Bacteriophage Therapy: From Lab to Clinical Practice

300 Pages·2018·8.424 MB·English

by  Joana Azeredo, Sanna Sillankorva (eds.)

Methods in
Molecular Biology 1693
Joana Azeredo
Sanna Sillankorva Editors
Bacteriophage
Therapy
From Lab to Clinical Practice
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire,AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Bacteriophage Therapy
From Lab to Clinical Practice
Edited by
Joana Azeredo
LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, CEB – Centre of Biological Engineering,
University of Minho, Braga, Portugal
Sanna Sillankorva
CEB – Centre of Biological Engineering, University of Minho, Braga, Portugal
Editors
JoanaAzeredo SannaSillankorva
LIBRO-LaboratoryofResearch CEB–CentreofBiologicalEngineering
inBiofilmsRosa´rioOliveira UniversityofMinho
CEB–CentreofBiologicalEngineering Braga,Portugal
UniversityofMinho
Braga,Portugal
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-7394-1 ISBN978-1-4939-7395-8 (eBook)
DOI10.1007/978-1-4939-7395-8
LibraryofCongressControlNumber:2017956899
©SpringerScience+BusinessMediaLLC2018
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Preface
This year we are celebrating the 100th anniversary of bacteriophage discovery. Bacterio-
phage therapy has had glorious and unfortunate periods. Since 1917, bacteriophages were
extensivelyandintensivelyusedasantimicrobialagentstocontrolbacterialinfections.Inthe
early part of the century many big pharmaceutical companies produced several bacterio-
phage products for different applications. The discovery of antibiotics allied to the indis-
criminate use of bacteriophages to treat every sort of infection, even nonbacterial, is
identifiedasoneofthemajorreasonsthatledtotheabandonmentofbacteriophagetherapy.
Antibiotics have now been used for approximately 70 years and have reduced illnesses and
deathscausedbyinfectiousdiseases.However,theemergenceofantibioticresistantbacteria
isamajorhealthconcern.Eachyearmillionsofpeoplebecomeinfectedwithmultiple-drug
resistantbacteria,whichconsequentlyleadstonumerousdeaths.Onthisaccount,thereisa
revival of interest in bacteriophage as therapeutic agents to control infectious diseases.
Despite this renewed interest, there is not yet any product broadly available for human
application. There are however a few exceptions where bacteriophages can be applied to
humanpatientsasalastresortundertheguidelinesoftheHelsinkitreatyandasatherapeu-
tic option in a few European countries. Accordingly, it is important to bring to medical
application the products that are being developed at the lab. Bacteriophage Therapy: From
Lab to Clinical Practice focuses on the methodology of product development and applica-
tioninclinicalcontexttoensureefficacy,safety,andregulatorycompliance.
This book has 21 chapters which have been subgrouped by dividing the experimental
approachessuitableforisolatingandcharacterizingbacteriophagestoformulatingbacterio-
phagemedicinalproductsandclinicalapplication.Regulatorycomplianceandsafetyaspects
ofbacteriophagetherapyarealsoaddressedinthebook.
Wewouldliketoexpressourgratitudetoallcontributingauthorswhoseexpertiseinthe
fieldishighlyrecognizedfortheircommitmenttothisbookbysharingtheirknowledgeina
simpleandcomprehensivewaytoguidebacteriophageresearchersthroughoutthedevelop-
mentofaproductformedicalapplication.Thisbookalsotargetsabroaderaudienceranging
fromclinicians,pharmaceutics,regulatoryauthorities,andstakeholders.
Braga,Portugal JoanaAzeredo
SannaSillankorva
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
PART I ISOLATION OF BACTERIOPHAGES
1 IsolationofBacteriophagesforFastidiousBacteria .......................... 3
ShigenobuMatsuzaki,JumpeiUchiyama,IyoTakemura-Uchiyama,
TakakoUjihara,andMasanoriDaibata
2 IsolationofBacteriophagesoftheAnaerobicBacteriaBacteroides............. 11
CristinaGarcı´a-Aljaro,MaiteMuniesa,andJuanJofre
3 IsolationofBacteriophagesforClinicallyRelevantBacteria................... 23
SannaSillankorva
PART II CHARACTERIZATION OF BACTERIOPHAGES
4 InVitroActivityofBacteriophagesAgainstPlanktonicand
BiofilmPopulationsAssessedbyFlowCytometry........................... 33
DianaP.PiresandLuı´sD.R.Melo
5 ObservationofBacteriophageUltrastructurebyCryo-electronMicroscopy.... 43
AnaCuervoandJose´L.Carrascosa
6 BacteriophageTaxonomy:AnEvolvingDiscipline .......................... 57
IgorTolstoy,AndrewM.Kropinski,andJ.RodneyBrister
PART III BACTERIOPHAGE SELECTION AND COCKTAIL FORMULATION
7 DeterminationoftheBacteriophageHostRange:
Culture-BasedApproach................................................. 75
AndreyV.LetarovandEugeneE.Kulikov
8 RecoveryandCharacterizationofBacteriaResistingInfection
byLyticBacteriophage .................................................. 85
LiberaLatinoandChristinePourcel
9 GuidelinestoComposeanIdealBacteriophageCocktail..................... 99
MaiaMerabishvili,Jean-PaulPirnay,andDanielDeVos
PART IV BIODISTRIBUTION, HOST INTERACTION AND CLINICAL APPLICATION
10 InteractionofBacteriophageswithMammalianCells........................ 113
ZuzannaKaz´mierczakandKrystynaDa˛browska
11 InVivoBacteriophageBiodistribution..................................... 123
NicolasDufour,Rapha¨elleDelattre,andLaurentDebarbieux
vii
viii Contents
12 InteractionofBacteriophageswiththeImmuneSystem:
InductionofBacteriophage-SpecificAntibodies ............................ 139
KrystynaDa˛browska
13 BacteriophageTreatmentofInfectedDiabeticFootUlcers .................. 151
VeraV.Morozova,YuliaN.Kozlova,DenisA.Ganichev,
andNinaV.Tikunova
14 CompassionateUseofBacteriophageTherapyforFootUlcer
TreatmentasanEffectiveStepforMovingTowardClinicalTrials............. 159
RandolphFish,ElizabethKutter,GordonWheat,BobBlasdel,
MziaKutateladze,andSarahKuhl
PART V PRODUCTION, PURIFICATION AND BACTERIOPHAGE STORAGE
15 BacteriophageProductioninBioreactors .................................. 173
MaryamAgboluajeandDominicSauvageau
16 ComputationalModelingofBacteriophageProductionfor
ProcessOptimization.................................................... 195
KonradKrysiak-Baltyn,GregoryJ.O.Martin,andSallyL.Gras
17 MethodsforBacteriophagePreservation................................... 219
MałgorzataB.Łobocka,AleksandraGłowacka,andPiotrGolec
PART VI SAFETY AND REGULATION
18 BacteriophageProductioninCompliancewith
RegulatoryRequirements................................................ 233
Jean-PaulPirnay,MaiaMerabishvili,HildeVanRaemdonck,
DanielDeVos,andGilbertVerbeken
19 GuidelinesforBacteriophageProductCertification ......................... 253
AlanFauconnier
PART VII NEW PHAGE THERAPYAPPROACHES
20 Nano/MicroFormulationsforBacteriophageDelivery...................... 271
PilarCorte´s,MaryCano-Sarabia,JoanColom,JenniferOtero,
DanielMaspoch,andMontserratLlagostera
21 SyntheticBiologytoEngineerBacteriophageGenomes ..................... 285
AnaRitaCosta,CatarinaMilho,JoanaAzeredo,
andDianaPriscilaPires
Index ...................................................................... 301
Contributors
MARYAMAGBOLUAJE (cid:1) ChemicalandMaterialsEngineering,UniversityofAlberta,
Edmonton,AB,Canada
JOANA AZEREDO (cid:1) LIBRO-LaboratoryofResearchinBiofilmsRosa´rioOliveira,CEB–
CentreofBiologicalEngineering,UniversityofMinho,Braga,Portugal
BOBBLASDEL (cid:1) LaboratoryofGeneTechnology,KULeuven,KasteelparkArenberg,Belgium
J.RODNEYBRISTER (cid:1) NationalCenter forBiotechnologyInformation,NationalLibraryof
Medicine,NationalInstitutesofHealth,Bethesda,MD,USA
MARYCANO-SARABIA (cid:1) CatalanInstituteofNanoscienceandNanotechnology(ICN2),CSIC
andTheBarcelonaInstituteofScienceandTechnology,Barcelona,Spain
JOSE´ L.CARRASCOSA (cid:1) DepartmentofStructureofMacromolecules,CentroNacionalde
Biotecnologı´a,Madrid,Spain
JOANCOLOM (cid:1) SchoolofVeterinaryMedicineandScience,UniversityofNottingham,
Nottingham,UK
PILARCORTE´S (cid:1) DepartamentdeGene`ticaiMicrobiologia,UniversitatAuto`nomade
Barcelona,CerdanyoladelValle`s,Spain
ANARITACOSTA (cid:1) LIBRO-LaboratoryofResearchinBiofilmsRosa´rioOliveira,CEB–
CentreofBiologicalEngineering,UniversityofMinho,Braga,Portugal
ANACUERVO (cid:1) DepartmentofStructureofMacromolecules,CentroNacionalde
Biotecnologı´a,Madrid,Spain
KRYSTYNADA˛BROWSKA (cid:1) InstituteofImmunologyandExperimentalTherapy,PolishAcademy
ofSciences,Wrocław,Poland
MASANORIDAIBATA (cid:1) DepartmentofMicrobiologyandInfection,KochiMedicalSchool,Kochi
University,Nankoku,Kochi,Japan
LAURENTDEBARBIEUX (cid:1) DepartmentofMicrobiology,MolecularBiologyofGenein
Extremophiles,InstitutPasteur,Paris,France
RAPHAE¨LLEDELATTRE (cid:1) DepartmentofMicrobiology,MolecularBiologyofGenein
Extremophiles,InstitutPasteur,Paris,France;INSERM,IAME,UMR1137,Paris,
France;Serviced’Anesthe´sie-Re´animation,AP-HP,HoˆpitalBeaujon,Clichy,France
NICOLASDUFOUR (cid:1) DepartmentofMicrobiology,MolecularBiologyofGeneinExtremophiles,
InstitutPasteur,Paris,France;ServicedeRe´animationMe´dico-Chirurgicale,Centre
HospitalierRene´Dubos,Pontoise,France;INSERM,IAME,UMR1137,Paris,France
ALANFAUCONNIER (cid:1) FederalAgencyforMedicinesandHealthProducts,Brussels,Belgium;
CultureinvivoASBL,Nivelles,Belgium
RANDOLPH FISH (cid:1) PhageBioticsResearchFoundation,Gray’sHarborCommunityHospital,
Aberdeen,WA,USA;WoundCentersatStJoseph’sMedicalCenter,Tacoma,WA,USA
DENIS A.GANICHEV (cid:1) RailwayClinicalHospital,Novosibirsk,RussianFederation
CRISTINAGARCI´A-ALJARO (cid:1) DepartmentofMicrobiology,UniversityofBarcelona,Barcelona,
Spain
ALEKSANDRAGŁOWACKA (cid:1) DepartmentofMicrobialBiochemistry,InstituteofBiochemistry
andBiophysicsofthePolishAcademyofSciences,Warsaw,Poland
PIOTRGOLEC (cid:1) LaboratoryofMolecularBiology(affiliatedwiththeUniversityofGdan´sk),
InstituteofBiochemistryandBiophysicsofthePolishAcademyofSciences,Gdan´sk,Poland
ix
x Contributors
SALLYL.GRAS (cid:1) TheBio21MolecularScienceandBiotechnologyInstitute,TheUniversityof
Melbourne,Parkville,VIC,Australia;TheDepartmentofChemicalEngineering,The
UniversityofMelbourne,Parkville,VIC,Australia
JUANJOFRE (cid:1) DepartmentofMicrobiology,UniversityofBarcelona,Barcelona,Spain
ZUZANNAKAZ´MIERCZAK (cid:1) InstituteofImmunologyandExperimentalTherapy,Polish
AcademyofSciences,Wrocław,Poland
YULIAN.KOZLOVA (cid:1) LaboratoryofMolecularMicrobiology,InstituteofChemicalBiologyand
FundamentalMedicineSBRAS,Novosibirsk,RussianFederation
ANDREWM.KROPINSKI (cid:1) DepartmentofFoodScience,UniversityofGuelph,Guelph,ON,
Canada;DepartmentofMolecular&CellularBiology,UniversityofGuelph,Guelph,ON,
Canada;DepartmentofPathobiology,UniversityofGuelph,Guelph,ON,Canada
KONRADKRYSIAK-BALTYN (cid:1) TheBio21MolecularScienceandBiotechnologyInstitute,The
UniversityofMelbourne,Parkville,VIC,Australia;TheDepartmentofChemical
Engineering,TheUniversityofMelbourne,Parkville,VIC,Australia
SARAHKUHL (cid:1) VANorthernCalifornia,Martinez,CA,USA;UniversityofCalifornia,San
Francisco,CA,USA
EUGENEE.KULIKOV (cid:1) WinogradskyInstituteofMicrobiologyRCBiotechnologyRAS,Moscow,
Russia;MoscowInstituteofPhysicsandTechnology,Dolgoprudny,MoscowRegion,Russia
MZIAKUTATELADZE (cid:1) GeorgeEliavaInstituteofBacteriophages,MicrobiologyandVirology–
3,Tbilisi,GA,USA
ELIZABETHKUTTER (cid:1) PhageBioticsResearchFoundation,Gray’sHarborCommunity
Hospital,Aberdeen,WA,USA;BacteriophageLab,TheEvergreenStateCollege,Olympia,
WA,USA
LIBERALATINO (cid:1) InstituteforIntegrativeBiologyoftheCell(I2BC),CEA,CNRS,Univ.
Paris-Sud,Universite´Paris-Saclay,Gif-sur-YvetteCedex,France
ANDREYV.LETAROV (cid:1) WinogradskyInstituteofMicrobiologyRCBiotechnologyRAS,Moscow,
Russia;LomonosovMoscowStateUniversity,Moscow,Russia;MoscowInstituteofPhysics
andTechnology,Dolgoprudny,MoscowRegion,Russia
MONTSERRATLLAGOSTERA (cid:1) DepartamentdeGene`ticaiMicrobiologia,Universitat
Auto`nomadeBarcelona,CerdanyoladelValle`s,Spain
MAŁGORZATAB.ŁOBOCKA (cid:1) DepartmentofMicrobialBiochemistry,InstituteofBiochemistry
andBiophysicsofthePolishAcademyofSciences,Warsaw,Poland;FacultyofAgriculture
andBiology,AutonomousDepartmentofMicrobialBiology,WarsawUniversityofLife
Sciences–SGGW,Warsaw,Poland
GREGORYJ.O.MARTIN (cid:1) TheDepartmentofChemicalEngineering,TheUniversityof
Melbourne,Parkville,VIC,Australia
DANIELMASPOCH (cid:1) CatalanInstituteofNanoscienceandNanotechnology(ICN2),CSIC
andTheBarcelonaInstituteofScienceandTechnology,Barcelona,Spain;ICREA,
Barcelona,Spain
SHIGENOBU MATSUZAKI (cid:1) DepartmentofMicrobiologyandInfection,KochiMedicalSchool,
KochiUniversity,Nankoku,Kochi,Japan
LUI´SD.R.MELO (cid:1) LIBRO–LaboratoryofResearchinBiofilmsRosa´rioOliveira,CEB–
CentreofBiologicalEngineering,UniversityofMinho,Braga,Portugal
MAIAMERABISHVILI (cid:1) LaboratoryforMolecularandCellularTechnology,QueenAstrid
MilitaryHospital,Brussels,Belgium
CATARINAMILHO (cid:1) LIBRO-LaboratoryofResearchinBiofilmsRosa´rioOliveira,CEB–
CentreofBiologicalEngineering,UniversityofMinho,Braga,Portugal
Contributors xi
VERAV.MOROZOVA (cid:1) LaboratoryofMolecularMicrobiology,InstituteofChemicalBiology
andFundamentalMedicineSBRAS,Novosibirsk,RussianFederation
MAITEMUNIESA (cid:1) DepartmentofMicrobiology,UniversityofBarcelona,Barcelona,Spain
JENNIFEROTERO (cid:1) DepartamentdeGene`ticaiMicrobiologia,UniversitatAuto`nomade
Barcelona,CerdanyoladelValle`s,Spain
DIANA P.PIRES (cid:1) LIBRO–LaboratoryofResearchinBiofilmsRosa´rioOliveira,CEB–
CentreofBiologicalEngineering,UniversityofMinho,Braga,Portugal
JEAN-PAULPIRNAY (cid:1) LaboratoryforMolecularandCellularTechnology,QueenAstrid
MilitaryHospital,Brussels,Belgium
CHRISTINEPOURCEL (cid:1) InstituteforIntegrativeBiologyoftheCell(I2BC),CEA,CNRS,
Univ.Paris-Sud,Universite´Paris-Saclay,Gif-sur-YvetteCedex,France
HILDE VANRAEMDONCK (cid:1) LaboratoryforMolecularandCellularTechnology,QueenAstrid
MilitaryHospital,Brussels,Belgium
DOMINIC SAUVAGEAU (cid:1) ChemicalandMaterialsEngineering,UniversityofAlberta,
Edmonton,AB,Canada
SANNASILLANKORVA (cid:1) CEB–CentreofBiologicalEngineering,UniversityofMinho,Braga,
Portugal
IYOTAKEMURA-UCHIYAMA (cid:1) SchoolofVeterinaryMedicine,AzabuUniversity,Sagamihara,
Kanagawa,Japan
NINAV.TIKUNOVA (cid:1) LaboratoryofMolecularMicrobiology,InstituteofChemicalBiologyand
FundamentalMedicineSBRAS,Novosibirsk,RussianFederation
IGORTOLSTOY (cid:1) NationalCenter forBiotechnologyInformation,NationalLibraryof
Medicine,NationalInstitutesofHealth,Bethesda,MD,USA
JUMPEIUCHIYAMA (cid:1) SchoolofVeterinaryMedicine,AzabuUniversity,Sagamihara,
Kanagawa,Japan
TAKAKOUJIHARA (cid:1) ScienceResearchCenter,KochiUniversity,Kohasu,Oko-cho,Nankoku,
Kochi,Japan
GILBERTVERBEKEN (cid:1) LaboratoryforMolecularandCellularTechnology,QueenAstrid
MilitaryHospital,Brussels,Belgium
DANIELDEVOS (cid:1) LaboratoryforMolecularandCellularTechnology,QueenAstridMilitary
Hospital,Brussels,Belgium
GORDON WHEAT (cid:1) PhageBioticsResearchFoundation,Gray’sHarborCommunityHospital,
Aberdeen,WA,USA;KaiserPermanenteNorthwest,SaintPeterHospitalFamilyMedicine
Residency,Olympia,WA,USA