361

Index

a – PCR 224 abdominal and intestinal anthrax 14 – – virus culture and antigen testing 224 abscesses 40 – prevention 340–341 acid-fast bacilli (AFB) 151 – protection 338–339 activated partial thromboplastin time (APTT) – treatment 342 219 Argentinian hemorrhagic fever (AHF) 213, Advisory Committee on Immunization 217, 219, 220 Practices (ACIP) 203 ‘‘Army Vaccine’’ 97 African bite fever (ATBF) 124, 129, 142 arthropod-borne infections 124, 125, 127, agar gel immunodiffusion (AGID) 181 128, 129, 139, 142 Agrobacterium 20 avian influenza viruses (AIVs) 177, 178 124 Amblyomma hebraeum 129 b Amblyomma variegatum 129 bacille Calmette–Guerin´ (BCG) 150, 153, amplified fragment length polymorphism 155 (AFLP) 159 Bacillus anthracis 5, 159 124, 126 – characteristics 5–6 Andes virus (ANDV) 273, 276, 277 – clinical and pathological findings anthrax. See Bacillus anthracis 13–14 antibiotic resistance 7–8 – – abdominal and intestinal anthrax 14 antigen detection 8 – – inhalation and pulmonary anthrax 14 Antiqua biovar 93 – – oropharyngeal anthrax 14 Arenaviridae 253 – clinical guidelines 297 arenaviruses 211–212 – decontamination 296 – clinical signs – diagnosis – – New World hemorrhagic fevers 214–215 – – antibiotic resistance 7–8 – – Old World hemorrhagic fevers 214 – – antigen detection 8 – decontamination 340 – – chromosome 10–11 – diagnostics COPYRIGHTED– – growth characteristics MATERIAL 6–7 – – serological tests 223 – – MLVA, SNR, and SNP typing 11 – disinfection 339–340 – – molecular identification 8–10 – epidemiology – – phage testing and biochemistry 8 – – New World 213–214 – – phenotypical identification 6 – – Old World 212–213 – – serological investigations 11 – pathogenesis 218–223 – disinfection 295, 296 – pathological signs – epidemiology 15 – – New World hemorrhagic fevers 217–218 – pathogenesis – – Old World hemorrhagic fevers 215–216 – – animals 12

BSL3 and BSL4 Agents: Epidemiology, Microbiology, and Practical Guidelines, First Edition. Edited by Mandy C. Elschner, Sally J. Cutler, Manfred Weidmann, and Patrick Butaye.  2012 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2012 by Wiley-VCH Verlag GmbH & Co. KGaA. 362 Index

Bacillus anthracis (contd.) ––animals 41–42 – – humans 12–13 – – human 40 – prevention 296 – clinical guidelines 302 – prophylaxis 296 – decontamination 301 – protection 295 – diagnosis 38 – treatment 297 – – antigen detection 39 Bacillus cereus 6, 8, 9, 10, 16 – – cultural identification 38 Bacillus mycoides 6 – – molecular based methods 39 Bacillus pseudomycoides 6 – – serology 39–40 Bacillus thuringiensis 6 – disinfection 301 Bacillus weihenstephanensis 6 – epidemiology 42–43 bacterial typing 160 – molecular typing 43 20, 62 – prophylaxis 302 Bartonellaceae 126 – protection 301 BCSP31 protein 26 – treatment 302 biofilm 91 Burkholderia oklahomensis 48 biovars 87, 92 Burkholderia pseudomallei 38, 39, 47–48 bluetongue virus 263 – clinical and pathological findings Bolivian hemorrhagic fever (BHF) 213 ––animals 50–51 botonneuse fever. See Mediterranean spotted – – humans 50 fever (MSF) – clinical guidelines 304 Brill–Zinsser disease 127, 137 – decontamination 303 26, 27, 30, 31 – diagnosis 48 Brucella canis 25, 27, 30, 31 – – antigen detection 49 Brucella inopinata 28 – – cultural identification 48–49 Brucella melitensis 20, 21, 22, 26, 27, 30, 31 – – molecular based methods 49 Brucella neotomae 30 – – serology 49–50 Brucella ovis 25, 30 – disinfection 303 Brucella species 19 – epidemiology 52 – characteristics 20–21 – molecular typing 52 – clinical and pathological findings 27–29 – prophylaxis 304 – clinical guidelines 300 – protection 303 – control strategies 31 – treatment 304 – diagnosis 22–25 – – immunological approaches 25 c – – polymerase chain reaction (PCR) assays caf1 gene 91 25–26 Callithrix jacchus 216, 243 – disinfection 298–299 Calomys callosus 213 – epidemiology 29 Calomys musculinus 213 – molecular typing methods 29–31 capA gene 10 – pathogenesis 26–27 capB gene 10 – prevention 299 capC gene 10 – prophylaxis 299 Cavia porcellus 216 – protection 298 Centers for Disease Control (CDC) 155 – treatment 300 Chapare virus (CHAPV) 213 Brucella suis 27, 30, 31 Chlamydiaceae 62 . See Brucella species Chlamydia pneumoniae 63 bubonic 94 Chlorocebus aethiops 242 Bundibugyo ebolavirus 237 Chordopoxvirinae 205 Bundibugyo virus (BDBV) 237, 242, 243 Clinical and Laboratory Standards Institute Bunyaviridae 253, 255, 256, 273, 274 (CLSI) 8 Burkholderia cepacia 48 clustered regularly interspaced short 37–38 palindromic repeats (CRISPRs) 93 – clinical and pathological findings coagulase 91 Index 363 complement fixation test (CFT) 39, 40 andersoni 125, 139 Corynebacterium 149 Dermacentor-borne necrosis erythema and cowpox virus 201, 203 lymphadenopathy (DEBONEL) 137 57–58 Dermacentor marginatus 138 – characteristics 58 Dermacentor reticularis 138 – clinical and pathological findings 63 Dermacentor variabilis 139 – – acute 63 Didelphis virginiana 140 – – chronic Q fever 64 discrimination index (DI) 161 – clinical guidelines 308 disseminated intravascular coagulation (DIC) – decontamination 307 219, 245, 258 – diagnosis 59 dksA-xerC intergenic spacer 134 – – cultivation 59–60 Dobrava virus (DOBV) 273, 276, 277 – – direct detection 59 – – serology 61–62 e – – specific DNA detection 60–61 Ebola virus (EBOV) 237, 239, 240, 242, 243 – disinfection 306, 307 Ebola virus disease (EVD) 239, 242–243, – epidemiology and molecular typing 64 245, 246 – – IS1111 typing 65 Echidnophaga gallinacea 106 – – MLVA typing 66 Eclipse probes 209 – – multispacer sequence typing 65 Ehrlichieae 126 – – plasmid types 64–65 endospores 58 ––RFLP 65 58 – pathogenesis 62–63 Enterococcus species 11 – prevention 307 enzootic state 86 – prophylaxis 307 enzyme-linked immunosorbent assay (ELISA) – protection 306 11, 39, 49, 72, 95, 96, 182, 223, 246, 279, 280 – treatment 308 epizootic hosts 102, 108 Coxiella species 124, 126 epizootic state 86 Crabtreella 20 escaro-nodular fever. See Mediterranean Crimean Congo hemorrhagic fever virus (MSF) (CCHFV) 255 eschar 136 – characteristics 256 – clinical and pathological findings 257 f – clinical guidelines 353 farcy 37 – decontamination 351 farcy buds 37 – diagnosis 258 Felis canadensis 109 – – antigen detection 259 Felis concolor 109 – – molecular methods 259 Fibrin degradation products (FDPs) 219 – – serology 259 Filoviridae 237, 253 – – virus isolation 259 filoviruses – disinfection 351 – characteristics 237–239 – epidemiology 256 – clinical signs 242–243 – pathogenesis 257–258 – decontamination 344–345 – prevention 352 – diagnostic procedures 246 – protection 351 – disease outbreaks 241 – treatment 352 – disease survivors, symptoms and clinical Ctenocephalides felis 140 signs of 244 Ctenocephalides felis strongylus 109 – disinfection 344–345 culling policy 39 – epidemiology 239–242 cutaneous anthrax 13 – pathogenesis 245–246 – pathological findings 243–245 d – prevention 345 Daeguia 20 – prophylaxis 345 decay-accelerating factor (DAF) 275 – protection 344 364 Index

filoviruses (contd.) hantavirus 273 – 238 – characteristics 274–275 – treatment 346 – clinical findings 277 Flaviviridae 253 ––HCPS 278 fleas 124, 128, 129, 130, 134, 136, 139, 140, – – HFRS 277–278 142 – clinical guidelines 359–360 Fleckfieber 126 – decontamination 358 fliCgene 49 – diagnosis 279 fluorescence melting curve analysis (FMCA) – – serology 279–280 206, 207 – – virus detection 280–281 focus reduction neutralization test (FRNT) – disinfection 358 280 – epidemiology 276–277 fopA gene 73 – pathogenesis 279 fowl plague 179 – prevention 359 Francisella novicida 71, 77, 78 – protection 358 71 – treatment 359 – characteristics 72 hantavirus cardiopulmonary syndrome – clinical and pathological findings (HCPS) 273, 274, 276, 277, 278, 279, 280 – – animals 74 hemagglutination inhibition test (HAI) – – humans 74, 76–77 181–182 – clinical guidelines 311 hemagglutinin (HA) protein 176, 181 – decontamination 309 hemorrhagic fevers. See arenaviruses; – diagnosis filoviruses – – direct isolation 72–73 hemorrhagic fever with renal syndrome – – molecular biology tools for identification (HFRS) 273, 274, 276, 277–278, 279, 280 73 highly pathogenic avian influenza (HPAI) – – phenotypical characteristics 73 175, 177, 178, 182 – – serology 72 – infection in animals 179–180 – disinfection 309 – epidemiology in H5N1 viruses in Africa – epidemiology and molecular typing 77–79 186 – pathogenesis 73–74 – genetic diversity of H5N1 virus 184 – prevention 310 – H5N1 virus chronology – prophylaxis 310 – – first wave 182–183 – protection 309 – – in Africa 185–187 – treatment 311 ––secondwave 183 – – third wave 183–185 g – infection in humans 180 . See Burkholderia mallei – virus outbreaks 187–188 gltA sequences 132 high performance liquid chromatography GP genes 237 (HPLC) 153, 154 Guanarito virus (GTOV) 213–214, 218 hms gene 91, 106 guinea pig model 216, 223 holarctica 71, 77, 78, 79 Holosporaceae 124 h human leukocyte antigen (HLA) 277 H5N1 virus 178 Hyalomma genus 255, 256 – chronology Hyalomma marginatum marginatum 255 – – first wave 182–183 hypervariable octameric oligonucleotide finger – – in Africa 185–187 prints (Hoof Prints) 30 – – second wave 183 – – third wave 183–185 i – infection in animals 179–180 immunefluorescence assay (IFA) 280 – infection in humans 180 indirect hemagglutination assay (IHA) 50 influenzae 26 indirect immunofluorescence antibody (IFA) Hantaan virus (HTNV) 273, 275, 276, 277 223 Index 365

Influenzavirus 175 l influenza virus 175 large cell variant (LCV) 58, 62 – characteristics large-sequence polymorphisms (LSPs) 166 – – antigenic drift and antigenic shift Lassa fever 212–213 176–177 Lassa virus (LASV) 211, 213, 214, 215, 216, – – genome and protein structure 176 218, 220, 221, 222 – – nomenclature 175–176 Lcr plasmid 89, 91 – – viral replication 176 LcrV 97 – clinical and pathological findings 58 – – HPAI (H5N1) infection in animals 63 179–180 lice 127, 128, 137, 139, 140, 142 – – HPAI (H5N1) infection in humans 180 Liponyssoides sanguineus 140 – decontamination 329 live vaccine 97 – diagnosis Lloviu virus (LLOV) 237, 239, 240, 242 ––direct 181 low pathogenic avian influenza (LPAI) 177, – – indirect 181–182 178, 182 – – pathotyping 182 L protein. See RNA-dependent RNA – disinfection 329 polymerase (RdRp) – H5N1 virus chronology Lujo virus (LUJV) 211, 213, 214, 215 – – first wave 182–183 – – in Africa 185–187 m ––secondwave 183 Macaca fascicularis 242 – – third wave 183–185 Macaca mulatta 216, 243 – HPAI virus outbreaks 187–188 Machupo virus (MACV) 213, 217, 219, 221 – LPAI virus outbreaks 188 malleinization 39 – pathogenesis Marburg marburgvirus 237 – – low and highly pathogenic influenza Marburgvirus 237 viruses 177 Marburg virus (MARV) 237, 239, 240, 242, – – molecular determinants 178–179 243 – – reservoir 177 Marburg virus disease (MVD) 242, 243, 245, – prevention 329–330 246 – prophylaxis 330 Marmotta bobac 108 – protection 328 mechanical mass transmission via soiled – treatment 331 mouth parts 107 – vaccines 330 mediasiatica 71, 77, 78 inhalation and pulmonary anthrax 14 Medievalis biovar 93 interferon (IFN)-gamma 155 Mediterranean spotted fever (MSF) 123, 128 interferon gamma release assays (IGRAs) . See Burkholderia pseudomallei 156, 157 microneutralization (MN) 182 invA gene 90 minimum inhibition concentrations (MICs) IS1111 typing 65 8 IS6110-RFLP analysis 161–162 monkeypox virus 201, 202 IS711 insertion sequence 25 motBgene 49 IS711 sequence 26 mppA-purC intergenic spacer 134 Isavirus 175 multilocus sequence analysis (MLSA) 165 139 multi-locus sequence typing (MLST) 30, 31, Ixodes ticks 128 159 multi-locus variable analysis (MLVA) 11, 30, j 52, 66, 78, 93 Jun´ın virus (JUNV) 211, 213, 217, 219, 220, multispacer sequence typing 65 221, 222 Mus musculus 140 mycobacterial interspersed repetitive units k (MIRU) 163 killed vaccine 97 Mycobacterium africanum 150, 165 366 Index

Mycobacterium avium 150, 153 n Mycobacterium bovis 150, 153, 155, 165 Nairovirus 273 Mycobacterium canettii 150, 165 natural plague 99 Mycobacterium caprae 150, 165 neopterin 258 Mycobacterium chelonae 150 neuraminidase (NA) protein 176, 179 Mycobacterium complex (MTBC) 165 neuraminidase inhibition (NI) assays 182 Mycobacterium fortuitum 150 Nocardia 149 Mycobacterium gordonae 150, 153 nodules 40, 41–42 Mycobacterium intracellulare 150 nonchromogens 150 Mycobacterium kansasii 150, 153 noncoding regions (NCRs) 274 Mycobacterium leprae 149, 150, 159 nontuberculosis mycobacteria (NTM) 149, Mycobacterium marinum 150 150, 152 Mycobacterium microti 150, 165 N protein 274 Mycobacterium pinnipedii 150, 165 NS1 protein 179 nucleic acid amplification tests (NAATs) Mycobacterium scrofulaceum 150 154–155 Mycobacterium simiae 150 nucleic acid hybridization 153 Mycobacterium szulgai 150 Mycobacterium tuberculosis 149 o – clinical guidelines 323 Ochrobactrum 20, 21 – clustering of strains 166 Ochrobactrum intermedium 20 – decontamination 323 Oenanthe isabellina 109 – diagnosis and immunological tests ompA protein 125, 132, 134 155–157 ompB protein 125, 132, 134 – diagnostic microbiology of 150–151 Orientalis 92, 98 – disinfection 323 126, 131, 133 – IS6110-RFLP analysis 161–162 oropharyngeal anthrax 14 – molecular epidemiology 157–159 Oropsylla montana 107 – mycobacteria cultivation 152–153 Orthobunyavirus 273 – mycobacteria identification Orthomyxoviridae 175 – – from culture 153–154 orthopoxviruses 201 – – directly from clinical specimens – cowpox virus 203 154–155 – human monkeypox 202 – performance criteria in microorganism – real-time PCR 204–205 molecular typing method selection 160 – – evaluation 205–206 – – discriminatory power 160–161 ––5 nuclease probes 207–208 – – genetic elements 161 – – formats 208 – – reproducibility 160 – – hybridization probes 206–207 – – typeability 161 – specimen collection 204 – prevention 323 – vaccinia virus 203 – prophylaxis 323 – variola virus 201–202 – protection 322 – single nucleotide polymorphism (SNP) p 165–166 Papio hamadryas 243 – spoligotyping 162–163 passive hemagglutination test (PHA) 95 – staining and microscopic examination Pasteurella pestis.See 151–152 -associated molecular patterns – treatment 323 (PAMPs) 27 – typing theoretical principles 160 pCD1 gene 91 – VNTR and MIRU analysis 163, 165 PCR-coupled restriction fragment length Mycobacterium ulcerans 150, 159 polymorphism (PCR-RFLP) 133, 134 Mycobacterium xenopi 150 Pediculus humanus humanus 126, 127, 128 Mycoplana 20 peripheral blood mononuclear cells (PBMCs) Mycoplasma pneumoniae 63 220 Index 367 pesticin 89–90, 91 Reston virus (RESTV) 237, 239, 242 pestoides 92 restriction fragment length polymorphisms pFra plasmid 89, 90, 91 (RFLPs) 65, 93, 158 pgm locus 90, 91 reversed transcription (RT)-PCR 280 phage testing and biochemistry 8 rhesus monkey model 216 Phlebovirus 273 Rhipicephalus sanguineus 124, 139 photochromogens 150 Rhizobium 20 Pichinde´ virus (PICV) 216, 218 Rhodococcus 149 pla gene 91 ribavirin 221–222 plague. See Yersinia pestis ribotypes 87, 93 plasmidic genes 91 aeschlimanii 129 pMT1 gene 91 126, 129, 142 pneumonic plague 94–95 124, 125, 126, 129, 134, 140 polymerase chain reaction (PCR) 25–26, 60, 124, 140 130, 133, 181 Rickettsia barbariae 124 – real-time 204–205 Rickettsia bellii 126, 129, 133 – – evaluation 205–206 Rickettsia canadensis 126, 129, 133 ––5 nuclease probes 207–208 124, 126 – – formats 208 123, 124, 126, 128, 132, 134, – – hybridization probes 206–207 136, 139 – virus culture and antigen testing 224 Rickettsia davousti 124 Polyplax spinulosa 140 124, 125, 126, 129, 134, 138, pPCP1 gene 91 140 pPla plasmid 91 Rickettsia helvetica 139 pRF genes 129 140 Propionibacterium 149 Rickettsia hoogstraalii 124 Prospect Hill virus (PHV) 276 58, 126 58 139 Proteus spp. 38 124 proventricular blockage 106–107 125, 139 psaA gene 90 123, 124, 125, 126, 127, Pseudochrobactrum 20 128, 131, 134, 136, 137, 138, 139, 140, 142 Pseudomonadaceae 38 124, 138 Pst plasmid. See pesticin 123, 124, 126, 128, 136, Pulex irritans 102, 106, 107 139 pulsed field gel electrophoresis (PFGE) 93 124, 129, 134 purified protein derivative (PPD) 155 Rickettsia sibirica mongolotimonae 124, 129, Puumala virus (PUUV) 273, 276, 277 137 Rickettsia slovaca 124, 138 q Rickettsia species 123–124, 129 Q fever. See Coxiella burnetii – characteristics 124–125 – clinical guidelines 320 r – decontamination 319 rapid diagnostic test (RDT) 95, 96 – diagnosis 130 Rattus norvegicus 128, 140 – – clinical 130–131 Rattus rattus 102, 128, 140 – – laboratory 131–134 Ravn virus (RAVV) 237, 239, 240, 243 – disinfection 319 real-time PCR 204–205, 246 – epidemiology 138–142, 141 – evaluation 205–206 – pathogenesis 134–136, 135 –5 nuclease probes 207–208 – – clinical and pathological findings – formats 208 136–138 – hybridization probes 206–207 – phylogenetic classification of 126 RecA gene 20 – – ancestral group 129–130 Reston ebolavirus 237 – – spotted fever group (SFG) 128–129 368 Index

Rickettsia species (contd.) smears 151–152 – – transitional group (TRG) 129 Spermophilus beechyii 107 – – fever group (TFG) 126–128 Spermophilus variegatus 107 – prevention 319 spoligotyping 162–163 – prophylaxis 319 spotted fever group (SFG) 128–129 – protection 318 Sudan ebolavirus 237 – treatment 320 Sudan virus (SUDV) 237, 240, 242, 243 124, 125, 126, 128, 130, 131, sylvatic plague 99 134, 136, 137, 139, 140 Rickettsieae 126 t rickettsioses. See Rickettsia species tabardillo 126 Rift Valley fever virus (RVFV) 263 Ta¨ı Forest ebolavirus 237 – characteristics 263–264 Ta¨ı Forest virus (TAFV) 237, 239, 242 – clinical and pathological findings in humans Thogotovirus 175 265 Thottapalayam virus (TPMV) 276 – decontamination 355 thrombocytopenia 218 – diagnosis and surveillance 267–268 tick-borne lymphadenopathy (TIBOLA) 137 – disinfection 354–355 ticks 123, 124, 125, 128–129, 134, 136, 137, – epidemiology 264–265 139, 140, 142 – pathogenesis 266–267 Tospovirus 273 – prevention 355 transitional group (TRG) 125, 126, 129 – prophylaxis and treatment 265–266 tuberculin skin test (TST) 155, 156–157 – protection 354 tuberculosis. See Mycobacterium tuberculosis – treatment 356 tul4 gene 73 RNA-dependent RNA polymerase (RdRp) See Francisella tularensis 274, 275 tumor necrosis factor (TNF)-alpha 155 Rochalimaea 126 type III secretion system (TTSS) 91 Rocky Mountain spotted fever (RMSF) 123, typhus exanthematique 126 124, 128, 137, 138 typhus fever group (TFG) 126–128 rpmE-tRNAfMet intergenic spacer 134 u s ulcers 40, 41 16S rRNA gene sequence 132 United States Plague (USP) vaccine. See Sabia´ virus 214 ‘‘Army Vaccine’’ 159 saspB gene 10 v sca1 gene 133 vaccinia virus (VACV) 201, 203 sca4 gene 134 variable number tandem repeats (VNTRs) sca gene 125, 132 11, 30, 93, 162, 163, 165 scotochromogens 150 variola virus (VARV) 201–202, 204, 205, 206, group (STG) 126 207, 208, 209 Seoul virus (SEOUV) 273 – decontamination 335 SEOV 276, 277 – disinfection 334–335 septicemic plague 94 – prevention 335 serological investigations 11 – protection 334 serum agglutination test 39 – treatment 336–337 shell vial technique 59 – vaccination 335–336 single nucleotide polymorphisms (SNP) 31, Venezuelan hemorrhagic fever 217 159 viral hemorrhagic fevers (VHFs) 239, 245, single nucleotide repeat (SNR) analysis 11 253 sin nombre virus (SNV) 273, 276 viral ribonucleoprotein (vRNP) 176 Siphonaptera 103 viral RNA (vRNA) 176, 181 small cell variants (SCVs) 58, 62 virulence plasmids small pox. See orthopoxviruses – pXO1 8 Index 369

– pXO2 9 – decontamination 313 Vulpes velox 109 – diagnosis 95–96 – – confirmed and suspected patient isolation w 96 Wolbachieae 126 – – vaccine 97 – disinfection 312, 313 x – epidemiology 98–99 Xenospylla cheopis 102, 103, 106, 107, 128, – – classical plague cycle 107–109 140 – – current plague distribution 99–100 – – flea biology 102–104 y – – historical perspective 100–102 yersiniabactin 86 – – plague transmission mechanism by fleas 25, 26, 88, 89 105–107 Yersinia microtus 92 – prevention 313 Yersinia pestis 85–89, 159 – prophylaxis 314, 315 – as biological weapon 97–98 – protection 312 – characteristics – treatment 314–315 – – chromosomal virulence genes Yersinia pseudotuberculosis 88, 89, 93, 97 90–91 yopM gene 91 – – microbiology 89 yp48 gene 93 – – molecular typing 92–93 yst gene 90 – – variants 92 – – virulence markers and pathogenesis z 89–90 Zaire ebolavirus 237 – clinical and pathological signs 93–95 zoonotic virus. See hantavirus – clinical guidelines 315 Zygodontomys brevicauda 214