Adaptive immunity, overview, 42, 44 Adhesin,

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265

Index

A

ActA, 128

Adaptive immunity, overview, 42, 44 Adhesin,

antigenic variation in mycoplasma, 185 Staphylococcus aureus genomic islet,

198–200 asd, 233

B

Bacille Calmette-Guérin (BCG), derivation and uses, 152, 156, 157

Bacteriophage, mycobacteria, 160

Staphylococcus aureus, 200, 201 Vibrio cholerae, 234, 235 BCG, see Bacille Calmette-Guérin Bordetella, virulence species origins, 26 Brucella, DNA microarray analysis,

32, 33

C

CagA, 98, 99 Campylobacter,

Campylobacter jejuni, genome sequencing, 64 glycomics,

capsular polysaccharides, 76, 77

flagellin glycosylation studies, 77, 78, 80

lipooligosaccharides, 73–75 mass spectrometry, 67, 69, 77, 78,

80, 81, 83

N-linked glycosylation, 80, 81, 83 nuclear magnetic resonance,

71–73, 78 overview, 64–67

prospects for study, 84, 85 therapeutic targeting, 83, 84 virulence factors, 64

comparative genomic analysis with Helicobacter species,

genome diversity sources, 101 prospects for study, 101, 102 sequence availability, 99 virulence, 99–101 culture, 256

diseases, 63, 64

genome sequencing, 91–93 CFP-10, 163, 164

Chlamydia, DNA microarray analysis, 33, 34

Cholera, see Vibrio cholerae Chromosome,

origins of replication, 6, 7

prophage influence on structure, 11 size distribution in microbes, 2, 3 topology and number, 3–5 ClfA, 199

ClfB, 199

Clusters of Orthologous Groups of proteins (COGs), Leptospira analysis, 115, 116

Coagulase, Staphylococcus aureus genomic islet, 197, 198

Codon usage, diversity among microbes, 6 COGs, see Clusters of Orthologous Groups

of proteins

Commensal bacteria, mucosal injury, 257, 258

Comparative genomic analysis,

Campylobacter vs Helicobacter species, genome diversity sources, 101 prospects for study, 101, 102 sequence availability, 99 virulence, 99–101

intraspecies comparisons, 5, 6

virulence gene identification, 260, 261 virulent vs nonvirulent strains, 32 Crohn’s disease, infectious etiology

evidence, 256, 257

(2)

D

DegU, 135 DNA microarray,

Brucella species, 32, 33 Chlamydia, 33, 34 Escherichia coli, 35

host–pathogen interaction studies, 35, 36 Porphyromonas gingivalis, 33

principles, 32

Streptococcus pneumoniae, 34, 35 DNA microarray, Vibrio cholerae virulence

gene expression analysis, 239, 240

E–G

ESAT-6, 161, 163, 164, 197 Escherichia coli,

DNA microarray analysis, 35 virulence strain origins, 24 ETA, see Exfoliative toxin A Exfoliative toxin A (ETA), 200 FlaC, 64

Flagellin, glycosylation studies in Campylobacter, 77, 78, 80 fnb genes, 198, 199

FUN genes, analysis, 31, 261 GBS, see Guillain-Barré syndrome GC content,

Leptospira genome, 111 variation in microbes, 5 Vibrio genomes, 229, 241, 242 GEIs, see Genetic elements and islands Gene cassette, comparative genomic

analysis, 10

Genetic elements and islands (GEIs), Staphylococcus aureus, 193, 206, 207 structure, distribution, and function, 12 Vibrio cholerae, 236, 237

virulence species origins, 24 Glycomics, Campylobacter jejuni,

capsular polysaccharides, 76, 77

flagellin glycosylation studies, 77, 78, 80 lipooligosaccharides, 73–75

mass spectrometry, 67, 69, 77, 78, 80, 81, 83

N-linked glycosylation, 80, 81, 83 nuclear magnetic resonance, 71–73, 78 overview, 64–67

prospects for study, 84, 85 therapeutic targeting, 83, 84

Group A Streptococcus, whole-genome polymerase chain reaction scanning, 36

Guillain-Barré syndrome (GBS), Campylobacter role, 63

H

Haemophilus influenzae, genome sequencing, 1

Helicobacter,

comparative genomic analysis with Campylobacter species, genome diversity sources, 101 prospects for study, 101, 102 sequence availability, 99 virulence, 99–101 culture, 256

enterohepatic species and pathogenicity, 95, 96

gastric species, 94, 95 genome sequencing, 91–93 Helicobacter pylori,

DNA microarray analysis, 35, 36 functional genomics, 97, 98 genome structure, 96, 97 history of study, 91, 94 population genetics, 97 virulence factors, 98, 99 virulence gene identification, 261 HGT, see Horizontal gene transfer hlyA, 233

Horizontal gene transfer (HGT), evolution role, 22

Vibrio cholerae, 231, 234 hsd genes, 206

I

IKKH, Toll-like receptor signaling, 53 InlA, 128–130, 139

InlB, 128–130, 133, 139 InlC, 133

Innate immunity, overview, 41, 42, 44 Insertion sequence (IS),

comparative genomic analysis, 8–10 Mycobacterium avian complex,

159 Integrons,

comparative genomic analysis, 10

Vibrio cholerae, 229, 237, 239

(3)

Interleukin-1 receptor-associated protein kinases (IRAKs), Toll-like receptor signaling, 49–51, 53, 54

Introns, structure, distribution, and evolution, 10, 11

IRAKs, see Interleukin-1 receptor- associated protein kinases IS, see Insertion sequence

J–L

JlpA, virulence factor function, 36, 37 Lactococcus lactis, probiotic use, 260 Leptospira,

classification, 109, 110 endoflagella, 118

gene expression regulation, 118 gene layout, 112, 113

genome annotation, 113–116, 121, 122 genome comparisons, 110, 111 genome features, 111, 112 lipopolysaccharide, 118, 119 lipoproteins, 120, 121 metabolism, 116, 117

protein secretion systems, 119, 120 serovars, 109

lgy, 186

Lipooligosaccharide, see Glycomics Lipopolysaccharide (LPS), Leptospira,

118, 119 Listeria monocytogenes,

diseases, 125

DNA microarray analysis, 35 genome features of strains, 128–130 genomics study prospects, 1341–143 hosts, 125

life cycle, 125–127 PrfA,

V

^B

regulon interactions, 139–141 target gene identification, 136–139 virulence factors,

cell wall linkage of proteins, 131, 132

comparative genomics in identification, 130

lipoprotein anchoring, 132, 133 lipotechoic acid anchoring of proteins,

133, 134

metabolism genes, 134

PrfA activity regulation, 135, 136

protein translocation across plasma membrane, 130

role in disease, 127, 128 surface protein anchoring, 131 transcriptional regulators, 135 LpeA, 132

LPS, see Lipopolysaccharide luk genes, 207

M

Mal, Toll-like receptor signaling, 51 Mammalian cell entry (MCE) proteins,

mycobacteria, 164, 165 Mass spectrometry (MS), glycomics

analysis, 67, 69, 77, 78, 80, 81, 83 MCE proteins, see Mammalian cell entry

proteins mdh, 233 mecA, 202, 203

MLEE, see Multilocus enzyme electrophoresis

MLSA, see Multilocus sequence analysis Mollicute, see Mycoplasma

MS, see Mass spectrometry

Multilocus enzyme electrophoresis (MLEE), Vibrio cholerae studies, 229, 231, 232

Multilocus sequence analysis (MLSA), Vibrio cholerae studies, 231, 233 Mycobacteria,

bacteriophages, 160 diseases, 151, 152

ESAT-6/CFP-10 antigens, 163, 164 lipid metabolism genes, 161, 163 mammalian cell entry proteins, 164, 165 Mycobacterium avian complex,

genome features, 158, 159 species, 158

Mycobacterium leprae, disease, 157

genome features, 157, 158 Mycobacterium marinum, 159, 160 Mycobacterium smegmatis, 160 Mycobacterium tuberculosis,

Bacille Calmette-Guérin, 152, 156, 157

complex, 155, 156

genome features, 154, 155

immune response, 153

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treatment, 153, 154

tuberculosis history and impact, 152, 153

Mycobacterium ulcerans, 159, 160 PE/PPE genes, 163

prospects for study, 166

resuscitation promoting factors, 165, 166 species, 152

Mycoplasma,

adaptation and pathogenicity, 186 adhesin antigenic variation, 185 human diseases, 176

mollicute host specificity, 175, 176 Mycoplasma penetrans,

gene conservation from ancestral bacteria, 179, 180 gene reduction events, 180

genome size, 179 paralogs, 180, 182 p35 paralogs,

Mycoplasma penetrans, 182 promoter switching, 182

paralog formation in phytoplasma, 185, 186

polymerase slippage, 183–185 reductive evolution,

essential genes for mollicutes, 178, 179

mollicutes, 177, 177 symbiosis, 176, 177 virulence species origins, 26 MyD88, Toll-like receptor signaling,

49–51

N–P ndk, 180

NMR, see Nuclear magnetic resonance Nonculturable organisms, approaches to

study, 255–257

Nuclear magnetic resonance (NMR), glycomics analysis, 71–73, 78 OpuC, 138

Origin of replication, comparative genomic analysis, 7, 8

p1, 185, 186

p35, see Mycoplasma

PAIs, see Pathogenicity islands Pathogenicity islands (PAIs),

Staphylococcus aureus, 204–206

structure, distribution, and function, 11, 12

Vibrio cholerae, 235, 236 virulence species origins, 24 PE genes, 163

Phage, see Bacteriophage Phospholipases, Listeria, 127 Plague, see Yersinia pestis Plasmids,

structure, size, topology, and evolution, 8 Vibrio cholerae, 237

Yersinia, 215 pls, 203

Porphyromonas gingivalis, DNA microarray analysis, 33

PPE genes, 163 PrfA,

activity regulation, 135, 136 function, 127

s

^B

regulon interactions, 139–141 target gene identification, 136–139 Probiotics, mechanisms of action and

prospects for study, 258–260

Prophage, see also Bacteriophage, distribution, influence on chromosome

structure, and virulence, 11 Staphylococcus aureus, 201 PrrF proteins, 13

PsaA, 132

Pseudogenes, Staphylococcus aureus, 194, 195

R

Recombination-based in vivo expression technology (RIVET), Vibrio cholerae virulence gene expression analysis, 239, 240

Restriction-modification (RM) systems, components, 23

distribution, 23

Resuscitation promoting factor (Rpf), mycobacteria, 165, 166 Rickettsia, virulence species origins, 25 RIVET, see Recombination-based in vivo

expression technology

RM systems, see Restriction-modification systems,

RNA interference, Listeria studies, 142

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Rpf, see Resuscitation promoting factor 16S rRNA, nonculturable organism studies

of genes, 255, 257 RstC, 234

RyhB, homologs, 13

S

Saccharomyces boulardii, probiotic use, 259 sar genes, 199

sdr genes, 199, 200

Seventh pandemic islands, Vibrio cholerae, 236, 237

Shigella,

comparative genomic analysis, 32 virulence species origins, 24, 32 SIGIRR, Toll-like receptor signaling

regulation, 54

Signature-tagged mutagenesis (STM), Vibrio cholerae virulence gene expression analysis, 239, 240 Single-locus sequence analysis (SLSA),

Vibrio cholerae studies, 231–233 SLSA, see Single-locus sequence analysis Small RNA (sRNA), gene distribution and

virulence role, 12, 13 Sortases, Listeria, 131, 132 sRNA, see Small RNA ssb, 186

ST2, Toll-like receptor signaling regulation, 54

Staphylococcus aureus, bacteriophage, 200, 201

genetic elements and islands, 206, 207 genome organization, 193, 194

genome sequencing of strains, 191, 192 genomic islets,

adhesin, 198–200 coagulase, 197, 198

MRSA252 SAR0285/0291 genomic islet, 195–197

infection, 191, 192

pathogenicity islands, 204–206 phenotypic trait correlation with small-

scale genetic variation, 200 pseudogenes, 194, 195

resistance, 192

Staphylococcal cassette chromosome elements, 202–204

virulence strain origins, 26

STM, see Signature-tagged mutagenesis Streptococcus pneumoniae, DNA

microarray analysis, 34, 35 SXT element, Vibrio cholerae, 239

T

T2K, Toll-like receptor signaling, 53 TIR domain, see Toll-like receptor TIRAP, see Mal

TLR, see Toll-like receptor Toll-like receptor (TLR),

features and ligands, TLR1, 47

TLR2, 46, 47 TLR3, 47 TLR4, 45, 46 TLR5, 47 TLR6, 47 TLR7, 48 TLR8, 48 TLR9, 47, 48 TLR11, 48, 49

innate immune response, 41, 42, 44 prospects for study, 54, 55

signaling,

MyD88-dependent signaling, interleukin-1 receptor-associated

protein kinases, 49–51 Mal, 51

overview, 49, 50 TRAF6, 49, 51

MyD88-independent signaling, IKKe, 53

overview, 51, 52 T2K, 53

TRAM, 53 TRIF, 52, 53

negative regulation, 53, 54 TIR domains, 44, 45

TRAF6, Toll-like receptor signaling, 49, 51

TRAM, Toll-like receptor signaling, 53 TRIF, Toll-like receptor signaling,

52, 53

TTSS, see Type III secretion system Tuberculosis, see Mycobacteria Type III secretion system (TTSS), see

Vibrio parahaemolyticus; Yersinia

pestis; Yersinia pseudotuberculosis

(6)

U–V udk, 180 VacA, 98 Vibrio cholerae,

bacteriophages, 234, 235 biotypes, 227

comparative genomic microarray analysis, 233

diseases, 227, 228

evolutionary relationship studies of strains,

multilocus enzyme electrophoresis, 229, 231, 232

multilocus sequence analysis, 231, 233

single-locus sequence analysis, 231–233

genome features,

comparison with other Vibrio species, 240, 243, 244

GC content, 229 integrons, 229

horizontal gene transfer, 231, 234 pathogenicity islands, 235, 236 plasmids, 237

seventh pandemic islands, 236, 237 super integrons, 237, 239

SXT element, 239 virulence genes,

expression analysis, 239, 240 global regulation, 239 virulence strain origins, 25 Vibrio fischeri, genome sequence and

features, 245 Vibrio parahaemolyticus,

diseases, 242

genome sequence and features, 242, 243

type III secretion system, 243, 248 Vibrio cholerae genome comparison,

243 virulence factors, 243 Vibrio vulnificus,

genome comparison with other Vibrio species, 244, 245

genome sequence and features, 244

Virulence species, origins, 23–27 vlhA, 184

W–Y

WGPScanning, see Whole-genome

polymerase chain reaction scanning Whipple’s disease, culture of causitive

organism, 255, 256

Whole-genome polymerase chain reaction scanning (WGPScanning), group A Streptococcus, 36 principles, 36

Yersinia enterocolitica, pathogenesis, 214 serogroups, 214

virulence species evolution, 214–216 Yersinia pestis,

comparative genomic analysis, 32 pathogenesis, 214

plague features, 213 serogroups, 213

type III secretion system,

chromosome-encoded system, 221, 222

flagellar gene clusters, 217 overview, 216, 217 prospects for study, 222 TTSS-2 gene inactivation, 222 virulence plasmid-encoded system,

217, 219

virulence species evolution, 25, 214–216 Yersinia pseudotuberculosis,

pathogenesis, 214 serogroups, 213

type III secretion system, chromosome-encoded system,

221, 222

flagellar gene clusters, 217 overview, 216, 217 prospects for study, 222

virulence plasmid-encoded system, 217, 219

YopT loss in O3 strain, 219–221 virulence species evolution, 214–216 YopT, loss in O3 Yersinia

pseudotuberculosis strain, 219–221