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Management of epidemics
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Fu rt he r i nf o rm at ion 95
An epidemic, as dened by the World Health Organization, occurs when
‘in a community or region [the] cases of an illness, specic health-related
behaviour, or other health-related events [are] clearly in excess of normal
expectancy’. Epidemics that are small-scale or conned to a small geographic area are informally referred to as ‘outbreaks’.
Epidemics are regularly caused where preventative measures break
down; examples include breaches of food safety procedures in restaurants resulting in outbreaks of enteropathogenic E. coli infection, failure
to adequately maintain cooling towers causing Legionella infections and
falls in vaccination coverage resulting in measles epidemics.
Epidemics can also arise from novel infectious agents such as the
SARS-CoV-1, MERS, SARS-CoV-2 and H1N1 viruses, for which new
preventative measures require to be developed. Where epidemics from
novel agents are not controlled locally, but instead spread beyond international borders, these are termed pandemics, of which SARS-CoV-2
and H1N1 are examples.
To detect epidemics early, public health agencies undertake surveillance. Surveillance involves the collection and review of cases that have
been identied via statutory notications, or health information systems
(such as microbiology reporting systems). For some infections such as
E. coli and Legionella, one challenge for public health agencies is to
distinguish epidemics from ‘sporadic’ cases at an early stage. This is
done using human judgement, for example, if a large number of cases of
E. coli occur in individuals who ate a specic food, although this task is
sometimes supported using computer algorithms.
Epidemics require an incident management team, some of whose
members have legal powers to impose measures to control infection.
The team establish a formal case denition for conrmed, probable and
possible cases (based on epidemiological features as well as clinical and/
or microbiological ndings), interview individuals with whom cases have
had signicant contact (termed contact tracing), test potential sources
of infections (e.g. foodstuffs or industrial cooling towers), and implement
control measures. The latter might include requiring infected individuals
to isolate for a time period (e.g. until they are asymptomatic or until they
test negative depending on the infectious agent), and/or ordering temporary closure of businesses thought to be sources of infection (e.g. a
restaurant with poor food hygiene practices).
Epidemic curves are crucial to the monitoring and management of
epidemics. Figure 5.6 shows a notional epidemic curve for an epidemic
caused by a single source, which is eliminated after 31 days. However,
they are also used in more complex epidemics where there is person-to-person spread. In the latter, epidemic curves are used to estimate key statistics such as the basic reproduction number (R0) in the
population, as well as to make projections about future infections. Where
the source of an epidemic is not apparent, comparative epidemiological
methods can be used to identify the likely source, for example, a case–
control design may identify a higher than expected consumption of a
given food – for example uncooked legumes – among cases compared
to controls prompting testing of foods, an education campaign and/or
product recalls.
The principles for managing pandemics are similar to those for managing epidemics but operate on a national or international scale. The
universality of pandemics, however, means that they pose special problems. First, they pose risks to the society-wide infrastructure needed
to deal with diseases, including, but not limited to health-care facilities.
Secondly, pandemics, unlike local and regional epidemics are rare, so
15
10
New cases
5
0
1
6 11 16 21 26 31 26 41
Days
Fig. 5.6 Epidemic curve for a notional outbreak within a single ongoing
source. Red line indicates time point where source of infection was removed (e.g.
closure of a restaurant).
agencies have little direct experience with their management. For this
reason, most settings develop pandemic plans and undertake regular table-top simulations to test and improve their preparedness. The
COVID-19 pandemic, caused by SARS-CoV-2, is a key example and is
discussed in detail in Chapter 13
Further information
Kindig D, Stoddart G. What is population health? Am J Publ Health 2003;93:
380–383.
UK Faculty of Public Health. What is public health? http://www.fph.org.uk/what_
is_public_health
Burden of disease
GBD Diseases and Injuries Collaborators. Global burden of 369 diseases and
injuries in 204 countries and territories, 1990–2019: a systematic analysis for
the Global Burden of Disease Study 2019. Lancet 2019; 2020(396):
1204–1222.
GBD Risk Factors Collaborators. Global burden of 87 risk factors in 204
countries and territories, 1990–2019: a systematic analysis for the Global
Burden of Disease Study 2019. Lancet 2019; 2020(396):1223–1249.
GBD Viewpoint Collaborators. Five insights from the Global Burden of Disease
Study 2019. Lancet 2019; 2020(396):1135–1159.
Screening
Gov.UK. Population screening programmes. https://www.gov.uk/topic/population-
screening-programmes Detailed information on 11 NHS population screening
programmes.
Immunisation
Gov.UK. Immunisation against infectious disease. https://www.gov.uk/
government/collections/immunisation-against-infectious-disease-the-greenbook The Green Book has the latest information on vaccines and vaccination
procedures, for vaccine-preventable infectious diseases in the UK.
Epidemiology
Burgess S, Davey Smith G, Davies NM, et al. Guidelines for performing Mendelian
randomization investigations. Wellcome Open Res 2020;4:186.
STROBE-MR Steering Group: STROBE-MR: Guidelines for strengthening the
reporting of Mendelian randomization studies. PeerJ https://peerj.com/
preprints/27857/
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Multiple Choice Questions
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5.2. Which of the following statements describe the current newborn
blood spot screening programme in the UK?
5.1. Which of the following are examples of large-scale screening
programmes across all of the UK in 2021?
A. Cervical cancer national screening programme in women
B. Prostate cancer national screening programme in men
C. Diabetic eye screening programme in both men and women
D. Newborn hearing screening programme
E. Abdominal aortic aneurysm screening programme in both men
and women
Answer: A, C and D.
Prostate cancer screening has not proven to be cost-effective and
thus is not approved by the UK National Screening Committee. An
abdominal aortic aneurysm screening programme operates only in men
65 years of age or over but not in women.
A. Ideally, blood spots should be collected on day 14
B. Babies who missed the screen can be tested up to 1 month
of age
C. Blood spots are screened for sickle-cell disease
D. Blood spots are screened for cystic brosis
E. Blood spots are screened for congenital hypothyroidism
Answer: C, D and E.
Ideally, blood spots should be collected on day 5. Babies who missed
the screen can be tested up to 1 year of age. Newborn blood spot
screens for: sickle-cell disease, cystic brosis, congenital hypothyroidism and inherited metabolic diseases (PKU, MCADD, MSUD, IVA, GA1
and HCU – see Fig. 5.2).
JAT Sandoe
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DH Dockrell
6
Principles of infectious disease
Agents causing infection 98
Normal microbial ora 100
Host–pathogen interactions 101
Investigation of infection 102
Direct detection of pathogens 103
Culture 104
Indirect detection of pathogens 105
Antimicrobial susceptibility testing 106
Epidemiology of infection 106
Infection prevention and control 108
Health care-associated infection 109
Outbreaks of infection 109
Immunisation 111
Antimicrobial stewardship 112
Treatment of infectious diseases 113
Principles of antimicrobial therapy 113
Antibacterial agents 116
Antimycobacterial agents 121
Antifungal agents 121
Antiviral agents 122
Antiparasitic agents 124
98 P RIN C IP L ES O F I NFE C TI O US D IS E AS E
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‘Infection’ in its strict sense describes the situation where microorganisms
or other infectious agents become established in the host organism’s
cells or tissues, replicate, induce a host response, and result in pathologic
changes in tissues. If a microorganism survives and replicates on an epithelial surface without causing pathological change the host is said to be ‘colonised’ by that organism. If a microorganism survives and lies dormant after
invading host cells or tissues, infection is said to be ‘latent’. When a microorganism, or the host response to it, is sufcient to cause illness or harm,
then the process is said to have caused infection, which may manifest by
symptoms or signs. In milder cases there can be asymptomatic infection
that may be identied by detection of a pathogen or the host response
to the pathogen. Most pathogens (agents that can cause infection) are
microorganisms but some are multicellular organisms. The manifestations
of disease may aid pathogen dissemination (e.g. diarrhoea or coughing).
The term ‘infection’ is often used interchangeably with ‘infectious disease’ but not all infections are ‘infectious’, i.e. transmissible from person
to person, and not all infections result in symptomatic disease. Infectious
diseases caused by pathogens that are transmitted between hosts can
also be called ‘communicable diseases’, whereas infection caused by
organisms that are already colonising the host are described as ‘endogenous’. The distinction is blurred in some situations, including health
care-associated infections such as meticillin-resistant Staphylococcus
aureus (MRSA) or Clostridioides (formerly Clostridium) difcile infection
(CDI), in which colonisation precedes infection but the colonising bacteria may have been recently transmitted between patients. The chain
of infection (Fig. 6.1) describes elements for communicable disease
transmission.
Despite dramatic advances in hygiene, immunisation and antimicrobial
therapy, infections still cause a massive burden of disease worldwide.
Key challenges remain in tackling infection in resource-poor countries.
Microorganisms are continually mutating and evolving; the emergence
of new infectious agents (e.g. SARS-CoV-2, see Ch. 13) and antimicrobial-resistant microorganisms is therefore inevitable. This chapter
describes the biological and epidemiological principles of infectious diseases and the general approach to their prevention, diagnosis and treatment. Specic infectious diseases are described in Chapters 13–15 and
many of the organ-based chapters.
Agents causing infection
The concept of an infectious agent was established by Robert Koch in
the 19th century (Box 6.1). Although fullment of ‘Koch’s postulates’
became the standard for conrming the cause of an infection, many
infectious agents do not full Koch’s postulates (e.g. uncultivable organisms and the causes of endogenous infections), and the postulates are
now of mainly historical interest. The groups of infectious agents that are
now recognised are described in the following sections.
6.1 Denition of an infectious agent – Koch’s postulates
1. The same organism must be present in every case of the disease.
2. The organism must be isolated from the diseased host and grown in pure
culture.
3. The isolate must cause the disease, when inoculated into a healthy, susceptible
animal.
4. The organism must be re-isolated from the inoculated, diseased animal.
A
B C
Fig. 6.1 The chain of infection can be linear (A) and cyclical (B and C). Campylobacter enteritis) require a portal of exit from
respiratory virus infection) require a mode of exit from the infected person, a mode of transmission (e.g. contaminated respiratory droplets or transmission via the surface of an
susceptible human host and a mode of transmission back to the insect vector. Many infections involve a combination of these modes of transmission (e.g. Lyme disease, which
has both an animal host and an insect vector) or several different modes of transmission.
Interaction between host receptor
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(determines host-specificity of the virus)
molecule and virus ligand
Adsorption
1
Agents caus ing i nfect ion 99
Lipid envelope
Capsid
Nucleic acid
Host cell
Complete virus particles are
released by budding of host cell
membrane (shown here) or
disintegration of host cell
Assembly of virus components
is mediated by host and/or
Nucleic acid and protein synthesis is mediated by
host and/or viral enzymes. This takes place in nucleus
or cytoplasm, depending on the specific virus
Release 6
Assembly 5
viral enzymes
Synthesis
4
2 Penetration
Receptor-mediated endocytosis
or, in some enveloped viruses,
membrane fusion (shown here)
3
Uncoating
Nucleic acid is liberated from the
phagosome (if endocytosed)
and/or capsid by complex
enzymatic and/or receptor-mediated
processes
Virus
Fig. 6.2 A generic virus life cycle. Life cycle components common to most viruses are host cell attachment and penetration, virus uncoating, nucleic acid and protein
synthesis, virus assembly and release. Virus release is achieved either by budding, as illustrated, or by lysis of the cell membrane. Life cycles vary between viruses.
Viruses
Viruses are incapable of independent replication. Instead, they subvert
host cellular processes to ensure synthesis of their nucleic acids and
proteins. Viruses’ genetic material (the genome) consists of single- or
double-stranded DNA or RNA. Retroviruses transcribe their RNA into
DNA in the host cell by reverse transcription. An antigenically unique protein coat (capsid) encloses the genome, and together these form the
nucleocapsid. In many viruses, the nucleocapsid is packaged within a
lipid envelope. Enveloped viruses are less able to survive in the environment and are spread by respiratory, sexual or blood-borne routes,
including arthropod-based transmission. Non-enveloped viruses survive
better in the environment and are predominantly transmitted by faecal–
oral or, less often, respiratory routes. A generic virus life cycle is shown
in Figure 6.2. A virus that infects a bacterium is a bacteriophage (phage).
6.2 How bacteria are identied
Gram stain reaction (see Fig. 6.3)
Gram-positive (thick peptidoglycan layer), Gram-negative (thin peptidoglycan) or
unstainable
Microscopic morphology
Cocci (round cells) or bacilli (elongated cells)
Presence or absence of capsule
Cell association
Association in clusters, chains or pairs
Colonial characteristics
Colony size, shape or colour
Effect on culture media (e.g. β-haemolysis of blood agar in haemolytic
streptococci; see Fig. 6.4)
Atmospheric requirements
Prokaryotes: bacteria (including mycobacteria and
actinomycetes)
Prokaryotic cells can synthesise their own proteins and nucleic acids, and
are able to reproduce autonomously, although they lack a nucleus. The
bacterial cell membrane is bounded by a peptidoglycan cell wall, which is
thick (20–80 nm) in Gram-positive organisms and thin (5–10 nm) in Gramnegative ones. The Gram-negative cell wall is surrounded by an outer membrane containing lipopolysaccharide. Genetic information is contained within
a chromosome but bacteria may also contain rings of extra-chromosomal
DNA, known as plasmids, which can be transferred between organisms,
without cells having to divide. Bacteria may be embedded in a polysaccharide capsule, and motile bacteria are equipped with agella. Although many
prokaryotes are capable of independent existence, some (e.g. Chlamydia tra-
chomatis, Coxiella burnetii) are obligate intracellular organisms. Bacteria that
can grow in articial culture media are classied and identied using a range
of characteristics (Box 6.2); examples are shown in Figures 6.3 and 6.4
Strictly aerobic (requires O
aerobic (grows with or without O
Biochemical reactions
Expression of enzymes (oxidase, catalase, coagulase)
Ability to ferment or hydrolyse various biochemical substrates
Motility
Motile or non-motile
Antibiotic susceptibility
Identies organisms with invariable susceptibility (e.g. to optochin in
Streptococcus pneumoniae or metronidazole in obligate anaerobes)
Matrix-assisted laser desorption/ionisation time-of-ight mass spectrometry
(MALDI-TOF-MS)
A rapid technique that identies bacteria and some fungi from their specic
molecular composition
Sequencing bacterial 16S ribosomal RNA gene
A highly specic test for identication of organisms in pure culture and in
), strictly anaerobic (requires absence of O
2
) or micro-aerophilic (requires reduced O
2
), facultatively
2
)
2
samples from normally sterile sites
Eukaryotes: fungi, protozoa and helminths
Eukaryotic cells contain membrane-bound organelles, including nuclei,
mitochondria and Golgi apparatus. Pathogenic eukaryotes are unicellular
(e.g. yeasts, protozoa) or complex multicellular organisms (e.g. nematodes, trematodes and cestodes).
Whole-genome sequencing
Although not yet in routine use, whole-genome sequencing (WGS) offers the potential
to provide rapid and simultaneous identication, sensitivity testing and typing of
organisms from pure culture and/or directly from clinical samples. As such, WGS is
likely to replace many of the technologies described above over the next few years
6
100 P RIN C IP L ES O F I NFE C TI O US D IS E ASE
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Gram stain
Gram-positive
Colony morphology (e.g.
haemolysis), Gram stain
appearance, agglutination
reactions, coagulase test,
Gram-positive cocci–clusters
Examples
Staphylococcus
aureus
Coagulase-negative
staphylococci
Gram-positive cocci–chains
Examples
Oral streptococci
Streptococcus
pneumoniae (often
pairs)
-haemolytic streptococci
Enterococci (short chains)
cocci
catalase
or
Gram-positive
Colony morphology, growth
characteristics (e.g. growth
in anaerobic atmosphere),
Gram stain appearance,
MALDI-TOF-MS identification
Examples
Actinomycetes
Arcanobacterium haemolyticum
Bacillus spp.
Corynebacterium diphtheriae
Lactobacillus spp.
Listeria monocytogenes
Nocardia spp.
Clostridium spp.
bacilli
Gram-negative
Colony morphology, growth
characteristics, oxidase
fermentation/MALDI-TOF-MS
Examples
Neisseria meningitidis
Neisseria gonorrhoeae
Moraxella catarrhalis
cocci
reaction, sugar
identification
Gram-negative
Colony morphology, growth
reaction, MALDI-TOF-MS
Examples
Escherichia coli
Klebsiella pneumoniae
Proteus spp.
Enterobacter spp.
Serratia spp.
Salmonella spp.
Shigella spp.
Yersinia spp.
Vibrio spp.
Pseudomonas aeruginosa
bacilli
characteristics, lactose
fermentation, oxidase
identification
Fig. 6.3 Flow chart for bacterial identication, including Gram lm appearances on light microscopy (×100). (MALDI-TOF-MS = matrix-assisted laser desorption/
ionisation time-of-ight mass spectroscopy).
A
Fig. 6.4
β-haemolytic streptococci (A) and α-haemolytic streptococci (B)
spread on each half of a blood agar plate (backlit). This image is half life-size.
× 0.5. ß-haemolysis renders the agar transparent around the colonies (A) and
α-haemolysis imparts a green tinge to the agar (B).
Fungi exist as either moulds (lamentous fungi) or yeasts. Dimorphic
fungi exist in either form, depending on environmental conditions (see
Fig. 13.62). The fungal plasma membrane differs from the human cell
membrane in that it contains the sterol, ergosterol. Fungi have a cell
wall made up of polysaccharides, chitin and mannoproteins. In most
D
B
fungi, the main structural component of the cell wall is β-1,3polysaccharide. These differences from mammalian cells are important
-glucan, a
because they offer useful therapeutic targets.
Protozoa and helminths are often referred to as parasites. Many parasites have complex multistage life cycles, which involve animal and/or
plant hosts in addition to humans.
Prions
Although prions are transmissible and have some of the characteristics
of infectious agents, they are not microorganisms, and are discussed on
page 1181.
Normal microbial ora
The human body is colonised by large numbers of microorganisms (collectively termed the human microbiota). Colonising bacteria, also referred to
as the ‘normal bacterial ora’, are able to survive and replicate on epithelial
Host–p athog en in terac tions 101
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Scalp
As for skin
Oral cavity
Oral streptococci (α-haemolytic)
Anaerobic Gram-positive bacilli
(including Actinomyces spp.)
Anaerobic Gram-negative bacilli
Prevotella spp.
Fusobacterium spp.
Candida spp.
Skin
Coagulase-negative staphylococci
Staph. aureus
Corynebacterium spp.
Propionibacterium spp.
Malassezia spp.
Hands
Resident: as for skin
Transient: skin flora (including
meticillin-resistant and other
Staph. aureus), bowel flora
(including Clostridioides difficile,
Candida spp. and Enterobacterales)
Vagina
Lactobacillus spp.
Staph. aureus
Candida spp.
Enterobacterales
Strep. agalactiae (group B)
Perineum
As for skin
As for large bowel
Nares
Staph. aureus
Coagulase-negative staphylococci
Pharynx
Haemophilus spp.
Moraxella catarrhalis
Neisseria spp. (including N. meningitidis)
Staph. aureus
Strep. pneumoniae
Strep. pyogenes (group A)
Oral streptococci (α-haemolytic)
Small bowel
Distally, progressively increasing
numbers of large bowel bacteria
Candida spp.
Large bowel
Enterobacterales
Escherichia coli
Klebsiella spp.
Enterobacter spp.
Proteus spp.
Enterococci
E. faecalis
E. faecium
Streptococcus anginosus group
Strep. anginosus
Strep. intermedius
Strep. constellatus
Anaerobic Gram-positive bacilli
Clostridium spp.
Anaerobic Gram-negative bacilli
Bacteroides spp.
Prevotella spp.
Candida spp.
6
Fig. 6.5 Human non-sterile sites and normal ora in health.
surfaces, e.g. skin and mucosal surfaces. The gastrointestinal tract and
the mouth are the two most heavily colonised sites in the body and they
have distinct microbiota, in both composition and function. Knowledge of
non-sterile body sites and their normal bacterial ora is required to inform
microbiological sampling strategies and interpret culture results (Fig. 6.5).
The microbiota is the total burden of microorganisms, their genes and
their environmental interactions, and is now recognised to have a profound
inuence on human health and disease. Maintenance of the normal ora is
benecial to normal immune function. Other functions include: lower gastrointestinal tract bacteria synthesise and excrete vitamins (e.g. vitamins K
and B
); colonisation with normal ora confers ‘colonisation resistance’ to
12
infection with pathogenic organisms by altering the local environment (e.g.
lowering pH), producing antibacterial agents (e.g. bacteriocins (small antimicrobial peptides/proteins), fatty acids and metabolic waste products),
and inducing host antibodies that cross-react with pathogenic organisms.
Conversely, some body sites are either sterile or contain very low numbers of colonising bacteria. For example, the submucosal tissues, blood
stream, peritoneal and pleural cavities are maintained as sterile by physical separation from the external environment; and the lower airways and
bladder, sites that were formerly believed to be sterile but are now known
to support limited microbiota, are protected from excessive contamination by the mucociliary escalator and urethral sphincter respectively, as
well as local immune responses.
Members of the normal ora can cause (endogenous) infection by
‘translocation’ from their normal habitat to other body sites or by excessive growth at the ‘normal’ site (overgrowth). Overgrowth is exemplied
by dental caries and ‘blind loop’ syndrome (p. 821). Translocation results
from spread along a surface or penetration through a colonised surface,
e.g. urinary tract infection caused by perineal/enteric ora, and surgical
site infections, particularly of prosthetic materials, caused by skin ora
such as staphylococci. Normal ora also contribute to disease by
cross-infection; organisms colonising one individual can cause disease
when transferred to another, more susceptible, individual.
The importance of limiting antimicrobial-induced perturbations of
microbiota is increasingly recognised. ‘Probiotics’ are proprietary
microbes or mixtures of microbes administered with the aim of restoring a benecial prole of gastrointestinal normal ora. Faecal microora
transplantation (FMT) has the same aim, by giving gastrointestinal microbiota from healthy people (ltered extract of faeces) to a patient. Although
the clinical effectiveness of probiotics remains a subject of debate, FMT
has proven benet in recurrent C. difcile infection.
Host–pathogen interactions
A ‘pathogen’ is a microorganism that can cause infection. The manifestations of infection, including a pathogen’s ability to cause severe disease
in a previously healthy host, are affected by its ‘virulence’. Virulence is
determined by the number and type of disease-causing proteins and
other factors that it can produce (‘virulence factors’).
Primary pathogens cause disease in a proportion of individuals to
whom they are exposed, regardless of the host’s immunological
status.
Opportunistic pathogens cause disease only in individuals whose
host defences are compromised, e.g. by an intravascular catheter,
or when the immune system is compromised, by genetic susceptibility or immunosuppressive therapy.
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Determinants of virulence
For a primary pathogen to cause infection in a healthy host it must
compete with colonising ora to reach target host cells. It can do this
in various ways, including sequestration of nutrients, adapting metabolism to exploit metabolites not used by commensal ora, production
of bacteriocins, and using motility to ‘swim’ to the site of infection.
Many microorganisms, including viruses, use ‘adhesins’ to initiate their
attachment to host cells. Some pathogens can invade through tissues. Many bacteria and fungi multiply after initial adhesion to a host
surface to form ‘biolms’. These are complex three-dimensional structures surrounded by a matrix of host and bacterial products, which
afford protection to the colony and limit the effectiveness of antimicrobials. Biolm-related infections on man-made medical devices such as
vascular catheters or grafts can be particularly difcult to treat.
Pathogens may produce toxins, microbial molecules that cause
adverse effects on host cells, either at the site of infection, or remotely
following carriage through the blood stream. Endotoxin is the lipid
component of Gram-negative bacterial outer membrane lipopolysaccharide. It is released when bacterial cells are damaged and has
generalised inflammatory effects. Exotoxins are proteins released by
living bacteria, which often have specific effects on target organs
(Box 6.3).
Intracellular pathogens, including viruses, bacteria (e.g. Salmonella
spp., Listeria monocytogenes and Mycobacterium tuberculosis), para-
sites (e.g. Leishmania spp.) and fungi (e.g. Histoplasma capsulatum), are
able to survive in intracellular environments, including after phagocytosis
by macrophages. Pathogenic bacteria express different genes, depending on environmental stress (pH, iron starvation, O2 starvation etc.) and
anatomical location.
Genetic diversity enhances the pathogenic capacity of bacteria. Some
virulence factor genes are found on plasmids or in phages and are
exchanged between different strains or species. The ability to acquire
genes from the gene pool of all strains of the species increases diversity and the potential for pathogenicity. Viruses exploit their rapid reproduction and potential to exchange nucleic acid with other strains of the
virus to enhance diversity. Once a new strain acquires sufcient virulence
genes, including those enhancing infectivity, it may become an epidemic
or pandemic strain, resulting in regional or global transmission, respectively. This phenomenon accounts for inuenza and COVID-19 pandemics (see Box 6.10 and Ch. 13).
The host response
Innate and adaptive immune and inammatory responses, which humans
use to control the normal ora and respond to pathogens, are reviewed
in Chapter 4
6.3 Exotoxin-mediated bacterial diseases
Disease Organism
Antibiotic-associated diarrhoea/
pseudomembranous colitis
Botulism Clostridium botulinum
Cholera Vibrio cholerae
Diphtheria Corynebacterium diphtheriae
Haemolytic uraemic syndrome Enterohaemorrhagic Escherichia coli
Necrotising pneumonia Staphylococcus aureus
Tetanus Clostridium tetani
Toxic shock syndrome Staph. aureus
Clostridioides difcile
(E. coli O157 and other strains)
Streptococcus pyogenes
Pathogenesis of infectious disease
The severity of an infection is determined by the virulence of the pathogen
and the host response. Whilst an intact host response protects against
infection or reduces its severity, an excessive response can be damaging.
Both the host immune response and pathogen-produced factors can
contribute to tissue injury and systemic manifestations of infection (see
‘Sepsis’, p. 198). The contribution of the immune response to disease
manifestations is exemplied by the immune reconstitution inammatory
syndrome (IRIS), which can be seen in human immunodeciency virus
(HIV) infection, post-transplantation neutropenia or tuberculosis (which
causes suppression of T-cell function): there is a paradoxical worsening
of the clinical condition as the immune dysfunction is corrected, caused
by an exuberant but dysregulated inammatory response.
Clinical manifestations of infection
The clinical manifestations of infection can be localised to the site of
infection or generalised. Examples of local manifestations include the
inammation of cellulitis, facial pain of sinusitis or neck stiffness of meningitis (Ch. 13). Generalised manifestations include sweats, chills (feeling
very cold, even with extra clothes/blankets), rigors, fevers, anorexia, lethargy and generalised aches, and many of these result from the immune
response to infection. While the presence of infection may be clinically
clear in some settings, often it is not. Identifying the responsible pathogen in patients with infection is usually not possible on clinical grounds,
neither is prediction of pathogen susceptibility and resistance to antimicrobial agents. Hence there is a need to carefully investigate suspected
infections to optimise, or avoid unnecessary, antimicrobial therapy.
Rigors are a clinical symptom (or sign if they are witnessed) characterised
by feeling very cold (‘chills’) and uncontrollable shivering, usually followed
by fever and sweating. Rigors occur when the thermoregulatory centre
attempts to correct a core temperature to a higher level by stimulating
skeletal muscle activity and shaking.
Thermoregulation can be altered during infection, causing both hyperthermia (fever) and hypothermia. Fever is mediated mainly by ‘pyrogenic
cytokines’ (e.g. interleukins IL-1 and IL-6, and tumour necrosis factor
(TNF)), which are released in response to various stimuli. including activation of pattern recognition receptors (PRRs) by microbial products (e.g.
lipopolysaccharide) and factors released by injured cells (Ch. 4). This
induces prostaglandin E
in the preoptic nucleus of the hypothalamus (thermoregulatory centre),
causing the core temperature to rise.
production, which binds to specic receptors
2
Investigation of infection
The aims of investigating a patient with suspected infection are: to conrm the presence of infection; identify the specic pathogen(s); and, where
appropriate, identify its susceptibility to specic antimicrobial agents in order
to optimise therapy. Pathogens may be detected directly (e.g. by culturing a
normally sterile body site) or their presence may be inferred by identifying the
host response to the organism (‘indirect detection’, Box 6.4), e.g. C-reactive
protein or procalcitonin as part of the acute phase response (p. 68), although
these are activated to varying extents by other inammatory stimuli. Careful
sampling increases the likelihood of diagnosis (Box 6.5). Culture results must
be interpreted in the context of the normal ora at the sampled site (see Fig.
6.5). The extent to which a microbiological test result supports or excludes
a particular diagnosis depends on its statistical performance (e.g. sensitivity,
specicity, positive and negative predictive value). Sensitivity and specicity
vary according to the type of test, sampling and processing techniques, and
time between infection and testing. Positive and negative predictive values
depend on the prevalence of the condition in the test population. The complexity of test interpretation is illustrated in Figure 6.8 below, which shows
the ‘windows of opportunity’ afforded by various testing methods. Given
this complexity, coordinated thought and action ensures appropriate test
application and timing; effective communication between clinicians and the
microbiologists facilitates optimal results and interpretation.
Inve st igati on of infe ction 103
https://t.me/medicina_free
6.4 Tests used to diagnose infection
Non-specic markers of inammation/infection
e.g. White cell count in blood sample (WCC), plasma C-reactive protein (CRP),
procalcitonin (PCT)*, serum lactate, cell counts in urine or cerebrospinal uid
(CSF), CSF protein and glucose
Direct detection of organisms or organism components
Microscopy
Detection of organism components (e.g. antigen, toxin)
Nucleic acid amplication tests (e.g. polymerase chain reaction)
Culture of organisms
± Antimicrobial susceptibility testing
Tests of the host’s specic immune response
Antibody detection
Interferon-gamma release assays (IGRA)
Although PCT is used increasingly in clinical practice, further evidence is required to establish
*
its precise role in distinguishing bacterial infections from other causes of inammation.
6.5 How to provide samples for microbiological sampling
Communicate with the laboratory
Discuss samples that require processing urgently or that may contain hazardous
or unusual pathogens with laboratory staff before collection
Communication is key to optimising microbiological diagnosis. If there is doubt about
any aspect of sampling, it is far better to discuss it with laboratory staff beforehand
than to risk diagnostic delay by inappropriate sampling or sample handling
Take samples based on a clinical diagnosis
Sampling in the absence of clinical evidence of infection is rarely appropriate
(e.g. collecting urine, or sputum for culture)
Use the correct container
Certain tests (e.g. nucleic acid and antigen detection tests) require proprietary
sample collection equipment
Follow sample collection procedures
Failure to follow sample collection instructions precisely can result in false-
positive (e.g. contamination of blood culture samples) or false-negative (e.g.
collection of insufcient blood for culture) results
Label sample and request form correctly
Label sample containers and request forms according to local policies, with
demographic identiers, specimen type and time/date collected
Include clinical details on request forms
Identify samples carrying a high risk of infection (e.g. blood liable to contain a
blood-borne virus) with a hazard label
Use appropriate packaging
Close sample containers tightly and package securely (usually in sealed plastic
bags)
Attach request forms to samples but not in the same compartment (to avoid
contamination, should leakage occur)
Manage storage and transport
Transport samples to the microbiology laboratory quickly
Consider pre-transport storage, conditions (e.g. refrigeration, incubation,
storage at room temperature) vary with sample type
Notify the receiving laboratory prior to arrival of unusual or urgent samples, to
ensure timely processing
Direct detection of pathogens
Some direct detection methods provide rapid results and enable detection of organisms that cannot be grown easily on articial culture media,
such as Chlamydia spp.; they can also provide information on antimicrobial susceptibility, e.g. M. tuberculosis.
Detection of whole organisms
Whole organisms are detected by examination of biological uids or tissue using a microscope.
Bright eld microscopy (in which the test sample is interposed
between the light source and the objective lens) uses stains to
enhance visual contrast between the organism and its background.
Examples include Gram staining of bacteria and Ziehl–Neelsen or
auramine staining of acid- and alcohol-fast bacilli (AAFB) in tuberculosis (the latter requires an ultraviolet light source). In histopathological examination of tissue samples, stains are used to demonstrate
not only the presence of microorganisms but also features of disease pathology.
Dark eld microscopy (in which light is scattered to make organisms
appear bright on a dark background) is used, for example, to examine genital chancre uid in suspected syphilis.
Electron microscopy may be used to examine stool and vesicle uid
to detect enteric and herpesviruses, respectively, but its use has
largely been supplanted by nucleic acid detection (see below).
Flow cytometry can be used to analyse liquid samples (e.g. urine) for
the presence of particles based on properties such as size, impedance and light scatter. This technique can detect bacteria but may
misidentify other particles as bacteria too.
Detection of components of organisms
Components of microorganisms detected for diagnostic purposes include
nucleic acids, cell wall molecules, toxins and other antigens. Commonly
used examples include SARS-CoV-2 antigen in respiratory secretions,
Legionella pneumophila serogroup 1 antigen in urine and cryptococcal
polysaccharide antigen in cerebrospinal uid (CSF). Most antigen detection methods are based on in vitro binding of specic antigen/antibody
and are therefore described with serological tests below. Other methods
may be used, such as tissue culture cytotoxicity assay for C. difcile toxin.
In toxin-mediated disease, detection of toxin may be of greater relevance
than identication of the organism itself (e.g. stool C. difcile toxin).
Nucleic acid amplication tests
In a nucleic acid amplication test (NAAT), specic sequences of microbial DNA or RNA are identied using a nucleic acid primer that is amplied exponentially by enzymes to generate multiple copies of a target
nucleotide sequence. The most commonly used NAAT is the polymerase
chain reaction (PCR; see Fig. 3.11). Reverse transcription PCR (RT-PCR)
is used to detect RNA from RNA viruses. The use of uorescent labels
in the reaction enables ‘real-time’ detection of amplied DNA; quantication is based on the principle that the time taken to reach the detection threshold is proportional to the initial number of copies of the target
nucleic acid sequence. In ‘broad range’ (bacterial) PCR the primers are
targeted to parts of the gene that encode 16S ribosomal RNA (rRNA)
that have shared DNA sequences across most bacteria. Between these
shared DNA sequences, the 16S rRNA gene varies between species;
so, using PCR, nucleotide sequencing of the product and comparison of
the DNA sequence information with large databases, bacterial detection
and species identication can be achieved. In multiplex PCR, multiple
primer pairs are used to enable detection of several different organisms
in a single reaction.
Determination of nucleotide sequences in a target gene(s) can be used
to assign microorganisms to specic strains, which may be relevant to
treatment and/or prognosis (e.g. in hepatitis C infection). Genes that are
relevant to virulence (such as toxin genes) or antimicrobial resistance can
also be detected; for example, the mecA gene can be used to screen
for MRSA.
NAATs are the most sensitive direct detection methods and are also
relatively rapid. They are used widely in virology, where the possibility
of false-positive results from colonising or contaminating organisms is
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