Fungi exist as either moulds (filamentous fungi) or yeasts. Dimorphic fungi exist in either form, depending on environmental conditions (see Fig. 13.57, p. 382). 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 manno-proteins. In most fungi, the main structural component of the cell wall is β-1,3-D-glucan, a glucose polymer.

Protozoa and helminths are often referred to as parasites. Many parasites have complex multi-stage life cycles, which involve animal and/or plant hosts in addition to humans.

Normal flora

Every human is host to an estimated 10¹³–10¹⁴ colonising microorganisms, which constitute the normal flora. Resident flora are able to survive and replicate at a body site, whereas transient flora are present only for short periods. Knowledge of non-sterile body sites and their normal flora is required to interpret culture results (Fig. 6.5).

The relationship between human host and normal flora is symbiotic, meaning that the organisms are in close proximity, and either mutualistic (both organisms benefit) or commensal (one organism benefits whilst the other derives neither benefit nor harm). The microbiome is the total burden of microorganisms, their genes and environmental interactions; the human microbiome is recognised increasingly as exerting a profound influence over human health and disease.

Maintenance of the normal flora is beneficial to health. For example, lower gastrointestinal tract bacteria synthesise and excrete vitamins (e.g. vitamins K and B₁₂); colonisation with normal flora confers ‘colonisation resistance’ to infection with pathogenic organisms by altering the local environment (e.g. lowering pH), producing antibacterial agents (e.g. bacteriocins, fatty acids and metabolic waste products), and inducing host antibodies which cross-react with pathogenic organisms.

Conversely, normally sterile body sites must be kept sterile. The mucociliary escalator transports environmental material deposited in the respiratory tract to the nasopharynx. The urethral sphincter prevents flow from the non-sterile urethra to the sterile bladder. Physical barriers, including the skin, lining of the gastrointestinal tract and mucous membranes, maintain sterility of the blood stream, peritoneal and pleural cavities, chambers of the eye, subcutaneous tissue and so on.

The normal flora contribute to endogenous disease by either excessive growth at the ‘normal’ site (overgrowth) or translocation to a sterile site. Overgrowth is exemplified by ‘blind loop’ syndrome (p. 882), dental caries and vaginal thrush, in which external factors favour overgrowth of specific components of the normal flora. Translocation results from spread along a surface or penetration of a closed barrier: for example, in urinary tract infection caused by perineal/enteric flora, and in surgical site infections, particularly of prosthetic materials, caused by skin flora such as staphylococci. Normal flora also contribute to disease by cross-infection, in which organisms that are colonising one individual cause disease when transferred to another, more susceptible, individual.

Host–pathogen interactions

Pathogenicity is the capability of an organism to cause disease and virulence is the extent to which a pathogen is able to cause disease. Pathogens produce proteins and other factors, termed virulence factors, which interact with host cells to contribute to disease.

• Primary pathogens cause disease in a proportion of individuals to whom they are exposed, regardless of their immunological status.

• Opportunistic pathogens cause disease only in individuals whose host defences are compromised; for example, by genetic susceptibility or immunosuppressive disease or therapy.

Characteristics of successful pathogens

Successful pathogens have a number of attributes. They compete with host cells and colonising flora by various methods, including sequestration of nutrients, use of metabolic pathways not used by competing bacteria, and production of bacteriocins (small antimicrobial peptides/proteins that kill closely related bacteria). Motility enables pathogens to reach their site of infection, often in sterile sites that colonising bacteria do not reach, such as the distal airway. Many microorganisms, including viruses, use ‘adhesins’ to attach to host cells at the site of infection. Other pathogens can invade through tissues.

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 A domain 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).

6.3 Exotoxin-mediated bacterial diseases

Disease	Organism
Antibiotic-associated diarrhoea/pseudo-membranous colitis	Clostridium difficile (p. 308)
Botulism	Clostridium botulinum (p. 1210)
Cholera	Vibrio cholerae (p. 344)
Diphtheria	Corynebacterium diphtheriae (p. 345)
Haemolytic uraemic syndrome	Escherichia coli O157 (and other strains) (p. 495)
Necrotising pneumonia	Staphylococcus aureus (p. 682)
Tetanus	Clostridium tetani (p. 1209)
Toxic shock syndrome	Staphylococcus aureus (p. 331)

Intracellular pathogens, including viruses, bacteria (e.g. Salmonella spp., Listeria monocytogenes and Mycobacterium tuberculosis), parasites (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 arrays of genes, depending on environmental stress (pH, iron starvation, O₂ starvation and so on) and anatomical location. In quorum sensing, bacteria communicate with one another to adapt their replication or metabolism according to local population density. Bacteria and fungi may respond to the presence of an artificial surface (e.g. prosthetic device, venous catheter) by forming a biofilm, which is a population of organisms encased in a matrix of extracellular molecules. Biofilm-associated organisms are highly resistant to antimicrobial agents.

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 (the ‘bacterial supragenome’) increases diversity and the potential for pathogenicity. Viruses exploit their rapid reproduction and potential to exchange nucleic acid with host cells to enhance diversity. Once a strain acquires a particularly effective combination of virulence genes, it may become an epidemic strain, accounting for a large subset of infections in a particular region. This phenomenon accounts for influenza pandemics.

The host response

Innate and adaptive immune and inflammatory responses which humans use to control the normal flora and respond to pathogens are reviewed in Chapter 4.

Pathogenesis of infectious disease

The harmful manifestations of infection are determined by a combination of the virulence factors of the organism and the host response to infection. Despite the obvious benefits of an intact host response, an excessive response is undesirable. Cytokines and antimicrobial factors contribute to tissue injury at the site of infection, and an excessive inflammatory response may lead to hypotension and organ dysfunction (p. 82). The contribution of the immune response to disease manifestations is exemplified by the immune reconstitution inflammatory syndrome (IRIS). This is seen, for example, in human immunodeficiency 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 inflammatory response.

The febrile response

Thermoregulation (p. 103) is altered in infectious disease. Microbial pyrogens or the endogenous pyrogens released during tissue necrosis stimulate specialised cells such as monocytes/macrophages to release cytokines, including interleukin (IL)-lβ, tumour necrosis factor-alpha (TNF)-α, IL-6 and interferon (IFN)-γ. Cytokine receptors in the pre-optic region of the anterior hypothalamus activate phospholipase A, releasing arachidonic acid as substrate for the cyclo-oxygenase pathway and producing prostaglandin E₂ (PGE₂), which in turn alters the responsiveness of thermosensitive neurons in the thermoregulatory centre. Rigors occur when the body inappropriately attempts to ‘reset’ core temperature to a higher level by stimulating skeletal muscle activity and shaking.

The role of the febrile response as a defence mechanism requires further study, but there are data to support the hypothesis that raised body temperature interferes with the replication and/or virulence of pathogens.

Patients in whom a diagnosis of infectious disease is being considered are investigated with non-specific tests that reflect innate immune and acute phase responses (p. 82), and specific tests, which detect either a microorganism or the host response to the organism (Box 6.4). Careful sampling increases the likelihood of diagnosis (Box 6.5). Culture results must be interpreted in the context of the normal flora 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, specificity, positive and negative predictive value, p. 5). Sensitivity and specificity vary according to the time between infection and testing, and 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 6.7 (p. 141), which shows the ‘windows of opportunity’ afforded by various testing methods. Given this complexity, effective communication between the clinician and the microbiologist is vital to ensure accurate test interpretation.

6.4 Tests used to diagnose infection

Non-specific markers of inflammation/infection

• e.g. Full blood count (FBC), plasma C-reactive protein (CRP), procalcitonin, cell counts in urine or cerebrospinal fluid (CSF), CSF protein and glucose

Direct detection of organisms or organism components

• Microscopy

• Detection of organism components (e.g. antigen, toxin)

• Nucleic acid amplification (e.g. polymerase chain reaction)

Culture of organisms

• ± Antimicrobial sensitivity testing

Tests of the host’s specific immune response

• Antibody detection

• Interferon-γ release assays (IGRA)

6.5 How to provide samples for microbiological sampling

Communication

• Discuss samples that may require forwarding to another laboratory or processing urgently or by an unusual method with laboratory staff before collection

• Communication is the most important requirement for good microbiological sampling. 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

Indication

• Screening (e.g. collecting ‘routine’ urine, intravenous cannulae or sputum) in the absence of clinical evidence of infection is rarely appropriate

Container

• Certain tests (e.g. nucleic acid and antigen detection tests) require proprietary sample collection equipment

Collection

• Follow sample collection instructions precisely (e.g. proper collection of mid-stream, terminal and early morning urine samples, skin decontamination prior to blood culture etc.) to increase diagnostic yield

Labelling

• Label sample containers and request forms according to local policies, with demographic identifiers, 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

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)

Storage and transport

• Transport samples to the microbiology laboratory quickly

• If pre-transport storage is required, conditions (e.g. refrigeration, incubation, storage at room temperature) vary with sample type

• Notify the receiving laboratory prior to arrival of samples, to ensure timely processing

Direct detection

Direct detection methods provide rapid results and may be applied to organisms that cannot be grown easily on artificial culture media, such as Chlamydia spp. They do not usually provide information on antimicrobial susceptibility or the degree to which organisms are related to each other (which is important in the investigation of possible outbreaks), unless relevant specific nucleic acid sequences are detected by polymerase chain reaction (PCR).

Detection of whole organisms

Whole organisms are detected by examination of biological fluids or tissue using a microscope.

• Bright field 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. In histopathological examination of tissue samples, multiple stains are used to demonstrate not only the presence of microorganisms, but also features of disease pathology.

• Dark field microscopy (in which light is scattered to make organisms appear bright on a dark background) is used, for example, to examine genital chancre fluid in suspected syphilis.

• Electron microscopy may be used to examine stool and vesicle fluid to detect enteric and herpesviruses, respectively, but its use has largely been supplanted by nucleic acid detection (see below).

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 Legionella pneumophila serogroup 1 antigen in urine and cryptococcal polysaccharide antigen in cerebrospinal fluid (CSF). Most antigen detection methods are based on in vitro binding of specific antigen/antibody and are described below (p. 141). However, other methods may be used, such as mouse bioassay for detection of Clostridium botulinum toxin or tissue culture cytotoxicity assay for C. difficile toxin. In toxin-mediated disease, detection of toxin may be of greater relevance than identification of the organism itself (e.g. stool C. difficile toxin).

Nucleic acid amplification tests (NAAT)

Specific sequences of microbial DNA and RNA are identified using a nucleic acid primer which is amplified exponentially by enzymes to generate multiple copies of the specific sequence. The most commonly used amplification method is the polymerase chain reaction (PCR; see Fig. 3.12, p. 60). Reverse transcription (RT) PCR is used to detect RNA from RNA viruses (e.g. hepatitis C virus and HIV-1). The use of fluorescent-labelled primers and probes enables ‘real-time’ detection of amplified DNA; quantification 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 multiplex PCR, multiple primer pairs are used to enable detection of several different organisms in a single assay.

Nucleic acid sequencing is also used to assign microorganisms to specific strains according to their genotype, which may be relevant to treatment and/or prognosis (e.g. in hepatitis C infection, p. 954). Genes that are relevant to pathogenicity (such as toxin genes) or antimicrobial resistance can also be detected. For example, detection of the mecA gene is used to screen for MRSA.

NAAT are the most sensitive direct detection methods and are particularly useful when a rapid diagnosis is required. They are used widely in virology, where the possibility of false-positive results from colonising or contaminating organisms is remote, and are applied to blood, respiratory samples, stool and urine. In bacteriology, PCR is used to examine CSF, blood, tissue and genital samples, and multiplex PCR is being developed for use in faeces. PCR is also being used increasingly in mycology and parasitology.

Culture

Microorganisms may be both detected and further characterised by culture from clinical samples (e.g. tissue, swabs and body fluids).

• In vivo culture (in a living organism) is not used in routine diagnostic microbiology.

• Ex vivo culture (tissue or cell culture) was widely used in the isolation of viruses, but has been largely supplanted by nucleic acid amplification techniques.

• In vitro culture (in artificial culture media) of bacteria and fungi is used for definitive identification, to test for antimicrobial susceptibility and to subtype the organism for epidemiological purposes.

However, culture has its limitations. Results are not immediate, even for organisms which are easy to grow, and negative culture rarely excludes infection completely. Organisms such as Mycobacterium tuberculosis are inherently slow-growing, typically taking at least 2 weeks to be detectable, even in specialised systems. Certain organisms, such as Mycobacterium leprae and Tropheryma whipplei, cannot be cultivated on artificial media, and others (e.g. Chlamydia spp. and viruses) grow only in ex vivo systems, which are slow and labour-intensive to use.

Blood culture

Rapid microbiological diagnosis is required for blood-stream infection (BSI; Fig. 6.6). To diagnose BSI, a liquid culture medium is inoculated with freshly drawn blood, transported to the microbiology laboratory and incubated in a system that monitors it constantly for products of microbial respiration (mainly CO₂), generally using fluorescence. If growth is detected, organisms are identified and sensitivity testing is performed. Traditionally, identification has been achieved by Gram stain and culture. However, MALDI-TOF (see Box 6.2) is being used increasingly, as it is rapid and inexpensive, and enables identification of organisms directly from the blood-culture medium.

Specific immunological tests

Immunological tests may be used to detect the host response to a specific microorganism, and can enable the diagnosis of infection with organisms that are difficult to detect by other methods or are no longer present in the host. The term ‘serology’ describes tests carried out on serum, and is used to include both antigen and antibody detection.

Antibody detection

Organism-specific antibody detection is applied mainly to blood (Fig. 6.7). Results are typically expressed as titres: that is, the reciprocal of the highest dilution of the serum at which antibody is detectable (for example, detection at serum dilution of 1 : 64 gives a titre of 64). ‘Seroconversion’ is defined as either a change from negative to positive detection or a fourfold rise in titre between acute and convalescent serum samples. An acute sample is usually taken during the first week of disease and the convalescent sample 2–4 weeks later. Earlier diagnosis can be achieved by detection of IgM antibodies, which are produced early in infection (p. 77). A limitation of these tests is that antibody production requires a fully functional host immune system, so there may be false-negative results in immunocompromised patients. Also, other than in chronic infections and with IgM detection, antibody tests usually provide a retrospective diagnosis.

Fig. 6.7 Detection of antigen, nucleic acid and antibody in infectious disease.
The acute sample is usually taken during the first week of illness, and the convalescent sample 2–4 weeks later. Detection limits and duration of detectability vary between tests and diseases, although in most diseases immunoglobulin (Ig) M is detectable within the first 1–2 weeks.

Antibody detection methods are described below (antigen detection methods are also described here as they share similar methodology).

Enzyme-linked immunosorbent assay

The principles of the enzyme-linked immunosorbent assay (ELISA, EIA) are illustrated in Figure 6.8. These assays rely on linking an antibody with an enzyme which generates a colour change on exposure to a chromogenic substrate. Various configurations allow detection of antigens or specific subclasses of immunoglobulin (e.g. IgG, IgM, IgA). ELISA may also be adapted to detect PCR products, using immobilised oligonucleotide hybridisation probe and various detection systems.

Immunoblot (Western blot)

Microbial proteins are separated according to molecular weight by polyacrylamide gel electrophoresis (PAGE) and transferred (blotted) on to a nitrocellulose membrane, which is incubated with patient serum. Binding of specific antibody is detected with an enzyme–anti-immunoglobulin conjugate similar to that used in ELISA, and specificity is confirmed by its location on the membrane. Immunoblotting is a highly specific test, which may be used to confirm the results of less specific tests such as ELISA.

Immunofluorescence assays

Immunofluorescence assays (IFAs) are highly specific. In indirect immunofluorescence, a serum sample is incubated with immobilised antigen (e.g. cells known to be infected with virus on a glass slide) and antibody binding is detected using a fluorescent-labelled anti-human immunoglobulin (the ‘secondary’ antibody). This method can also detect organisms in clinical samples (usually tissue or centrifuged cells) using a specific antibody in place of patient serum. In direct immunofluorescence, clinical samples are incubated directly with fluorescent-labelled specific antibodies to detect antigen, eliminating the need for secondary antibody.

Complement fixation test

In a complement fixation test (CFT), patient serum is heat-treated to inactivate complement, and added to specific antigen. Any specific antibody present in the serum will complex with the antigen. Complement is then added to the reaction. If antigen–antibody complexes are present, the complement will be ‘fixed’ (consumed). Sheep erythrocytes, coated with an anti-erythrocyte antibody, are added. The degree of erythrocyte lysis reflects the remaining complement and is inversely proportional to the level of the specific antigen–antibody complexes.

Agglutination tests

When antigens are present on the surface of particles (e.g. cells, latex particles or microorganisms) and cross-linked with antibodies, visible clumping (or ‘agglutination’) occurs.

• In direct agglutination, patient serum is added to a suspension of organisms that express the test antigen. For example, in the Weil–Felix test, host antibodies to various rickettsial species cause agglutination of Proteus bacteria because they cross-react with bacterial cell surface antigens.

• In indirect (passive) agglutination, specific antigen is attached to the surface of carrier particles which agglutinate when incubated with patient samples that contain specific antibodies.

• In reverse passive agglutination (an antigen detection test), the carrier particle is coated with antibody rather than antigen.

Other tests

Immunodiffusion involves antibodies and antigen migrating through gels, with or without the assistance of electrophoresis, and forming insoluble complexes where they meet. The complexes are seen on staining as ‘precipitin bands’. Immunodiffusion is used in the diagnosis of endemic mycoses (p. 381) and some forms of aspergillosis (p. 697).

Immunochromatography is used to detect antigen. The system consists of a porous test strip (e.g. a nitrocellulose membrane), at one end of which there is target-specific antibody, complexed with coloured microparticles. Further specific antibody is immobilised in a transverse narrow line some distance along the strip. Test material (e.g. blood or urine) is added to the antibody–particle complexes, which then migrate along the strip by capillary action. If these are complexed with antigen, they will be immobilised by the specific antibody and visualised as a transverse line across the strip. If the test is negative, the antibody–particle complexes will bind to a line of immobilised anti-immunoglobulin antibody placed further along the strip, which acts as a negative control. Immunochromatographic tests are rapid and relatively cheap to perform, and are appropriate for point-of-care testing, e.g. in HIV 1.

Antibody-independent specific immunological tests

Interferon-gamma release assays (IGRA) are being used increasingly to diagnose tuberculosis (p. 692). The principle of the assay is that T lymphocytes of patients infected with Mycobacterium tuberculosis (MTB) release IFN-γ when they are exposed to MTB-specific peptides. The absence of these peptides in bacille Calmette–Guérin (BCG; see Box 6.14) vaccine results in IGRA tests being more specific for the diagnosis of tuberculosis infection than the tuberculin skin test (p. 692), because the latter may be positive as a result of previous BCG vaccination.

Antimicrobial susceptibility testing

If growth of microorganisms in culture is inhibited by the addition of an antimicrobial agent, the organism is considered to be susceptible. Bacteriostatic agents cause reversible inhibition of growth and bactericidal agents cause cell death; the terms fungistatic/fungicidal are equivalent for antifungal agents, and virustatic/virucidal for antiviral agents. The lowest concentration of antimicrobial agent at which growth is inhibited is the minimum inhibitory concentration (MIC), and the lowest concentration that causes cell death is the minimum bactericidal concentration (MBC). If the MIC is less than or equal to a predetermined breakpoint threshold, the organism is considered susceptible, and if the MIC is greater than the breakpoint, it is resistant.

Breakpoints are determined for each antimicrobial agent from a combination of pharmacokinetic and clinical data. The relationship between in vitro antimicrobial susceptibility and clinical response is complex, as response also depends on immune status, pharmacokinetic variability (p. 21), comorbidities that may influence pharmacokinetics or pharmacodynamics, and antibiotic dosing, as well as MIC/MBC. Thus, susceptibility testing does not guarantee therapeutic success.

Susceptibility testing is most often carried out by disc diffusion (Fig. 6.9). Antibiotic-impregnated filter paper discs are placed on an agar plate containing bacteria. The antibiotic diffuses through the agar, resulting in a concentration gradient centred on the disc. Bacteria are unable to grow where the antibiotic concentration exceeds the MIC, which may therefore be inferred from the size of the zone of inhibition. Susceptibility testing methods using antimicrobials diluted in liquid media are generally more accurate and reproducible, and are used for generating epidemiological data.

Epidemiology of infection

The communicability of infectious disease means that, once a clinician has diagnosed an infectious disease, potential exposure of other patients must be considered. The patient may require treatment in isolation, or an outbreak of disease may need to be investigated in the community (Ch. 5). The approach will be specific to the microorganism involved (Chs 13–15) but the principles are outlined below.

Geographic and temporal patterns of infection

Endemic disease

Endemic disease has a constant presence within a given geographic area or population. The infectious agent may have a reservoir, vector or intermediate host that is geographically restricted, or may itself have restrictive environmental requirements (e.g. temperature range, humidity). The population affected may be geographically isolated, or the disease may be limited to unvaccinated populations. Factors that alter geographical restriction include:

• expansion of an animal reservoir (e.g. Lyme disease from reforestation)

• vector escape (e.g. airport malaria)

• extension of host range (e.g. schistosomiasis from dam construction)

• human migration (e.g. severe acute respiratory syndrome (SARS) coronavirus)

• public health service breakdown (e.g. diphtheria in unvaccinated areas)

• climate change.

Emerging and re-emerging disease

An emerging infectious disease is one that has newly appeared in a population, or has been known for some time but is increasing in incidence or geographic range. If the disease was previously known and thought to have been controlled or eradicated, it is considered to be re-emerging. Many emerging diseases are caused by organisms which infect animals and have undergone adaptations that enable them to infect humans. This is exemplified by HIV, which is believed to have originated in higher primates in Africa. The geographical pattern of some recent emerging and re-emerging infections is shown in Figure 6.10.

Reservoirs of infection

The US Centers for Disease Control (CDC) define a reservoir of infection as ‘one or more epidemiologically connected populations or environments in which a pathogen can be permanently maintained, and from which infection is transmitted to a defined target population’. Reservoirs of infection may be human, animal or environmental.

Human reservoirs

Colonised individuals or those with clinical infectious disease may act as reservoirs, e.g. for Staph. aureus (including MRSA), which is carried in the nares of 30–40% of humans, and C. difficile. For infected humans to act as reservoirs, the infections caused must be long-lasting and/or non-fatal, at least in a proportion of those affected, to enable onward transmission (e.g. tuberculosis, sexually transmitted infections). Humans are the only reservoir for some organisms (e.g. smallpox and measles).

Animal reservoirs

The World Health Organization (WHO) defines a zoonosis as ‘a disease or infection that is naturally transmissible from vertebrate animals to humans’. The infected animal may be asymptomatic. Zoonotic agents may be transmitted via any of the routes described below. Primary infection with zoonoses may be transmitted onward between humans, causing secondary disease (e.g. Q fever, brucellosis, Ebola).

Environmental reservoirs

Many infective pathogens are acquired from an environmental source. However, some of these are maintained in human or animal reservoirs, with the environment acting only as a conduit for infection.

Transmission of infection

Infectious agents may be transmitted by one or more of the following routes:

• Respiratory route: inhalation.

• Faecal–oral route: ingestion of infectious material originating from faecal matter.

• Sexually transmitted infections: direct contact between mucous membranes.

• Blood-borne infections: direct inoculation of infected blood or body fluids.

• Direct contact: very few organisms are capable of causing infection by direct contact with intact skin. Most infection by this route requires inoculation or contact with damaged skin.

• Via a vector or fomite: the vector/fomite bridges the gap between the infected host or reservoir and the uninfected host. Vectors are animate, and include mosquitoes in malaria and dengue, fleas in plague and humans in MRSA. Fomites are inanimate, and include items such as door handles, water taps, ultrasound probes and so on, which are particularly associated with health care-associated infection.

The likelihood of infection following transmission of an infectious agent depends on organism factors and host susceptibility. The number of organisms required to cause infection or death in 50% of the exposed population is referred to as the ID₅₀ (infectious dose) and LD₅₀ (lethal dose), respectively. The incubation period is the time between exposure and development of disease, and the period of infectivity is the period after exposure during which the patient is infectious to others. Knowledge of incubation periods and periods of infectivity is important in controlling the spread of disease, although for many diseases these estimates are imprecise (Boxes 6.6 and 6.7).

6.6 Periods of infectivity in childhood infectious diseases ¹

Disease	Infectious period
Chickenpox	From 4 days before² until 5 days after appearance of the rash³
Measles	From 1–2 days before onset of rash; duration unknown³
Mumps	Unknown⁴
Rubella	Unknown, but most infectious during prodromal illness³
Scarlet fever	Unknown⁵
Whooping cough	Unknown^5,6

¹ From Richardson M, Elliman D, Maguire H, et al. Pediatr Infect Dis J 2001; 20:380–388. These recommendations may differ from local or national guidance.

² Transmission before 48 hrs prior to the onset of rash is rare.

^3,4,5 Exclude from contact with non-immune and immunocompromised people for 5 days from ³onset of rash, ⁴onset of parotitis or ⁵start of antibiotic treatment.

⁶ Exclude for 3 weeks if untreated.

6.7 Incubation periods of important infections ¹

Infection	Incubation period
Short incubation periods
Anthrax, cutaneous³	9 hrs to 2 wks
Anthrax, inhalational³	2 days²
Bacillary dysentery⁵	1–6 days
Cholera³	2 hrs to 5 days
Dengue haemorrhagic fever⁶	3–14 days
Diphtheria⁶	1–10 days
Gonorrhoea⁴	2–10 days
Influenza⁵	1–3 days
Meningococcaemia³	2–10 days
Norovirus¹	1–3 days
SARS coronavirus³	2–7 days²
Scarlet fever⁵	2–4 days
Intermediate incubation periods
Amoebiasis⁶	1–4 wks
Brucellosis⁴	5–30 days
Chickenpox⁵	11–20 days
Lassa fever³	3–21 days
Malaria³	10–15 days
Measles⁵	6–19 days
Mumps⁵	15–24 days
Poliomyelitis⁶	3–35 days
Psittacosis⁴	1–4 wks
Rubella⁵	15–20 days
Typhoid⁵	5–31 days
Whooping cough⁵	5–21 days
Long incubation periods
Hepatitis A⁵	3–7 wks
Hepatitis B⁴	6 wks to 6 mths
Leishmaniasis, cutaneous⁶	Weeks to months
Leishmaniasis, visceral⁶	Months to years
Leprosy³	5–20 yrs
Rabies⁴	2–8 wks²
Trypanosoma brucei gambiense infection⁶	Months to years
Tuberculosis⁵	1–12 mths

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