Bacteria are probably the most important group of micro‐organisms in terms of infection prevention and control because they are responsible for the majority of opportunistic infections in healthcare. A healthy human being will typically be host to a quadrillion (1000 trillion or 10¹⁵) bacteria – around ten times as many organisms as there are cells in the human body – and we need most of these to survive.

The so‐called ‘human microbiome’ is increasingly being recognized as an essential part of human health (Bhalodi et al. [7], Young [132]) and a variety of conditions – such as Crohn's disease, ulcerative colitis, irritable bowel syndrome, obesity, type 2 diabetes, Parkinson's disease, chronic fatigue syndrome, arthritis and even asthma – may all be related to disturbance of the balance of micro‐organisms in the gut, although the question remains as to whether this is a cause or effect (Otter [90], Tosh and McDonald [113], Wang et al. [120]). See Table 4.2 for examples of how the human microbiome can be protective.

In normal circumstances, the relationship between bacteria and their host is symbiotic and the organisms are considered to be commensal (i.e. their presence does not cause the host any problems) and mutually beneficial; however, if the host has lowered resistance or a bacteria gains access to a different site, it can become an opportunistic pathogen. For example, E. coli from the gut may cause a urinary tract infection (with associated symptoms) if it enters the urethra and ascends the urinary tract.

Despite the fact that we are surrounded by unquantifiable numbers of bacteria in our world, relatively few are pathogenic to us. There is an important balance to be struck in our home lives; we should not try to disinfect everything we come into contact with, and indeed many things around us are going to be contaminated (money, cash point buttons, our mobile phones and the handles on public transport, to name a few). If we are healthy and have good immunity and intact skin, this will often be of little consequence to us as long as we follow simple precautions such as practising hand hygiene, environmental hygiene (cleaning) and food hygiene.

For a patient receiving interventional healthcare, however, things can be very different and we need to do as much as possible to ensure items introduced into the care environment are free of pathogens. Our increasing understanding of the normal commensal micro‐organisms in humans suggests that restoring and maintaining the microbiome may provide a key to preventing colonization and infection, including with multi‐drug‐resistant organisms (Otter [90], Tosh and McDonald [113]), which can be ‘selected out’ when exposed to antibiotics. This means that bacteria that are sensitive to the antibiotics are killed but any resistant ones are left to replicate and become the dominant type. A developing form of treatment is the ‘faecal microbiota transplant’, or stool transplant, which involves replacing the stool in an affected gut with stool from a healthy donor. This has been shown to be very effective for treatment of intractable C. difficile (van Nood et al. [115]) and may be helpful in other conditions.

Sometimes a patient will be ‘colonized’ with a species of bacteria, which means it is present but not causing them harm. However, if the bacteria are transferred to another patient and gain access to a portal of entry, that person may suffer harm, so there is a need for effective precautions. Whether or not any particular situation will result in an infection depends on a wide range of factors and these are not always predictable. What is certain is that bacterial infections cannot occur when bacteria are not present, hence the importance of measures designed to minimize the risk of transmission.

The presence of an organism in a specimen result does not on its own imply that an infection has occurred. Any laboratory results must always be interpreted in association with an assessment of the patient's condition and symptoms, which will guide the need for treatment.

Viruses are much smaller, and even simpler, than bacteria. Nobel laureate Peter Medawar is said to have described viruses as ‘bad news wrapped in protein’ and indeed they are little more than a protein capsule containing some genetic material. They rely on other organisms for their survival and reproduce within a host cell, using the cell's own mechanisms to reproduce, which leads to the death of the host cell (Goering et al. [47]). The life cycle of a virus is illustrated in Figure 4.4. The small size of viruses (e.g. poliovirus is only 30 nanometres across) means that most are smaller than the wavelengths of visible light. They can only be ‘seen’ with a specialist instrument such as an electron microscope, which will only be available in a very few hospital microbiology laboratories. Diagnosis of viral infections is normally based on the patient's symptoms, with confirmation by laboratory tests designed to detect either the virus itself or antibodies produced by the patient's immune system as a response to infection (Goering et al. [47]). Modern laboratories use PCR to amplify the genes in the sample to make them detectable quickly.

There are viruses that specifically infect humans, other animals or plants, or even bacteria. This is one characteristic that can be used in classifying them. However, the main basis for classification is by the type of genetic material they contain – DNA (deoxyribonucleic acid) or RNA (ribonucleic acid), in either a double or single strand. Other characteristics include the shape of the viral particle and the sort of disease caused by infection (Gillespie and Bamford [45]).

A final point to consider in relation to viral structure and infection prevention and control is the presence or absence of a lipid envelope enclosing the viral particle. Viruses that have a lipid envelope, such as herpes zoster virus (responsible for chickenpox and shingles), are much more susceptible to destruction by alcohol than those without. Norovirus and or rotavirus, which are common causes of viral gastroenteritis (WHO [124]), are examples of viruses without a lipid envelope. For this reason, alcohol hand sanitizers are not recommended during outbreaks of norovirus in hospitals.

Like bacteria, fungi exist in many environments on earth, including occasionally as commensal organisms on human beings. Fungi are familiar to us as mushrooms and toadstools and the yeast that is used in brewing and baking. They also have many uses in the pharmaceutical industry, particularly in the production of antibiotics. Fungi produce spores, both for survival in adverse conditions, as bacteria do, and to provide a mechanism for dispersal in the same way as plants (Goering et al. [47]).

A few varieties of fungi are able to cause opportunistic infections in humans. These are usually found in one of two forms: either as single‐celled yeast‐like forms, which reproduce in a similar fashion to bacteria (by dividing or budding), or as plant‐like filaments called ‘hyphae’. A mass of hyphae together forms a ‘mycelium’. Some fungi may appear in either form, depending on environmental conditions. Fungal infections are referred to as ‘mycoses’. Superficial mycoses, such as ringworm and thrush (Candida albicans), usually involve only the skin or mucous membranes and are normally mild, if unpleasant; however, deeper mycoses involving major organs can be life threatening. These occur in patients who have severely impaired immune systems and may be an indicator of such impairment; for example, pneumonia caused by Pneumocystis jirovecii (previously carinii) is considered a clinical indication of AIDS (acquired immune deficiency syndrome). Superficial infections are generally transmitted by physical contact, whereas deeper infections can result from spores being inhaled. This is why it is important to ensure that patients with impaired immunity are protected from situations where the spores of potentially pathogenic fungi, such as Aspergillus spp., are likely to be released, for example during building work (Goering et al. [47]).

Protozoa are single‐celled animals, some species of which are medically important parasites of human beings, particularly in tropical and subtropical parts of the world, where diseases such as malaria are a major public health issue. Unlike bacteria, their relationship with humans is almost always parasitic. The life cycles of protozoa can be complex and may involve stages in different hosts.

Medically important protozoa include Plasmodium spp., the cause of malaria; Giardia spp. and Cryptosporidium spp., which can cause gastroenteritis; and Trichomoniasis spp., which is a sexually transmitted cause of vaginitis (Gillespie and Bamford [45]).

The most common routes of infection of protozoa are by consuming them in food or water or via an insect vector such as a mosquito (Goering et al. [47]). Cross‐infection in the course of healthcare is uncommon but not unknown.

‘Helminths’ is a generic term for parasitic worms. A number of worms from three different groups affect humans: tapeworms (cestodes), roundworms (nematodes) and flukes (trematodes). Transmission generally occurs via ingestion of eggs or larvae, or infected animals or fish, but some are transmitted via an insect vector and some, notably the nematode Strongyloides spp., have a larval stage that is capable of penetrating the skin (Gillespie and Bamford [45]).

Helminth infections can affect almost every part of the body, and the effects can be severe. For example, Ascaris worms can cause bowel obstruction if there are large numbers present; Brugia spp. and Wuchereria spp. obstruct the lymphatic system and eventually cause elephantiasis as a result; and infection with Toxocara spp. (often after contact with dog faeces) can result in epilepsy or blindness (Goering et al. [47]). However, cross‐infection in healthcare is not normally considered a significant risk.

Arthropods (insects) are most significant in infectious disease in terms of their function as vectors of many viral, bacterial, protozoan and helminth‐caused diseases. Some flies lay eggs in the skin of mammals, including humans, and the larvae feed and develop in the skin before pupating into the adult form, whereas some, such as lice and mites, are associated with humans for the whole of their life cycle. Such arthropod infestations can be uncomfortable, and there is often significant social stigma attached to them, possibly because the creatures are often visible to the naked eye. The activity of the insects and the presence of their saliva and faeces can result in quite severe skin conditions that are then vulnerable to secondary fungal or bacterial infection (Goering et al. [47]).

Species of Pediculus infest the hair and body of humans, feeding by sucking blood from their host. The adult animal is around 3 mm long and wingless, moving by means of claws. It cannot jump or fly, and dies within 24 hours if away from its host, so cross‐infection normally occurs via direct contact or transfer of eggs or adults through sharing personal items (Cummings et al. [15]).

Scabies is caused by the mite Sarcoptes scabiei, an insect less than 1 mm long that burrows into the top layers of skin. The female mites lay eggs in these burrows and the offspring can spread to other areas of the body. Infestation usually starts around the wrists and in between the fingers because acquisition normally occurs via close contact with an infected individual (e.g. by holding hands). The burrows are visible as a characteristic rash in the areas affected. The skin starts to itch a few weeks after infestation, which is a reaction to the faeces of the mite. A delay in recognition can lead to mass infestation, especially within families or in settings where there is a lot of interpersonal care, such as a nursing home. In immunocompromised hosts and those unable to practise normal levels of personal hygiene, very high levels of infestation can occur, often with thickening of the skin and the formation of thick crusts. This is known as ‘Norwegian scabies’ and is associated with a much higher risk of cross‐infection than the normal presentation.

Scabies is most often associated with long‐stay care settings, but there have been outbreaks associated with more acute healthcare facilities (Cassell et al. [12]). Treatment with scabicide must be co‐ordinated to ensure untreated hosts do not reinfect those already treated.

Prions are thought to be the causative agents of a group of diseases called transmissible spongiform encephalopathies (TSEs), the most well known of which are Creutzfeldt–Jakob disease (CJD) and its variant (vCJD) (Table 4.4). These are fatal neurodegenerative diseases with a lengthy incubation period (up to 50 years) and no conventional host response, making them difficult to detect.

TSEs can be naturally occurring, inherited or acquired (Table 4.4). They are characterized by ‘plaques’ in the brain that are surrounded by holes that give the appearance of a sponge, hence the name. The causative ‘organism’ is a prion, defined in 1982 by Stanley Prusiner as a proteinaceous infectious particle resistant to procedures that modify nucleic acid.

From an infection control perspective, the key point is that prions contain no genetic material; therefore, it can be argued that they are not alive and so cannot be killed. Control is achieved via recognition of risk and physical removal through cleaning procedures. Prions are not affected by routine decontamination processes such as autoclaving or chemical disinfection. This has led to extensive reviews of decontamination procedures in the UK with increased emphasis on effective washing to remove any residual organic material, and on the tracking of instruments to individual patients to facilitate any look‐back exercise. Modern decontamination services are now capable of removing prions from the surface of even complex instruments; however, where risk is identified, single‐use instruments are usually recommended, especially for neurological work.

In the 1990s there was a lot of concern about the emergence of vCJD, which was associated with consumption of contaminated beef from cattle who had bovine spongiform encephalopathy (BSE). With intense input from public health initiatives and what was then called the Ministry of Agriculture, Fisheries and Food, beef was made safe again. However, UK citizens born before 1992 are still considered at risk of vCJD due to its long incubation period.

There were also several cases of CJD associated with contaminated medical products, such as human pituitary hormone, dura mater grafts and medical instruments. For this reason, all patients undergoing surgery should be assessed for risk of CJD by asking the following questions:

A patient with CJD or vCJD is not infectious to other people under routine circumstances so no special precautions are required other than if dealing with cerebrospinal fluid (CSF). A spillage of CSF should be cleaned up with a strong disinfectant such as 10,000 ppm of chlorine.