BSL3 and BSL4 Agents: Epidemiology, Microbiology, and Practical Guidelines

385 Pages·2012·3.16 MB·English

Editedby
MandyC.Elschner,SallyJ.Cutler,
ManfredWeidmann,and
PatrickButaye
BSL3andBSL4Agents
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Edited by Mandy C. Elschner, Sally J. Cutler,
Manfred Weidmann, and Patrick Butaye
BSL3 and BSL4 Agents
Epidemiology, Microbiology, and Practical Guidelines
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V
Contents
Acknowledgment XIX
Preface XXI
ListofContributors XXIII
PartA Pathogens 1
PartI Bacteria 3
1 Bacillusanthracis:Anthrax 5
MarkusAntwerpen,PaolaPilo,PierreWattiau,PatrickButaye,
JoachimFrey,andDimitriosFrangoulidis
1.1 Introduction 5
1.2 CharacteristicsoftheAgent 5
1.3 Diagnosis 6
1.3.1 PhenotypicalIdentification 6
1.3.2 GrowthCharacteristics 6
1.3.3 AntibioticResistance 7
1.3.4 PhageTestingandBiochemistry 8
1.3.5 AntigenDetection 8
1.3.6 MolecularIdentification 8
1.3.6.1 VirulencePlasmidpXO1 8
1.3.6.2 VirulencePlasmidpXO2 10
1.3.7 Chromosome 10
1.3.8 MLVA,SNR,andSNPTyping 11
1.3.9 SerologicalInvestigations 11
1.4 Pathogenesis 12
1.4.1 Animals 12
1.4.2 Humans 12
1.5 ClinicalandPathologicalFindings 13
1.5.1 OropharyngealAnthrax 14
1.5.2 AbdominalorIntestinalAnthrax 14
1.5.3 InhalationalorPulmonaryAnthrax 14
1.6 Epidemiology 15
VI Contents
1.7 Conclusion 15
References 16
2 BrucellaSpecies:Brucellosis 19
SallyJ.Cutler,MichelS.Zygmunt,andBrunoGarin-Bastuji
2.1 Introduction 19
2.2 CharacteristicsoftheAgent 20
2.3 Diagnosis 22
2.3.1 ImmunologicalApproaches 25
2.3.2 PolymeraseChainReactionAssays 25
2.4 Pathogenesis 26
2.5 ClinicalandPathologicalFindings 27
2.6 Epidemiology,MolecularTyping,andControl
Strategies 29
2.6.1 Epidemiology 29
2.6.2 MolecularTypingMethods 29
2.6.3 ControlStrategies 31
2.7 Conclusions 31
References 32
3 Burkholderiamallei:Glanders 37
LisaD.SpragueandMandyC.Elschner
3.1 Introduction 37
3.2 CharacteristicsoftheAgent 37
3.3 Diagnosis 38
3.3.1 CulturalIdentification 38
3.3.2 MolecularBasedMethods 39
3.3.3 AntigenDetection 39
3.3.4 Serology 39
3.4 ClinicalandPathologicalFindingsinHumans 40
3.5 ClinicalandPathologicalFindingsinAnimals 41
3.6 Epidemiology 42
3.7 MolecularTyping 43
3.8 Conclusions 43
References 43
4 Burkholderiapseudomallei:Melioidosis 47
LisaD.SpragueandMandyC.Elschner
4.1 Introduction 47
4.2 CharacteristicsoftheAgent 47
4.3 Diagnosis 48
4.3.1 CulturalIdentification 48
4.3.2 AntigenDetection 49
4.3.3 MolecularBasedMethods 49
4.3.4 Serology 49
Contents VII
4.4 ClinicalandPathologicalFindingsinHumans 50
4.5 ClinicalandPathologicalFindingsinAnimals 50
4.6 Epidemiology 52
4.6.1 MolecularTyping 52
4.7 Conclusions 52
References 53
5 Coxiellaburnetii:QFever 57
MatthiasHanczaruk,SallyJ.Cutler,RudolfToman,and
DimitriosFrangoulidis
5.1 Introduction 57
5.2 CharacteristicsoftheAgent 58
5.3 Diagnosis 59
5.3.1 DirectDetection 59
5.3.2 C.burnetiiCultivation 59
5.3.3 DetectionofC.burnetiiSpecificDNA 60
5.3.4 Serology 61
5.4 Pathogenesis 62
5.5 ClinicalandPathologicalFindings 63
5.5.1 AcuteQFever 63
5.5.2 ChronicQFever 64
5.6 Epidemiology,IncludingMolecularTyping 64
5.6.1 PlasmidTypes 64
5.6.2 RFLP 65
5.6.3 IS1111Typing 65
5.6.4 MultispacerSequenceTyping 65
5.6.5 MLVATyping 66
5.7 Conclusion 66
References 66
6 Francisellatularensis:Tularemia 71
AndersJohansson,HerbertTomaso,PlamenPadeshki,AndersSjo¨stedt,
NigelSilman,andPaolaPilo
6.1 Introduction 71
6.2 CharacteristicsoftheAgent 72
6.3 Diagnosis 72
6.3.1 Serology 72
6.3.2 DirectIsolation 72
6.3.3 PhenotypicalCharacteristics 73
6.3.4 MolecularBiologyToolsforIdentification 73
6.4 Pathogenesis 73
6.5 ClinicalandPathologicalFindings 74
6.5.1 Animals 74
6.5.2 Humans 74
6.6 EpidemiologyandMolecularTyping 77
VIII Contents
6.7 Conclusion 79
References 80
7 Yersiniapestis:Plague 85
AnneLaudisoit,WernerRuppitsch,AnnaStoeger,andArianePietzka
7.1 Introduction 85
7.2 CharacteristicsoftheAgent 88
7.2.1 ThePlagueBacterium:Yersiniapestis 88
7.2.1.1 YersiniapestisMicrobiology 89
7.2.1.2 YersiniapestisVirulenceMarkersandPathogenesis 89
7.2.1.3 ChromosomalVirulenceGenes 90
7.2.1.4 YersiniapestisVariants 92
7.2.2 MolecularTyping 92
7.3 Pathogenesis 93
7.3.1 ClinicalandPathologicalSigns 93
7.3.2 Diagnosis 95
7.3.2.1 PlaguePreventionandTreatment 96
7.3.3 PlagueasaBiologicalWeapon 97
7.4 Epidemiology 98
7.4.1 PlagueDistributionToday 99
7.4.2 PlagueinItsHistoricalPerspective 100
7.4.3 AnUpdatedPlagueCycle? 102
7.4.3.1 Flea-BornePlagueTransmission 103
7.4.4 ClassicalPlagueCycle 107
7.5 Conclusion 109
References 110
8 RickettsiaSpecies:Rickettsioses 123
AliceN.Maina,StephanieSpeck,EvaSpitalska,RudolfToman,
GerhardDobler,andSallyJ.Cutler
8.1 Introduction 123
8.2 CharacteristicsoftheAgent 124
8.3 PhylogeneticClassificationofRickettsiae 126
8.3.1 TyphusFeverGroup 126
8.3.2 SpottedFeverGroup 128
8.3.3 TransitionalGroupRickettsiae 129
8.3.4 AncestralGroupRickettsiae 129
8.4 Diagnosis 130
8.4.1 ClinicalDiagnosis 130
8.4.2 LaboratoryDiagnostics 131
8.5 Pathogenesis 134
8.5.1 ClinicalandPathologicalFindings 136
8.6 Epidemiology 138
8.7 Conclusions 142
Acknowledgments 142
References 143
Contents IX
9 Mycobacteriumtuberculosis:Tuberculosis 149
StefanPanaiotov,MassimoAmicosante,MarcGovaerts,PatrickButaye,
ElizabetaBachiyska,NadiaBrankova,andVictoriaLevterova
9.1 Introduction 149
9.2 DiagnosticMicrobiologyofMycobacteria 150
9.3 StainingandMicroscopicExamination 151
9.4 CultivationofMycobacteria 152
9.5 IdentificationofMycobacteriafromCulture 153
9.6 IdentificationofMycobacteriaDirectlyfromClinicalSpecimens 154
9.7 ImmunologicalTestsfortheDiagnosisofMycobacteriumtuberculosis
Infection 155
9.8 MolecularEpidemiologyofTuberculosis 157
9.9 TheoreticalPrinciplesofTyping 160
9.10 PerformanceCriteriaAppliedinSelectingtheMethodforMolecular
TypingofMicroorganisms 160
9.10.1 Reproducibility 160
9.10.2 DiscriminatoryPower 160
9.10.3 Typeability 161
9.11 GeneticElementsinM.tuberculosisthatContributetoDNA
Polymorphism:CurrentMethodsAppliedforGenotyping
ofM.tuberculosis 161
9.12 IS6110-RFLPAnalysis 161
9.13 SpacerOligonucleotideTyping–Spoligotyping 162
9.14 VNTRandMIRUAnalysis 163
9.15 SingleNucleotidePolymorphism 165
9.16 TheClusteringQuestion? 166
9.17 Conclusions 167
References 167
PartII Viruses 173
10 InfluenzaVirus:HighlyPathogenicAvianInfluenza 175
ChantalJ.Snoeck,NancyA.Gerloff,RaduI.Tanasa,F.XavierAbad,and
ClaudeP.Muller
10.1 Introduction 175
10.2 CharacteristicsoftheAgent 175
10.2.1 Nomenclature 175
10.2.2 GenomeandProteinStructure 176
10.2.3 ViralReplication 176
10.2.4 AntigenicDriftandAntigenicShift 176
10.3 Pathogenesis 177
10.3.1 Reservoir 177
10.3.2 LowandHighlyPathogenicInfluenzaViruses 177
10.3.3 MolecularDeterminantsofPathogenicity 178
10.4 ClinicalandPathologicalFindings 179
X Contents
10.4.1 HPAI(H5N1)InfectioninAnimals 179
10.4.2 HPAI(H5N1)InfectioninHumans 180
10.5 Diagnosis 181
10.5.1 DirectDiagnosis 181
10.5.2 IndirectDiagnosis 181
10.5.3 Pathotyping 182
10.6 EvolutionandGeographicSpreadofHPAI(H5N1)Viruses 182
10.6.1 ChronologyofH5N1Virus 182
10.6.1.1 FirstWave 182
10.6.1.2 SecondWave 183
10.6.1.3 ThirdWave 183
10.6.2 FocusonAfrica 185
10.7 EpidemiologyofOtherInfluenzaSubtypes 187
10.7.1 HPAIVirusOutbreaks 187
10.7.2 LPAIVirusOutbreaks 188
10.8 Conclusion 188
References 189
11 Variola:Smallpox 201
AndreasNitscheandHermannMeyer
11.1 Introduction 201
11.2 VariolaVirus 201
11.3 HumanMonkeypox 202
11.4 VacciniaVirus 203
11.5 CowpoxVirus 203
11.6 CollectionofSpecimens 204
11.7 Real-TimePolymeraseChainReaction 204
11.8 EvaluationofReal-TimePCRAssays 205
11.9 Real-TimePCRAssayswithHybridizationProbes 206
11.10 Real-TimePCRAssayswith5(cid:2)NucleaseProbes 207
11.11 OtherReal-TimePCRFormats 208
11.12 Conclusions 209
References 209
12 Arenaviruses:HemorrhagicFevers 211
AmyC.Shurtleff,StevenB.Bradfute,SheliR.Radoshitzky,PeterB.
Jahrling,JensH.Kuhn,andSinaBavari
12.1 Characteristics 211
12.2 Epidemiology 212
12.2.1 OldWorldArenaviruses 212
12.2.2 NewWorldArenaviruses 213
12.3 ClinicalSigns 214
12.3.1 OldWorldArenaviralHemorrhagicFevers 214
12.3.2 NewWorldArenaviralHemorrhagicFevers 214
12.4 PathologicalFindings 215