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Index| Volume 33, ISSUE 3, P731-748, September 2013

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Index

        Note: Page numbers of article titles are in boldface type.

        A

        Acanthamoeba, 484–485
        Achromobacter, MALDI-TOF mass spectrometry for, 572
        Actinomyces, MALDI-TOF mass spectrometry for, 574
        Adenoviruses, 448–449, 451, 453, 528, 534–536
        Adrenomedullin, in sepsis, 417, 420
        Aeromonas, 528, 535
        Affirm VPIII assay, 473, 489
        African trypanosomiasis, 467–468
        Aichi virus, 534
        Alere Determine TB-LAM Ag lateral flow test, 559
        Algorithms, clustering, in MALDI-TOF mass spectrometry, 620–622
        Amebiasis, 485–488
        American trypanosomiasis (Chagas disease), 476–477
        Amoeba, free-living, 470, 484–485
        Amplicor Mycobacterium tuberculosis test, 554
        Amplified Mycobacterium tuberculosis Direct Test, 554
        AmpliVue C difficile test, 530–531, 534
        Anaerobic bacteria
         in blood cultures, 652
         MALDI-TOF mass spectrometry for, 574
        Ancylostoma, 487–488
        Antibiotic Resistance Genes Database, 644
        Antigen85, in tuberculosis, 561
        Antigen-detection tests, for respiratory viruses, 440
        Antimicrobial resistance
         in blood culture pathogens, 665–667
         MALDI-TOF mass spectrometry for, 602, 623
        Antimicrobial susceptibility testing, 415, 695
        Aptamers, in tuberculosis, 560–561
        Aptima Trichomonas vaginalis assay, 473, 489
        Arabinitol, in fungal infections, 540–541
        Ascaris lumbricoides, 486–488
        Aspergillosis
         biomarkers in, 506–511
         molecular diagnosis of, 512–519
        Aspergillus, MALDI-TOF mass spectrometry for, 575–597, 616
        Aspergillus Real-Time PCR Panel, 512–514, 516
        Astroviruses, 528, 534–535
        Auroeobasidium/Hormonema, MALDI-TOF mass spectrometry for, 576
        Automation, 567–588
         business case for, 584–587
         digital imaging in, 579–582
         history of, 706–707
         importance of, 567–569
         liquid microbiology and, 569–571
         of blood culture microorganism detection, 651–652, 664–665
         of polymicrobial blood culture identification, 614–615
         preanalytical, 571–578
         total laboratory, 582–584

        B

        Babesiosis, 446, 475–476
        BACcel, for blood cultures, 671, 673
        Bacillus, MALDI-TOF mass spectrometry for, 574
        BacT FX system, for blood cultures, 652
        BacT/ALERT system, for blood cultures, 652, 664–665
        BACTEC Lytic/10 bottles, for blood cultures, 665
        BACTEC Plus, for blood cultures, 665
        BACTEC/ALERT, for blood cultures, 671–672
        Bacteremia, sepsis in. See Sepsis.
        Bacteria, MALDI-TOF mass spectrometry for, 572–595
        Bacterial strain typing. See Strain typing.
        Bacteriophages, in Keypath MRSA/MSSA Blood Culture Test, 668
        Bacteroides fragilis, MALDI-TOF mass spectrometry for, 603, 623
        Balmuthia mandrillaris, 484–485
        BD Max System, 655–656
        BDG Fungitell assay, 509–510
        Beta-lactamase, Mycobacterium tuberculosis, 561
        Bile solubility test, for blood cultures, 664, 673
        Binary typing, 633, 643–645
        BinaxNOW Staphylococcus aureus assay, for blood cultures, 668, 673
        BioFire assays, for respiratory viruses, 451–453
        Bioinformatics, 645
        Biomarkers
         for fungal infections, 506–511, 519
         for gastroenteritis, 543
         for Mycobacterium tuberculosis, 558–562
         for sepsis, 415–422
        bioMérieux VITEX 2ID, 671–672, 709
        bioMérieux VITEX MS
         description of, 590–592, 612
         for bacteria identification, 592–595
         for blood cultures, 671–672
         for fungi identification, 595–597
        Biosensors, for gastroenteritis, 541–543
        Blastocystis hominis, 487
        Blastomyces dermatitidis, 509
        Blood cultures
         contamination of, 652
         microorganism detection in, 651–684
        Candida, 665–666, 669–671
        Enterococcus, 656–658, 669–670
        Escherichia coli, 658, 669–670
        Exoserohilum rostratum, 519
        false-negative results of, 652
        fungi, 505–506, 615–617, 657–661
        Gram-negative bacteria, 657–661
        Gram-positive bacteria, 615, 657–661
        history of, 651–653
        in sepsis, 414–415, 422–423, 426, 428
        Klebsiella, 669–670
        Listeria, 656
        MALDI-TOF mass spectrometry for, 601, 613–617
        nanotechnology for, 656–657
        nucleic acid amplification tests for, 653–662
        polymicrobial, 614–615
        Pseudomonas aeruginosa, 669–670
        pyrosequencing, 659
        rapid, 707
        specimen processing for, 613–614
        Staphylococcus, 653–656
        Staphylococcus aureus, 665, 668, 674
        Streptococcus, 659, 672
        Streptococcus pneumoniae, 664, 671
         subculture of, 652
        Bloodstream infections. See also Blood cultures.
         MALDI-TOF mass spectrometry for, 613–617
         sepsis in. See Sepsis.
        Bocaviruses, 535
        Bordetella pertussis, 540
        Bovine herpes virus, 544
        Bovine respiratory syncytial virus, 544
        Bovine viral diarrhea virus, 541
        Breath, tuberculosis biomarkers in, 559–560
        Bronchoalveolar fluid analysis, in fungal infections, 506–508
        Brugia malayi, 468, 479–480
        Bruker MALDI BioTyper, 612
         description of, 590–592
         for bacteria identification, 592–595
         for blood cultures, 671–672
         for fungi identification, 595–597
        Burkholderia
         MALDI-TOF mass spectrometry for, 574
         strain typing of, 642

        C

        CALC-1 gene, in sepsis, 418
        Campylobacter, 536, 539
        Campylobacter coli, 535
        Campylobacter jejuni, 528, 534–535, 541
        Candida
         biomarkers in, 506–511
         in blood cultures, 665–667, 669–673
         MALDI-TOF mass spectrometry for, 575–597, 614–617
         molecular diagnosis of, 511–528
        Candida albicans germ tube antibody assay, 509
        Candida Real-Time PCR Panel, 512–513, 515–516
        Capillary gel electrophoresis, for strain typing, 636, 638
        Capillary Sanger sequencing, for strain typing, 639
        Capillary sequence platforms, for strain typing, 636, 638
        Carbapenamases, MALDI-TOF mass spectrometry for, 602
        Card agglutination test, for African trypanosomiasis, 478
        Cell culture, for respiratory viruses, 440
        Cell lysis, for blood cultures, 613–614
        Cell-analysis, real-time, for gastroenteritis, 545–546
        Centrifugation, of urine specimens, for MALDI-TOF mass spectrometry, 617–618
        Cepheid assays, for respiratory viruses, 443–445
        Cestodes, 487–488
        cfiA gene, Bacteroides fragilis, 623
        Chagas disease, 466, 476–477
        Chemical protein extraction, for blood cultures, 613–614
        Chemiluminescence assay, for sepsis, 417, 421
        Chemiluminescence sandwich immunoassay, for procalcitonin, 418
        Chlamydophila, strain typing of, 639
        Cholera toxin, 542
        CHROMagar Candida, for blood cultures, 665–667
        CHROMagar MRSA, for blood cultures, 667
        Chromogenic agar, for blood cultures, 665–667, 673
        Ciphergen Protein-Chip System, for African trypanosomiasis, 479
        ClinProTools, 619
        Clonality, MALDI-TOF mass spectrometry for, 622
        Clonorchis sinensis, 488
        Clostridium, strain typing of, 635
        Clostridium difficile, 528, 530–534–536, 545–546, 721
         MALDI-TOF mass spectrometry for, 622
         typing of, 632, 636–637
        Clostridium perfringens, 535, 546
        Clustered, regularly interspersed short palindromic repeats (CRISPRs), for strain typing, 632
        Clustering algorithms, in MALDI-TOF mass spectrometry, 620–622
        Coinfections, of respiratory viruses, 455
        CompassXport tool, 618–619
        Compensatory antiinflammatory response syndrome, 415
        Comprehensive Antibiotic Resistance Database, 644
        Computers, in sequencing, 694
        Conductometric biosensors, for gastroenteritis, 542
        Confusion matrix, in MALDI-TOF mass spectrometry, 620–621
        Consensus multilocus sequence typing, 632, 639–640
        Coronaviruses, molecular diagnosis of, 451, 454
        Corynebacterium, MALDI-TOF mass spectrometry for, 574
        C-reactive protein
         in gastroenteritis, 543
         in sepsis, 416–418
        CRISPRs (clustered, regularly interspersed short palindromic repeats), for strain typing, 632
        Crohn disease, 543
        Cronobacter, strain typing of, 635
        Cryptococcus, MALDI-TOF mass spectrometry for, 575–576
        Cryptosporidiosis, 471, 485–488, 536, 544
        Culture-independent diagnostic testing, 645–646
        Cultures. See also Blood cultures.
         for free-living amoeba, 485
         for fungal infections, 505–506
         for gastroenteritis, 528–529
         for leishmaniasis, 481
        α-Cyano-4-hydroxycinnamic acid, in MALDI-TOF mass spectrometry, 612, 623
        Cytokines
         in gastroenteritis, 543–544
         in sepsis, 417, 421

        D

        Data storage, in sequencing, 691
        Databases, for sequencing, 692
        Decision support, 723
        Definitions Biomarkers Working Group, 506
        Determine TB-LAM Ag lateral flow test, 559
        Diafiltration, of urine specimens, for MALDI-TOF mass spectrometry, 617–618
        Diarrhea. See also Gastroenteritis.
         in parasitic disease, 470–472, 485–488
        Dientamoeba fragilis, 471, 487
        Differential centrifugation, for blood cultures, 613–614
        Digital imaging, 579–582
        Direct Amplification Disk, 446
        Direct bile solubility test, for blood cultures, 664, 673
        Direct tube coagulation test, for blood culture, 662
        Disk diffusion susceptibility test, 708
        Diversity, in sequencing, 690
        DNase test, thermostable, for blood cultures, 664, 673

        E

        Electrical impedance detection methods, for gastroenteritis, 545
        Electrochemical impedimetric immunosensors, for gastroenteritis, 541–542
        Electron microscopy, for gastroenteritis, 528–529
        Electronic medical records, 722–723
        Electrophoresis, pulsed field gel, for strain typing, 631–632, 634–636
        Electrospray ionization mass spectrometry, 659–670
         for babesiosis, 476
        emm gene, for strain typing, 632, 639
        Encephalitozoon, 489–490
        Endotoxin, in sepsis, 417, 421–422
        Endotoxin activity assay, for sepsis, 417, 421
        Entamoeba gingivalis, 486
        Entamoeba histolytica, 536
        Entamoeba histolytica/dispar, 470, 485–488
        Enterobacteriaceae, MALDI-TOF mass spectrometry for, 601
        Enterococcus
         in blood cultures, 656, 669–670
         strain typing of, 635
         vancomycin resistance and susceptibility in, MALDI-TOF mass spectrometry for, 601, 603, 622
        Enterocytozoon, 489–490
        Enteroviruses, 452, 454, 534
        Enzyme immunoassay, for gastroenteritis, 528
        Enzyme-linked immunosorbent assay
         for filariasis, 480
         for gastroenteritis, 543
         for tuberculosis, 561
         Hyplex BloodScreen assay with, 661–662
        Epidemiology, MALDI-TOF mass spectrometry for, 622
        Epstein-Barr virus, PCR for, 718–719
        Escherichia, strain typing of, 635, 638
        Escherichia coli, 528, 534–536, 541–542
         antibiotic resistance in, 602
         in blood cultures, 658, 669–670
         misidentification of, 612
         strain typing of, 643
        eSensor Respiratory Viral Panel, 449
        ESwab, 570
        European Aspergillus PCR Initiative, 518
        European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group, 508
        Exoserohilum rostratum, 519

        F

        Filariasis, 467–468
        FilmArray Blood Culture Identification panel, 657–659, 662–663
        FilmArray GI assay, 487
        FilmArray Respiratory Panel, 451–453
        Filter paper, of urine specimens, for MALDI-TOF mass spectrometry, 617–618
        Fluconazole resistance, in blood cultures, 666
        Flukes, 487–488
        Fluorescence microscopy. See PNA FISH (peptide nucleic acid fluorescent in situ hybridization assay).
        Fluorescent resonance energy transfer (FRET), for malaria, 463
        Focus Diagnostic assays, for respiratory viruses, 445–446
        Fontana Masson strain, for fungi, 519
        Formalin-fixed paraffin-embedded tisues, fungi in, 519
        Foundation for Innovative New Diagnostics, 479
        Free-living amoebae, 484–485
        Fructobacillus, MALDI-TOF mass spectrometry for, 622
        Fungal infections, 505–525
         biomarkers for, 506–511, 519
         MALDI-TOF mass spectrometry for, 615–617
         molecular diagnosis of, 511–518
        Fungitell assay, 509–510
        Fusarium, MALDI-TOF mass spectrometry for, 597, 616

        G

        Galactomannan, in fungal infections, 506–509
        Ganglioside-sensitized liposomes, for gastroenteritis, 542
        Gastroenteritis, 528–552
         biosensors for, 541–545
         genomic assays for, 529–540
         historical detection methods for, 527–529
         multiplex PCR for, 534–537, 721
         proteomics for, 529, 541–546
         real-time cell analysis systems for, 545–546
        Gel-based separation, for blood cultures, 613–614
        GeneOhm Cdiff Assay, 530–531
        GeneOhm StaphSR assay, 655–656, 662–663
        GeneXpert Flu Assay, 443–444
        GeneXpert MRSA/SA blood culture assay, 653–664, 672–674, 709
        GeneXpert Xpert MTV/RIF test, 556–558
        GenMark assays, for respiratory viruses, 448–449
        Genome analysis, for gastroenteritis, 539
        Genomic assays, for gastroenteritis, 529–540
        Genotype MTDR test, 555–556
        GenoType Mycobacteria Direct test, 554
        Giardiasis, 471, 485–488, 536
        1,3-ß-D-Glucan, in fungal infections, 509–540
        Glutamate dehydrogenase antigen test, for gastroenteritis, 528
        Gold nanotechnology, for blood cultures, 656–657
        G-protein--coupled receptors, for gastroenteritis, 545
        Gram-negative organisms, MALDI-TOF mass spectrometry for, 602, 715–717
        Gram-positive bacteria, MALDI-TOF mass spectrometry for, 615

        H

        HACEK organisms, MALDI-TOF mass spectrometry for, 597
        Helicase method, for Staphylococcus detection, 654
        Helicobacter pylori, 544
        HeliScope System, for gastroenteritis, 539–540
        Helminths, intestinal, 470–472, 485–488
        High-resolution fragment analysis, for strain typing, 632, 636–638
        Histoplasma capsulatum, in blood cultures, 652
        Hologic assays, for respiratory viruses, 442–443
        Human metapneumovirus, molecular diagnosis of, 442–443, 448, 451
        Hyplex BloodScreen assay, 661–663
         for sepsis, 423, 427

        I

        Illumigene C difficile Assay, 530–532
        Immunochromatography
         for blood cultures, 668
         for filariasis, 480
        Immunocytotoxicity assay, in gastroenteritis, 545
        Immunoenzymatic microplate sandwich assay, for fungal infections, 506
        Immunoglobulin, salivary, in gastroenteritis, 544
        Immunoluminometric procalcitonin assay, for sepsis, 419
        Immunoparalysis, in sepsis, 415
        Immunosensors, for gastroenteritis, 541–543
        Incidental findings, in sequencing, 694–695
        Incubators, digital imaging in, 579–582
        Infectious Diseases Society of America, fungal infection guidelines of, 508
        Influenza virus, molecular diagnosis of, 443–453
        INNO-LiPA TB test, 555
        Innova plating instrument, 571–572, 574–575
        InocuLAB, 573
        InoquIA plating instrument, 571–572, 575–576
        Interferons
         in gastroenteritis, 543–544
         in Mycobacterium tuberculosis, 559, 561
        Interleukins
         in gastroenteritis, 543–544
         in sepsis, 417, 421
        Intestinal parasites, 470–472, 485–488
        Ion Proton System, for gastroenteritis, 540
        IQuum assays, for respiratory viruses, 445
        Isoplater, 571, 573

        K

        Keypath MRSA/MSSA Blood Culture Test, 668
        Klebsiella, in blood cultures, 669–670
        K-mer based approaches, to strain typing, 632, 642

        L

        Label-free detection methods, for gastroenteritis, 545
        Lactococcus, MALDI-TOF mass spectrometry for, 622
        LCx, M tuberculosis test, 554
        LDMS, for malaria, 465
        Leishmaniasis, 469, 481–482
        Leishmanin skin test, 481–482
        Leuconostoc, MALDI-TOF mass spectrometry for, 622
        LIASON BRAHMS PCT-immunoluminometric assay, for procalcitonin, 419
        Liat Influenza A/B assay, 445
        Line probe assays, for Mycobacterium tuberculosis, 558
        Lipoarabinomannan, in tuberculosis, 559
        Lipopolysaccharide-binding protein, in sepsis, 417, 419–420
        Liquid microbiology, 569–571
        Listeria
         in blood cultures, 656
         MALDI-TOF mass spectrometry for, 574, 603
         strain typing of, 603, 639
        Loa loa, 468, 479–480
        Loop-mediated isothermal amplification
         for African trypanosomiasis, 467–468, 478–479
         for leishmaniasis, 469
         for malaria, 465, 474–475
         for Mycobacterium tuberculosis, 557–558
         for toxoplasmosis, 470, 484
        Luminex assays
         for intestinal parasites, 486
         for respiratory viruses, 449–451
        Luminex Multiplex PCR xMAP assay, for fungal infections, 512–513
        Luminex xMAP technology, for gastroenteritis, 535
        Lymphatic filariasis, 467–468
        Lysis centrifugation, for blood cultures, 652

        M

        Malaria, 462–465, 474–475, 540
        MALDI Sepsityper kit, 601, 671–673
        MALDIquant, 620
        MALDI-TOF mass spectrometry, 589–609, 709–717
         clinical utility of, 710–717
         commercial systems for, 590–592
         costs of, 598, 710
         dangers of, 711
         description of, 710
         disadvantages of, 711
         economics of, 710
         emerging uses of, 611–628
        bloodstream infections, 613–617
        classification, 619–620
        clustering algorithms, 620–622
        limitations of, 612–613
        postanalytical, 618–622
        spectra refinements, 618–619
        urinary tract infections, 617–618
         for antimicrobial resistance detection, 602, 623
         for blood cultures, 673, 715–717
         for clonality studies, 622
         for epidemiologic information, 622
         for microbial identification
        advantages of, 597–598
        bacteria, 592–595
        direct, 601–602
        disadvantages of, 599–600
        fungi, 517, 595–597
        Gram-negative, 715–717
        principles of, 590–592
        Streptococcus, 716
         for strain typing, 602–603, 622
         future applications of, 600–603
         history of, 589–599
         implementation of, 714
         patient benefits of, 714
         unusual organisms found in, 712–714
         work flow with, 710–711
        Mannan, in fungal infections, 540–541
        Mansonella, 479–480
        Mass spectrometry
         for babesiosis, 476
         for malaria, 475
         matrix-assisted laser desorption ionization-time-of-flight. See MALDI-TOF mass spectrometry.
         PCR with, for blood cultures, 663
        MassSpecWavelet, 620
        MATLAB, 620
        Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF). See MALDI-TOF mass spectrometry.
        MEDIC (Multicenter Endotoxin Detection in Critical Illness) trial, 417, 421
        Medical education, for sequencing, 696
        Medical laboratory technologists, 569
        Meningitis outbreak of 2012, investigation of, 519
        Meningococcus Genome Informatics Platform, 639
        Metabolomics, for Mycobacterium tuberculosis, 561
        Metagenomics, 689–690
        Methicillin resistance, in Staphylococcus aureus. See MRSA (methicillin-resistant Staphylococcus aureus).
        Microscopy
         for African trypanosomiasis, 478
         for filariasis, 480
         for free-living amoebae, 485
         for gastroenteritis, 528
         for intestinal helminths, 487–488
         for leishmaniasis, 481
         for microsporidia, 489
         for trichomoniasis, 488–489
        Microsporidiosis, 473, 489–490
        Minimum Information for Publication of Quantitative Real-Time PCR Experiments guidelines, 511
        Mixed inflammatory response syndrome, 415
        MLST (multilocus sequence typing), 632, 639–640
        Molecular diagnosis, 717–722. See also individual methods and infections.
         for fungal infections, 511–518
         for Mycobacterium tuberculosis, 554–558
         for respiratory viruses, 441–455
         for sepsis, 422–429
         product selection for, 717–718
         quantitative testing in, 718
        Molecular phylogeny, 687–689
        MolYsis Basic kit, 601
        Moraxella, MALDI-TOF mass spectrometry for, 621
        MRSA (methicillin-resistant Staphylococcus aureus)
         antibiotic resistance in, MALDI-TOF mass spectrometry for, 602
         in blood cultures, 653–657, 663, 665–668, 674
         in sepsis, 422, 424–425
         MALDI-TOF mass spectrometry for, 602–603, 622
         strain typing of, 632, 638–640
        MRSA ID, 667
        Mucorales, MALDI-TOF mass spectrometry for, 597
        Multicenter Endotoxin Detection in Critical Illness (MEDIC) trial, 417, 421
        Multilocus sequence typing, 632, 639–640
        Multiple locus VNTR analysis, for strain typing, 636, 638
        Multiplex PCR, 719
         for African trypanosomiasis, 478–479
         for babesiosis, 476
         for blood cultures, 658
         for free-living amoebae, 485
         for gastroenteritis, 534–538, 721
         for intestinal parasites, 486–487
        Multiplex protein/antigen liquid arrays, for gastroenteritis, 543–544
        Multiplex xTAG Fungal ASR Luminex assay, 512, 514
        MycAssay Aspergillus, 512, 515–516
        Mycobacterium
         in blood cultures, 652
         MALDI-TOF mass spectrometry for, 574
         strain typing of, 635, 643
        Mycobacterium tuberculosis, 553–566
         biomarkers for, 558–562
         MALDI-TOF mass spectrometry for, 574
         molecular diagnosis of, 554–558
         multidrug-resistant, 555–556, 568

        N

        NAATs. See Nucleic acid amplification tests; specific tests.
        Naegleria fowleri, 484–485
        Nanosphere assays, for respiratory viruses, 446–448
        Nanotechnology, for blood cultures, 656–657
        National Institute of Allergy and Infectious Diseases Mycoses Study Group, 508–511
        Necator americanus, 487–488
        Neisseria, strain typing of, 639, 642
        Nematodes, 487–488
        NeutrAvidin, for gastroenteritis, 542
        Next-generation sequencing-based microbiota determination, for gastroenteritis, 538–540
        Nitrocellulose nanofibrous membrane, for gastroenteritis, 541
        Nitrous oxide, in gastroenteritis, 543–544
        Nocardia, MALDI-TOF mass spectrometry for, 574
        Noninstrumented nucleic acid platform, for malaria, 465, 475
        Norovirus, 528, 534–536
        Nosema, 489–490
        Nucleic acid amplification tests
         for African trypanosomiasis, 478–479
         for babesiosis, 475–476
         for blood cultures, 653–662
         for intestinal helminths, 487–488
         for malaria, 463–465, 474–475
         for microsporidia, 489–490
         for Mycobacterium tuberculosis, 554–558
         for respiratory viruses, 441–455
         for sepsis, 422–429
        Nucleic acid lateral flow immunoassay (NALFIA), for malaria, 475
        Nucleic acid sequencing. See Sequencing.
        Nucleic acid-based sequenced -based amplification (NASBA)
         for African trypanosomiasis, 479
         for malaria, 474–475

        O

        Oligochromatography, for African trypanosomiasis, 467, 479
        Oligonucleotides, in tuberculosis, 560–561
        Onchcerca volvulus, 479–480
        Optoelectric immunosensors, for gastroenteritis, 542–543

        P

        Paecilomyces, 513
        Paraffin-embedded tissues, fungi in, 519
        Paraflagellar rod protein A, in African trypanosomiasis, 478–479
        Parainfluenza viruses, 448, 451, 453–454, 544
        Parasitic diseases, 461–503
         blood, 462–468, 474–480
         intestinal, 470–472, 485–488
         tissue, 469–470, 481–485
         urogenital, 483, 488–489
         versus microsporidia, 489–490
        Parechoviruses, 534
        PCR. See Polymerase chain reaction.
        PCR-ribotyping, for strain typing, 632, 636–637
        Penicillium, MALDI-TOF mass spectrometry for, 616
        Pentraxin 3, in sepsis, 417, 421
        Peptide nucleic acid fluorescent in situ hybridization assay. See PNA FISH (peptide nucleic acid fluorescent in situ hybridization assay).
        Phenotypic methods, for blood cultures, 662, 664–672
        Phoenix automated identification system, for blood cultures, 664–665
        Pichia, MALDI-TOF mass spectrometry for, 576
        Plasmodium, 540
        Platelia kit, for fungal infections, 507–508
        Platelia mannan antigen test, 510
        Plating techniques, automation for, 569–582
        PLEX-ID BAC Spectrum assay, 424, 428, 476
        PLEX-ID Broad Fungal Assay, 512, 515–516
        PNA FISH (peptide nucleic acid fluorescent in situ hybridization assay), 709
         for African trypanosomiasis, 467
         for blood cultures, 668–673
         for fungal infections, 514, 518
        Pneumocystis, biomarkers in, 510
        Polymerase chain reaction
         electrospray ionization mass spectrometry with, 659–670
         for African trypanosomiasis, 467–468, 478–479
         for babesiosis, 466, 475–476
         for blood culture microorganisms, 653–662
         for Chagas disease, 466, 476–477
         for cryptosporidiosis, 471
         for Dientamoeba fragilis, 471, 487
         for Entamoeba histolytica/dispar, 470
         for Epstein-Barr virus, 718–719
         for filariasis, 468, 480
         for free-living amoebae, 470, 485
         for fungal infections, 511–518
         for gastroenteritis, 534–538
         for giardiasis, 471
         for intestinal parasites, 473–474, 486–488
         for leishmaniasis, 469, 481–482
         for malaria, 465–466, 474–475
         for microsporidiosis, 474
         for Mycobacterium tuberculosis, 554–555
         for respiratory viruses, 441–455
         for schistosomiasis, 473
         for sepsis, 422–429
         for toxoplasmosis, 470, 482–484
        Polymicrobial blood cultures, 614–615, 672
        Portrait Toxigenic C difficile Assay, 530–531, 533
        Postanalytical approach, MALDI-TOF mass spectrometry for, 618–622
        Post-transplant lymphoproliferative disease, 718–719
        Preanalytical automation, 571–578
        PREVI Isola plating instrument, 571–572, 578
        Principal-component analysis, in MALDI-TOF mass spectrometry, 620
        Privacy issues, in sequencing, 694
        Pro-adrenomedullin, in sepsis, 417, 420
        ProbeTec Direct Test, for Mycobacterium tuberculosis, 554
        Procalcitonin, in sepsis, 417–419
        Prodesse kits, for respiratory viruses, 442–443
        ProGastro CD assay, 530–532
        Proteomics
         for gastroenteritis, 529, 541–546
         for Mycobacterium tuberculosis, 561
        Provasopressin, in sepsis, 417, 420
        Prove-it Sepsis assay, 423, 426–427, 661, 663
        Pseudomonas aeruginosa
         in blood cultures, 669–670
         MALDI-TOF mass spectrometry for, 574
        Pulsed field gel electrophoresis, for strain typing, 631–632, 634–636
        PulseNet, 634–635, 638
        PyroMark ID platform, for gastroenteritis, 539
        Pyrosequencing
         for blood cultures, 659, 663
         for gastroenteritis, 538–539

        Q

        QuantiFERON-TB Gold Tube assay, 559
        Quantitative testing, in molecular diagnosis, 718
        QuickFISH, for blood cultures, 670–671, 673
        Quidel assay, for respiratory viruses, 443

        R

        Rapid antigen test, for gastroenteritis, 529
        Rapid detection
         from blood cultures, 651–684
         history of, 706–707
        RapID NF O Plus, in MALDI-TOF mass spectrometry, 621
        readBruker Flex Data tool, 618
        Real-time cell-analysis, for gastroenteritis, 545–546
        Recognition capability, in MALDI-TOF mass spectrometry, 620
        RenDx Fungiplex panel, 516–517
        Resistance, antimicrobial. See Antimicrobial resistance.
        Respiratory syncytial virus, molecular diagnosis of, 441–443, 445–448
        Respiratory viruses, 439–460
         molecular diagnosis of, 719–720
         NAATS for, 441–455
        Results, communication of, 722–723
        Rhinoviruses, molecular diagnosis of, 442, 448, 452, 454
        Rhodotorula, MALDI-TOF mass spectrometry for, 575
        Ribospacer PCR, for strain typing, 632, 636–637
        RNA FISH, for fungi, 519
        Rotaviruses, 528, 534–536
        Round worms, 487–488
        rRNA genes, in pyrosequencing, 659

        S

        Saccharomyces, MALDI-TOF mass spectrometry for, 575
        Salivary immunoglobulin, in gastroenteritis, 544
        Salmonella, 528, 535–536, 544
         strain typing of, 603, 635, 638, 643
        Salmonella enterica, 534
        Sapovirus, 534–535
        Scedosporium, 513, 519
        Schistosomiasis, 473
        Seeplex Diarrhea ACE Detection, 535
        Seeplex Diarrhea Virus Panel, 535
        SELDI-TOF, for African trypanosomiasis, 467
        Selective reporting, 723
        Sepsis, 413–437
         agents causing, 652
         biomarkers for, 415–422
         clinical continuum of, 414–415
         incidence of, 414
         molecular diagnosis of, 422–429
        SepsiTest
         for blood cultures, 662–663
         for sepsis, 424, 428
        Sepsityper kit, 601, 613–614, 671
        SeptiFast
         for blood cultures, 660–661, 663
         for fungal infections, 512, 515–516
         for sepsis, 424, 427–428
        Sequencing, 685–704
         clinical microbiology use of, 686–687
         computer limitations in, 693–694
         data interpretation in, 692–693
         data storage problems with, 691
         database quality and, 692
         diversity findings in, 690
         errors in, 692
         evolution of, 686
         for antimicrobial susceptibility, 695
         for strain typing, 638
         incidental findings in, 694–695
         integrating into clinical diagnostics, 691
         medical education for, 696
         metagenomics and, 689–690
         microbiome and, 695–696
         open nature of, 690
         privacy issues in, 694
         standards for, 691–692
         unexpected byproducts of, 687–689
        Sequencing by Oligonucleotide Ligation and Detection (SOLiD), for gastroenteritis, 539
        Serology
         for Chagas disease, 477
         for intestinal helminths, 487
         for leishmaniasis, 481
         for toxoplasmosis, 482–484
        Shear horizontal surface acoustic wave device, for gastroenteritis, 542
        Shigella, 534–536
         misidentification of, 612
         strain typing of, 635
        Shock, septic. See Sepsis.
        Simplexa assays, for respiratory viruses, 445–446
        Simplexa C difficile Universal Direct Test, 530–533
        Single number polymorphisms, in strain typing, 641–642
        Single-molecule real-time sequencing, for gastroenteritis, 540
        Smart Leish re-time PCR assay, 482
        Solexa sequencing platform, for gastroenteritis, 539
        SOLiD (Sequencing by Oligonucleotide Ligation and Detection), for gastroenteritis, 539
        Spa gene, for strain typing, 632, 638–639
        Specimen(s), MALDI-TOF mass spectrometry, 601–602, 613–614
        Specimen collection, swab methods for, 569–571
        Spectra MRSA, 667
        Spectral preprocessing, in MALDI-TOF mass spectrometry, 620
        Spirometra erinacei, 488
        Sputum, tuberculosis biomarkers in, 560–561
        Staph ID/R Blood Culture Panel, 654, 663
        Staph SR assay, for sepsis, 422–425
        StaphPlex assay, for sepsis, 423, 425
        Staphylococcus
         in blood cultures, 653–656, 665, 668, 674
         strain typing of, 635
        Staphylococcus aureus, 540
         classification of, 621
         in sepsis, 422, 424–425
         MALDI-TOF mass spectrometry for, 621
         methicillin-resistant. See MRSA (methicillin-resistant Staphylococcus aureus).
        Staphylococcus M assay, for sepsis, 423, 425
        Stool culture, for gastroenteritis, 528–529
        Strain typing, 639–650
         amplified fragment length polymorphism analysis for, 631, 634–636
         binary typing, 633, 643–645
         bioinformatics for, 645
         clustered, regularly interspersed short palindromic repeats for, 632
         culture independent testing and, 645–646
        emm gene typing, 632, 639
         high-resolution fragment analysis, 632, 636–638
         importance of, 629–630
         k-mer based approaches, 632, 642
         MALDI-TOF mass spectrometry for, 602–603, 622
         methods selection for, 630–631
         multilocus sequence typing for, 632, 639–640
         pulsed field gel electrophoresis for, 631–632, 634–636
        spa gene, 632, 638–639
         superMLST, 633, 643–645
         whole-genome sequencing for, 632, 640–642
        Streptococcal antigen testing, for blood cultures, 664, 673
        Streptococcus
         in blood cultures, 656
         MALDI-TOF mass spectrometry for, 572, 716
         misidentification of, 612
        Streptococcus pneumoniae
         in blood cultures, 664, 671
         strain typing of, MALDI-TOF mass spectrometry for, 603
        Strongyloides stercoralis, 487–488
        SuperMLST, for strain typing, 633, 643–645
        Supervised clustering, in MALDI-TOF mass spectrometry, 620–622
        Support vector machine, for MALDI-TOF mass spectrometry, 619–620
        Surface acoustic wave device, for gastroenteritis, 542
        Surface second harmonic generation techniques, for gastroenteritis, 542–543
        Swabs, for specimen collection, 569–571
        Systemic inflammatory response syndrome. See Sepsis.

        T

        T2 Biosystems fungal assays, 517
        Taenia, 488
        Tapeworms, 487–488
        TaqMan Array Card assay, for intestinal parasites, 486
        Technology, in clinical practice, 705–729. See also specific instruments and techniques.
        Thermostable DNase test, for blood cultures, 664
        Time-resolved amplified cryptate emission (TRACE) technology, for procalcitonin, 419
        Total laboratory automation, 582–584
        Toxoplasmosis, 470, 544
        TRACE (Time-resolved amplified cryptate emission) technology, for procalcitonin, 419
        Transcriptiomics, for Mycobacterium tuberculosis, 561
        Transcription-mediated amplification assay, for trichomoniasis, 473
        Trematodes, 487–488
        Trichomoniasis, 473, 488–489
        Trichophyton, MALDI-TOF mass spectrometry for, 576
        Trichuris trichiura, 486
        Trypanosomiasis
         African, 467–468
         American (Chagas disease), 476–477
        Tube coagulase test, for blood cultures, 673
        Tuberculosis. See Mycobacterium tuberculosis.
        Typing and subtyping. See Strain typing.

        U

        Ulcerative colitis, 543
        Urine
         MALDI-TOF mass spectrometry for, direct microorganism detection in, 601–602, 617–618
         tuberculosis biomarkers in, 559

        V

        Vancomycin resistance and susceptibility, Enterococcus, 601, 603, 622, 657
        Variable number tandem repeats, for strain typing, 636
        Vasopressin, in sepsis, 417, 420
        Verigene C difficile Test, 530–531, 533–534
        Verigene Gram-Negative Blood Culture Nucleic Acid Test, 663
        Verigene Gram-Positive Blood Culture Nucleic Acid Test, 423, 426, 656–657, 662–663
        Verigene RV+, for respiratory viruses, 446–448
        Vibrio, 528, 535, 542, 548, 639
        Vibrio cholerae, 546
        VIDAS enzyme-linked fluorescent immunoassay, for procalcitonin, 419
        Viral infections
         gastrointestinal, 528, 534–535, 544
         respiratory, 439–460
        Virulence Factors Database, 644
        Virus neutralization assays, for gastroenteritis, 545
        VITEK 2, for blood cultures, 664–665
        Vitek AutoMicrobic system, 706, 708
        VITEK MS. See bioMérieux VITEX MS.
        Vittaforma, 489–490
        VYOO assay, for sepsis, 424, 428

        W

        Walk-Away Specimen Processor, 571–572, 576–577, 708
        Wampole Isolator, 652
        Whole-genome sequencing, 632, 640–642
        Workforce shortages, 645
        Worms, intestinal, 487–488
        Wuchereria bancrofti, 468, 479–480

        X

        Xpert C difficile assay, 530–532
        Xpert C difficile/Epi assay, 530–532
        Xpert MRSA/SA assay, 423–425, 663
        Xpert MTV/RIF test, 556–558
        xTAG Fungal ASR Luminex assay, 512, 514
        xTAG Gastrointestinal Pathogen Panel, 486–487, 536–537, 721–722
        xTAG Respiratory Virus Panel, 449–451
        xTAG RVP FAST assays, 449–451

        Y

        Yeast Traffic Light PNA FISH assay, 512, 514
        Yersinia, 535
        Yersinia enterocolitica, 528, 535