylococcusaureusmorethanadecadebeforemethicillinwassynthesizedandintroducedintheclinic[9].Anotheravenuetodeterminethefrequencyofanti-bioticresistanceintheenvironmentistosurveyisolatedecosystems,ideallywherehumaninfluencehasbeenminimalornon-existent.SuchsitesarechallengingtoidentifyintheAnthropocenebutwehavereportedongenomicsequencesobtainedfrombacteriasampledfromageologicallyisolatedcaveenvironmenttorevealthatorganismsseparatedfromphylogeneticallycloserelativesformillionsofyearsareresistanttomultipleclassesofantibiotics[10].Onehypothesistoaccountforthisobservationisthatincreasedcompetitioninnutrient-limitedenvironmentscoupledwithslowgrowthratessuchasthosefoundinsealedcaveenvironmentsincreasesthevalueofantibioticproductionandsub-sequentlyalsoresistance.Identifyingantibioticproduc-tioninsituintheseenvironmentsremainschallenging.Suchdirectobservationswouldilluminatethecycleofproductionandresistanceandwouldclarifytheroleofantibioticsinsuchpristinenaturalenvironments.Anal-ternativehypothesisisthatthecadreofresistanceele-mentsthatarecommoninvariousgeneraandspeciesareonlyslowlylost,especiallywhenlocatedinthegen-omeratherthanmobileelements,evenwithoutselectionandespeciallyforslowgrowingmicrobes[11].Theselinesofinvestigationallconvergeonthefollow-ing:antibioticsandresistancearecoupled,andbothareancientfeaturesoftheprokaryoticlifestyle,deeplyem-beddedinmicrobialgenomes.Nevertheless,whereverthepreviousequilibriumbetweenthesephenomenahadlain,humanshaverepurposedantibioticsforbothmed-icalandagriculturalapplicationsinmoderntimes.Anti-bioticproductionandusearenowmeasuredintensofthousandsoftonsperyearand,asaresult,microbesareexperiencingunprecedentedlevelsofantimicrobialex-posure.Consequently,weareexperiencingashiftinthefrequencyofresistanceinbothenvironmentalandclin-icalorganismsinresponsetotheanthropogenicuseofantibiotics.Addressingthisshiftrequiresadetailedun-derstandingofthestrategiesorganismsusetobecomeresistanttoantibioticsandtheforcesthatshapehowtheyareemployedanddistributed.TheevolutionofresistanceDeterminantsofresistancecanbeclassifiedintoseveralcategoriesdependingonthenatureoftheantibiotictar-getandthebiochemicalmechanismofresistance[12].Thesimplestcaseinvolvesacquiringoneormoremuta-tionsintheproteinorgenetargetoftheantibioticthatFig.1.Pastandpresentcyclesofantibioticdiscoveryandresistance.Forapproximately70years(1930s–1990s)pathogenicbacteriaandthediseasestheycausewerecontrolledwiththediscoveryofmanynewantibioticscaffoldsandderivatives.Resistanceinevitablyemerged,bythecaptureofmobileresistanceelementsorintrinsicmechanisms,butwascounteredwithnewdrugdiscovery.Inthepresentsituation,thelackofnewantibioticdrugsandtheriseofmulti-drug-resistantpathogensthatharbormanyresistanceelementspresentsagravepublichealthchallengeWaglechnerandWrightBMCBiology (2017) 15:84 Page2of8
preventsbinding,whichisachievablethroughsimplese-lectivepressureandimperfectchromosomereplication[13].Itisimpossibletoovercomeorpreventthistypeofresistancefromoccurringasitreflectstheintrinsicfidel-ityrestrictionsofDNAsynthesis,anditisoftenthefirstoutcomeofantibioticselectionwhereasinglegenemodificationcanresultinresistance.Incaseswhereahosthasmultiplecopiesofanessentialgenetarget,onlyoneorafewofthesecopiesmaybecomeresistantandatitrationeffectmaybeobserveduntilenoughresistantallelesarepresenttoovercometheantibiotic.Thiscanoccurthroughsuccessiveacquisitionsofmutations,throughduplicationofthetargetinthehostgenome,orbyup-regulatingtheexpressionoftheresistanttargettotitrateouttheeffectoftheantibiotic[14].Therearealsomanywaystoinfluencetheeffectofanantibioticthroughtheacquisitionofgenesthatencodeproteinsthatpreventorattenuatetheeffectivebindingofantibioticstotheirmoleculartargets[15].Similarly,thereareenzymesthatmodifytheantibiotictargettopreventdrugbinding[16].Inthiscase,acquisitionofsuchelementsmeansthehostcellgainsfunctionalitydenovooracquiresitfromapre-existingdeterminantfromanexternalsource.Whatgovernstherateandpropensityforgeneratingentirelynewresistancedeterminantsisanopenquestion.Microbeshaveseveralwaysofdecreasingtheeffectiveconcentrationofanantibiotic.Thereareresistancede-terminantsthatcanenzymaticallyactonanantibiotictodegradeorotherwisechemicallymodify(viadonormo-leculessuchasATPoracetyl-CoA)anantibioticsuchthatitisnolongerinanactiveform[17].Examinationofthestructureandmechanismofsuchenzymesrevealsthattheyarelikelyrepurposedfromcatalystswithotherfunctionsinthecell,withperhapsweakactivitytowardstheantibioticthatwasenhancedthroughnaturalselec-tion[18].Wecoinedtheterm‘proto-resistance’torefertothosegenesandassociatedproteins,whicharepre-sumablyperformingotherfunctionsintheirusualcon-textbutmaybeadaptedbyselectionintosourcesofantibioticresistance[12].Theintracellularconcentrationofantibioticsmaybereducedthroughtheactionofeffluxpumps,whicharefoundubiquitouslyinmicroorganisms[19].Effluxpumpsoftenhavebroadsubstratespecificitiesandcantransportawidevarietyofmoleculesacrossthecellmembraneofthehost,reflectingtheirprimaryrolesingeneraldetoxification.Narrowsubstraterangetrans-portersarecommonlyfoundinnaturalproductbiosyn-theticgeneclustersandhavespecificallyarisentoexportproductsintotheextracellularenvironment.Thesemayrepresentasourceofantibioticresistancewhenfoundinanon-producingcell[20].Anotherstrategytoaltertrans-portistoreducecellularpermeabilitytoantibiotics.Gram-negativebacteriapossessanoutermembranethatgreatlyreducestheabilityofmanymoleculestoaccu-mulateinsideacellatconcentrationshighenoughtobeinhibitory.Additionally,cellsmayevolvetobelessperme-abletoantibioticsthroughselectiononthenumberandexpressionlevelsofmembrane-spanningporinsthatallowdiffusionintothehost[21].Ithasbeenproposedthatan-tibioticselectionwasthedrivingforcebehindtheevolu-tionoftheGram-negativecellwallarchitecture[22].Whentheantibiotictargetisnotasinglegeneproductitisthoughttobemoredifficulttoevolveresistance.Examplesofthisincludeantibioticsthatfunctionbyinteractingwithordisruptingthecellmembraneitself,orantibioticsthattargettheprecursorsofcellstructureslikethebuildingblocksofcellwallpolymers[23].Incaseswhereresistanceisknownforsuchantibiotics,itisoftenachievedbyaccessingpre-existingdiversityinthesecell-wallstructures.Alteringthebiosynthesisofthesestruc-tureschangestheirphysicochemicalpropertiesbyusingoneormorealternativebiosyntheticgenes,andthesechangescanbeleveragedtogenerateresistance[24].Nearlyalloftheseresistancemechanismsareobservedinthebiosyntheticgeneclustersthatencodetheproduc-tionofantibiotics.Insomecases,theantibioticpro-ducers’ownself-resistancegeneshavebeenarguedtobetheancestorsoftheresistancedeterminantsfoundinnon-producingorganisms[25].Itisunclearhoworwhenthishasoccurredbutitmayhavebeenrecentinsomecases[26].Comparativestudiesusingtheincreas-ingnumberofbiosyntheticgeneclustersequencesmayhelptoestablishatestablescenarioforhorizontalgenetransfertoplayaroleinthemobilizationofresistancedeterminants.Considerthebirthofanovelbiosyntheticclustercomposedofcomponentsfrompre-existingclustersthatrecombinetogenerateanewsmallmoleculewithantibioticactivity.Thehostcarryingthisbiosyntheticgeneclusterwouldrequireaformofself-resistancethatleavesthenewmoleculeintactlesttheinnovationiswastedwhilebeingabletoexploitsusceptibilityinotherorganisms.Overtimeitmaybeexpectedthatacopyofthisself-resistancedeterminant,perhapsafteraduplicationevent,wouldbecomepartoftheclusterasisfrequentlyobservedinotherbiosyntheticgeneclustersanditsexpressionbecomeregulatedwiththecluster.Horizontalgenetrans-fer(HGT)ofentireclustershasbeenproposedtoplayaroleintheevolutionofsecondarymetabolism[27].Oncethesegenesbecomemobilizedamongphylogeneticallyrelatedorganisms,selectionmayfavorHGTofthere-sistancegenesaloneamonganevenbroaderpopulationtocountertheadvantageofantibioticproduction.ThespreadofresistancethroughbacterialpopulationsWhileantibioticsandresistanceareancient,inmostcasesresistancetospecificantibioticshasemergedWaglechnerandWrightBMCBiology (2017) 15:84 Page3of8
independentlyseveraltimes.Thisisreflectedinthedi-versityofresistancestrategiesthatwecurrentlyencoun-terforallclassesofantibiotics.Theaminoglycosideantibioticsareagoodexample.Resistancecanoccurthrougheffluxmechanisms,bytargetmutationtoin-sensitivevariants,bytargetmodification,andbythreedistinctclassesofchemicalmodificationoftheantibioticmolecule(Fig.2).Wecanreadilyidentifysuchresistanceelementsinmanybacterialgenomesofnon-aminoglycosideproducersandsomehaveredundantmechanisms.Howdidthisoccur?Onecanimagineascenariowhereproducingorganismscanestablishanad-vantageinalocalenvironment;resistanceinaneighbor-ingpopulation(likelyaproducerofitsownantibiotic)iseitheracquiredviaHGTordevelopeddenovo,resultinginecological‘détente’overtime.Theabundanceofre-sistanceelementsinthechromosomesofenvironmentalbacteriaisconsistentwithsuchanidea,reflectingthelongnaturalhistoryofinteractionsamongbacteria.Bac-teriawill,therefore,acquire,overtime,resistanceele-mentsthatreflecttheircurrentandpastencounterswithantibioticproducers.Unlesstheresistanceelementprovidesasignificantfitnesscost,suchelementsshouldpersistinthechromosomeunscathed,thoughperhapstranscriptionallyattenuated.Thenumberof‘silent’re-sistantelementsinthechromosomeofbacteriasupportsthishypothesis.Thesituationinpathogensisdifferent.Manypatho-gensarecommon,thoughminimal,componentsofthehumanmicrobiotaorarespecialistswithnarrowhostranges.Byvirtueoftheiruniqueenvironment(resourcerich,shortergrowthcycles,specializedecologicalniches)theyhavedevelopedfewerbiosyntheticgeneclustersen-codingbroadspectrumantibiotics,andhaveinsteadinvestedinmolecularmachinerytocloakthemselvesorotherwiseevadetheimmunesystem.Giventheireco-logicalniche,theyhavelimitedtheproductionofanti-microbialagentstohighlyspecificandnarrowspectrumagentssuchasbacteriocins.Consequently,theyhavefewerdedicatedresistanceelementsintheirchromo-somes(thehighlyregulatedAmpCinEnterobacteriaceaeistheexception)andingeneralarehighlysusceptibletoantibiotics.Historicalcollectionsofsuchorganismsre-vealanumberofplasmids,butfewmobileantibioticre-sistanceelements[28,29].Withthedawnoftheantibioticerainthe1930s,thisscenariohaschanged,andresistancegeneshaveaccumulatedintheseplasmidsandoftenbeenmobilizedtothechromosome.Aparsimoniousexplanationforthisobservationisthatstochasticcaptureofresistancegenesoccursonmobileelementsregularly,butatanunknownfre-quency,intheenvironment(consistentwiththeac-cretionofresistancegenesinenvironmentalbacteriadiscussedabove).Thehumanuseofantibioticsoverthelastsevendecadeshasresultedinanintensivese-lectivepressurethatpromotesfixationofmobileele-mentsthatcarryresistancegenesintopathogens.Theinitialcaptureofresistancedeterminantsintomobileelementsis,however,likelytobeveryrare.Giventhegeneticandmechanisticdiversityofresistanceintheenvironment,thefrequencyofsuchtransfersmustalsobequitelow,andobviouslyonlyoccurswheresuchpopulationsmixreadily,suchasinmanures,watertreatmentfacilities,andsimilarsettings[30].Whatisunknowniswhatmakesoneresistanceelementmorelikelytobemobilizedoveranother.Again,theamino-glycosidesprovideagoodexamplewherenewgenesencodingantibioticmodifyingenzymesappearedinFig.2.Gentamicinresistance,anexampleofgeneticandbiochemicaldiversity.Resistancetogentamicinoccursinavarietyofways.Alteredmembranepotential,efflux,and16SrRNAmethylationallconferresistancebutleavetheantibioticunaltered.Variousgroup-transferreactionsaddphosphoryl,nucleotidyl,oracetylgroupsatseveralpositionsonthemoleculeWaglechnerandWrightBMCBiology (2017) 15:84 Page4of8
pathogensregularlysincetheirfirstclinicaluseinthelate1940s(kinases,acetyltransferases,nucleotidyl-transferases),butribosomemethyltransferases,whichconferhigh-levelpan-aminoglycosideresistanceinen-vironmentalbacteria,werenotdetectedinpathogensuntiltheearly2000s.Whatthisimpliesisthatforanyantibioticusedinmedicineoragriculture,thespectrumofresistanceele-mentsintheenvironmentmustbecatalogedandmo-nitoredforpossiblemobilizationtotheclinic.Suchstudieswillprovideanearlywarningsystemforthepre-dictabledevelopmentofresistanceinpathogens.Weex-pect,however,thatitisunlikelythatwecanaccuratelypredictwhichmechanismswill1)escapethereservoirofresistanceintheenvironment,and2)besuccessfullymobilizedacrossabroadspectrumofpathogens.Barrierstopan-resistanceIfresistanceisancient,multifactorial,andmobile,whyisn’teverythingresistanttoeverything?Amidthealarmbeingraisedaboutresistance,itisimportanttonotethatantimicrobialresistanceisnottotalanduniversal.Eventhoughcertainimportantpathogensareincreasinglyresistanttosomeorallclinicallyusedantibiotics,itshouldnotbeexpectedthatallantibioticseverywherewillsuddenlybecomeuselessagainstallbacteria.Thebacterialresistomeconsistsofallresistancedetermi-nantsinprokaryotes[31].Inanalogytothepan-genomeconcept,itisdifficulttosayiftheresistomeisopen(un-limiteddiversity)orclosed(constraineddiversity)andhowmuchworkisrequiredtoelaborateitfully.WithinformaticresourcessuchastheComprehensiveAnti-bioticResistanceDatabase(https://card.mcmaster.ca/),theinsilicoidentificationofresistanceisadvancingfaraheadoftherateatwhichdeterminantsarebeingbio-chemicallycharacterized[32].Nevertheless,questionsmaybeaskedaboutthestructureoftheresistomeasitiscurrentlyunderstoodandhowitischangingasare-sultoftheuseofantibiotics.Ithasbeenarguedthatonlythedeterminantsidentifiedinspecificcontextsneedtobeconsideredtrueresistance,comparedtotheoper-ationaldefinitionthatanydeterminantthatcausesade-creaseinsusceptibilityisaresistancedeterminant[33].Theargumentstatesthatinordertoproperlyestimatetheriskofresistancethekeyeventisthatadeterminantbecomesdecontextualizedfromitssource,whereitmaynothavefunctionedasatrueresistancegene,andmobi-lizedintoanewcontextthroughHGTandonlythenitbecomesatrueresistancegeneofpublichealthormed-icalimpact[33].Whilewefeelthatthisisanunneces-saryrestrictiononthestudyoftheresistomeasawhole,theveryreasonformakingthisdistinctionillustratesabarriertopan-resistance;manydeterminantsofresist-ance,accordingtotheoperationaldefinition,havenotbeenobservedoutsideoftheiroriginalcontexts,havenotbeenmobilizedintonewhosts,andarenotguaran-teedtobecomemobilizedinthefuture.Fueledbylow-costgenomeandmetagenomesequen-cingandgrowingdatabasesthatcollectmicrobialgen-omicinformation,effortshavebeenmadetodescribetheresistomeinvariousgenera.OurrecentworkinBacillusandPaenibacillushasrevealedthatthereareundiscovereddeterminantsandmechanismsofresist-ancetobefound[34].Consistentwithobservationsintheclinic,notallresistancedeterminantsarefoundinallorganisms.Whyisthis?Whatarethebarrierstogenemobilizationandcapture?Ithasbeensuggestedthatphylogenystructuresantibioticresistance,wherecertainfamiliesoforganismsaremorelikelytosharemoreoftheirresistomes[11].Whilethisisbroadlytrueathighertaxonomiclevels,genomicsurveyssuggesttheindividualresistomesofdifferentspeciesaremosaicinnature[34].Thereiscertainlyarolehereaswellforsharedinsertionsequencesandothercommonelementsthatcanfavorhomologousrecombinationandinfluencegenemosaicity.HumansandthebacterialresistomeSinceantibioticsareexcellentselectiveagents,itiscri-ticaltoknowhowtheactionsofhumansareaffectingthebacterialresistome.Ofthemolecularmechanismsdescribedabove,selectionforresistantmutationsistheleastavoidable.Idealantibiotictargetsareessential,andessentialcellularcomponentsarehighlyconserved.Changestooneormoreofthesesystemsareoftenmildlyormoderatelydeleterious.Thisisgoodnewssinceitmeansthatresistantorganismsareoftenatadis-advantageintermsofabsolutegrowthraterelativetosensitiveorganismsandthatresistantvariantsofthesetargetsmaynoteasilysubstitutefortheoriginalsifacquired.Thissuggeststhepossibilitythatresistancecanbereversedovertimeintheabsenceofselection,thoughinpracticecompleteeliminationfrompopulationsisunlikely[35].Whereresistancerequiresthepresenceofotherdeter-minantsbeyondtheactualtargetoftheantibiotic,manyauxiliaryfactorscomeintoplay.Theseresistancedeter-minantsareeitherdistributednarrowlywithinoneorafewtaxa,ortheyhavebecomemobilizedongeneticelementssuchastransposons,insertionsequences,plas-mids,andphageandbecomesubjecttoHGT.Thepre-vailingviewofbacterialgenomedynamicssuggeststhatHGTisconstantandoccursmorefrequentlybetweenmorecloselyrelatedtaxa.Effortshavebeenmadetode-terminethegeneralfitnesscostofbothpassivelycarry-ingandactivelyexpressingthesedeterminants[36,37].TheburdenofcarryingextrageneticmaterialisthoughttobelowingeneralandexpandinggenomesizedoesWaglechnerandWrightBMCBiology (2017) 15:84 Page5of8
notappeartobeasignificantbarriertoaccumulatingmanyresistancegenes,atleastinenvironmentalbac-teria.Ifaveragegenomesizesoforganismsareatequi-librium,theremustalsobeaconcomitantlossofgenes[38].Adegreeofplasticityseemstobeanimportantfacetoftheevolutionofbacterialgenomesandsuggeststhatintheabsenceofselection,antimicrobialresistancedeterminantsalongwithmanyothergenesmaydriftintoandoutofgenomeswithregularity[38].Thissug-geststhatresistancemaybereversedbydrift.However,thisrequiressufficienttimewithoutselection,anditisunlikelythatanylineagewillremainunexposedtoselec-tionforlongenoughforallcellstobepurgedofresis-tanceelements.Whetherornotmobilizedresistancedeterminantsbe-comewidelydistributeddependsontwofactorsinadditiontoselectionbyantibiotics:compatibilityandproximity[39].Compatibilityreferstotheabilityofanorganismtoacceptandexpressnewlyacquiredgeneticmaterial.ItmayrefertotheabilityoftheorganismtoparticipateintheexchangeofDNA,butmayalsorefertotheabilitytoexpressafunctionalresistancedeter-minantinthecorrectcontext.Obviousbarrierstocom-patibilitycanincludeplasmidcompatibilitymismatches,phageincompatibility,celltypeincompatibility(aGram-positiveorganismmaynotbeabletoexpressaGram-negativeoutermembraneprotein,forexample),DNAGCcontentmismatch,codonbias,genetoxicity,andfunctionalincompatibilitywheretherecipientcellre-quiresadditionalcomponentsnottransferredfromthedonor[40].Allofthesebarriersseemtoincreasewithincreasingtaxonomicdistance.Ithasalsobeensug-gestedthatnaturallycompetentorganismsmaybeabletotakeupenvironmentalDNA,whichmayincluderesistancedeterminants,andissubjecttothesamebar-riers.Thetypesofantibioticresistancedeterminantsthataremobilizedmosteasilymightrepresentaclassleastaffectedbythesebarriers[41].ThoughavarietyofHGTmechanismsarecapableofspreadingresistancedeterminants,itremainsunclearhowrecipientcellsincorporatetheproperregulatorycontrolofnewlyacquiredgenesintotheirexpressionnetworks[42].Inopenpan-genomes,thediscoveryoflargeanddiverseaccessorygenomesinvariousbacterialfamilieshasspurredinvestigationintohowandwhentheseacquiredgenesmaybeexpressedandhasimport-antconsequencesforourunderstandingofmobilizedantibioticresistance[43].Ifthemajorityoftheseac-quiredgenesaredormant,itmayonlyrequirebriefselectiontoactivatetheirexpression.Mobileelementscancarrymanydifferentdeterminantsandarepartici-patingintheirownevolutionarydynamics.Thecapabil-itytotunetheexpressionofhitchhikinggenesmighthelpmobileelementsmitigatedeleteriouseffectsofexpressinggenesinthewrongcontext,whichwouldshowthatplasticityprovidestherawmaterialforselection[42].Theproximityoforganismsreferstothecontactthatmicrobeshavewheretheycanexchangecompatiblegen-eticmaterial.Organismswithnarrowenvironmentalniches,suchasendosymbioticbacteriaorpathogenswithrestrictedhostranges,mayneverhavetheoppor-tunitytoacquireforeigngeneticmaterial[44].Itwouldbeaninterestingexercisetodetermineiftaxawithclosedpan-genomeshavesimilarlyreducedresistomesandviceversa.Anotherexampleofabarrierreferstoantibioticswithnarrowerspectrums.Whenanantibioticonlytargetscertainbacteria,forexample,duetoin-trinsicresistance,thereisnopressureonun-targetedbacteriatoacquireresistancegenes.ResistancetotheglycopeptideantibioticvancomycinisonlyobservedinGram-positivebacteria,despitethefactthatGram-negativebacteriamaybesusceptibletotheseantibioticsundercertaincircumstances,yettheresistancedetermi-nantshaveneverbeenobservedinGram-negativesinspiteofthefactthattheyco-existinmanyenvironmentswithGram-positives[45].Prospects—‘irresistibleantibiotics?’Theevidenceisnowclearthattheenvironmentalresis-tomeoffersanearlimitlessdiversityofantibioticresist-anceelementsthatareatoncehighlyspecific—forexample,inactivatingenzymes—andbroad—forexample,effluxsystems,tocounterallantibiotics,eventhosesyn-thesizedinthelab.Theabilitytocaptureandmobilizegeneshorizontallythroughbacterialpopulationsandtoenhancethesebynaturalselectionfrommodestresistanceactivityintomorerobustphenotypesmeansthatthede-velopmentofan‘irresistibleantibiotic’ishighlyunlikelyifnotimpossible.Tosuggestotherwiseistolackhumilitybeforethevastnessofmicrobialgenesandtheirhistoryontheplanet.Whatisalsoclearisthatwecannotcompletelyavoidresistance.Byunderstandinghowresistanceemergesandisspreadthroughpopulations,wecanbetterselectanddeploythenextgenerationsofdrugs[46].ThiswillrequiremoreunderstandingofthefundamentalmechanismsofresistanceandtheprecisedegreetowhichHGThasshapedpathogengenomesingeneralandresistomesspecifically.Fortunately,theunprecedentedgrowthofsequencedataistransformingthekindsofanalysisthatcanbeperformedonwholeprokaryoticgenomes,ofbothclinicallyimportantorganismsandtheenvironmentalorganismsthatsurroundus.Thisrequiresaconcertedpushforbettersurveillance,datasharinganddissemin-ation,andthedevelopmentofmethodstoleveragethesedata.Ultimately,thiswillbeaneffortofriskmanagementthatrequirestheparticipationofeverystakeholderfrompolicymakersdowntobasicresearcherswithclearWaglechnerandWrightBMCBiology (2017) 15:84 Page6of8
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