Antibiotics and Antibiotics Resistance Genes in Soils: Monitoring, Toxicity, Risk Assessment and Management PDF
Preview Antibiotics and Antibiotics Resistance Genes in Soils: Monitoring, Toxicity, Risk Assessment and Management
Soil Biology Muhammad Zaff ar Hashmi Vladimir Strezov Ajit Varma Editors Antibiotics and Antibiotics Resistance Genes in Soils Monitoring, Toxicity, Risk Assessment and Management Soil Biology Volume 51 Series Editor Ajit Varma, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida, UP, India Moreinformationaboutthisseriesathttp://www.springer.com/series/5138 Muhammad Zaffar Hashmi (cid:129) Vladimir Strezov (cid:129) Ajit Varma Editors Antibiotics and Antibiotics Resistance Genes in Soils Monitoring, Toxicity, Risk Assessment and Management Editors MuhammadZaffarHashmi VladimirStrezov DepartmentofMeteorology FacultyofScienceandEngineering, COMSATSInstituteofInformation DepartmentofEnvironmentalSciences Technology MacquarieUniversity Islamabad,Pakistan Sydney,NewSouthWales Australia AjitVarma AmityInstituteofMicrobialTechnology AmityUniversityUttarPradesh Noida,UP India ISSN1613-3382 ISSN2196-4831 (electronic) SoilBiology ISBN978-3-319-66259-6 ISBN978-3-319-66260-2 (eBook) DOI10.1007/978-3-319-66260-2 LibraryofCongressControlNumber:2017957062 ©SpringerInternationalPublishingAG2017 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilarmethodologynowknownorhereafterdeveloped. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publicationdoesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexempt fromtherelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthis book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained hereinor for anyerrors oromissionsthat may havebeenmade. Thepublisher remainsneutralwith regardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. Printedonacid-freepaper ThisSpringerimprintispublishedbySpringerNature TheregisteredcompanyisSpringerInternationalPublishingAG Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland Preface Worldwide consumption of antibiotics has increased drastically in the past few decades. The application of antibiotics has led to the production of antibiotic resistancegenes(ARGs)whichrepresentagrowingandserioushumanhealththreat worldwide. Recent research highlighted that the main sources, reservoirs, and recipients of antibiotics and ARGs are water, air, and soil. Antibiotics and ARGs areincreasinglybeingrecognizedasemergingcontaminants,threateningeffective treatment of infections and carrying a great risk to public health. Anthropogenic activitiessuchastheriseinantibioticuseformedicalandagriculturalpurposesare considered a major cause for escalating the threat. The environmental risks of pharmaceuticals,ingeneral,werefirstidentifiedinthe1990sfollowedbyaseries ofmonitoringandeffectstudies. Theoverarchingthemeofthisbookistosummarizethecurrentstateofknowl- edge of antibiotics and ARGs in the soil environment. The book covers a wide rangeoftopicsforunderstandingtheantibioticsandARGsinsoils,theirrisktothe environment, and options for effective control. It presents some very important tools and methodologies that can be used to address antibiotics and ARGs in a consistent, efficient, and cost-effective manner. Furthermore, this book includes antibioticproducingmicroorganisms,theroutesofentryandfateofantibioticsand resistance genes, biomonitoring approaches, dissemination of ARGs in soils, risk assessment, the impact of antibiotics and ARGs on the soil microbial community and other biota, bioremediation and biodegradation approaches, as well as soil management strategies for antibiotics and ARG-contaminated soils. Special emphasiswasgiventodisseminationmechanismsofARGsinsoil,assoilplaysa crucial role in the development of antibiotic resistance traits in bacteria and the distributionofantibiotic-resistantmicrobialspecies,resistantgeneticmaterial,and antibiotic compounds. Resistance genes appear to be everywhere in nature—in pathogens,commensals,andenvironmentalmicroorganisms.Weinviteyoutogain a broader insight into the role of the soils in the mechanisms of resistance devel- opment,thedisseminationofantibiotic-resistantgeneticelements,andthetransport v vi Preface ofARGsorantibioticsasenvironmentalcontaminantsthroughthepresentationsof ourcontributingauthorsinthisbook. Antibioticsareproducedbyseveralgroupsofmicrobessuchasbacteria,fungi, andactinomycetesastheirnaturaldefensesystemagainstothermicrobeslivingin their vicinity. Soil microorganism had always been the primary source for the productionofantibioticsandstillcontinuestomaintainitssignificance.Butindis- criminate use of antibiotics and disinfectants in medicine, agriculture, and fish cultureandtheirreleaseinenvironmenthavegivenbirthtoanothercriticalproblem of multidrug-resistant pathogenic microbes, and hence, we are still in need of effective metabolites that can be used as antibiotics to combat these resistant strains.Thefirstchaptersofbookincludethehistory,consumption,physicochem- ical properties, and sources of antibiotics in soil, monitoring, mode of action, and applicationsofantibiotics.Recentreportsshowedthatdosinglivestockanimalwith antibioticsincreasesgreenhousegasemissionsespeciallyfromthecowdung.The use of antibiotics also disrupts the microbes, and microbes may not perform vital functions to combat against the climate change. These antibiotics change the microbes present in the digestive system of dung beetles, which are considered important in carbon cycling and improving soil. Some chapters provide an over- viewofantibioticsinsoil–plantsystemincludingtheaccumulationofantibioticsin differentplants.Asantibioticsareusedinescalatingquantities,thereisagrowing concernoverthepresence,toxicity,andfateofantibioticsinsoilwhichmaypose adverse effects on plants, soil biology, crop yield, and quality of production. Keeping in view latest advances in the instrument to detect antibiotics and ARGs suchasapplicationofnext-generationsequencing,othermetagenomictechniques, antimicrobialresistancedashboardapplication,andpointofcare(POC),i.e.,labon a chip, and gas chromatography techniques, their strengths and limitations were alsodiscussed.ButsuccessfulassessmentofantibioticsandARGsrequiresappro- priateresearchquestions. Thisbookprovidesabriefoverviewofrecentresearchindeterminingtheimpact of antibiotics, their bioactive metabolites, and ARGs that enter the soil on the structure,diversity,andfunctionofsoilmicrobialcommunitiesandhumanhealth. It has been established that the release of these drugs, their residues, and/or metabolites disturbs the environment and threatens soil inhabitants such as earth- worms.Invitroandinvivoassayshavelargelyfocusedontheacutegenotoxicity and biochemical toxicity of these compounds in earthworms. These drugs can be poisonoustoearthwormsandotherinhabitantsofsoilecosystems;themajorityof themhavebeenidentifiedasgenotoxicandmanyascausingbiochemicaltoxicity. Inthelongterm,genomedisturbancesduetogenotoxicityaswell asbiochemical toxicitymayimpairgrowth,reproduction,andpopulationdynamicsintheseorgan- isms. The book also describes the risk assessment process developed by various governmentbodiesinordertodeterminetherisksofreleasingantibioticsandARGs intothesoilandalsoidentifiestheexistingchallenges. Indeed, regional management regimes for agricultural and clinical use of anti- biotics, together with good hygiene, have in many cases proved successful in minimizing resistance on a national basis. The last chapter aims to identify Preface vii managementoptionsforreducingthespreadofantibioticsandantibioticresistance determinants via environmental pathways. Management options with respect to bioremediationasasustainablesoilmanagement;limitingagriculturalsources;and treatmentofhospital,domestic,andindustrialwastewaterwerealsodiscussed. Mostchaptersinthebookarewrittentoafairlyadvancedlevelandshouldbeof interest to the graduate student and practicing scientist. We also hope that the subjectmattertreatedwillbeofinteresttopeopleoutsidemedicine,soil,biology, and chemistry and to scientists in industry as well as government and regulatory bodies. Islamabad,Pakistan MuhammadZaffarHashmi Sydney,Australia VladimirStrezov Noida,India AjitVarma Contents 1 AntibioticsProducingSoilMicroorganisms. . . . . . . . . . . . . . . . . . 1 NiharikaChandraandSunilKumar 2 AntibioticsResistanceGenes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 AhmadHasnain,WajidNasim,HussaniMubarak,NosheenMirza, SohaibKhan,XiaomeiSu,SarfrazAhmed, andMuhammadZaffarHashmi 3 AReviewonAntibioticsConsumption,Physico-Chemical PropertiesandTheirSourcesinAsianSoil. . . . . . . . . . . . . . . . . . . 39 SijaArun,MoitraiyeeMukhopadhyay,andParomitaChakraborty 4 EntryRoutesofVeterinaryAntibioticsintheEnvironment. . . . . . 49 ReepP.TashoandJaeYoungCho 5 MonitoringofAntibioticsandAntibioticResistanceGenes inAgroecosystems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 SarfrazAhmed,MuhammadIbrahim,RabiaKhushiMuhammad, IqraNaseem,RubbeaIdrees,MuhammadZaffarHashmi, andAteeq-ur-Rehman 6 RoleofAntibioticsinClimateChange. . . . . . . . . . . . . . . . . . . . . . 91 RidaAkram,MuhammadZaffarHashmi,andWajidNasim 7 PotentialDisseminationofARBandARGsintoSoilThrough theUseofTreatedWastewaterforAgriculturalIrrigation:IsIt aTrueCauseforConcern?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99 NadaAl-JassimandPei-YingHong 8 AntibioticResistanceGeneDuetoManureApplication. . . . . . . . . 135 SrujanaKathi 9 AntibioticsandAntibioticsResistanceGenesDissemination inSoils. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145 EddieCytryn,ZdzisławMarkiewicz,andMagdalenaPopowska ix x Contents 10 DisseminationMechanismofAntibioticResistanceGenes inEnvironment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185 ManojKumar,RamPrasad,ShiveshSharma,AjitVarma, andVivekKumar 11 FateofAntibioticsinSoil. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201 RidaAkram,AsadAmin,MuhammadZaffarHashmi,AbdulWahid, MuhammadMubeen,HafizMohkumHammad,ShahFahad, andWajidNasim 12 UptakeofAntibioticsbyPlants. . . . . . . . . . . . . . . . . . . . . . . . . . . . 215 SandraA.YoussefandIsamI.Bashour 13 RecentAdvancesinMethodsfortheDetectionofAntibiotics andAntibioticsResistanceGenesinSoil. . . . . . . . . . . . . . . . . . . . . 233 HussaniMubarak,NosheenMirza,andMuhammadZaffarHashmi 14 ElucidationofEmergingNanomaterialsImpactsonAntibiotic ResistanceAgainstSoilandAquaticMicroflora. . . . . . . . . . . . . . . 253 ToqeerAhmed 15 TheEffectsofAntibioticsontheStructure,Diversity, andFunctionofaSoilMicrobialCommunity. . . . . . . . . . . . . . . . . 277 AnnaPiotrowska-Długosz 16 SoilAntibioticsandTransferofAntibioticResistanceGenes AffectingWildlife. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307 VanessaSilva,IsabelCarvalho,GilbertoIgrejas,andPatr´ıciaPoeta 17 GenotoxicityandBiochemicalToxicityofSoilAntibiotics toEarthworms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321 SarfrazAhmed,MuhammadIbrahim,RashemWaheed, AbuBakarHassanAzdee,MuhammadZaffarHashmi, andShabirAhmed 18 PotentialEnvironmental,EcologicalandHealthEffectsofSoil AntibioticsandARGs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335 BiljanaBalabanova 19 RiskAssessmentofAntibioticsandAntibiotic-ResistantGenes inSoil. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361 KhushbuSalianandVladimirStrezov 20 AntibioticsintheSoil:Sources,EnvironmentalIssues, andBioremediation. . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . .. . 381 UmeshB.Jagtap
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