Clinical Microbiology Procedures Handbook 3 Vol Set

Clinical Microbiology Procedures Handbook, 2nd Edition.......Page 1
VOLUME 1......Page 2
Copyright......Page 5
Contents......Page 6
Editorial Board......Page 8
Contributors......Page 10
How To Use This Handbook......Page 16
Abbreviations......Page 18
Preface......Page 22
Acknowledgments......Page 24
Reader Response Form......Page 26
Disclaimer......Page 28
SECTION 1 - Procedure Coding, Reimbursement, and Billing Compliance......Page 30
1.1 Introduction......Page 31
1.2 Procedure Coding, Reimbursement, and Billing Compliance......Page 36
SECTION 2 - Specimen  Collection, Transport, and Acceptability......Page 46
2.1 Collection, Transport, and Manipulation of Clinical Specimensand Initial Laboratory Concerns......Page 47
SECTION 3 - Aerobic Bacteriology......Page 75
3.1 Introduction to the section......Page 80
3.2.1 Gram Stain......Page 83
3.2.2 Acridine Orange Stain......Page 106
3.2.3 Wet Mount for Detection of Leukocytes and Microorganisms......Page 110
3.3.1 Paratechnical Processing of Specimens for Aerobic Bacteriology......Page 116
3.3.2 Interpretation and RapidIdentification of Bacterial Growth on Primary Culture Media......Page 125
3.4.1 General Detection and Interpretation......Page 139
3.4.2 Brucella Cultures......Page 158
3.4.3 Bartonella Cultures......Page 164
3.5 Body Fluid Cultures (ExcludingBlood, Cerebrospinal Fluid, and Urine)......Page 169
3.6 Catheter Tip Cultures......Page 177
3.7 Cerebrospinal Fluid Cultures......Page 183
3.8.1 Fecal Culture for Aerobic Pathogens of Gastroenteritis......Page 190
3.8.2 Fecal Culture for Campylobacter and Related Organisms......Page 211
3.8.3 Clostridium difficile Toxin Detection......Page 230
3.8.4 Helicobacter pylori Cultures......Page 237
3.8.5 Screen for Vancomycin-Resistant Enterococci in Fecal Cultures......Page 243
3.9.1 Guidelines for Performance of Genital Cultures......Page 247
3.9.2 Group B Streptococcus Cultures......Page 261
3.9.3 Neisseria gonorrhoeae Cultures......Page 267
3.9.4 Haemophilus ducreyi Cultures......Page 281
3.10 Ocular Cultures......Page 286
3.11.1 Guidelines for Performance of Respiratory Tract Cultures......Page 294
3.11.2 Lower Respiratory Tract Cultures......Page 296
3.11.3 Respiratory Cultures from Cystic Fibrosis Patients......Page 311
3.11.4 Legionella Cultures......Page 320
3.11.5 Otitis Cultures......Page 334
3.11.6 Bordetella Cultures......Page 340
3.11.7 Corynebacterium diphtheriae Cultures......Page 354
3.11.8 Group A Streptococcus Culture and Direct Antigen Detection......Page 363
3.11.9 Nasal Sinus Cultures......Page 370
3.12 Urine Cultures......Page 374
3.13.1 Wound and Soft Tissue Cultures......Page 405
3.13.2 Quantitative Cultures of Wound Tissues......Page 421
3.14 Leptospira Culture......Page 425
3.15 Mycoplasma pneumoniae, Mycoplasma hominis, and Ureaplasma Cultures from Clinical Specimens......Page 430
3.16 Guidelines for Identification of Aerobic Bacteria......Page 447
3.17.1 Acetamide Utilization Test......Page 464
3.17.2 Acetate Utilization Test......Page 466
3.17.3 ALA (d-Aminolevulinic Acid) Testfor Porphyrin Synthesis......Page 468
3.17.4 Antimicrobial Disk Tests for Identification (Especially of Staphylococci)......Page 471
3.17.5 Bile-Esculin and Esculin Tests......Page 476
3.17.6 Bile Solubility Test......Page 479
3.17.7 Butyrate Esterase Test......Page 482
3.17.8 CAMP Factor Tests (Standard and Rapid)......Page 485
3.17.9 Carbohydrate Utilization Tests......Page 489
3.17.10 Catalase Test......Page 495
3.17.11 Cetrimide Test......Page 497
3.17.12 Citrate Utilization Test (Simmons)......Page 499
3.17.13 Coagulase Test-Protein A/Clumping Factor Agglutination Method......Page 501
3.17.14 Coagulase Test-Rabbit Plasma Method......Page 505
3.17.15 Decarboxylase-Dihydrolase Tests......Page 508
3.17.16 DNase Test-Rapid Thermonuclease Test......Page 512
3.17.17 Fluorescent-Pigment Agars for Pseudomonas Identification......Page 515
3.17.18 Gelatin Liquefaction......Page 518
3.17.19 Glucan and Polysaccharide Production......Page 521
3.17.20 Gram Reaction Enzymatic Test......Page 523
3.17.21 Hippurate Hydrolysis Rapid Test......Page 525
3.17.22 Hydrogen Sulfide Production......Page 528
3.17.23 Indole Test......Page 531
3.17.24 Indoxyl Acetate Disk Test......Page 535
3.17.25 Kligler’s Iron Agar Test and Triple Sugar Iron Agar Test......Page 537
3.17.26 LAP (Leucine Aminopeptidase) Test......Page 540
3.17.27 Lecithinase and Lipase Detection......Page 542
3.17.28 Lipophilism Test for Corynebacterium......Page 545
3.17.29 Malonate Test......Page 547
3.17.30 MGP (Methyl Glucopyranoside) Test......Page 549
3.17.31 Motility Tests......Page 552
3.17.32 MRS Broth......Page 556
3.17.33 MR-VP (Methyl Red–Voges-Proskauer) Tests......Page 558
3.17.34 MUG (4-Methylumbelliferyl-b-D-Glucuronide) Test......Page 562
3.17.35 Nitrate/Nitrite Reduction Test......Page 565
3.17.36 O/129 Disk Susceptibility Testing for Vibrio and Aeromonas spp.......Page 569
3.17.37 ONPG (o-Nitrophenyl-b-D-Galactopyranoside) Test......Page 572
3.17.38 Optochin Susceptibility Test......Page 574
3.17.39 Oxidase Test......Page 577
3.17.40 Phenylalanine Deaminase Test......Page 580
3.17.41 PYR (L-Pyrrolidonyl-b-Naphthylamide) Test......Page 583
3.17.42 Quellung Reaction for Pneumococci......Page 586
3.17.43 6.5% Salt and Temperature Tolerance Test......Page 589
3.17.44 Satellite Test......Page 592
3.17.45 SPS (Sodium Polyanetholesulfonate) Disk Test......Page 595
3.17.46 SS (Salmonella-Shigella) Agar Test for Growth......Page 597
3.17.47 Starch Hydrolysis Test......Page 599
3.17.48 Urea Test......Page 601
3.18.1 Identification of Gram-Positive Bacteria......Page 604
3.18.2 Identification of Gram-NegativeBacteria......Page 619
SECTION 4 - Anaerobic Bacteriology......Page 640
4.1 Introduction......Page 642
4.2 Collection and Transport of Clinical Specimens for Anaerobic Culture......Page 643
4.3 Culture Media for Anaerobes......Page 650
4.4 Examination of Primary Culture Plates for Anaerobic Bacteria......Page 659
4.5 Incubation Techniques for Anaerobic Bacteriology Specimens......Page 665
4.6.1 Introduction......Page 669
4.6.2 Spot Indole Test......Page 670
4.6.3 Nitrate Disk Reduction Test......Page 672
4.6.4 Catalase Test......Page 674
4.6.5 Identification by Using Special-Potency Disks......Page 676
4.6.6 Sodium Polyanethol Sulfonate Disk for Differentiation of Anaerobic Cocci......Page 678
4.6.7 Bile Test/Bacteroides Bile Esculin Agar for Differentiation of Anaerobic Gram-Negative Rods......Page 680
4.6.8 Fluorescence......Page 681
4.6.9 Lipase Test......Page 683
4.6.10 Lecithinase Test......Page 684
4.6.11 Pigment Production......Page 685
4.6.12 Urease Test......Page 687
4.6.13 Appendixes to Procedure 4.6......Page 688
4.7 Microbiochemical Systems for the Identification of Anaerobes......Page 693
4.8 Rapid Enzymatic Systems for the Identification of Anaerobes......Page 696
4.9.1 Introduction......Page 700
4.9.2 Alkaline Phosphatase......Page 701
4.9.3 Glutamic Acid Decarboxylase......Page 702
4.9.4 L-Alanyl-Alanylaminopeptidase......Page 704
4.9.5 L-Proline-Aminopeptidase......Page 705
4.9.6 4-Methylumbelliferone Derivative Substrates......Page 706
4.9.7 Combination Enzymatic Tabletsfor Nitrophenol, Aminopeptidase, and Methylumbelliferyl Substrates......Page 707
4.9.8 Appendixes to Procedure 4.9......Page 709
4.10 Anaerobic Gram-Negative Bacilli......Page 711
4.11 Anaerobic Gram-Positive Bacilli......Page 724
4.12 Anaerobic Cocci......Page 733
VOLUME 2......Page 741
SECTION 5 - Antimicrobial SusceptibilityTesting......Page 745
5.1 Disk Diffusion Test......Page 747
5.2 Broth Microdilution MIC Test......Page 762
5.3 Beta-Lactamase Tests......Page 779
5.4 Oxacillin Salt-Agar Screen Test To Detect Oxacillin (Methicillin)-Resistant Staphylococcus aureus......Page 785
5.5 Screen Tests To Detect High-Level Aminoglycoside Resistance in Enterococcus spp.......Page 789
5.6 Agar Screen Test To Detect Vancomycin Resistance in Enterococcus spp.......Page 794
5.7 Broth Microdilution MIC Test for Anaerobic Bacteria......Page 798
5.8 Etest......Page 806
5.9 Agar Dilution MIC Test for Anaerobic Bacteria......Page 814
5.10.1 Minimum Bactericidal Concentration Testing......Page 826
5.10.2 Time-Kill Assay......Page 843
5.10.3 Time-Kill Assay for Determining Synergy......Page 855
5.11 Serum Inhibitory and Bactericidal Titers......Page 861
5.12 Synergism Testing: Broth Microdilution Checkerboard and Broth Macrodilution Methods......Page 877
5.13 Quality Assurance Measures for Antimicrobial Susceptibility Testing......Page 900
5.14.1 McFarland Standards......Page 918
5.14.2 Antimicrobial Stock Solutions......Page 922
5.14.3 Preparation of Agar and Broth Media Used in Routine Antimicrobial Susceptibility Tests......Page 929
5.15 Preparation of Broth Microdilution MIC Trays......Page 939
5.16 Selecting Antimicrobial Agents for Testing and Reporting......Page 957
5.17 Evaluating Antimicrobial Susceptibility Test Systems......Page 966
5.18.1 Sources of Supplies for  Antimicrobial Susceptibility Tests......Page 977
5.18.2 General References for Antimicrobial Susceptibility Testing......Page 979
SECTION 6 - Aerobic Actinomycetes......Page 980
6.1 Specimen Examination and Primary Isolation......Page 981
6.2 Media and Methods Used for the Identification of Aerobic Actinomycetes......Page 989
6.3.1 Clinical Diseases in Humans Associated with Aerobic Actinomycetes......Page 1000
6.3.2 Suppliers......Page 1001
6.3.3 Medium Composition and Preparation......Page 1003
6.3.4 Cell Wall Determination of Diaminopimelic Acid Isomers......Page 1007
SECTION 7 - Mycobacteriology and Antimycobacterial Susceptibility Testing......Page 1010
7.1.1 Safety and Levels of Laboratory Service......Page 1012
7.1.2 Digestion-Decontamination Procedures......Page 1014
7.1.3 Reporting......Page 1023
7.2 Acid-Fast Stains......Page 1025
7.3 Solid Media for Isolation......Page 1029
7.4.1 BACTEC 460TB Radiometric System......Page 1033
7.4.2 BACTEC MGIT 960 Automated System......Page 1040
7.4.3 VersaTREK (ESP Culture System II)......Page 1044
7.4.4 MB/BacT Mycobacterial Detection......Page 1051
7.4.5 Wampole ISOLATOR Tube......Page 1055
7.5 Septi-Chek AFB Biphasic Medium......Page 1058
7.6.1 Conventional Biochemicals......Page 1061
7.6.2 Gen-Probe AccuProbe Mycobacterial Culture Identification Test......Page 1073
7.6.3 BACTEC NAP Test......Page 1076
7.7 Susceptibility Tests by Modified Agar Proportion......Page 1079
7.8.1 BACTEC 460TB (Radiometric)System Indirect Susceptibility Testing for Mycobacterium tuberculosis......Page 1083
7.8.2 BACTEC 460TB System Indirect Susceptibility Tests with Pyrazinamide for Mycobacterium tuberculosis......Page 1090
7.8.3 BACTEC 460TB System Indirect Susceptibility Tests for Slow-Growing Mycobacteria other than Mycobacterium tuberculosis......Page 1093
7.8.4 BACTEC 460TB System Direct Susceptibility Test for Mycobacterium tuberculosis......Page 1096
7.8.5 BACTEC MGIT 960 SIRE Nonradiometric Susceptibility Testing for Mycobacterium tuberculosis......Page 1098
7.8.6 BACTEC MGIT 960 PZA Susceptibility Testing for Mycobacterium tuberculosis......Page 1103
7.8.7 VersaTREK (Formerly ESP Culture System II) Indirect Susceptibility Testing for Mycobacterium tuberculosis......Page 1107
7.8.8 VersaTREK (Formerly ESP Culture System II) Indirect Susceptibility Tests with Pyrazinamide for Mycobacterium tuberculosis......Page 1111
SECTION 8 - Mycology and Antifungal Susceptibility Testing......Page 1114
8.1 Introduction and General Considerations......Page 1115
8.2 Specimen Selection, Collection, and Transport......Page 1117
8.3 Specimen Examination......Page 1122
8.4 Processing Specimens for Fungal Culture......Page 1131
8.5 Examination and Evaluation of Primary Cultures......Page 1137
8.6 Presumptive Identification Tests for Yeasts Isolated on Primary Culture......Page 1147
8.7 Identification of Moulds on Primary Culture......Page 1157
8.8 Full Identification of Yeasts......Page 1163
8.9 Mould Identification......Page 1176
8.10 Antifungal Susceptibility Testing......Page 1235
SECTION 9 - Parasitology......Page 1242
9.1 Introduction......Page 1245
9.2.1 Collection of Fresh Specimens......Page 1255
9.2.2 Preservation of Specimens......Page 1259
9.2.3 Shipment of Specimens......Page 1266
9.3.1 Macroscopic Examination of Fecal Specimens: Age and Physical Description......Page 1268
9.3.2 Calibration of Microscope with an Ocular Micrometer......Page 1271
9.3.3 Microscopic Examination of Fecal Specimens: Direct Smears......Page 1274
9.3.4 Microscopic Examination of Fecal Specimens: Concentration by Formalin-Ethyl Acetate Sedimentation......Page 1278
9.3.5 Microscopic Examination of Fecal Specimens: Concentration by Zinc Sulfate Flotation......Page 1283
9.3.6 Microscopic Examination of Fecal Specimens: Permanent Stained Smear (Trichrome)......Page 1287
9.3.7 Microscopic Examination of Fecal Specimens: Iron Hematoxylin Stain (Modified Spencer-Monroe Method)......Page 1293
9.3.8 Calcofluor White for Detection of Microsporidial Spores and Acanthamoeba Cysts......Page 1300
9.4.1 Special Stains for Coccidia, Including Cyclospora cayetanensis: Modified Kinyoun’s Acid-Fast Stain (Cold)......Page 1305
9.4.2 Special Stains for Coccidia, Including Cyclospora cayetanensis: Modified Ziehl-Neelsen Acid-Fast Stain (Hot)......Page 1309
9.4.3 Special Stains for Microsporidia: Weber Green......Page 1313
9.4.4 Special Stains for Microsporidia: Ryan Blue......Page 1317
9.4.5 Special Stains for Microsporidia: Acid-Fast Trichrome Stain for Cryptosporidium and the Microsporidia......Page 1322
9.5.1 “Culture” of Larval-Stage Nematodes: Baermann Technique......Page 1327
9.5.2 “Culture” of Larval-Stage Nematodes: Harada-Mori Technique......Page 1331
9.5.3 “Culture” of Larval-Stage Nematodes: Petri Dish-Filter Paper Slant......Page 1334
9.5.4 “Culture” of Larval-Stage Nematodes: Agar Plate Culture for Strongyloides stercoralis......Page 1337
9.5.5 Determination of Egg Viability: Schistosomal Egg Hatching......Page 1341
9.5.6 Recovery of Scolices and Proglottids of Cestodes......Page 1344
9.6.1 Examination for Pinworm: Cellulose Tape Preparation......Page 1347
9.6.2 Sigmoidoscopy Specimen: Direct Wet Smear......Page 1350
9.6.3 Sigmoidoscopy Specimen: Permanent Stained Smear......Page 1354
9.6.4 Duodenal Contents: String Test (Entero-Test Capsule)......Page 1357
9.6.5 Duodenal Contents: Duodenal Aspirate......Page 1361
9.6.6 Urogenital Specimens: Direct Saline Mount......Page 1365
9.6.7 Urogenital Specimens: Permanent Stained Smear (Giemsa)......Page 1369
9.6.8 Urine Concentration: Centrifugation......Page 1373
9.6.9 Urine Concentration: Membrane Filter (Nuclepore)......Page 1377
9.7.1 Expectorated Sputum: Direct-Mount and Stained Preparations......Page 1381
9.7.2 Induced Sputum: Stained Preparations for Detection of Pneumocystis carinii......Page 1385
9.7.3 Aspirates and Bronchoscopy Specimens......Page 1393
9.7.4 Biopsy Specimens......Page 1399
9.8.1 Detection of Blood Parasites......Page 1406
9.8.2 Preparation of Thin Blood Films......Page 1409
9.8.3 Preparation of Thick Blood Films......Page 1411
9.8.4 Combination Thick and Thin Blood Films (Can Be Stained as Either)......Page 1414
9.8.5 Giemsa Stain......Page 1417
9.8.6 Wright’s Stain......Page 1422
9.8.7 Determination of Parasitemia......Page 1426
9.8.8 Delafield’s Hematoxylin Stain......Page 1430
9.8.9 Concentration Procedures: Buffy Coat Concentration......Page 1434
9.8.10 Concentration Procedures: Membrane Filtration Concentration......Page 1437
9.8.11 Concentration Procedures: Knott Concentration......Page 1440
9.8.12 Concentration Procedures: Triple Centrifugation Concentration......Page 1443
9.9.1 Parasite Culture: Entamoeba histolytica......Page 1445
9.9.2 Parasite Culture: Acanthamoeba and Naegleria spp.......Page 1453
9.9.3 Parasite Culture: Trichomonas vaginalis......Page 1461
9.9.4 Parasite Culture: In Pouch TV System for Trichomonas vaginalis......Page 1467
9.9.5 Parasite Culture: Leishmania spp. and Trypanosoma cruzi......Page 1471
9.10.1 Identification Aids: Artifacts......Page 1477
9.10.2 Information Tables......Page 1481
9.10.3 Common Problems in Organism Identification......Page 1500
9.10.4 Quality Control Recording Sheets......Page 1507
9.10.5 Flowcharts for Diagnostic Procedures......Page 1512
9.10.6 Commercial Supplies and Suppliers......Page 1515
9.10.7 Appendix 9.10.7-1 Current OSHA Regulations on the Use of Formaldehyde......Page 1529
9.10.8 CPT Codes (Parasitology)......Page 1530
VOLUME 3......Page 1533
SECTION 10 - Viruses and Chlamydiae......Page 1539
10.1 Laboratory Diagnosis of Viral Infections: Introduction......Page 1540
10.2 Selection, Maintenance, and Observation of Uninoculated Monolayer Cell Cultures......Page 1550
10.3 Cell Culture Techniques: Serial Propagation and Maintenance of Monolayer Cell Cultures......Page 1561
10.4 Specimen Collection and Processing......Page 1570
10.5 Viral Culture: Isolation of Viruses in Cell Cultures......Page 1581
10.6 Isolation of Chlamydia spp. in Cell Culture......Page 1622
10.7 Direct Detection of Viruses and Chlamydia in Clinical Samples......Page 1634
SECTION 11 - Immunology......Page 1644
11.1.1 Introduction......Page 1646
11.1.2 Immunologic Assays Used in the Serologic Diagnosis of Infectious Diseases......Page 1647
11.1.3 Emerging Immunological Assays......Page 1663
11.2.1 Introduction......Page 1667
11.2.2 Anti-Streptolysin O......Page 1669
11.2.3 Anti-DNase B Test......Page 1673
11.3 Detection of Legionella Antigen by Direct Immunofluorescence......Page 1676
11.4 Urinary Antigen Detection for Legionella spp.......Page 1683
11.5.1 Introduction......Page 1689
11.5.2 Direct Fluorescent-Antibody Test for Treponema pallidum......Page 1693
11.5.3 Rapid Plasma Reagin Test......Page 1695
11.5.4 Serodia Treponema pallidum Particle Agglutination Test......Page 1699
11.6 Detection of Borrelia burgdorferi Antibodies......Page 1702
11.7.1 Introduction......Page 1712
11.7.2 Indirect Fluorescent-Antibody Test......Page 1714
11.7.3 Solid-Phase (Dot Blot) EIA......Page 1721
11.7.4 Latex Agglutination......Page 1724
11.8 Immunoassay Detection of Shiga Toxin-Producing Escherichia coli......Page 1727
11.9 Serodiagnosis of Helicobacter pylori......Page 1735
11.10 Total Viable Cell Counting Procedure......Page 1740
11.11 Peripheral Blood Mononuclear Cell Cryopreservation Method......Page 1742
11.12 Lymphocyte Proliferation Assay......Page 1744
11.13 Natural Killer Cell Assay......Page 1749
11.14 Quantitation of Human Interleukin 4, Interleukin 6, and Gamma Interferon......Page 1755
11.15 Flow Cytometry Whole-Blood Intracellular-Cytokine Assay Using Phorbol Myristate Acetate, Ionomycin, and Brefeldin A......Page 1761
11.16 Whole-Blood Lymphocyte Immunophenotyping Using Cell Surface Markers by Flow Cytometry......Page 1765
11.17 Neutrophil Function Whole-Blood Flow Cytometric Test for Leukocyte Adhesion Deficiency......Page 1773
11.18 Flow Cytometric Test for Chronic Granulomatous Disease......Page 1777
SECTION 12 - Molecular Biology......Page 1781
12.1 Introduction......Page 1783
12.2.1 Introduction......Page 1788
Part 1 - Gen-Probe PACE 2 Nucleic Acid Hybridization Test for Detecting Chlamydia trachomatis and Neisseria gonorrhoeae......Page 1789
Part 2 - Solution Hybridization Antibody Capture Assay for the Chemiluminescent Detection and Quantitation of Human Cytomegalovirus DNA in WBCs......Page 1794
Part 3 - Solution Hybridization Antibody Capture Chemiluminescent Assay for the Detection of Human Papillomavirus Types in Cervical Specimens......Page 1799
Part 1 - Detection of Chlamydia trachomatis in Genitourinary Specimens by Using the Roche Amplicor PCR Kit......Page 1804
Part 2 - Detection of Mycobacterium tuberculosis in Respiratory Specimens by Using the Roche Amplicor PCR Kit......Page 1810
Part 3 - Detection of Mycobacterium tuberculosis in Respiratory Specimens by Using the Gen-Probe Amplified Mycobacterium tuberculosis Direct Test......Page 1816
Part 4 - Detection of Mycobacterium tuberculosis Complex in Respiratory Specimens by Using the BD ProbeTecET Direct Detection Assay......Page 1822
Part 5 - Quantitative Measurement of Human Immunodeficiency Virus Type 1 RNA by Using the Roche Amplicor PCR Kit......Page 1826
Part 6 - Quantitative Measurement of Human Immunodeficiency Virus Type 1 RNA by Using the Roche Amplicor Ultrasensitive PCR Kit......Page 1833
Part 7 - Qualitative Detection of Hepatitis C Virus RNA by Using the Roche Amplicor Reverse Transcriptase PCR Kit......Page 1841
Part 8 - Quantitative Measurement of Hepatitis C Virus RNA by Using the Roche Amplicor HCV Monitor Reverse Transcriptase PCR Kit......Page 1847
Part 9 - Detection of Herpes Simplex Virus in CSF by PCR......Page 1854
Part 10 - Detection of Mycoplasma pneumoniae in Respiratory Specimens by PCR......Page 1865
Part 11 - Detection of Bordetella pertussis by PCR......Page 1877
12.3.1 Introduction......Page 1885
12.3.2 Identification of Bacteria and Fungi by Using Nucleic Acid Probes......Page 1886
12.3.3 DNA Probes for the Identification of Mycobacteria......Page 1890
12.4.1 Introduction......Page 1894
12.4.2 Plasmid Fingerprinting of Gram-Negative Organisms......Page 1895
12.4.3 Plasmid Fingerprinting of Staphylococci......Page 1899
12.4.4 Method for Ribotyping by Using a Chemiluminescent Probe......Page 1904
12.4.5 Chromosomal Restriction Fragment Analysis by Pulsed-Field Gel Electrophoresis: Application to Molecular Epidemiology......Page 1909
12.4.6 Characterization of Pathogenic Microorganisms by Genomic Fingerprinting with Arbitrarily Primed PCR......Page 1916
12.4.7 Genotyping of Hepatitis C Virus by INNO-LiPA HCV II......Page 1919
12.5.1 Introduction......Page 1924
12.5.2 Detection of Enterococcal Vancomycin Resistance by Multiplex PCR......Page 1925
12.5.3 Detection of Methicillin Resistance in Staphylococci by PCR......Page 1929
12.6-1 Companies Which Supply Reagents for PCR for Bordetella pertussis and Mycoplasma pneumoniae......Page 1932
SECTION 13 - Epidemiologic and Infection Control Microbiology......Page 1933
13.1 Introduction......Page 1935
13.2 Laboratory Support for Infection Control: Optimization by Policy and Procedure......Page 1936
13.3 Policies for Environmental Sampling and Culturing for Infection Control......Page 1940
13.5 Epidemiologic Strain Typing......Page 1943
13.6 Culture of Hospital Water for Legionellaceae......Page 1948
13.7 Culture and Endotoxin Assay of Hemodialysis Fluids......Page 1962
13.8 Culture of Peritoneal Dialysis Fluid......Page 1968
13.9 Air Cultures for Fungi......Page 1975
13.10 Microbiological Assay of Environmental and Medical-Device Surfaces......Page 1982
13.11 Surveillance Cultures from Immunocompromised Hosts......Page 1994
13.12 Culture of Intravascular Devices......Page 1998
13.13 Culture of Blood Bank Products......Page 2004
13.14 Microbiological Assessment of Orthopedic Surgery Sites......Page 2008
13.15 Quantitative Culture of Small-Bowel Contents......Page 2014
13.16.1 Introduction......Page 2018
13.16.2 Dienes Typing for Proteus spp.......Page 2019
13.16.3 Slime Test for Staphylococci......Page 2021
13.16.4 Synergistic Hemolysis......Page 2023
13.16.5 Appendix to Procedure 13.16......Page 2025
13.17 Prospective, Focused Surveillance for Oxacillin-Resistant Staphylococcus aureus and Vancomycin-Resistant Enterococci......Page 2026
SECTION 14 - Quality Assurance, Quality Control, Laboratory Records, and Water Quality......Page 2029
14.1 Quality Assessment and Improvement (Quality Assurance)......Page 2030
14.2 Quality Control......Page 2059
14.3 Laboratory Records......Page 2093
14.4 Preparation and Quality Control of Laboratory Water......Page 2112
SECTION 15 - Biohazards and Safety......Page 2122
15.1 Introduction......Page 2123
15.2.1 Routes of Infection and Laboratory Activities......Page 2124
15.2.2 Safe Work Practices......Page 2126
15.2.3 Decontamination......Page 2129
15.2.4 Biohazardous Spills......Page 2134
15.3.1 Introduction......Page 2137
15.3.2 Risk Assessment......Page 2138
15.3.3 Biosafety Levels......Page 2141
15.3.4 Biological Safety Cabinet......Page 2143
15.3.5 PPE and Engineering Controls......Page 2147
15.4.1 Introduction......Page 2149
15.4.2 Autoclave......Page 2150
15.4.3 Centrifuge......Page 2153
15.4.4 Gas Cylinders......Page 2157
15.4.5 Pneumatic Tube System......Page 2160
15.4.6 Specimen/Microorganism Storage and Retention......Page 2162
15.4.7 Other Equipment and Devices......Page 2164
15.5 Packaging and Shipping Infectious Substances......Page 2165
15.6 Management of Laboratory Accidents......Page 2171
15.7 Management of Infectious Waste......Page 2178
SECTION 16 Bioterrorism......Page 2185
16.1 General Introduction to Bioterrorism......Page 2186
16.2 Levels of Laboratory Safety......Page 2192
16.3 Packaging, Labeling, and Shipment of Infectious Specimens......Page 2198
16.4 Anthrax-Bacillus anthracis......Page 2202
16.5 Botulinum Toxin-Clostridium botulinum......Page 2210
16.6 Brucellosis-Brucella spp.......Page 2213
16.7 Plague-Yersinia pestis......Page 2218
16.8 Tularemia-Francisella tularensis......Page 2223
16.9 Smallpox-Variola Major......Page 2226
Index......Page 2231