District Laboratory Practice in Tropical Countries Part 2

442 Pages·2005·7.02 MB·English

by  Monica Cheesbrough

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District
Laboratory
Practice in
Tropical
Countries
Part 2
Second Edition
Monica Cheesbrough
CAMBRIDGEUNIVERSITY PRESS
Cambridge, New York, Melbourne, Madrid, Cape Town, Singapore, São Paulo
Cambridge University Press
The Edinburgh Building, Cambridge CB2 8RU, UK
Published in the United States of America by Cambridge University Press, New York
www.cambridge.org
Information on this title: www.cambridge.org/9780521676311
© Monica Cheesbrough 2000, 2006
This publication is in copyright. Subject to statutory exception and to the provision of
relevant collective licensing agreements, no reproduction of any part may take place
without the written permission of Cambridge University Press.
First published in print format 2006
ISBN-13 978-0-511-34842-6 eBook (EBL)
ISBN-10 0-511-34842-8 eBook (EBL)
ISBN-13 978-0-521-67631-1 paperback
ISBN-10 0-521-67631-2 paperback
Cambridge University Press has no responsibility for the persistence or accuracy of urls
for external or third-party internet websites referred to in this publication, and does not
guarantee that any content on such websites is, or will remain, accurate or appropriate.
Every effort has been made in preparing this book to provide accurate and up-to-date
information which is in accord with accepted standards and practice at the time of
publication. Nevertheless, the authors, editors and publisher can make no warranties that
the information contained herein is totally free from error, not least because clinical
standards are constantly changing through research and regulation. The authors, editors
and publisher therefore disclaim all liability for direct or consequential damages resulting
from the use of material contained in this book. Readers are strongly advised to pay careful
attention to information provided by the manufacturer of any drugs or equipment that
they plan to use.
Part 2
Contents
Chapter 7 Microbiological tests
7.1 Microbiology practice and quality assurance in district laboratories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Pages 1–9
7.2 Features and classification of microorganisms of medical importance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9–35
7.3 Microscopical techniques used in microbiology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35–45
7.4 Culturing bacterial pathogens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45–62
7.5 Biochemical tests to identify bacteria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62–70
7.6 Examination of sputum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71–76
7.7 Examination of throat and mouth specimens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76–79
7.8 Examination of pus, ulcer material and skin specimens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80–85
7.9 Examination of effusions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85–90
7.10 Examination of urogenital specimens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90–97
7.11 Examination of faecal specimens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97–105
7.12 Examination of urine. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105–115
7.13 Examination of cerebrospinal fluid (c.s.f.). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116–124
7.14 Culturing blood. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124–130
7.15 Examination of semen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130–132
7.16 Antimicrobial susceptibility testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132–143
7.17 Water-related diseases and testing of water supplies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143–157
7.18 Summary of the clinical and laboratory features of microorganisms
Bacterial pathogens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157–234
Fungal pathogens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 234–247
Viral pathogens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248–266
COLOUR SECTION. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . between p. 266 and p. 267
Chapter 8 Haematological tests
8.1 Haematology in district laboratories and quality assurance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268–271
8.2 Functions of blood, haematopoiesis and blood disorders. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271–295
8.3 Collection of blood. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295–299
8.4 Measurement of haemoglobin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299–309
8.5 PCV and red cell indices. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309–313
8.6 Counting white cells and platelets. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313–319
8.7 Blood films. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 319–329
8.8 Erythrocyte sedimentation rate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329–331
8.9 Reticulocyte count. Methaemoglobin reduction test. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331–334
8.10 Investigation of sickle cell disease . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 334–340
8.11 Investigation of bleeding disorders. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 340–347
Chapter 9 Blood transfusion tests
9.1 Blood transfusion services at district level and quality assurance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 348–351
9.2 Blood donation and storage of blood . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352–361
9.3 Blood grouping. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 362–369
9.4 Compatibility testing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 369–378
Recommended Books. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 379
Details of Part 1. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380
Appendix I
Preparation of reagents and culture media. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 382–407
Appendix II
Useful addresses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 410–416
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 417–434
iii
Preface
Since the publication of the first edition of Part 2 District Laboratory Practice in Tropical Countries in 2000,
the work of many district laboratories continues to be dominated by the on-going HIV/AIDS pandemic,
increases in the prevalence of tuberculosis and other HIV-related infections and more recently, the
requirement for laboratory monitoring of antiretroviral therapy.
This new edition includes an update on HIV disease/AIDS, recently developed HIV rapid tests to diagnose
HIV infection and screen donor blood, and current information on antiretroviral drugs and the laboratory
monitoring of antiretroviral therapy.
Information on the epidemiology and laboratory investigation of other pathogens has also been brought up
to date. Several new, rapid, simple to perform immunochromatographic tests to assist in the diagnosis of
infectious diseases are described, including those for brucellosis, cholera, dengue, leptospirosis, syphilis and
hepatitis. Recently developed IgM antibody tests to investigate typhoid fever are also described. The new
classification of salmonellae has been introduced.
Details of manufacturers and suppliers now include website information and e-mail addresses. Websites are
also included that provide up to date information on water and sanitation initiatives, and diseases such as
tuberculosis, cholera, leptospirosis, mycetoma, HIV/AIDS and other sexually transmitted infections.
Where required the haematology and blood transfusion chapters have been updated, including a review of
haemoglobin measurement methods in consideration of the high prevalence of anaemia in developing
countries.
It is hoped that this new edition of Part 2 and recently published second edition of Part 1 District
Laboratory Practice in Tropical Countries will continue to help and motivate those working in district
laboratories and those responsible for the management of district laboratory services, training and
continuing education of district laboratory personnel.
Monica Cheesbrough, November 2005
iv
Acknowledgements
The author wishes to thank all those who have corresponded and contributed their suggestions for this
second edition Part 2 District Laboratory Practice in Tropical Countries, particularly those working in district
laboratories and training laboratory personnel in tropical and developing countries.
Gratitude and thanks are also due to those who have helped to prepare the new edition:
Mr Steven Davies, Microbiology Specialist Advisor, Institute of Biomedical Sciences (IBMS) for reading
through and commenting on the microbiology chapter and contributing text on antimicrobials and the
Etest. Also acknowledged for their suggestions are Mr Stephen Mortlock, Member of the IBMS
Microbiology Advisory Panel and Mr Mark Tovey, Microbiology Department, Sheffield.
Mr Simon Hardy, Senior Lecturer in Microbiology, University of Brighton, for also assisting in the revision
of the microbiology chapter.
Dr Eric Bridson, Microbiologist, for reading through the text and checking microbial nomenclature.
Dr Mohammed Tofiq, NMK Clinic, for corresponding with the author and making suggestions for the
microbiology text.
In the preparation of the text covering laboratory monitoring of antiretroviral therapy, gratitude is
expressed to Dr Jane Carter, AMREF, Nairobi, Dr Steve Gerrish, Kara Clinic, Lusaka, Major Peter Disney,
Tshelanyemba Hospital, Zimbabwe and Mr Derryck Klarkowski, Laboratory Specialist, Médecins Sans
Frontières, for their helpful contributions.
Dr Henk Smits, Molecular Biologist, Biomedical Research Royal Tropical Institute, Amsterdam, for supplying
information on rapid tests for brucellosis and leptospirosis.
Professor Asma Ismail, Director Institute for Research in Molecular Medicine, University Sains Malaysia, for
providing text and artwork for the Typhirapid test.
Ms M Marilyn Eales, Haematology Tutor, Pacific Paramedical Training Centre, Wellington, New Zealand, for
reading through and commenting on the haematology and blood transfusion chapters.
The author also wishes to thank Fakenham Photosetting for their careful and professional preparation of the
new edition.
Acknowledgements for colour artwork: These can be found on page 267.
v

MICROBIOLOGICAL TESTS 1
7
Microbiological tests
develop and validate standard treatments and
7.1 control interventions, and ensure antimicrobial
Microbiology practice
drugs are purchased appropriately and used
and quality assurance in district correctly.
laboratories
Infections are particularly prevalent where poverty,
malnutrition, and starvation are greatest, sanitation is
inadequate, personal hygiene poor, water supplies
are unsafe or insufficient, health provision the least
In tropical and developing countries, there is an developed, and disease control measures are lacking
urgent need to strengthen clinical microbiology and or ineffective.
public health laboratory services in response to: War and famine in developing countries have
(cid:2) The high prevalence and increasing incidence of greatly increased the number of people that have
become refugees, suffer illhealth and die prema-
infectious diseases.
turely from infectious diseases.
HIV disease/AIDS, acute respiratory tract infections In rural areas, distances to health centres and
(particularly pneumonia), typhoid, cholera, dysentery,
hospitals are often too great to be travelled by
tuberculosis, meningitis, whooping cough, plague,
patients or mothers with young children requiring
sexually transmitted diseases (including gonorrhoea and
syphilis), viral hepatitis, yellow fever, dengue, and viral immunization.
haemorrhagic fevers are major infectious diseases that In many countries, increasing urbanization has
cause high mortality and serious ill health in tropical and resulted in an increase in the incidence of diseases
developing countries. Climatic changes, particularly
associated with inadequate and unsafe water, poor
global warming and extreme rainfall, are increasing the
distribution of some infectious diseases, especially those sanitation, and overcrowded living conditions.
that are mosquito-borne and water-borne. In areas of high HIV prevalence, major
(cid:2) The threat posed by the re-emergence and rapid pathogens such as M. tuberculosisand Streptococcus
pneumoniae and a range of opportunistic pathogens
spread of diseases previously under control or in
associated with immunosuppression, are responsible
decline such as tuberculosis, plague, diphtheria,
for infections, often life-threatening, in those infected
dengue, cholera and meningococcal meningitis.
with HIV.
(cid:2) The emergence of opportunistic pathogens
This subunit includes information on:
associated with HIV, new strains of pathogens
such as Vibrio cholerae serotype 0139 and ● Clinical microbiology and public health labora-
viruses causing severe acute respiratory tory activities at district level.
syndrome (SARS) and avian influenza. ● Quality assurance and standard operating
procedures (SOPs) in microbiology.
(cid:2) The rapid rate at which bacterial pathogens are ● Collection of microbiological specimens.
becoming resistant to commonly available and ● Safe working practices.
affordable antimicrobials.
Drug resistance is causing problems in the treatment and
control of infections caused by pathogens such as CLINICAL MICROBIOLOGY AND PUBLIC HEALTH
Streptococcus pneumoniae, Haemophilus influenzae,
LABORATORY ACTIVITIES AT DISTRICT LEVEL
Staphylococcus aureus, Pseudomonas aeruginosa,
Neisseria gonorrhoeae, and enterococci. Some strains of A network of district microbiology and regional
M.tuberculosishave developed multi-drug resistance.
public health laboratories is needed to provide to the
(cid:2) The need for reliable microbiological data to community, accessible microbiological services.
7.1
2 DISTRICT LABORATORY PRACTICE IN TROPICAL COUNTRIES
Important: District laboratories require the support of which require microbiological investigations based
the regional public health laboratory in the prep- on a consideration of:
aration and implementation of microbiological
– local disease patterns,
standard operating procedures (SOPs), safe working
– clinical relevance and frequency of isolation,
practices, on-site training, quality assurance, and
– severity of disease and outcome,
provision of essential supplies (e.g. reagents, culture
– possibility of effective intervention,
media, controls, antisera).
– need for surveillance to monitor drug resistance
and epidemic potential,
Operating microbiological laboratory services – cost benefit ratio of isolation and, or, identifi-
with minimal resources cation,
The high cost of culture media and reagents, lack – laboratory capacity and resources available,
of a rational approach to the selection and use of – availability of trained personnel to perform
microbiological investigations, and a shortage of microbiological investigations and ensure the
trained technical staff and clinical microbiologists are quality of work and reports.
important factors in preventing the establishment
Such an approach helps to target resources where
and extension of essential microbiological services in
they are most needed, enables a list of essential
developing countries.
culture media and diagnostic reagents to be
To ensure the optimal use of available resources,
identified, sourced and costed, and training in micro-
it is important for health authorities to identify those
biology techniques and their application to be more
pathogens of greatest public health importance
specific.
QUALITY ASSURANCE AND SOPs IN MICROBIOLOGY
Providing appropriate, reliable and The principles of quality assurance (QA) and general
affordable microbiological services guidelines on how to prepare standard operating
Laboratory personnel, clinicians, community procedures (SOPs) are described in subunit 2.4 in
health officers and sanitary officers must work Part 1 of the book.
closely together in deciding the microbiological
services that are required and ensuring the
services provided are appropriate, reliable, and
Need for quality assurance and SOPs in
affordable.
microbiology
This involves identifying:
Microbiological investigations are important in
● The infectious diseases that require labora- the diagnosis, treatment, and surveillance of
tory investigation (priority pathogens). infectious diseases and policies regarding the
● Role of district laboratories in surveillance selection and use of antimicrobial drugs. It is
therefore essential that test reports:
work and the investigation of epidemics.
● Techniques (SOPs) to be used to collect – are reliable,
– standardized,
specimens, identify pathogens and perform
– provide the information that is required at
antimicrobial susceptibility tests.
the time it is needed,
● Most appropriate systems for reporting and
– in a form that can be understood.
recording the results of microbiological
Quality assurance is also required to minimize
investigations, collating and presenting data
waste and ensure investigations are relevant
for surveillance purposes.
and used appropriately.
● Quality assurance.
● Training requirements, supervision, and on-
going professional support.
WHO in its publication Basic laboratory procedures
● Equipment and microbiological supplies in clinical bacteriology1 states that quality assurance
needed and systems for distribution of in microbiology must be:
supplies.
– comprehensive: to cover every step in the cycle
● Costs involved. from collecting the specimen to sending the final
report to the doctor as shown opposite;
7.1