Medical bacteriology : a practical approach / edited by Peter Hawkey and Deirdre Lewis.

Format:

Book

Contributor:

Hawkey, P. M. (Peter M.)

Lewis, D. A. (Deirdre A.)

Series:

Practical approach series ; no. 265.

Practical approach series ; no. 265

Language:

English

Subjects (All):

Diagnostic bacteriology--Laboratory manuals.

Diagnostic bacteriology.

Medical bacteriology.

Bacteriology.

Medical Subjects:

Bacteriology.

Genre:

Laboratory manuals.

Physical Description:

xxvi, 409 pages : illustrations ; 26 cm.

Edition:

Second edition.

Place of Publication:

Oxford ; New York : Oxford University Press, 2004.

Summary:

The first edition of this book, published in 1995, established itself as the most popular practical guide to frequently used procedures in clinical microbiology laboratories. Because that book and this new edition describe methods in the order in which they would be encountered in the laboratory it is the perfect bench companion, both for the novice in clinical microbiology, and the experienced microbiologist who needs to confirm a detail. This new edition, extensively up-dated, encapsulates the practical experience of a group of expert clinical microbiologists and scientists imparting valuable tips and solutions to both the methodology and interpretation of clinical microbiology results. The book represents a state-of-the-art training aid for the diagnostic microbiology laboratory, and will prove to be an invaluable aid to microbiologists preparing for higher professional examinations such as membership of the Royal College of Pathologists and the American Board of Medical Microbiology.

Contents:

1 Bacteriology of urine / Eleri M. Davies, Deirdre A. Lewis 1

2 Specimen collection and transport 1

3 Microscopy and other rapid screening methods 5

3.1 Reagent strips/dipsticks 5

3.2 Microscopy 6

3.3 Automated screening methods for urine 8

4 Interpretation of findings on microscopy 9

4.1 Leukocytes 9

4.2 Red cells 10

4.3 Epithelial cells 10

4.4 Bacteria 10

4.5 Casts and crystals 10

5 Culture 11

5.1 Choice of media 11

5.2 Culture methods 12

5.3 Localization of site of infection 13

5.4 Culture of urine for Mycobacterium tuberculosis 15

6 Interpretation of culture results 16

6.1 The concept of significant bacteriuria 16

6.2 Interpretation and reporting of specimens from patients with indwelling catheters and ileal conduits 17

6.3 Interpretation and reporting of suprapubic aspirate and ureteric catheter specimens 18

6.4 Asymptomatic bacteriuria of pregnancy 19

7 Identification of bacteria 19

7.1 Yeasts 19

7.2 Identification of difficult or 'fastidious' organisms 19

8 Sensitivity testing 21

8.1 Choice of first-line and second-line agents for sensitivity testing 21

8.2 Primary sensitivity testing 23

8.3 Reporting of sensitivities 23

9 Further tests 24

9.1 Detection of antimicrobial substances in urine (51) 24

2 Bacteriology of normally sterile body fluids / Olive Murphy, Roger Freeman 27

2 Methods for the examination of blood 27

2.1 Principles of blood culture 27

2.2 Principles of blood culture methods 30

2.3 Blood culture methods 35

2.4 Blood culture diagnosis of catheter-related sepsis 38

2.5 Alternative methods to broth cultures 39

3 Methods for the examination of cerebrospinal fluid 40

3.2 Bacteriological aspects of specimen collection 40

3.3 Microscopy 41

3.4 Culture 43

3.5 Additional tests 44

3.6 Interpretation of results 45

3.7 Tuberculous meningitis (TBM) 46

4 Methods for the examination of peritoneal dialysis effluents 47

4.1 Definition of CAPD peritonitis 47

4.2 Sampling PDE 47

4.3 Interpretation of culture results 49

4.4 Identification and sensitivity testing 49

4.5 Culture negative peritonitis 49

5 Methods for the examination of serous fluids 50

5.1 Examination of non-purulent serous fluids 50

3 Bacteriology of the respiratory tract / Steve O'Hara J. Andrew Lowes, Grace Smith 55

2 Upper respiratory tract 55

2.1 The nose 55

2.2 The nasopharynx 57

2.3 The throat 59

2.4 The ear 63

2.5 The maxillary sinuses 64

3 Lower respiratory tract (LRT) 65

3.1 Specimen collection 65

3.2 Routine microscopy and culture 66

3.3 Special microscopy and culture 73

3.4 Non-cultural methods of diagnosis 83

4 Bacteriology of the genital tract / Catherine A. Ison, Alun J. Davies, Peter M. Hawkey 93

1.1 Normal vaginal flora 93

1.2 Changes in normal vaginal flora 94

1.3 Pathogens associated with specific clinical conditions 96

2 Collection and transport of specimens 96

3 Assessment of specimens in the laboratory 98

3.1 Microscopy 98

3.2 Detection of antigen in specimens by enzyme immunoassay 100

4 Culture 101

4.1 Selective medium for the isolation of N. gonorrhoeae 101

4.2 Blood agar and blood agar with neomycin 108

4.3 MacConkey's agar 108

4.4 Chlamydia transport medium 109

5 Serological methods 109

5.1 Serological diagnosis of syphilis 109

5.2 Serological diagnosis of chlamydial infections 116

6 Molecular methods 116

6.1 Chlamydial trachomatis 116

6.2 Neisseria gonorrhoeae 117

6.3 Treponema pallidum 117

7 Antibiotic susceptibility testing 117

7.1 Antibiotic susceptibility testing of N. gonorrhoeae 117

7.2 Antibiotic sensitivity testing of other pathogens 118

5 Bacteriology of superficial and deep tissue infection / Nicola Baker, Ann Bushell, Peter M. Hawkey 121

1.1 Taking good samples 121

1.2 Transport 122

2 General methods 123

2.1 Pus 123

2.2 Swabs 125

2.3 Fluids 126

2.4 Tissue 126

3 Anaerobic methods 127

3.1 Gas-liquid chromatography (GLC) 127

3.2 Culture of anaerobes 129

3.3 Identification of anaerobes 132

3.4 Anaerobic sensitivity testing 141

4 Skin and soft tissue infections 141

4.1 Pyoderma and cellulitis 141

4.2 Wound infections 150

4.3 Gangrene, myositis, and fasciitis 152

4.4 Burns, varicose ulcers, ischaemic ulcers, pressure sores 153

4.5 Sinuses 153

4.6 Fistulae 154

4.7 Vesicles and bullae 154

4.8 Suppurative lymphadenitis 155

4.9 Chronic ulcers 156

5 Infection associated with the gastrointestinal tract 157

5.1 Intra-abdominal abscess 157

5.2 Peritonitis 158

5.3 Wound infections 160

5.4 Biliary infections 160

5.5 Liver abscesses 162

5.6 Abscesses 162

6 Gynaecological and post-partum infections 163

6.1 Post-operative infections 163

6.2 Tubo-ovarian sepsis 164

6.3 Infection associated with intrauterine contraceptive devices (IUCDs) 164

6.4 Post-partum infections 166

7 Infections of the skeletal system 167

7.1 Acute osteomyelitis 167

7.2 Chronic osteomyelitis 168

8 Joint infections 169

8.1 Prosthetic joint infections 169

9 CNS infections 170

9.1 Cerebral abscess 170

10 Eye infections 171

10.1 Acute conjunctivitis 171

10.2 Endophthalmitis 172

10.3 Periocular infections 173

6 Bacteriology of intestinal disease / Stephen Pedler, Clive Graham 177

2 Bacterial enteric pathogens 178

3 Culture media 178

3.1 Media for the isolation of salmonellae and shigellae 178

3.2 Screening identification media for salmonellae and shigellae 182

3.3 Media for the isolation of Escherichia coli 0157, Yersinia enterocolitica, and other commonly encountered gastrointestinal pathogens 184

4 Routine specimen processing 184

4.1 Specimen collection 187

4.2 Microscopy 187

4.3 Culture 188

4.4 Reading the plates 188

4.5 Serotyping of salmonellae and shigellae 191

4.6 Biochemical identification 201

4.7 Sensitivity testing of salmonellae and shigellae 202

4.8 Reporting to the clinician 202

5 Specimen processing for organisms other than salmonellae, shigellae, and campylobacters 203

5.1 Escherichia coli 203

5.2 Yersinia enterocolitica 205

5.3 Vibrio cholerae and V. parahaemolyticus 206

5.4 Clostridium difficile 207

5.5 'Food poisoning' due to Clostridium perfringens, Staphylococcus aureus, and Bacillus cereus 208

5.6 Helicobacter pylori 211

7 Antimicrobial susceptibility testing / Derek F. J. Brown, Jenny Andrews, Trevor Winstanley, Alasdair P. MacGowan 215

2 Disc diffusion methods for antimicrobial susceptibility testing 216

2.1 Factors affecting diffusion tests 217

2.2 Methods of disc diffusion susceptibility testing 220

2.3 Selection of agents for routine testing 234

2.4 Specific problems in testing 235

2.5 Quality assurance 239

2.6 Primary susceptibility tests 240

3 Methods for determining minimum inhibitory concentrations 241

3.1 Agar dilution 241

3.2 Broth dilution methods 247

3.3 Etest 256

4 Breakpoint methods 256

5 Serum bactericidal tests and determination of minimum bactericidal concentrations 258

6 Automated methods 259

7 Expert systems 260

8 Clinical relevance and epidemiological outputs 263

8 Antimicrobial assays / David S. Reeves, Les O. White 267

2 Clinical application of antimicrobial assays 268

2.1 General considerations 268

2.2 Indications for monitoring 270

3 Taking specimens for assays 271

4 Methods of assay 273

4.1 Characteristics of assay methods: microbiological vs.

non-microbiological 273

5 Microbiological assays 276

6 Immunoassays 276

6.2 Reagent constitution and storage 278

6.3 Calibration 278

6.4 Internal control 279

6.5 Fluorescence polarization immunoassay (FPIA) 279

7 High performance liquid chromatography (HPLC) 282

7.1 General principles and terms 282

7.2 Characteristics 283

7.3 Principles of separation

reverse phase 283

7.4 Equipment 284

7.5 Sample preparation 285

7.6 Calibration 286

7.7 Methods for individual antimicrobials 287

8 Quality assurance 289

8.1 Internal controls 289

8.2 External quality assessment (EQA) 289

9 Clinical interpretation 290

9 Laboratory computing in medical microbiology / Andrew M. Lovering 295

2 Laboratory computers in microbiology 295

2.1 Stand-alone systems (Laboratory Information Management Systems

LIMS) 295

2.2 Systems integrated with other hospital systems (Hospital Information Systems

HIS) 296

2.3 Feeder systems to electronic patient records (Integrated Laboratory Information Management Systems

ILIMS) 296

3 Core elements of a microbiology computer system 297

3.1 Requesting 297

3.2 Result entry 299

3.3 Validation, system actions, and authorization 301

3.4 Returning results to requesters 302

4 Secondary functions 304

4.1 Access, security, and audit 304

4.2 Laboratory management functions 305

4.3 Data extraction 305

5 System maintenance and development 306

6 Procurement of a new system 306

10 Quality control and quality assurance / W. A. Hyde, P. K. Curley 309

2 Personnel 310

2.1 Recruitment policies and staffing structures 310

2.2 Training and organization 310

2.3 Standard operating procedures 311

2.4 Logistics and organization 312

2.5 Specimen collection and transport 313

2.6 Specimen handling and report validation 313

3 Culture media quality issues 314

3.1 Storage conditions 314

3.2 Preparation of culture media 315

3.3 User problems 318

4 Maintenance and storage of control organisms 321

4.1 Long-term storage 321

4.2 Short-term storage for ready access 322

5 Equipment monitoring 322

5.1 Temperature control 322

5.2 Control of anaerobic cabinets 323

5.3 pH meter electrodes 323

5.4 Autoclaves and preparators 324

5.5 Pipettes 325

6 Quality control of laboratory tests and reagents 325

6.1 Chemicals and dyes 325

6.2 Staining techniques 325

6.3 Kits and identification systems 325

6.4 United Kingdom National External Quality Assessment Scheme (UKNEQAS) 326

6.5 Internal quality control 326

7 Near patient testing 327

8 Audit and error logging 327

11 Laboratory investigation of health care-associated infection / Peter M. Hawkey, Kevin G. Kerr 331

1.1 Administration 332

2 Sample collection 333

2.1 Surveillance 333

2.2 Sampling protocols 334

3 Specimen processing 341

3.1 Criteria for organism identification 341

3.2 Use of selective and differential media 341

4 Bacterial typing systems 342

4.1 Principles and use of bacterial typing systems 342

4.2 Biotyping 343

4.3 Antibiogram and resistogram typing 344

4.4 Serotyping 344

4.5 Bacteriophage typing 345

4.6 Bacteriocin typing 345

4.7 Molecular typing methods 346

12 Epidemiological methods in the investigation of acute bacterial infections / Stephen R. Palmer 355

2 Basic concepts in infectious disease epidemiology 355

2.1 Reservoir of infection 355

2.2 Source of infection 356

2.3 Mode of transmission 356

2.4 Occurrence 356

2.5 Incubation period 357

2.6 Host response 357

2.7 Analysis and presentation of data 357

2.8 Communicability 359

3 Epidemiological methods 359

3.1 Descriptive methods 359

4 Analytical methods 361

4.1 Case-control studies 362

4.2 Cohort studies 366

4.3 Statistical analysis of case-control and cohort studies 367

5 A practical approach to the investigation of an acute incident 369

5.1 Identification and confirmation of the problem 369

I Staining procedures 373

1 Gram's stain (Preston and Morrell's modification) 373

1.1 Solutions required 373

1.2 Staining procedure 373

2 Giemsa stain 374

2.1 Solutions required 374

2.2 Staining procedure 374

3 Stains for acid-fast bacilli 375

3.1 Auramine phenol 375

3.2 Ziehl-Neelsen 375

3.3 Kinyoun's acid-fast stain 376

4 Stains for metachromatic (volutin) granules 377

4.1 Loeffler's methylene blue 377

4.2 Albert's stain, modified 377

4.3 Neisser's stain 378

5 Spore stain (Schaeffer and Fulton's method) 378

5.1 Staining procedure 378

II Bacteriological media not usually commercially available 379

1 Transport media 379

1.1 Chlamydia transport medium 379

2 Selective/differential media 380

2.1 Deoxycholate citrate, crystal violet, cefazolin, rhamnose agar (DCCR) 380

2.2 Deoxyribonuclease, toluidine blue, cefalothin agar (DTBCA) 380

2.3 Leeds Acinetobacter medium (LAM) 381

2.4 MacConkey, inositol, carbenicillin agar (MICA) 381

2.5 Nalidixic acid, cetrimide agar 382

2.6 Phenanthroline, C-3911 agar 382

2.7 Proteeae identification medium 383

2.8 Salt, phenolphthalein, methicillin agar (SPMA) 383

2.9 Toluidine blue deoxynucleic acid agar (TDA) 384

2.10 Vancomycin imipenem agar (VIA) 384

III Principles of biochemical tests for the identification of bacteria 387

1.1 Catalase test 387

1.2 Citrate test 388

1.3 Decarboxylase and dehydrolase tests 388

1.4 Hippurate hydrolysis test 389

1.5 Hydrogen sulfide test 389

1.6 Indole test 390

1.7 Methyl red and Voges-Proskauer test 391

1.8 Nitrate reduction test 392

1.9 ONPG (o-nitrophenyl-[beta]-D-galactopyranoside) test 393

1.10 Oxidase test 393

1.11 Phenylalanine deaminase test 394

1.12 Urease test 395.

Notes:

Previous ed.: IRL Press at Oxford University Press, 1989.

Includes bibliographical references and index.

ISBN:

0199637792

0199637784

OCLC:

51964709