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Medical Microbiology 3rd Revised edition [Mīkstie vāki]

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(Formerly of the Microbiology Department, Freeman Hospital, Newcastle Upon Tyne)
  • Formāts: Paperback / softback, 568 pages, height x width x depth: 247x189x23 mm, weight: 1088 g
  • Sērija : Fundamentals of Biomedical Science
  • Izdošanas datums: 05-Jun-2019
  • Izdevniecība: Oxford University Press
  • ISBN-10: 0198818149
  • ISBN-13: 9780198818144
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Medical Microbiology 3rd Revised editionPalielināt
  • Formāts: Paperback / softback, 568 pages, height x width x depth: 247x189x23 mm, weight: 1088 g
  • Sērija : Fundamentals of Biomedical Science
  • Izdošanas datums: 05-Jun-2019
  • Izdevniecība: Oxford University Press
  • ISBN-10: 0198818149
  • ISBN-13: 9780198818144
Citas grāmatas par šo tēmu:
Permanent link: https://www.kriso.lv/db/9780198818144.html
Keywords:
Biomedical scientists are the foundation of modern healthcare, from cancer screening to diagnosing HIV, from blood transfusion for surgery to food poisoning and infection control. Without biomedical scientists, the diagnosis of disease, the evaluation of the effectiveness of treatment, and research into the causes and cures of disease would not be possible.

The Fundamentals of Biomedical Science series has been written to reflect the challenges of practicing biomedical science today. It draws together essential basic science with insights into laboratory practice to show how an understanding of the biology of disease is coupled to the analytical approaches that lead to diagnosis. Assuming only a minimum of prior knowledge, the series reviews the full range of disciplines to which a Biomedical Scientist may be exposed - from microbiology to cytopathology to transfusion science.

The series: · Understands the complex roles of Biomedical Scientists in the modern practice of medicine. · Understands the development needs of employers and the Profession. · Addresses the need for understanding of a range of fundamental sciences in the context of Biomedicine. · Places the theoretical aspects of Biomedical Science in their practical context via clinical case studies.

Medical Microbiology covers a range of key laboratory techniques used in the diagnosis of important human diseases caused by microorganisms. From sample collection, through to analysis and laboratory investigation, the text covers a wide range of procedures and highlights how and why results are generated. The third edition has been expanded to cover a wider range of topics, including a new chapter on Whole Genome Sequencing and extended coverage of syphilis and MALDI.

Recenzijas

This third edition is a valuable update and just like the previous editions, I believe it will also be a useful textbook for students of Biomedical Sciences. * Sudeshna Saha, University of California San Diego Health, USA, Microbiology Society * I am very pleased to see the new chapter on whole genome sequencing * Dr Lewis Bingle, University of Sunderland * [ The] best text book around for undergraduate Biomedical Sciences students * Dr Cheryl Walter, University of Hull * [ I] would certainly adopt the third [ edition]... I think the inclusion of chapter on whole genome sequencing is very welcome * Dr Christopher Ring, Middlesex University *

An introduction to the Fundamentals of Biomedical Science series xv
Contributors xx
Abbreviations xxi
1 Introduction to microbiology
1(11)
Michael Ford
1.1 Classification
2(1)
1.1.1 Prokaryotes and eukaryotes
2(1)
1.2 The bacterial cell
2(2)
1.2.1 Flagella
3(1)
1.2.2 Fimbriae/pili
4(1)
1.2.3 Sex pili
4(1)
1.3 Bacterial growth
4(2)
1.4 Sterilization and disinfection
6(2)
1.4.1 Sterilization
6(1)
1.4.1.1 Heat
6(1)
1.4.1.2 Filtration
7(1)
1.4.1.3 Irradiation
7(1)
1.4.2 Disinfection
7(1)
1.4.2.1 Alcohols
8(1)
1.4.2.2 Halogen disinfectants
8(1)
1.4.2.3 Aldehydes
8(1)
1.5 Bacterial colony recognition
8(4)
Chapter summary
10(1)
Further reading
10(1)
Discussion questions
11(1)
2 Culture media
12(19)
John Perry
2.1 Microbial requirements for growth
12(1)
2.2 Ingredients of culture media
13(3)
2.2.1 Water
13(1)
2.2.2 Protein derivatives
13(1)
2.2.3 Yeast extract
14(1)
2.2.4 Gelling agents
14(1)
2.2.5 Buffers
14(1)
2.2.6 Blood and serum
15(1)
2.2.7 Charcoal
15(1)
2.2.8 Other additives for fastidious bacteria and anaerobes
15(1)
2.3 Selective media
16(1)
2.4 Differential media
17(2)
2.5 Enrichment media
19(1)
2.6 Chromogenic media
19(5)
2.6.1 Detection of Salmonella and E. coli O757 using chromogenic media
20(1)
2.6.2 Detection of S. aureus (including MRSA) using chromogenic media
21(1)
2.6.3 Chromogenic media for urinary tract pathogens
21(2)
2.6.4 Chromogenic media for detection and differentiation of yeasts
23(1)
2.7 Media for antimicrobial susceptibility testing
24(1)
2.8 Preparation and sterilization of culture media
25(2)
2.8.1 Sterilization
26(1)
2.8.2 Dispensing media
26(1)
2.9 Quality control
27(4)
2.9.1 Sterility testing
27(1)
2.9.2 Choice of bacterial strains
27(1)
2.9.3 Inoculum
28(1)
2.9.4 Batch failure
28(1)
Chapter summary
29(1)
Further reading
29(1)
Discussion questions
30(1)
3 Identification tests
31(23)
John Perry
3.1 Biochemical tests
32(8)
3.1.1 Catalasetest
32(1)
3.1.2 Oxidase test
32(1)
3.1.3 Detection of bacterial hydrolases--glycosidases
33(2)
3.1.4 Peptidases
35(1)
3.1.5 Esterases
36(1)
3.1.6 Phosphatases
36(1)
3.1.7 Deoxyribonuclease (DNase)
37(1)
3.1.8 Hydrolysis of gelatine
37(1)
3.7.9 Amino acid metabolism
38(1)
3.1.10 Carbohydrate oxidation/fermentation
39(1)
3.2 Miscellaneous biochemical tests
40(2)
3.2.1 Urease
40(1)
3.2.2 Hydrogen sulphide production
40(1)
3.2.3 Reduction of nitrate
40(1)
3.2.4 Coagulase
41(1)
3.2.5 Lecithinase (phosphatase C)
42(1)
3.3 Carbon source utilization tests
42(1)
3.4 Susceptibility to antibiotics and chemical inhibitors
43(1)
3.5 Tolerance to environmental conditions
44(1)
3.6 Requirement for growth factors
44(1)
3.7 Identification schemes
45(1)
3.8 Commercial kits
46(1)
3.9 Automated biochemical identification systems
47(1)
3.10 MALDI-TOF
48(2)
3.11 Immunological tests
50(1)
3.12 Pitfalls and quality issues with biochemical identification tests
51(3)
Chapter summary
52(1)
Further reading
53(1)
Discussion questions
53(1)
4 Susceptibility testing and antibiotic assay
54(27)
Jenny Andrews
4.1 Rationale for antimicrobial susceptibility testing
55(1)
4.2 Commonly used antibiotics
56(1)
4.3 Antimicrobial susceptibility testing
56(7)
4.3.1 Disc susceptibi/ity testing
56(1)
4.3.2 Disc susceptibility testing---inoculum required
56(1)
4.3.3 Depth of agar
57(1)
4.3.4 Application and storage of discs
57(1)
4.3.5 Incubation and atmospheric conditions
58(1)
4.3.6 What do zones of inhibition mean-what do they relate to?
58(2)
4.3.7 Interpretation of disc susceptibility tests
60(1)
4.3.8 Direct susceptibility testing
61(1)
4.3.9 Double disc/combination disc techniques
62(1)
4.3.10 Gradient method of susceptibility testing
62(1)
4.4 Broth methods
63(1)
4.5 Automated susceptibility testing
64(1)
4.6 Enzymatic methods of resistance β-lactamases)
65(2)
4.6.1 Class A β-lactamases
65(1)
4.6.2 Class B β-lactamases
66(1)
4.6.3 Class C β-lactamases
66(1)
4.6.4 Class D β-lactamases
66(1)
4.7 Detection of mechanisms of resistance and the application of expert rules
67(1)
4.7.1 Natural (inherent/intrinsic) resistance
68(1)
4.8 Additional tests
68(2)
4.8.1 Antibiotic combination and synergy testing
68(1)
4.8.2 Chequerboard titrations
69(1)
4.8.3 Time kill curves
69(1)
4.9 Control of antimicrobial susceptibility testing
70(1)
4.9.1 Control strains
70(1)
4.9.2 Maintenance of control strains
71(1)
4.10 Antibiotic assays
71(5)
4.10.1 Assay methods--microbiological assays
72(2)
4.10.2 Non-microbiological methods--enzyme-based assays
74(1)
4.10.3 Immunoassays
75(1)
4.10.4 High-performance liquid chromatography (HPLC)
75(1)
4.11 Detection of antimicrobial resistance by molecular methods
76(5)
Chapter summary
78(1)
Further reading
79(1)
Discussion questions
80(1)
5 Blood cultures
81(28)
Derek Law
5.1 Laboratory investigation of blood culture samples
82(5)
5.1.1 Blood culture methods
82(1)
5.7.2 Procedures for sample taking, transport, and processing
82(3)
5.1.3 Principles of common blood culture systems
85(1)
5.7.4 Types of media used in blood culture systems
85(1)
5.7.5 Traditional non-automated blood culture systems
85(1)
5.1.6 Automated blood culture systems
86(1)
5.7.7 Radiometric methods
86(1)
5.1.8 Non-radioactive detection methods
86(1)
5.1.8.1 Lysis centrifugation methods
87(1)
5.1.8.2 Neutralization of antimicrobial agents and other inhibitory factors
87(1)
5.2 Procedure for dealing with negative bottles
87(1)
5.3 Procedure for dealing with positive bottles
88(6)
5.3.1 Microscopy of positive blood cultures
89(1)
5.3.2 Differentiation of bacterial types based on microscopy results
89(1)
5.3.3 Procedures in the event of negative microscopy
89(2)
5.3.4 Culture regimes following microscopy
91(1)
5.3.5 Culture of positive bottles
91(1)
5.3.6 Direct susceptibility tests
91(2)
5.3.7 Additional tests
93(1)
5.4 Bacterial pathogens
94(5)
5.4.1 Pathogens likely to be a cause of septicaemia and bacteraemia
94(3)
5.4.2 Polymicrobial bacteraemia
97(1)
5.4.3 Mycobacteria
97(1)
5.4.4 Bacteraemia in children
98(1)
5.4.5 Bacteraemia in immunocompromised patients
98(1)
5.5 False-positive results
99(3)
5.5.1 Blood culture contamination
99(1)
5.5.2 Determining the significance of a possible contaminated culture
99(1)
5.5.3 Factors to consider when determining the significance of an isolate
100(1)
5.5.3.1 Number of positive bottles
100(1)
5.5.3.2 Time for the bottles to become positive
100(1)
5.5.3.3 Clinical information
100(1)
5.5.4 Non-cultural markers of septicaemia
101(1)
5.5.5 Reducing the incidence of blood culture contamination
101(1)
5.6 Endocarditis
102(7)
5.6.1 Principles of how bacteria cause endocarditis
102(1)
5.6.2 Bacteria associated with endocarditis
103(1)
5.6.3 Signs and symptoms of endocarditis
104(1)
5.6.4 Diagnosis of endocarditis
104(1)
5.6.5 Identification and susceptibility testing
104(3)
Chapter summary
107(1)
Further reading
107(1)
Discussion questions
108(1)
6 Investigation of urine samples
109(26)
Clive Graham
6.1 Overview of the urinary tract
110(2)
6.1.1 Normal flora of the urinary tract
110(1)
6.1.2 Mechanisms designed to prevent infection
110(1)
6.7.3 Mechanism of infection in the catheterized patient
111(1)
6.2 Urinary tract pathogens
112(5)
6.2.1 Virulence factors of microbes causing urinary tract infection
114(1)
6.2.2 Epidemiology
114(1)
6.2.3 Infections of the lower urinary tract
114(1)
6.2.4 Infections of the upper urinary tract
114(1)
6.2.5 Asymptomatic bacteriuria
115(1)
6.2.6 Asymptomatic pyuria
115(1)
6.2.7 Common fungal pathogens
115(1)
6.2.8 Atypical and fastidious organisms
116(1)
6.2.9 Mycobacteria
116(1)
6.2.10 Parasites
116(1)
6.3 Urinary samples
117(1)
6.3.1 Specimen collection
117(1)
6.3.2 Midstream urine (MSU)
117(1)
6.3.3 Clean catch urine
117(1)
6.3.4 `Pad' urine
117(1)
6.3.5 `Bag' urine
118(1)
6.3.6 `In-out catheter' urine
118(1)
6.3.7 Catheter stream urine (CSU)
118(1)
6.3.8 Suprapubic aspirate
118(1)
6.4 Transport of specimens to the laboratory
118(1)
6.5 Initial processing of samples
119(4)
6.5.1 Leucocyte esterase
119(1)
6.5.2 Nitrate reductase (Greiss test)
119(1)
6.5.3 Urine microscopy
120(1)
6.5.3.1 Eukaryotic cell types in urine
120(1)
6.5.3.2 Significance of casts in urine wet films
120(1)
6.5.3.3 Types of pathological crystals found in urine
121(1)
6.5.3.4 Parasitic infection and detection
121(1)
6.5.4 Automated techniques available for processing urine samples in the laboratory and point of care testing (POCT)
122(1)
6.5.4.1 Automated dipstick method
122(1)
6.5.4.2 Automated microscopy
122(1)
6.5.4.3 Flow cytometry
122(1)
6.5.4.4 Other automated methods for detecting bacteriuria
123(1)
6.6 Culture
123(3)
6.6.1 Significant culture results
123(1)
6.6.2 Procedures for quantifying urine cultures
124(1)
6.6.3 Common isolation media
124(2)
6.6.4 Confirmatory tests
126(1)
6.65 Contaminated urine samples
126(4)
6.6.6 Antimicrobial susceptibility testing
127(2)
6.6.7 Direct susceptibility testing
129(1)
6.6.8 Automated identification and susceptibility
129(1)
6.6.9 Hazardous organisms
130(1)
6.7 Urinary antibiotics
130(5)
6.7.1 Trimethoprim
130(1)
6.7.2 Cefalexin
130(1)
6.7.3 Amoxicillin
130(1)
6.7.4 Co-amoxiclav
130(1)
6.7.5 Nitrofurantoin
131(1)
6.7.6 Ciprofloxacin
131(1)
6.7.7 Gentamicin
131(1)
6.7.8 Treatment failure
131(1)
6.7.9 Detection of antimicrobial substances
132(1)
Chapter summary
132(1)
Further reading
133(1)
Discussion questions
134(1)
7 Investigation of wound, tissue, and genital samples
135(35)
Steve Davies
Mark Tovey
7.1 The skin and mucosa
136(1)
7.1.1 Overview of the skin
136(1)
7.1.2 Normal flora of the skin
137(1)
7.2 Skin infections and their causes
137(4)
7.2.1 Skin infections
138(1)
7.2.1.1 Cellulitis
138(1)
7.2.1.2 Folliculitis
139(1)
7.2.1.3 Boils and carbuncles
139(1)
7.2.1.4 Abscesses
139(1)
7.2.1.5 Impetigo
139(1)
7.2.1.6 Ulceration
140(1)
7.2.1.7 Erysipelas
140(1)
7.2.1.8 Erysipeloid
140(1)
7.2.1.9 Necrotizing fasciitis
140(1)
7.2.1.10 Gangrene
141(1)
7.3 Mucosal infections
141(4)
7.3.1 Eye infections
141(1)
7.3.1.1 Conjunctivitis
141(1)
7.3.1.2 Ophthalmia neonatorum
142(1)
7.3.1.3 Chlamydia and viral conjunctivitis
142(1)
7.3.1.4 Keratitis
142(1)
7.3.1.5 Orbital cellulitis
142(1)
7.3.2 Ear infections
143(1)
7.3.2.1 Otitis externa
143(1)
7.3.2.2 Otitis media
143(1)
7.3.3 Nasal swabs
143(1)
7.3.4 Throat infections
143(1)
7.3.4.1 Pharyngitis
143(1)
7.3.4.2 Diphtheria
144(1)
7.3.4.3 Epiglottitis
144(1)
7.3.4.4 Vincent's angina
144(1)
7.3.4.5 Fusobacterium necrophorum
145(1)
7.4 Organisms, virulence factors, and toxin production
145(4)
7.4.1 Staphylococcus aureus
145(1)
7.4.2 Group A streptococci (S. pyogenes)
146(1)
7.4.2.1 Pseudomonas aeruginosa
147(1)
7.4.2.2 Clostridium perfringens
147(1)
7.4.2.3 Corynebacterium diphtheriae
148(1)
7.4.3 Mycobacteria
148(1)
7.5 Sample processing
149(3)
7.5.1 Microscopy techniques
149(1)
7.5.2 Common isolation media
150(2)
7.6 Orthopaedic samples
152(1)
7.6.1 Orthopaedic sample processing
152(1)
7.7 Genital tract and associated specimens
153(11)
7.7.1 Normal flora of the genital tract
153(1)
7.7.2 Specimen quality and type
154(1)
7.7.3 Sexually transmitted infections (STIs)
154(1)
7.7.3.1 Gonorrhoea
154(1)
7.7.3.2 Trichomoniasis
155(1)
7.7.3.3 Genital herpes
156(1)
7.7.3.4 Chlamydia
156(1)
7.7.3.5 Syphilis
156(3)
7.7.3.6 Chancroid
159(1)
7.7.3.7 Human papillomavirus (HPV) infection
160(1)
7.7.3.8 Mycoplasma genitalium
161(1)
7.7.4 Non-sexually transmitted genital tract infections
161(3)
7.8 Neisseria gonorrhoeae: virulence factors
164(1)
7.9 Sample processing
164(2)
7.10 Medicolegal issues
166(4)
Chapter summary
168(1)
Further reading
169(1)
Discussion questions
169(1)
8 Examination of cerebrospinal fluid and fluids from sterile sites
170(26)
Derek Law
8.1 Investigation of cerebrospinal fluids
171(17)
8.7.1 Bacterial meningitis
172(1)
8.1.2 Viral meningitis
173(1)
8.7.3 Cryptococcal meningitis
173(1)
8.7.4 Processing of CSF samples
174(1)
8.1.4.1 Appearance of CSF
175(1)
8.1.4.2 Cell count
175(3)
8.1.4.3 Centrifugation of CSF
178(1)
8.1.4.4 Gram stains
178(1)
8.1.4.5 Culture of CSF
179(1)
8.1.5 Characteristics and identification of common meningitis pathogens
179(2)
8.1.6 Antigen testing
181(1)
8.1.7 Molecular testing
181(1)
8.1.8 Viral meningitis
182(1)
8.1.9 Tuberculosis meningitis
182(2)
8.1.10 Cryptococcal meningitis
184(1)
8.1.11 Neurosurgical patients
185(1)
8.1.12 Treatment of meningitis
186(1)
8.1.13 Prevention of meningitis---the role of vaccination
186(2)
8.2 Other sterile body fluids
188(8)
8.2.1 Synovial and bursa fluids
188(1)
8.2.2 Pleural fluid
188(1)
8.2.3 Pericardial fluid
188(1)
8.2.4 Ascitic or peritoneal fluid
189(1)
8.2.5 Processing of fluids
189(1)
8.2.5.1 Cell count
189(1)
8.2.5.2 Microscopy and culture
190(1)
8.2.5.3 Additional tests
190(1)
8.2.5.4 TB culture
191(1)
8.2.6 Continuous ambulatory peritoneal dialysis (CAPD) fluids
191(1)
8.2.6.1 Processing CAPD fluid
192(1)
8.2.6.2 Cell count
192(1)
8.2.6.3 Gram stain
192(1)
8.2.6.4 Culture of CAPD fluid
193(1)
8.2.6.5 Treatment of CAPD peritonitis
193(1)
8.2.6.6 Prevention of CAPD infection
194(1)
Chapter summary
194(1)
Further reading
194(1)
Discussion questions
195(1)
9 Investigation of respiratory samples
196(34)
Louise Hill-King
9.1 The respiratory tract
197(6)
9.7.1 Overview of the respiratory tract
197(1)
9.7.2 Respiratory tract membranes
197(1)
9.7.3 Normal flora of the respiratory tract
198(1)
9.7.4 Disruption of the normal flora
198(1)
9.7.5 Infections of the lower respiratory tract
199(1)
9.7.6 Common bacterial pathogens
199(1)
9.7.7 Community-acquired pneumonia
199(1)
9.7.8 Typical and atypical pneumonia
199(1)
9.7.9 Hospital-acquired pneumonia
200(1)
9.1.10 Predisposing factors
200(1)
9.7.11 Lung abscesses
201(1)
9.7.12 Whooping cough
201(1)
9.7.13 Common fungal pathogens
201(1)
9.1.13.1 Yeasts
201(1)
9.1.13.2 Moulds
202(1)
9.1.14 Parasites
202(1)
9.2 Processing of lower respiratory samples
203(9)
9.2.1 Sample types
203(1)
9.2.2 Sample processing
204(1)
9.2.2.1 Homogenization of sputum samples
204(1)
9.2.2.2 Concentration of lower respiratory samples
205(1)
9.2.3 Microscopy techniques
205(1)
9.2.3.1 Gram staining
205(2)
9.2.3.2 Microscopy for detection of Legionella spp.
207(1)
9.2.3.3 Microscopy for PCP
207(1)
9.2.3.4 Differential staining of WBC (eosinophils)
207(1)
9.2.4 Common isolation media
208(2)
9.2.5 Confirmatory tests
210(1)
9.2.6 Antimicrobial susceptibility testing
211(1)
9.3 Cystic fibrosis
212(4)
9.3.1 Aetiology, symptoms, and outcome of cystic fibrosis
212(1)
9.3.2 Organisms associated with CF
213(1)
9.3.3 Culture of CF samples
214(1)
9.3.4 Identification of pathogens from CF samples
214(1)
9.3.5 Further identification of Bcc organisms
215(1)
9.3.6 Antimicrobial susceptibility testing of CF isolates
215(1)
9.3.7 Antimicrobial strategies for CF
216(1)
9.4 Mycobacteria
216(8)
9.4.1 Common mycobacterial types
217(1)
9.4.2 Microscopy for Mycobacterium spp.
218(2)
9.4.3 Conventional culture for mycobacteria
220(1)
9.4.4 Solid and liquid culture media for mycobacteria
220(1)
9.4.4.1 Solid media
220(1)
9.4.4.2 Liquid media
221(1)
9.4.5 Automated mycobacterial culture methods
221(1)
9.4.6 Identification of Mycobacterium spp.
222(1)
9.4.7 Antimicrobial susceptibility testing
222(2)
9.4.8 Typing of mycobacteria
224(1)
9.4.9 Immunodiagnostic tests
224(1)
9.5 Hazardous organisms
224(6)
9.5.1 Classification of hazardous organisms
225(1)
9.5.2 Containment Levels
225(1)
9.5.3 Microbiological safety cabinets
226(1)
9.5.4 Personal protective equipment (PPE)
227(1)
9.5.5 Spillages
227(1)
Chapter summary
228(1)
Further reading
229(1)
Discussion questions
229(1)
10 Investigation of gastrointestinal specimens
230(35)
Michael Ford
Kathy Nye
10.1 The general principles of the investigation of gastrointestinal disease
231(3)
10.2 Bacterial pathogens associated with gastrointestinal disease
234(6)
10.2.1 Campylobacter species
235(1)
10.2.2 Salmonella species
235(1)
10.2.3 Shigella species
236(1)
10.2.4 Escherichia coli
236(1)
10.2.5 Vibrio species
237(1)
10.2.6 Yersinia species
238(1)
10.2.7 Bacillus cereus
238(1)
10.2.8 Staphylococcus aureus
239(1)
10.2.9 Clostridium difficile
239(1)
10.2.10 Clostridium perfringens
239(1)
10.3 Mechanisms involved in the production of disease by bacterial causes of intestinal infection
240(1)
10.4 Isolation media and how they work
241(2)
10.5 Identification of bacterial pathogens isolated from faeces samples
243(7)
10.5.1 Agglutination tests
245(2)
10.5.2 Non-cultural methods for the detection of bacteria) causes of gastrointestinal disease
247(1)
10.5.2.1 Immunomagnetic separation (IMS)
247(1)
10.5.2.2 Molecular bacteriology
247(1)
10.5.3 Bacterial toxin detection
248(1)
10.5.3.1 Tissue culture
248(1)
10.5.3.2 Enzyme immunoassay (EIA)
249(1)
10.5.4 Typing techniques
249(1)
10.5.4.1 Serotyping
249(1)
10.5.4.2 Phage typing
250(1)
10.5.4.3 PCR ribotyping
250(1)
10.6 Patient management and control of infection
250(1)
10.7 Therapeutic regimes
251(1)
10.8 Non-bacterial causes of gastrointestinal disease
251(4)
10.8.1 Viral pathogens
251(1)
10.8.1.1 Laboratory detection
252(1)
10.8.1.2 Patient management and infection control
253(1)
10.8.2 Parasitic infections
253(1)
10.8.2.1 Protozoa
253(2)
10.9 The role of the reference laboratory
255(1)
10.10 Food and water microbiology
255(10)
10.10.1 Water microbiology
255(1)
10.10.2 Emerging waterborne pathogens
256(1)
10.10.2.1 Helicobacter pylori and other unusual waterborne pathogens
256(1)
10.10.3 Microbiological analysis of water
257(2)
10.10.4 Food microbiology
259(3)
Chapter summary
262(1)
Further reading
263(1)
Discussion questions
264(1)
11 Clinical parasitology
265(27)
Tony Worthington
11.1 What are parasites?
266(1)
11.2 Clinical parasitology in the twenty-first century
266(2)
11.3 Protozoa
268(6)
11.3.7 Amoebae
269(1)
11.3.1.1 Entamoeba histolytica
269(1)
11.3.2 Flagellates
270(1)
11.3.2.1 Giardia intestinalis
270(1)
11.3.3 Apicomplexans
271(1)
11.3.3.1 Cryptosporidium spp.
271(1)
11.3.4 Toxoplasma gondii
272(1)
11.3.5 dilates
273(1)
11.3.5.1 Balantidium coli
273(1)
11.4 Helminths
274(5)
11.4.1 Nematodes (roundworms)
274(1)
11.4.2 Ascaris lumbricoides (giant roundworm)
275(1)
11.4.3 Trichuris trichiura (whipworm)
276(1)
11.4.4 Enterobius vermicularis (pinworm/threadworm)
277(1)
11.4.5 Anisakis simplex
277(2)
11.5 Cestodes (tapeworms)
279(2)
11.5.1 Taenia saginata (beef tapeworm) and Taenia solium (pork tapeworm)
279(1)
11.5.2 Echinococcus granulosus
280(1)
11.6 Trematodes
281(2)
11.6.1 Fasciola hepatica
281(2)
11.6.2 Paragonimus westermani
283(1)
11.7 Diagnosis of gastrointestinal parasitic infections acquired through the gastrointestinal tract
283(1)
11.8 Examination of faeces for ova, cysts, and parasites (OCP)
284(4)
11.8.1 Eyepiece calibration
287(1)
11.9 Immunological techniques
288(1)
11.10 Molecular techniques
288(2)
11.11 Treatment of parasitic infections acquired through the gastrointestinal tract
290(2)
Chapter summary
290(1)
Further reading
291(1)
Discussion questions
291(1)
12 Infection prevention and control
292(27)
Sheila Morgan
Michael Ford
12.1 What is infection prevention and control?
293(1)
12.2 MRSA screening
293(6)
12.2.1 Consequences of MRSA colonization
293(1)
12.2.2 Justification for MRSA screening
294(1)
12.2.3 Sample types and collection
294(1)
12.2.4 Sample processing
295(1)
12.2.4.1 Enrichment culture
295(1)
12.2.4.2 Selective media (non-chromogenic)
296(1)
12.2.4.3 Selective media (chromogenic)
297(1)
12.2.4.4 Molecular methods
298(1)
12.2.5 Panton--Valentine leukocidin-producing S. aureus
299(1)
12.3 Vancomycin-resistant enterococci (VRE)
299(3)
12.3.1 Sample processing
300(1)
12.3.1.1 Selective media
301(1)
12.3.1.2 Chromogenic VRE media
301(1)
12.3.1.3 Enrichment culture
301(1)
12.4 Routes of transmission and detection of pathogens that require initiation of a screening programme
302(2)
12.4.1 Surveillance of pathogens
303(1)
12.5 Importance of Clostridium difficile (C. difficile) in hospital environments
304(3)
12.5.1 Laboratory diagnosis of C. difficile
305(2)
12.6 Gram-negative outbreaks
307(1)
12.7 Other resistance screening and media
308(1)
12.8 Infection prevention and control
309(10)
12.8.1 Hand hygiene
309(2)
12.8.2 Standard Precautions
311(1)
12.8.3 Isolation nursing
311(1)
12.8.3.1 Source isolation
312(1)
12.8.3.2 Protective isolation
312(1)
12.8.4 Management of cohorts
312(1)
12.8.5 Disinfection policy
313(1)
12.8.5.1 Sterilization
313(1)
12.8.5.2 Ward routine
313(1)
12.8.5.3 Other departments/units
313(1)
12.8.6 Waste management
314(1)
12.8.7 Monitoring Air Quality in Theatres
314(3)
Chapter summary
317(1)
Further reading
318(1)
Discussion questions
318(1)
13 Laboratory investigations of viral infections
319(34)
Jayne Harwood
13.1 General properties and structure of viruses
320(2)
13.1.1 Viral morphology
321(1)
13.1.2 Viral classification
321(1)
13.2 Viral pathogenesis
322(1)
13.2.1 Host cellular response to viral infection
322(1)
13.3 Samples required for the diagnosis of viral infection
323(2)
13.3.1 Swabs
324(1)
13.3.2 Respiratory samples
324(1)
13.3.3 Cerebrospinal fluid (CSF)
324(1)
13.3.4 Vesicle fluid
324(1)
13.3.5 Faeces
324(1)
13.3.6 Clotted blood
324(1)
13.3.7 BDTA blood
324(1)
13.4 Diagnostic methods in virology
325(5)
13.4.1 Overview of diagnostic methods
325(1)
13.4.2 Direct detection of viruses
325(1)
13.4.3 Electron microscopy (EM) morphology/immune EM
325(1)
13.4.4 Histopathological appearance
326(1)
13.4.5 Antigen detection
327(1)
13.4.6 Molecular techniques for the detection of viral genomes
327(1)
13.4.7 Indirect examination
328(2)
13.5 Serology
330(7)
13.5.1 Complement fixation test (CFT)
331(2)
13.5.2 Detection of IgM
333(1)
13.5.3 Enzyme-linked immunosorbent assay (EUSA)
333(1)
13.5.3.1 Competitive methods
334(1)
13.5.3.2 Sandwich methods
334(1)
13.5.3.3 Antibody capture method
334(1)
13.5.4 Assay characteristics
335(1)
13.5.5 Criteria used for diagnosing a re-infection/re-activation
335(1)
13.5.6 Limitation of serological diagnosis
336(1)
13.6 Antiviral chemotherapy
337(1)
13.6.1 Resistance of viruses to inhibitors
337(1)
13.6.2 Site of action of common antiviral agents
338(1)
13.7 Common viral infections
338(15)
13.7.1 Respiratory tract
338(1)
13.7.1.1 Adenoviruses
338(1)
13.7.1.2 Rhinoviruses
338(1)
13.7.1.3 Influenza
339(1)
13.7.2 Childhood disease
339(1)
13.7.2.1 Measles
339(1)
13.7.2.2 Mumps
339(1)
13.7.2.3 Respiratory syncytial virus (RSV)
340(1)
13.7.3 Common viral gastroenteritis
340(1)
13.7.3.1 Rotavirus
340(1)
13.7.3.2 Adenovirus
340(1)
13.7.3.3 Norovirus
340(1)
13.7.4 Herpesviruses
340(1)
13.7.4.1 Herpes simplex (HSV)
340(1)
13.7.4.2 Varicella zoster virus (VZV, chickenpox)
341(1)
13.7.4.3 Cytomegalovirus (CMV)
341(1)
13.7.5 Hepatitis viruses
341(1)
13.7.5.1 Hepatitis A (HAV)
341(1)
13.7.5.2 Hepatitis B (HBV)
341(1)
13.7.5.3 Hepatitis C (HCV)
342(1)
13.7.6 Human immunodeficiency virus (HIV)
342(1)
13.7.7 Congenital infections
343(1)
13.7.7.1 Toxoplasmosis
343(1)
13.7.7.2 Rubella
344(1)
13.7.7.3 Herpes simplex virus (HSV)
345(1)
13.7.7.4 Varicella zoster virus (VZV)
346(1)
13.7.7.5 Cytomegalovirus (CMV)
346(1)
13.7.7.6 Parvovirus B19
347(4)
Chapter summary
351(1)
Further reading
351(1)
Discussion questions
352(1)
14 Clinical mycology
353(32)
Derek Law
14.1 What are fungi?
353(2)
14.2 Clinical mycology in the twenty-first century
355(2)
14.3 Common fungal infections of humans
357(1)
14.4 Infections of the skin, nails, and hair
358(9)
14.4.1 Sources of dermatophyte infection
358(2)
14.4.2 Diagnosis of dermatophyte infections
360(1)
14.4.3 Collection of samples for diagnosis of dermatophyte infection
361(1)
14.4.4 Laboratory procedures for diagnosis of dermatophyte infection
362(1)
14.4.4.1 Microscopy
362(2)
14.4.4.2 Culture for dermatophytes
364(1)
14.4.5 Confirmation of dermatophyte isolation
364(2)
14.4.6 Non-dermatophyte fungi as a cause of skin infections
366(1)
14.4.7 Treatment of skin, nail, and hair infections
367(1)
14.5 Candida infections of the mucosa
367(4)
14.5.1 Diagnosis of mucosal Candida infections
369(2)
14.5.2 Treatment of mucosal Candida infections
371(1)
14.6 Invasive fungal infections
371(9)
14.6.1 Invasive Candida infections
372(1)
14.6.1.1 Diagnosis of invasive candidiasis
373(1)
14.6.2 Cryptococcal meningitis
374(1)
14.6.3 Aspergillus infections
374(2)
14.6.3.1 Diagnosis of ABPA and aspergilloma
376(1)
14.6.3.2 Diagnosis of invasive aspergillosis
377(1)
14.6.3.3 Treatment of invasive aspergillosis
378(1)
14.6.4 Other filamentous fungi as a cause of invasive disease
379(1)
14.6.5 Fungal infections of the eye
379(1)
14.7 Antifungal susceptibility testing
380(2)
14.7.1 Antifungal agents
380(1)
14.7.2 Methods of susceptibility testing
380(2)
14.8 The role of the reference laboratory
382(3)
Chapter summary
383(1)
Further reading
383(1)
Discussion questions
384(1)
15 Bacterial pathogenesis
385(38)
Lynn G. Dover
15.1 Fundamental themes
385(2)
15.7.1 Important sites of bacterial infection
387(1)
15.2 Virulence factors
387(1)
15.3 Gaining a foothold--early events in infection
388(5)
15.3.1 Bacterial adhesins
388(1)
15.3.2 MSCRAMMs
389(1)
15.3.3 Adhesin structural biology
390(1)
15.3.4 Fimbrial adhesins of Gram-negative bacteria
390(2)
15.3.5 Fimbrial adhesins of Gram-positive bacteria
392(1)
15.3.6 Non-fimbrial adhesins
392(1)
15.3.7 Trimeric autotransporter adhesins (TAAs)
393(1)
15.4 Invasion by bacteria
393(8)
15.4.1 Integrin-mediated invasion
395(2)
15.4.2 Enterobacterial T3SSpromote invasion or intimacy
397(4)
15.5 Avoiding the immune response
401(11)
15.5.1 Detection of microbial-associated molecular patterns (MAMPs)
401(2)
15.5.2 Opsonization and evasion strategies
403(2)
15.5.3 Binding host complement inhibitors
405(1)
15.5.4 Bacterial complement inhibitors
406(1)
15.5.5 Proteolysis of complement and immunoglobulins
406(1)
15.5.6 Antiphagocytic outer polysaccharidic layers
407(1)
15.5.7 Antiphagocytic and anti-inflammatory action of T3SS effectors
408(1)
15.5.8 S. aureus produces superantigens that influence lymphocyte populations
409(1)
15.5.9 Staphylococcal Protein A is a superantigen that kills specialized B-lymphocytes
410(1)
15.5.10 Toxic shock syndromes are elicited by T-cell specific superantigens
411(1)
15.6 Toxinogenesis
412(8)
15.6.1 Toxins that subvert membrane receptor signalling
412(1)
15.6.2 Cytolytic toxins
413(1)
15.6.3 Phospholipases
413(3)
15.6.4 Cholesterol-dependent cytolysins (CDCs)
416(1)
15.6.5 Toxins that enter cells and disrupt cellular physiology
416(2)
15.6.6 Diphtheria and cholera toxins modify key host proteins by ADP-ribosylation
418(2)
15.7 Pan-genomes, mobile genetic elements, and the acquisition virulence factors
420(3)
Chapter summary
421(1)
Further reading
421(1)
Discussion questions
422(1)
16 Molecular diagnostics
423(22)
Jayne Harwood
16.1 Polymerase chain reaction (PCR)
424(4)
16.1.1 Detection of PCR products
428(1)
16.2 Variations of PCR
428(4)
16.2.1 Reverse transcriptase PCR (RT-PCR)
428(1)
16.2.2 Real-time PCR
428(1)
16.2.3 Nested PCR
429(1)
16.2.4 Multiplex PCR
430(1)
16.2.5 Ligase chain reaction (ICR)
431(1)
16.3 Advantages and disadvantages of PCR
432(1)
16.4 Applications
433(1)
16.4.7 HIV viral load monitoring
433(1)
16.5 DNA Sequencing
434(1)
16.6 DNA microarrays
434(3)
16.6.1 Applications of DNA microarrays
437(1)
16.7 Nucleic acid hybridization
437(8)
16.7.1 Southern blot
438(1)
16.7.2 Northern blot
438(1)
16.7.3 In situ hybridization
439(4)
Chapter summary
443(1)
Further reading
443(1)
Discussion questions
444(1)
17 Whole genome sequencing in microbiology
445(25)
Michael Ford
17.1 Whole genome sequencing (WGS) techniques
446(3)
1.1.1 Sanger sequencing
447(2)
17.2 Automated whole genome sequencing
449(1)
17.3 Next generation sequencing (NGS)
449(1)
17.4 Data analysis and e-infrastructure
450(1)
17.5 Detection of microbial drug resistance using WGS
451(7)
17.5.1 Use of WGS for predicting susceptibility in S. aureus and MRSA
452(1)
17.5.2 WGS susceptibility prediction in Gram-negative organisms
453(2)
17.5.3 WGS and Neissera gonorrhoeae susceptibility
455(1)
17.5.4 Mycobacterium tuberculosis (MTB) and WGS resistance prediction
456(1)
17.5.5 Viral resistance and WGS
457(1)
17.6 Use of WGS in determining virulence properties in microorganisms
458(2)
17.7 WGS sequencing and vaccine development
460(2)
17.7.1 Development of MenB vaccine using reverse vaccinology
461(1)
17.7.2 Influenza vaccine
461(1)
17.8 Bacterial identification using WGS
462(1)
17.9 Use of WGS in bacterial strain typing and epidemiological investigation
463(7)
17.9.1 Multilocus sequence typing (MIST)
463(1)
17.9.2 Restriction fragment length polymorphism (RFLP)
464(4)
Chapter summary
468(1)
Further reading
468(1)
Discussion questions
469(1)
18 Procedures for sample collection, transport, and processing
470(29)
Malcolm Holliday
18.1 The importance of sample collection
471(2)
18.2 Overview of different sample types and specimen containers
473(2)
18.2.1 Sterile plastic or glass `universal' containers
473(1)
18.2.2 Boric acid containers
473(1)
18.2.3 Dipslides
473(1)
18.2.4 Sterile plastic universal with spoons (faeces containers)
474(1)
18.2.5 Swabs
474(1)
18.2.6 Blood cultures
474(1)
18.3 Methods of sample collection
475(9)
18.3.7 Urine samples
476(1)
18.3.1.1 Midstream urine (MSU)
476(1)
18.3.1.2 Catheter stream urine (CSU)
476(1)
18.3.1.3 Bag urine
476(1)
18.3.1.4 Pad urine
477(1)
18.3.1.5 Supra-pubic aspirate (SPA)
477(1)
18.3.2 Swab samples
477(1)
18.3.2.1 Wound swabs
477(1)
18.3.2.2 Nasal swabs
478(1)
18.3.2.3 Throat swabs
478(1)
18.3.2.4 Eye swabs
478(1)
18.3.2.5 Ear swabs
478(1)
18.3.2.6 Pernasal swabs (for Bordetella pertussis)
478(1)
18.3.3 Blood samples
478(1)
18.3.3.1 Blood cultures
478(2)
18.3.3.2 Blood samples for antibiotic levels
480(1)
18.3.3.3 Blood samples for bacterial and viral serology
480(1)
18.3.3.4 Blood samples for molecular investigations
481(1)
18.3.4 Cerebrospinal fluid (CSF)
481(1)
18.3.5 Sterile body fluids (e.g. joint fluid, pleural fluid, etc.)
481(1)
18.3.6 Vesicle fluids for virology
481(1)
18.3.7 Catheter and line tips
481(1)
18.3.8 Skin, hair, and nails for dermatophyte fungi
482(1)
18.3.8.1 Skin scrapings
482(1)
18.3.8.2 Hair
482(1)
18.3.8.3 Nail
482(1)
18.3.9 Tissue, prostheses, etc.
482(1)
18.3.10 Sputum
482(1)
18.3.11 Nasopharyngeal aspirates (NPAs) for virology
483(1)
18.3.12 Faeces
483(1)
18.3.12.1 Rectal swabs
483(1)
18.3.13 Perianal swabs and Sellotape™ preparations
483(1)
18.3.14 Vaginal swabs
483(1)
18.3.15 Cervical swabs
484(1)
18.3.16 Penile (urethral) swabs
484(1)
18.4 Methods of sample transport
484(1)
18.5 Transport regulations
485(3)
18.6 Basic sample processing
488(1)
18.7 Inoculation of culture media
489(6)
18.7.1 Urine samples
490(1)
18.7.2 Swab samples
491(1)
18.7.3 Blood cultures
491(1)
18.7.4 Fluids, pus, and CSF
491(1)
18.7.5 Tissue and biopsy samples
491(1)
18.7.6 Prostheses
491(1)
18.7.7 Catheter tips
491(1)
18.7.8 Skin, hair, and nails
492(1)
18.7.9 Sputum
492(1)
18.7.10 Faeces
493(1)
18.7.11 Smears and wet preparations for microscopy
493(1)
18.7.12 Spreading culture plates
494(1)
18.8 Safety considerations
495(4)
Chapter summary
496(1)
Further reading
497(1)
Discussion questions
497(2)
Hints and tips for Discussion questions 499(5)
Self-check answers 504(9)
Glossary 513(9)
References 522(7)
Index 529
Dr Michael Ford has worked in Microbiology for over 30 years and was appointed Microbiology Laboratory Manager for the Newcastle Upon Tyne NHS Foundation Trust in 2014. Michael has a wide experience in all areas of diagnostic service provision. He has recently worked very closely with Public Health England which resulted in the transfer of their Newcastle services into the Trust. A key part of this was the setting up of a new molecular diagnostic service for Newcastle. His main research area involved developing novel methods of bacterial identification, which resulted in a number of publications and two successful patents for the development of novel selective media. He has been a lecturer at Northumbria University on both the BSc and MSc Microbiology programmes. Michael has also been a key member of the IBMS Scientific Advisory Panel for Microbiology and IBMS Deputy Chief Examiner.