Male urethritis

Inflammation of the male urethra can be either infectious, caused by sexually transmitted diseases, or due to trauma following urological procedures, intermittent catheterization, insertion of foreign bodies, anatomical abnormalities or following accidental injury. Traditionally, the infectious causes have been divided into gonococcal urethritis, caused by N. gonorrheae, or non-gonococcal (also known as ‘non-specific’ urethritis, NSU). Chlamydia trachomatis is the most common agent of NSU, but other agents include Ureaplasma urealyticum, Mycoplasma hominis and Trichomonas vaginalis. Mixed infections can occur in a minority of cases. Other rare causes include lymphogranuloma venereum, herpes genitalis, syphilis, mycobacterium and typical bacteria (usually gram-negative rods) that are associated with cystitis in the presence of a urethral stricture. In vitro experiments have demonstrated that some bacteria, in particular the urogenital pathogens, can adhere to spermatozoa; this property might be an important mechanism by which infections may be spread throughout the female reproductive tract, with sperm acting as vectors of disease (Hosseinzadeh et al., 2000). Urethritis may also be seen in association with other infectious syndromes such as epididymitis, orchitis, prostatitis, proctitis, Reiter's syndrome, iritis, pneumonia, otitis media or urinary tract infection.

Signs and symptoms

Infections may be asymptomatic; patients sometimes present following partner screening. Symptoms may include urethral discharge, urethral itch, and dysuria. Urinary frequency and urgency are typically absent and, if present, should suggest prostatitis or cystitis.

Intoduction

Medical mycology studies fungi that may produce disease in humans and other animals. Fungi are not related to bacteria: bacteria are prokaryotes, without a membrane-bound nucleus or intracellular organelles; fungi are eukaryotes that have both sexual and asexual reproductive phases, and have membrane-bound organelles including nuclei, mitochondria, golgi apparatus, endoplasmic reticulum, lysosomes, etc. Initially, fungi were thought to be part of the Kingdom of Plantae, albeit lower members of this Kingdom. When the Five Kingdom division of life forms came into general use, however, the fungi were separated into their own Kingdom, separate from the plants, due to their lack of chloroplasts or chlorophyll, the composition of their cell wall and their asexual reproduction by means of spores. Whereas eukaryotes such as plants and algae contain chlorophyll that allows them to generate energy by photosynthesis (autotrophic), fungi lack chlorophyll: they are heterotrophic, and must absorb nutrients from their environment or host. They can be saprophytes, living on dead organic matter (e.g. mushrooms, toadstools, bread mould) or parasites utilizing living tissues (e.g. yeast infections). Fungi are aerobic and non-motile; they have rigid cell walls composed of complex polysaccharides such as chitins or glucans and their plasma membrane contains sterols, principally ergosterol. They grow best at a neutral pH in a moist environment, but can tolerate a range of pH.

Introduction

Viruses are obligate intracellular parasites, i.e. they require an animal, plant or bacterial cell for growth, survival and replication. The virus genome can consist of either DNA or RNA, and they use the host cell replication and protein synthesis machinery for their own growth and replication. Viruses do not have features that previously were thought to be necessary for any living organism: they do not respire, move or grow, produce waste products, utilize energy or display irritability; they do, however, have the ability to replicate inside eukaryotic or prokaryotic host cells. Viruses that infect bacteria are known as bacteriophages, and there are large numbers of viruses that infect plants, with significant impact on horticulture and crops.

Until the recent discovery of prions, viruses were described as the smallest known entities that can cause disease. Their size ranges from 20 nm (poliovirus) to around 400 nm (poxviruses). The smallest known bacterium is around 200 nm (mycoplasma), and the larger ones such as staphylococci are around 500 nm in size. Viruses therefore pass readily through bacterial filters (normally 220 nm) and they can only be visualized by electron microscopy, using negative staining (see Fig. 1.3).

Virus structure

The viral nuclei acid genome may consist of DNA or RNA (but never both), and this can be double-stranded, single-stranded, segmented or non-segmented, with positive or negative strand orientation.

Infection occurs when a susceptible part of the human body is exposed to a microorganism; this exposure may, or may not, lead to disease. Only the body, never the environment, is infected. Contamination may refer to the body (e.g. a wound can be contaminated), or to the working environment. Contamination occurs in the laboratory setting when a microorganism comes into contact with aseptic or sterile materials or supplies being handled or manipulated: contamination with environmental organisms has a negative impact on embryo culture. Gametes or embryos may be contaminated by exposure to organisms in the environment, exposure to pathogens found in body fluids of patients undergoing treatment, or from microorganisms carried by ART staff. When gametes or embryos are exposed to pathogenic organisms, there is the potential to transmit disease to several targets, including the developing embryo, the couple undergoing ART treatment, neighbouring gametes and embryos and subsequently other couples undergoing ART treatment, as well as ART health-care personnel. This unique situation, with multiple targets for contamination and infection, make infection and contamination control crucial in the ART laboratory.

Tissue culture systems used in the ART laboratory are designed to provide a physiological environment that can support and sustain cell metabolism and division, making them an ideal medium for the replication of a variety of microorganisms.

Bacteria are unicellular organisms that belong to the kingdom of Prokaryotae. Whereas eukaryotes have membrane-bound cytoplasmic organelles designed to carry out specific functions, bacteria have no welldefined nucleus, nuclear membrane or membranebound organelles. Their bacterial genome consists of a single, double-stranded, closed circular DNA molecule that lies within the cytoplasm, along with mesosomes, ribosomes, and various cytoplasmic granules, all of which are enclosed within a thin elastic trilaminar membrane. The majority of bacteria also lack the cytoskeleton that gives support and structure to eukaryotes. With the exception of the mycoplasmas, bacteria contain a cell wall of unique chemical composition. They are microscopic in size, with species ranging from 0.25 μm to 1 μm in width and 1 μm to 10 μm in length. Some bacterial species have capsules, flagella, or pili, and some species produce endospores.

Bacteria are divided into Orders, Families, Genera, and species, and named according to genus and species: e.g. Escherichia (genus) coli (species). Bacteria within the same genus and species also may be designated as subspecies, based upon differences in geographic distribution, transmission, clinical manifestation, and pathogenicity, e.g. Treponema pallidum subsp. pallidum, and T. pallidum subsp. pertenue. They may also be classified in serogroups, serotypes, or serovars based upon surface or subsurface antigens or according to the type of capsule surrounding the bacterium. For example, streptococci are grouped on the basis of specific cell wall polysaccharide antigens (Lancefield groups).

History of microbiology

The history of microbiology, the scientific study of microorganisms, had its origins in the second half of the seventeenth century, when Anton van Leeuwenhoek (1632–1723), a tradesman in Delft, Holland, learned to grind lenses in order to make microscopes that would allow him to magnify and observe a wide range of materials and objects. Although he had no formal education and no knowledge of the scientific dogma of the day, his skill, diligence and open mind led him to make some of the most important discoveries in the history of biology. He made simple powerful magnifying glasses, and with careful attention to lighting and detail, built microscopes that magnified over 200 times. These instruments allowed him to view clear and bright images that he studied and described in meticulous detail. In 1673 he began writing letters to the newly formed Royal Society of London, describing what he had seen with his microscopes. He corresponded with the Royal Society for the next 50 years; his letters, written in Dutch, were translated into English or Latin and printed in the Philosophical Transactions of the Royal Society. These letters include the first descriptions of living bacteria ever recorded, taken from the plaque between his teeth, and from two ladies and two old men who had never cleaned their teeth:

Prion protein

‘Prions’ (proteinaceous infectious particles) are particles made up of an abnormal glycoprotein that is capable of causing a cell to produce more abnormal protein. The Prion particle is a unique agent, infectious by biological and medical criteria, but different from all known conventional microbes because it contains no elements of nucleic acid genetic material. Prusiner identified and classified prion diseases in 1982, and his work in describing prions as infectious protein particles that cause neurodegenerative disorders (Prusiner, 1991, 1995) gained the Nobel Prize in 1997. All known prion diseases are fatal; they are known as ‘spongiform encephalopathies’ because they cause the brain to be riddled with holes or ‘spongy’, with accompanying symptoms of progressive neurological degeneration. The spongiform change occurs without inflammation, inclusion bodies, or apparent immune response.

Prion diseases

Prion diseases, known as transmissible spongiform encephalopathies, (TSEs) can be infectious/ iatrogenic (5%), inherited (10%), or sporadic (‘Classical’, 85%).

Animal

The first neurological disease of this kind was described in sheep during the early eighteenth century. Affected sheep rub or ‘scrape’ their coat against a tree, as if it itches – hence it was given the name ‘scrapie’ in England. In France, it was known as ‘La tremblante’ because the animals shake due to ataxia. In 1966, Alper showed that the infectious agent responsible for scrapie in sheep was very UV-resistant, compared with known viruses. This finding led to the suggestion that scrapie might be infectious without the involvement of a nucleic acid.

The female genital tract hosts a variety of microbial organisms: composition of the normal flora varies according to the woman's age, site in the genital tract and hormonal status (prepubertal, different phases of the menstrual cycle, pregnancy, oral contraceptive use, hormone replacement therapy and postmenopausal). Vaginal secretions are usually clear, scanty and have a pH below 4.5. Normal vaginal flora usually favours colonization by the hydrogen peroxide producing Lactobacillus spp.; these organisms use epithelial glycogen and produce lactic acid, leading to the resultant normally acid pH of vaginal secretions. Imbalance in the vaginal flora or infection with some sexually transmitted pathogens may lead to abnormal vaginal discharges associated with inflammation. Not all vaginal discharges are vaginal in origin – uterine infections or mucopurulent cervicitis will also result in a discharge from the vagina.

Vulvo-vaginitis can have several different etiologies; three types of vulvo-vaginitis syndromes will be reviewed here:

1. trichomoniasis, caused by the protozoan Trichomonas vaginalis;

2. candidiasis (‘thrush’), caused by the yeast Candida albicans;

3. bacterial vaginosis, due to overgrowth with the anaerobic bacteria, Mycoplasma hominis and Gardnerella vaginalis or other Candida spp.

The vaginitis syndromes are significant from several standpoints.

• Trichomoniasis, and rarely some candidal infections, are considered to be sexually transmitted. The mode of transmission for bacterial vaginosis is unknown. Although there is some evidence to suggest that bacterial vaginosis is sexually transmitted, this conclusion is not supported by the bulk of the evidence.

The eye is a sense organ designed to focus light onto receptor cells and to control the amount of light reaching these receptors. Its optimal functioning requires the presence of certain accessory structures which include the eyebrows, eyelids, eyelashes, and the lacrimal apparatus.

Anatomy and physiology of the eye

The basic anatomy of the eye and its accessory structures are shown in Figure 3.1. The eyeball is approximately 2.5 cm in diameter and is bounded by a white, fibrous, protective layer of connective tissue (the sclera) at the back and by a transparent fibrous layer (the cornea) at the front. Apart from the cornea, the front of the eye is covered by a transparent layer of modified skin (the conjunctiva), which also lines the eyelid. Inside the sclera is a layer of vascular tissue (the choroid), which supplies nutrients to it. The region of the choroid beneath the cornea is modified to form the iris and ciliary body, which are muscular structures involved in controlling, respectively, the amount of light entering the eye and the shape of the lens. The innermost layer of the eye is the retina, which extends back from the ciliary body to cover the rear three–quarters of the surface of the eyeball. The retina contains the light–sensitive cells and has its own blood and nerve supply.

The gastrointestinal tract (GIT) and the accessory digestive organs (teeth, tongue, salivary glands, liver, gallbladder, and pancreas) together constitute the digestive system whose function is to break down dietary constituents into small molecules and then to absorb these molecules for subsequent distribution throughout the body. The GIT is, basically, a continuous tube extending from the mouth to the anus (Figure 7.1). The main regions of the GIT include the oral cavity, the oropharynx, and laryngopharynx (which are also part of the respiratory tract), oesophagus, stomach, small intestine (duodenum, jejunum, and ileum), and the large intestine (caecum, colon, and rectum). Because of differences in their anatomy, physiology, organisation, and location, each of these regions provides a different set of environmental conditions for potential microbial colonisers and has, therefore, a distinctive microbiota. Although each of these regions is distinctly different, the oral cavity has some unique features (e.g., a complex anatomy leading to a great variety of habitats, the presence of non–shedding surfaces; i.e., teeth, which enable biofilm formation and a high oxygen content), which render it very different from the rest of the GIT. In contrast, the other regions of the GIT have a far simpler structure (basically, tubular in nature), which results in a lower habitat diversity within a particular region, non–shedding surfaces are absent, most regions (below the stomach) are anaerobic, and many regions (within the large intestine) have a lumen which is usually filled with material.

The oral cavity is not simply the entrance to the gastrointestinal tract (GIT), but consists of a complex system of tissues and organs with a variety of functions which together are involved in selecting food that is suitable for intake and processing the food into a form that is suitable for passage into the rest of the GIT. Another major function of the oral cavity is speech production. With regard to its feeding function, the oral cavity contains several sensory systems which are involved in perceiving the taste, smell, touch, and temperature of the food. This sensory information is analysed in the central nervous system and used to determine the acceptability of the food. If it is regarded as acceptable, then saliva is secreted, chewing is initiated, and eventually swallowing takes place.

Anatomy and physiology of the oral cavity

The oral cavity is formed from the cheeks, the hard and soft palates, and the tongue (Figure 8.1). It contains accessory digestive structures, the teeth, and is connected to the pharynx by an opening known as the fauces. The total surface area of the oral cavity is approximately 200 cm2. The surfaces of the teeth comprise 20% of this, with the remainder being attributable to the oral mucosa. The oral mucosa, like other mucosal surfaces, consists of two layers – an epithelium and an underlying layer of connective tissue, the lamina propria.

The skin, together with its accessory structures (hair, nails, glands, sensory receptors, muscles, and nerves), constitute what is known as the integumentary system. The skin itself is an organ composed of several tissues (epidermal, connective, nervous, and muscular) and is one of the largest organs of the body in terms of its surface area (approximately 1.75 m2) and weight (approximately 5 kg). It has a variety of functions, chief among which is protecting underlying tissues from microbes.

Anatomy and physiology of human skin

It is important to realise that the structure of skin is not uniform over the whole body surface, and profound differences occur at different body sites. Obvious examples are the presence or absence of hair and sudoriferous glands. Nevertheless, certain features are common to skin regardless of its location. Hence, it is basically composed of two layers – an inner dermis and an outer epithelium known as the epidermis (Figure 2.1). The epidermis is a keratinised, stratified, squamous epithelium within which five layers can be distinguished (Table 2.1 and Figure 2.2). Its thickness varies from 0.5 to 3 mm, depending on its location and, being the outermost layer of the skin, it is obviously an important site for microbial colonisation. The most common cell of the epidermis (comprising approximately 90% of all the cells of the skin) is the keratinocyte. New keratinocytes are constantly being produced in the stratum basale and, as they are pushed towards the surface, they undergo a process known as keratinisation.

The respiratory system consists of a series of tubes (the respiratory tract) for conducting air to the respiratory membrane where oxygen and carbon–dioxide exchange occurs with the bloodstream, as well as a ventilatory system consisting of the lungs, diaphragm, and associated muscles. The primary function of the respiratory system is to supply oxygen to, and remove carbon dioxide from, the blood. The blood is transported to all cells of the body by the cardiovascular system. The site of interaction between the two systems is the lung – this organ being responsible for the exchange of gases between them. Other functions of the respiratory system include (1) regulating blood pH, (2) producing sounds, (3) eliminating water and heat, and (4) housing the receptors responsible for the sense of smell. Only the respiratory tract of the system is colonised by microbes and the ventilatory system is not described further.

Anatomy and physiology of the respiratory tract

The respiratory tract, which is also referred to as the “conducting portion” of the respiratory system, delivers air to the lungs (known as the “respiratory portion”), where gas exchange takes place. The conducting portion consists of the nose, pharynx, larynx, trachea, and bronchi, whereas the respiratory portion consists of the bronchioles, alveolar ducts, alveolar sacs, and alveoli (Figure 4.1). The conducting portion, apart from the bronchi, is heavily colonised by microbes, whereas the respiratory portion is generally sterile.

It has been recognised for many years that the indigenous microbiota has an important role to play in maintaining the health of an individual by preventing colonisation by exogenous pathogens. However, this “barrier” function is far from being the only contribution that the microbiota makes to the well–being of its host (Table 9.1). It is well established that resident microbes contribute significantly to human development and nutrition and are an effective means of neutralising potentially toxic dietary components. Most (approximately 1014) of the microbial inhabitants of a human being are located in the colon, which also harbours one of the most diverse of the resident microbial communities. The activities of this microbiota, therefore, are likely to have the greatest impact on human development and health, and have been the most extensively investigated. Studies of the role played by microbial communities inhabiting other sites in maintaining human health have largely been devoted to their ability to prevent colonisation by exogenous pathogens. Ethical considerations limit the type of experiments that can be carried out using humans; therefore, much of our knowledge of the role of the indigenous microbiota on mammalian development and health have come from studies involving animals.

Colonisation resistance

Exclusion of exogenous microbes

Co–evolution has ensured that each exposed surface of a human being is colonised by microbes exquisitely adapted to that particular environment.

Although the previous chapter has emphasised the benefits which we derive from the presence of our indigenous microbiota, it must be remembered that the microbiota of each body site also contains organisms that are able to cause disease. Methods of altering the microbiota of a site to increase the benefits it confers or to decrease its ability to cause disease are, therefore, of great interest and practical importance. An obvious way of altering the microbiota of a body site is to use antibiotics, and these chemotherapeutic agents have been used widely to prevent and treat infections due to indigenous microbes. The availability of effective and cheap antibiotics in the latter half of the twentieth century revolutionised the treatment of infectious diseases and, for developed countries at least, reduced their impact as major causes of death and disability. Indeed, the Nobel laureate immunologist, Macfarlane Burnett, stated in 1962 that “by the late twentieth century we can anticipate the virtual elimination of infectious disease as a significant factor in social life”. However, the development of resistance to a range of antibiotics by some important pathogens, including many indigenous organisms (e.g., Staph. aureus, Strep. pneumoniae, N. meningitidis, H. influenzae, E. coli), has raised the possibility of a return to the pre–antibiotic “dark ages”. Other adverse effects of antibiotic administration on the indigenous microbiota were also described in Chapters 2–9. There is, therefore, great interest in the development of other approaches to manipulating the indigenous microbiota that do not result in such side effects.