Proteus mirabilis: Methods and Protocols

343 Pages·2019·7.773 MB·English

by  Melanie M. Pearson

Methods in
Molecular Biology 2021
Melanie M. Pearson Editor
Proteus
mirabilis
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
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JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire, UK
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Proteus mirabilis
Methods and Protocols
Edited by
Melanie M. Pearson
Department of Microbiology and Immunology, University of Michigan Medical School,
Ann Arbor, MI, USA
Editor
MelanieM.Pearson
DepartmentofMicrobiology
andImmunology
UniversityofMichiganMedicalSchool
AnnArbor,MI,USA
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-9600-1 ISBN978-1-4939-9601-8 (eBook)
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Covercaption:ScanningelectronmicrographofP.mirabilisswarmingoveranagarsurface.Swarmfrontswerecaptured
duringactivemigrationusingain situvapor fixationtechnique. This revealedtheorganization of flagellarfilaments
duringswarming,showingtheseareinterwoveninphasetoformhelicalconnectionsbetweenadjacentswarmercells.
ImageprovidedbyDr.BrianV.Jones.
ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer
Nature.
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Preface
ProteusmirabiliswasnamedbyGustavHauserin1885,whoobservedbacteriaculturedon
gelatin that morphed from short, nearly spherical rods to lively, moving long bacilli. He
namedthebacteriumafterProteusfromHomer’sOdyssey,whowasabletochangeshapeat
will to avoid capture and questioning. Over 60 years later, in 1949, Johannes Kvittingen
summedupcontinuedeffortstostudyP.mirabiliswiththeconclusion:“Inthecourseofthe
timethisworkonthelife-cycleofProteushasbeengoingon,andasnewdetailshavebeen
clarified,thefeelinghasincreasedthatthefullunderstandingofthebiologyandsociologyof
themicrobebecomesincreasinglyevasive.”WilliamsandSchwarzhoffin1978,whilenoting
advancesinthefield,wrote“theswarmingphenomenoncontinuestoescapeourcomplete
understanding.”
P. mirabilis is an opportunistic bacterial pathogen, most often known as a causative
agent of complicated urinary tract infection. It is also a model organism for swarming
motility, wherein bacteria move as a coordinated population across a surface. Despite its
geneticrelatednesstowidelyrecognizedspeciessuchasEscherichiacoli,specializedhandling
techniquesareoftennecessary.Thisvolumecontainsessentialprotocolsforresearcherswho
study,orhopetostudy,P.mirabilis.Withrenewedappreciationforthemedicalimpactand
environmental adaptability of this organism, coupled with continued fascination for its
dynamicbehavior,wepresentthisvolumetoaidfurtherpursuitofanswers.
AnnArbor,MI,USA MelanieM.Pearson
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 ProteusmirabilisOverview............................................... 1
HarryL.T.Mobley
2 CultureMethodsforProteusmirabilis..................................... 5
MelanieM.Pearson
3 MethodsforStudyingSwarmingandSwimmingMotility.................... 15
MelanieM.Pearson
4 TestingtheAbilityofCompoundstoInduceSwarming ..................... 27
ChelsieE.Armbruster
5 PurificationofNativeFlagellin............................................ 35
Marı´aJose´Gonza´lez,VictoriaIribarnegaray,PabloZunino,
andPaolaScavone
6 AnalysisofProteusmirabilisSocialBehaviorsonSurfaces .................... 45
KristinLittleandKarineA.Gibbs
7 InsertionalMutagenesisProtocolforConstructingSingleorSequential
Mutations.............................................................. 61
MelanieM.Pearson,StephanieD.Himpsl,andHarryL.T.Mobley
8 AllelicExchangeMutagenesisinProteusmirabilis........................... 77
KristenE.HoweryandPhilipN.Rather
9 QuantificationofUreaseActivity.......................................... 85
ShawnRichmondandAlejandraYep
10 SiderophoreDetectionUsingChromeAzurolSandCross-Feeding
Assays ................................................................. 97
StephanieD.HimpslandHarryL.T.Mobley
11 UsingHemagglutination,SurfaceShearing,andAcidTreatment
toStudyFimbriaeinProteusmirabilis..................................... 109
StephanieD.Himpsl,MelanieM.Pearson,andHarryL.T.Mobley
12 PhaseVariationofthemrpFimbrialPromoter.............................. 121
MelanieM.Pearson
13 AdherenceofProteusmirabilistoUroepithelialCells........................ 129
Marı´aJose´Gonza´lez,VictoriaIribarnegaray,PaolaScavone,
andPabloZunino
14 AnInVitroBladderModelforStudyingCatheter-AssociatedUrinary
TractInfectionandAssociatedAnalysisofBiofilms.......................... 139
JonathanNzakizwanayo,HarrietPelling,ScarletMilo,
andBrianV.Jones
15 IndependentTransurethralUrinaryTractInoculationinaMurine
ModelofAscendingInfectionwithProteusmirabilis........................ 159
SaraN.Smith
vii
viii Contents
16 CochallengeInoculationwithProteusmirabilisinaMurine
TransurethralUrinaryTractModelofAscendingInfection .................. 173
SaraN.Smith
17 IndwellingUrinaryCatheterModelofProteusmirabilisInfection ............ 187
SaraN.SmithandChelsieE.Armbruster
18 VaccinationtoProtectAgainstProteusmirabilisChallenge
UtilizingtheAscendingModelofUrinaryTractInfection................... 201
SaraN.Smith,StephanieD.Himpsl,andHarryL.T.Mobley
19 CharacterizationofProteusmirabilisLipopolysaccharideSamples
byInfraredSpectroscopyandSerologicalMethods.......................... 217
KatarzynaDurlik,GrzegorzCzerwonka,PaulinaZ˙arnowiec,
andWiesławKaca
20 IsolationandPurificationofProteusmirabilisBacteriophage................. 231
AgnieszkaMaszewskaandAntoniR(cid:1)oz˙alski
21 DetectionofNeutrophilExtracellularTrapsinUrine........................ 241
YanbaoYu,KeehwanKwon,andRembertPieper
22 UsingProteomicstoIdentifyInflammationDuringUrinary
TractInfection ......................................................... 259
YanbaoYuandRembertPieper
23 AssessmentofProteusmirabilisAntigenImmunological
ComplexesbyAtomicForceMicroscopy .................................. 273
WiesławKaca,JoannaGlen´ska-Olender,IwonaKonieczna,
J(cid:1)ozefGawe˛da,andSławomirSe˛k
24 ConsiderationsforModelingProteusmirabilisSwarming.................... 285
BruceP.Ayati
25 TransposonInsertionSiteSequencinginaUrinaryTractModel.............. 297
ValerieS.Forsyth,HarryL.T.Mobley,andChelsieE.Armbruster
Index ...................................................................... 339
Contributors
CHELSIEE.ARMBRUSTER (cid:1) DepartmentofMicrobiologyandImmunology,JacobsSchoolof
MedicineandBiomedicalSciences,StateUniversityofNewYorkatBuffalo,Buffalo,NY,
USA
BRUCEP.AYATI (cid:1) DepartmentofMathematics,UniversityofIowa,IowaCity,IA,USA
GRZEGORZCZERWONKA (cid:1) DepartmentofMicrobiology,InstituteofBiology,JanKochanowski
UniversityinKielce,Kielce,Poland
KATARZYNADURLIK (cid:1) DepartmentofMicrobiology,InstituteofBiology,JanKochanowski
UniversityinKielce,Kielce,Poland
VALERIES.FORSYTH (cid:1) DepartmentofMicrobiologyandImmunology,UniversityofMichigan
MedicalSchool,AnnArbor,MI,USA
JO´ZEFGAWE˛DA (cid:1) S´wie˛tokrzyskieRheumatologyCentre,St.LukasHospital,Kon´skie,Poland
KARINEA.GIBBS (cid:1) DepartmentofMolecularandCellularBiology,HarvardUniversity,
Cambridge,MA,USA
JOANNAGLEN´SKA-OLENDER (cid:1) DepartmentofMicrobiology,InstituteofBiology,Jan
KochanowskiUniversityinKielce,Kielce,Poland;RegionalScienceandTechnologyCenter,
S´wie˛tokrzyskiBiobank,Che˛ciny,Poland
MARI´AJOSE´ GONZA´LEZ (cid:1) DepartamentodeMicrobiologı´a,InstitutodeInvestigaciones
Biol(cid:1)ogicasClementeEstable,Montevideo,Uruguay
STEPHANIED.HIMPSL (cid:1) DepartmentofMicrobiologyandImmunology,Universityof
MichiganMedicalSchool,AnnArbor,MI,USA
KRISTEN E.HOWERY (cid:1) DepartmentofMicrobiologyandImmunology,EmoryUniversity,
Atlanta,GA,USA
VICTORIA IRIBARNEGARAY (cid:1) DepartamentodeMicrobiologı´a,InstitutodeInvestigaciones
Biol(cid:1)ogicasClementeEstable,Montevideo,Uruguay
BRIAN V.JONES (cid:1) DepartmentofBiologyandBiochemistry,UniversityofBath,Bath,UK
WIESŁAW KACA (cid:1) DepartmentofMicrobiology,InstituteofBiology,JanKochanowski
UniversityinKielce,Kielce,Poland
IWONA KONIECZNA (cid:1) DepartmentofMicrobiology,InstituteofBiology,JanKochanowski
UniversityinKielce,Kielce,Poland
KEEHWANKWON (cid:1) TheJ.CraigVenterInstitute,Rockville,MD,USA
KRISTIN LITTLE (cid:1) DepartmentofMolecularandCellularBiology,HarvardUniversity,
Cambridge,MA,USA
AGNIESZKAMASZEWSKA (cid:1) DepartmentofBiologyofBacteria,FacultyofBiologyand
EnvironmentalProtection,UniversityofLodz,Lodz,Poland
SCARLETMILO (cid:1) DepartmentofChemistry,UniversityofBath,Bath,UK
HARRYL.T.MOBLEY (cid:1) DepartmentofMicrobiologyandImmunology,Universityof
MichiganMedicalSchool,AnnArbor,MI,USA
JONATHANNZAKIZWANAYO (cid:1) DepartmentofBiologyandBiochemistry,UniversityofBath,
Bath,UK
MELANIEM.PEARSON (cid:1) DepartmentofMicrobiologyandImmunology,Universityof
MichiganMedicalSchool,AnnArbor,MI,USA
HARRIETPELLING (cid:1) DepartmentofBiologyandBiochemistry,UniversityofBath,Bath,UK
REMBERTPIEPER (cid:1) TheJ.CraigVenterInstitute,Rockville,MD,USA
ix
x Contributors
PHILIP N.RATHER (cid:1) DepartmentofMicrobiologyandImmunology,EmoryUniversity,
Atlanta,GA,USA;ResearchService,AtlantaVAMedicalCenter,Decatur,GA,USA
SHAWNRICHMOND (cid:1) DepartmentofBiologicalSciences,CaliforniaPolytechnicState
University,SanLuisObispo,CA,USA
ANTONI RO´Z˙ALSKI (cid:1) DepartmentofBiologyofBacteria,FacultyofBiology
andEnvironmentalProtection,UniversityofLodz,Lodz,Poland
PAOLA SCAVONE (cid:1) DepartamentodeMicrobiologı´a,InstitutodeInvestigacionesBiol(cid:1)ogicas
ClementeEstable,Montevideo,Uruguay
SŁAWOMIRSE˛K (cid:1) FacultyofChemistry,BiologicalandChemicalResearchCentre,University
ofWarsaw,Warsaw,Poland
SARAN.SMITH (cid:1) DepartmentofMicrobiologyandImmunology,UniversityofMichigan
MedicalSchool,AnnArbor,MI,USA
ALEJANDRAYEP (cid:1) BiologicalSciencesDepartment,CaliforniaPolytechnicStateUniversity,
SanLuisObispo,CA,USA
YANBAOYU (cid:1) TheJ.CraigVenterInstitute,Rockville,MD,USA
PAULINAZ˙ARNOWIEC (cid:1) DepartmentofMicrobiology,InstituteofBiology,JanKochanowski
UniversityinKielce,Kielce,Poland
PABLO ZUNINO (cid:1) DepartamentodeMicrobiologı´a,InstitutodeInvestigacionesBiol(cid:1)ogicas
ClementeEstable,Montevideo,Uruguay