Despite dramatic advances in hygiene, immunisation and antimicrobial therapy, infectious diseases are still a major cause of disease worldwide. Key challenges remain in tackling infection in resource-poor countries and in the emergence of new infectious agents and antimicrobial-resistant microorganisms. This chapter describes the biological and epidemiological principles of infectious diseases and the general approach to their prevention, diagnosis and treatment. Specific infectious diseases are described in Chapters 13–15 and many of the organ-based chapters. Prions are unique amongst infectious agents in that they are devoid of any nucleic acid. They appear to be transmitted by acquisition of a normal mammalian protein (prion protein, PrPC) which is in an abnormal conformation (PrPSC, containing an excess of beta-sheet protein); the abnormal protein inhibits the 26S proteasome, which can degrade misfolded proteins, leading to accumulation of the abnormally configured PrPSC protein instead of normal PrPC. The result is accumulation of protein which forms amyloid in the central nervous system, causing a transmissible spongiform encephalopathy (see Box 13.40, p. 329, and p. 1211). Prokaryotic cells are capable of synthesising 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 Gram-negative ones. The Gram-negative cell wall is surrounded by an outer membrane containing lipopolysaccharide. Plasmids are rings of extra-chromosomal DNA within bacteria, which can be transferred between organisms. Bacteria may be embedded in a polysaccharide capsule, and motile bacteria are equipped with flagella. Although many prokaryotes are capable of independent existence, some (e.g. Chlamydia trachomatis, Coxiella burnetii) are obligate intracellular organisms. Bacteria that replicate in artificial culture media are classified and identified using a range of characteristics (Box 6.2), with examples in Figures 6.3 and 6.4. Eukaryotes contain functional organelles, including nuclei, mitochondria and Golgi apparatus. Eukaryotes involved in human infection include fungi, protozoa (unicellular eukaryotes with a flexible cell membrane, p. 353) and helminths (complex multicellular organisms including nematodes, trematodes and cestodes, p. 369). 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. • 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. 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. 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). 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. • 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. 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. 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. • 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. 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). 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. 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. • 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) 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).
Principles of infectious disease
The infectious agent is the organism that causes the disease. The reservoir is the place where the population of an infectious agent is maintained. The portal of exit is the point from which the infectious agent leaves the reservoir. Transmission is the process by which the infectious agent is transferred from the reservoir to the human host, either directly or via a vector or fomite. The portal of entry is the body site that is first accessed by the infectious agent. Finally, in order for disease to ensue, the person to whom the infectious agent is transmitted must be a susceptible host.
Infectious agents
Prions
Viruses
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.
Prokaryotes: bacteria (including mycobacteria and actinomycetes)
A Alpha-haemolytic streptococci. The colonies cause partial haemolysis, which imparts a green tinge to the agar. The organism shown is Strep. pneumoniae from the cerebrospinal fluid of a patient with meningitis (note also the susceptibility to optochin (O), which is another feature used to identify this organism). B Beta-haemolytic streptococci. The colonies cause complete haemolysis, which renders the agar transparent. The organism shown is Strep. pyogenes (group A β-haemolytic streptococci) from a superficial wound swab.
Eukaryotes: fungi, protozoa and helminths
Host–pathogen interactions
Investigation of infection
Direct detection
Detection of whole organisms
Detection of components of organisms
Nucleic acid amplification tests (NAAT)
Culture
Blood culture
Specific immunological tests
Antibody detection
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.
Enzyme-linked immunosorbent assay
This can be configured in various ways. A Patient Ab binds to immobilised specific Ag, and is detected by addition of anti-immunoglobulin–enzyme conjugate and chromogenic substrate. B Patient Ab binds to immobilised Ig subclass-specific Ab, and is detected by addition of specific Ag, followed by antibody–enzyme conjugate and chromogenic substrate. C Patient Ab and antibody–enzyme conjugate bind to immobilised specific Ag. Magnitude of colour change reaction is inversely proportional to concentration of patient Ab. D Patient Ag binds to immobilised Ab, and is detected by addition of antibody–enzyme conjugate and chromogenic substrate. In A, the conjugate Ab is specific for human immunoglobulin. In B–D, it is specific for Ag from the disease-causing organism.
Agglutination tests
Other tests
Antibody-independent specific immunological tests
Epidemiology of infection
Geographic and temporal patterns of infection
Endemic disease
Emerging and re-emerging disease
(MDR-TB = multidrug-resistant tuberculosis; SARS = severe acute respiratory syndrome; vCJD = variant Creutzfeldt–Jakob disease; VRSA = vancomycin-resistant Staph. aureus) Adapted from Samaranayake 2006 – see p. 164.
Transmission of infection
Principles of infectious disease
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