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1 Index Note: Page numbers of article titles are in boldface type. A Absidia infections, 324 AccuProbe, for nontuberculous mycobacteria, 282 Achromobacter infections, in cystic fibrosis, Acid-fast microscopy, for nontuberculous mycobacteria, Acinetobacter infections, nosocomial, , 264 Adamantanes, for influenza, 390, 392, 399 Adenovirus 14 infections clinical presentation of, diagnosis of, 420 discovery of, 410 epidemiology of, microbiology of, 411 pathogenesis of, 417 treatment of, Amantadine, for influenza, 366, 392 Amikacin, resistance to, 301, 304 Amphotericin B, for Histoplasma infections, Anaerobic infections, nosocomial, 259 Antibiotic resistance Achromobacter, 208 Legionella, 229 Mycobacterium tuberculosis complex, nontuberculous Mycobacterium, 209 nosocomial respiratory organisms, Staphylococcus aureus, Stenotrophomonas, 208 Streptococcus pneumoniae, 229 Antibiotics, susceptibility testing of. See Susceptibility testing. Antigen detection, influenza virus, 368, Antiviral resistance, in influenza virus, Aspergillomas, 324 Aspergillosis clinical presentation of, diagnosis of, , epidemiology of, in cystic fibrosis, microbiology of, pathogenesis of, 318 Aspergillus Technology Consortium, Atypical mycobacteria. See Nontuberculous mycobacteria. Clin Lab Med 34 (2014) /14/$ see front matter ª 2014 Elsevier Inc. All rights reserved. labmed.theclinics.com

2 432 Index B BACTEC systems, for nontuberculous mycobacteria, 281 BD Veritor test, for influenza virus, 373 Bedaquiline, resistance to, 301 BG (1,3-b-D-glucan) test, for fungal infections, 316, , 359 BinaxNOW test, for Streptococcus pneumoniae, 225 BioFire FilmArray, for influenza virus, Blood culture, for respiratory infections, 224, 226 Bocavirus infections. See Human bocavirus type 1 infections. Bordetella bronchiseptica infections. See Pertussis. Bordetella holmnesii infections. See Pertussis. Bordetella parapertussis infections. See Pertussis. Bordetella pertussis infections. See Pertussis. Bronchoalveolar lavage for fungal infections, 322 for nosocomial infections, 261 Bronchoscopes, nontuberculous mycobacteria contaminating, 278 Broth microdilution assay, nontuberculous mycobacteria, 287 Broth-based culture systems, for nontuberculous mycobacteria, 281 Bruker system, for Burkholderia cepacia, 207 Burkholderia cepacia complex infections, in cystic fibrosis, Burkholderia cepacia selective agar, for fungi, 210 for nontuberculous Mycobacterium, Burkholderia gladioli infections, in cystic fibrosis, C Candida infections, in cystic fibrosis, Capreomycin, resistance to, 301, 304 Carbol fuchsin stain, for nontuberculous mycobacteria, Catalase test, for Staphylococcus aureus, 203 Chocolate agar, for Pseudomonas aeruginosa, 204 CMN group, nontuberculous mycobacteria in, 272 Colonization, by nontuberculous mycobacteria, 275 Cough, whooping. See Pertussis. Cryptococcal antigen test, 316, 320, Cryptococcosis, 316, Culture-based drug susceptibility testing, in tuberculosis, 299, 302 Cultures adenovirus 14, 420 Bordetella, influenza virus, 368, 370 Middle East respiratory syndrome coronavirus, 420 nontuberculous mycobacteria, nosocomial organisms, Cystic fibrosis, clinical presentation of, epidemiology of, infections in

3 Index 433 Achromobacter, Burkholderia cepacia complex, diagnosis of, 199 fungal, microbiology of, 199 microbiome analysis for, Mycobacterium, Pseudomonas aeruginosa, Staphylococcus aureus, Stenotrophomonas, susceptibility testing for, 199 viral, 210 D DAS181, for influenza, 392 Decontamination, of nontuberculous mycobacteria specimens, Direct fluorescent antibody test for adenovirus 14, 420 for Bordetella, Disk diffusion test, for Pseudomonas aeruginosa, 204 DNA sequencing, for nontuberculous mycobacteria, E Emerging viral infections, Enterobacter infections, nosocomial, 259, Enzyme immunoassays for Crytococcus, 319 human bocavirus type 1, 421 Enzyme-linked immunosorbent assay for Bordetella, for Legionella, 223, 225 Enzyme-linked immunospot method, in interferon-gamma release assay, 342 Epidemiologic cut-offs, for nontuberculous mycobacteria, 287 Escherichia coli infections, nosocomial, 259, 266 E-test for Pseudomonas aeruginosa, 204 for Staphylococcus aureus, 203 Ethambutol, resistance to, 300, 303 European Aspergillus PCR Initiative, European Organization for Research and Treatment of Cancer, 318 F Favipiravir, for influenza, Filamentous hemagglutinin, 241, FilmArray Respiratory Panel, 245, Flu A/B RSV Direct test, Fluorescent immunoassay, for influenza virus, 373 Fluorescent method, for nontuberculous mycobacteria, Focus Flu A/B RSV Direct test,

4 434 Index Fungal infections. See also specific organisms. clinical presentation of, diagnosis of, , epidemiology of, in cystic fibrosis, microbiology of, pathogenesis of, 318 treatment of, 326 Fungitec-G test, 320 Fungitell test, 320 G Galactomannan test for fungal infections, 316, , GeneXpert MTB/RIF assay, GenoType MTBDRplus and strips, 305, 307 Genotype Mycobacteria Direct test, 280 Genotype Mycobacterium CM and AS assays, 284 Genotyping, of nontuberculous mycobacteria, 286 Global Pertussis Initiative Conference, 242 1,3-b-D-Glucan (BG) test, for fungal infections, 316, Gram-negative infections, nosocomial, 259, 265 Growth detection, of nontuberculous mycobacteria, H Haemophilus influenzae infections, nosocomial, 259, 266 Halo sign, in aspergillosis, 317 Health care associated respiratory infections. See Nosocomial respiratory infections. Histoplasma infections clinical presentation of, 222 diagnosis of, 224, epidemiology of, 222 microbiology of, 220 pathogenesis of, 222 treatment of, HIV infections cryptococcosis with, fungal infections with, 315, Pneumocystis jirovecii infections with, tuberculosis with, , 344 Hospital-acquired respiratory infections. See Nosocomial respiratory infections. Human bocavirus type 1 infections clinical presentation of, diagnosis of, 421 discovery of, 410 epidemiology of, 415 microbiology of, pathogenesis of, treatment of, 422

5 Index 435 I Immunochromatography, for Aspergillus, 323 Immunofluorescence assay, for influenza virus, Immuno-Myologics enzyme immunoassay, for Histoplasma, Infections, respiratory. See Respiratory infections. Influenza, clinical presentation of, 366, 389 diagnosis of, methods for, 368, principles of, 367, 369 sample collection and transport for, epidemiology of, 389 microbiology of, , pathogenesis of, 366, 389 surveillance programs for, treatment of, , 388, , Influenza virus antiviral resistance in, genetics of, phenotyping of, susceptibility testing for, Interferon-gamma release assays, for tuberculosis, Invader assay, for nontuberculous mycobacteria, 283 iquum LIAT influenza A/B assay, Isoniazid for latent tuberculosis, 345 resistance to, Itraconazole, for Histoplasma infections, 230 K Kanamycin, resistance to, 301, 304 Kinyoun stain, for nontuberculous mycobacteria, Klebsiella pneumoniae infections, nosocomial, 259, L Lananimivir, for influenza, Lateral flow assay for Aspergillus, 323 for cryptococcosis, 319, 326 for influenza virus, 371 for Legionella, 223, 225 Latex agglutination test for cryptococcosis, 319 for Staphylococcus aureus, 203 Legionella infections clinical presentation of, 221 diagnosis of, epidemiology of, 221 microbiology of, 220

6 436 Index Legionella (continued) nosocomial, 259, 266 pathogenesis of, 221 treatment of, 229 Levofloxacin, resistance to, 303 LIAT influenza A/B assay, LightCycler Mycobacterium Detection Kit, 280 Line probe assays for Mycobacterium tuberculosis, 307 for nontuberculous mycobacteria, 284 Loop-mediated isothermal amplification, for Bordetella, 247 M MacConkey agar, for Pseudomonas aeruginosa, 204, 249 Macrolides, for Bordetella, 249 MALDI-TOF MS for Achromobacter, 208 for Burkholderia cepacia, 207 for nontuberculous mycobacteria, for nosocomial organisms, 263 for Pseudomonas aeruginosa, 204 for Staphylococcus aureus, 203 for Stenotrophomonas, 208 Mannitol salts agar, for Staphylococcus aureus, Maruha test, 320 Maternal immunization, for pertussis, 241 Matrix-assisted laser desorption ionization-time of flight mass spectroscopy. See MALDI-TOF MS. Mechanical ventilation, respiratory infections in. See Nosocomial respiratory infections. Methicillin-resistant Staphylococcus aureus, , 259, Microarray analysis for influenza virus, 397 for nosocomial organisms, 263 Microbiome analysis, in cystic fibrosis, Microscopy, acid-fast, for nontuberculous mycobacteria, Middle East respiratory syndrome coronavirus infections clinical presentation of, 415 diagnosis of, 420 discovery of, 410 epidemiology of, 413 microbiology of, pathogenesis of, 417 treatment of, 421 Minimum inhibitory concentration for nontuberculous mycobacteria, 287 for Pseudomonas aeruginosa, 204 for Staphylococcus aureus, 203 Miravista Diagnostics enzyme immunoassay, for Histoplasma, MiSeq platform, for Mycobacterium tuberculosis, 308

7 Index 437 Molecular assays, for respiratory infections, 224 Molecular beacon assays, for Mycobacterium tuberculosis, 304, 306 Molecular drug susceptibility testing, in tuberculosis, 299, Moraxella catarrhalis infections, nosocomial, 259 Moxifloxacin, resistance to, 303 MRSA (methicillin-resistant Staphylococcus aureus) infections in cystic fibrosis, nosocomial, 259, MTBDRplus and strips, 305, 307 Mucoid form, of Pseudomonas aeruginosa, Mucormycosis, 318, 324 Multicombinational bactericidal testing, for Pseudomonas aeruginosa, 204 Multidrug resistance, in nosocomial respiratory organisms, Multiplex methods, for influenza virus, MycAssay, for Aspergillus, Mycobacteria, nontuberculous. See Nontuberculous mycobacteria. Mycobacterium tuberculosis complex infections. See Tuberculosis. Mycosis Study Group, 318 N Nanosphere Verigene Assay, for influenza virus, 375 Neuraminidase inhibitors, , Next-generation sequencing for influenza virus, for Mycobacterium tuberculosis, 303, 308 Nontuberculous mycobacteria infections, clinical significance of, diagnosis of, acid-fast microscopy for, criteria for, 277 growth detection in, identification in, specimen processing for, genotyping of, 286 in cystic fibrosis, microbiology of, , 338 newly described, opportunistic, 275 pathogenesis of, sources of, susceptibility testing of, Nosocomial respiratory infections, clinical presentation of, 260 diagnosis of, epidemiology of, etiology of, pathogenesis of, treatment of, 259, Nucleic acid amplification tests for adenovirus 14, 420

8 438 Index Nucleic (continued) for Bordetella, for fungi, 210 for influenza virus, 368, for Mycobacterium tuberculosis, 308 for nontuberculous mycobacteria, 280, for nosocomial organisms, 262 for tuberculosis, 299 for viruses, 210 O Ofloxacin, resistance to, 303 Oseltamivir, for influenza, , 392, 399 P Pediatric patients, latent tuberculosis testing in, 344 Peramivir, for influenza, Pertussis, case definitions of, 242 clinical presentation of, 240 diagnosis of, 242 epidemiology of, immunity to, laboratory testing for, microbiology of, 238 pathogenesis of, toxins in, treatment of, 249 vaccines for, virulence factors in, 241 Phenotyping for Achromobacter, 208 for influenza virus, for Stenotrophomonas, 208 Platelia Aspergillus enzyme immunoassay, Pneumocystis jirovecii infections diagnosis of, 316, , in cystic fibrosis, 210 Pneumonia adenovirus 14, fungal. See Fungal infections. Histoplasma, 220, 222, human bocavirus type 1, in cystic fibrosis, influenza virus, 366, 389 Legionella, , 229 Middle East respiratory syndrome coronavirus, 415 nosocomial. See Nosocomial respiratory infections. pneumococcal, rhinovirus C, 416

9 Index 439 Polymerase chain reaction for Aspergillus, for Bordetella, for fungi, 322 for human bocavirus type 1, 421 for influenza virus, 368, , 397 for Middle East respiratory syndrome coronavirus, 420 for Mycobacterium tuberculosis, 304, 306 for nontuberculous mycobacteria, 280, for nosocomial organisms, for Pneumocystis jirovecii, for rhinovirus C, Pontiac fever, 221 Protected brush specimens, for nosocomial infections, 261 Pseudomonas aeruginosa infections in cystic fibrosis, nosocomial, , 264, 266 Pyrazinamide, resistance to, 300, 303 Pyrosequencing for influenza virus, for Mycobacterium tuberculosis, 305, Q QuantiFERON-TB Gold In-Tube test, Quidel Sofia Influenza A 1 B fluorescent immunoassay, 373 Quinolones, resistance to, 301, 303 R Radiography, for nosocomial infections, 261 Respiratory infections. See also specific organisms. antibiotic resistance in, emerging viruses in, fungal, , in cystic fibrosis, nontuberculous mycobacterial, nosocomial, pertussis, urine antigen tests for, Respiratory Virus Plus test, for influenza virus, Restriction fragment length polymorphism analysis, for nontuberculous mycobacteria, Rhinovirus C infections clinical presentation of, 416 diagnosis of, discovery of, 410 epidemiology of, microbiology of, 412 pathogenesis of, 417, 419 treatment of, 422

10 440 Index Rhinovirus infections, in cystic fibrosis, 210 Rhizopus infections, 324 Rifabutin, resistance to, 302 Rifampin for latent tuberculosis, 345 resistance to, 300, 302, Rifapentine, for latent tuberculosis, 345 Rimantadine, for influenza, 366, 392 R-mix test, for influenza virus, 372 RNA sequencing for Achromobacter, 208 for Burkholderia cepacia, for nontuberculous mycobacteria, 209, 280, for Stenotrophomonas, 208 S Sanger sequencing for influenza virus, for Mycobacterium tuberculosis, 303, 305, 307 Scedosporium infections, in cystic fibrosis, SeptiFast test, for Aspergillus, Serologic tests for Bordetella, 244, for human bocavirus type 1, 421 for respiratory infections, 224 Serratia infections, nosocomial, 266 Sofia Influenza A 1 B fluorescent immunoassay, 373 Speed-oligo Mycobacteria test, 284 Sputum analysis for nontuberculous mycobacteria, for respiratory infections, 224, 226 Staphylococcus aureus infections in cystic fibrosis, methicillin-resistant, , 259, nosocomial, 259, 261, 263, 266 small-colony variants of, in cystic fibrosis, Stenotrophomonas infections, in cystic fibrosis, Streptococcus pneumoniae infections clinical presentation of, diagnosis of, epidemiology of, microbiology of, 220 nosocomial, 259, 266 pathogenesis of, treatment of, 229 vaccines for, 222 Susceptibility testing Achromobacter, 208 Burkholderia cepacia complex, influenza virus,

11 Index 441 Mycobacterium tuberculosis complex, nontuberculous mycobacteria, 209, Pseudomonas aeruginosa, 204 Staphylococcus aureus, Stenotrophomonas, 208 SYBR dye assays, for influenza virus, 375 T T-705 (favipiravir), for influenza, M Rapid Detection system, for influenza virus, 373 Trichosporon infections, in cystic fibrosis, Trimethoprim-sulfamethoxazole for Bordetella, 249 resistance to, 199 T-SPOT.TB test, Tuberculin skin test, 338, 341 Tuberculosis, antibiotic resistance in, clinical presentation of, , diagnosis of, epidemiology of, 298, extrapulmonary, 299 latent, interferon-gamma release assays for, microbiology of, 298, 338 molecular diagnosis of, multidrug resistant, 298 pathogenesis of, 299, treatment of, 345 U United Kingdom Fungal Polymerase Chain Reaction Consensus Group, Urine antigen tests, for respiratory infections, clinical presentation of, diagnosis of, epidemiology of, microbiology of, 220 pathogenesis of, treatment of, V Vancomycin, resistance to, Ventilator-associated respiratory infections. See Nosocomial respiratory infections. Veritor test, for influenza virus, 373 Viral infections. See also specific viruses. emerging,

12 442 Index W Wako fungal tests, 320 Whole genome sequencing, for nontuberculous Mycobacterium, 209 Whooping cough. See Pertussis. X Xpert Flu test, for influenza virus, Z Zanamivir, for influenza, , 392, 399

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