The urinary system consists of two kidneys, two ureters, a bladder, and a urethra. When considering the microbiota of this system, it is convenient to deal with the male and female urinary systems separately for a number of reasons. Firstly, the anatomy of the system in males and females differs significantly. Secondly, in males, the terminal portion of the urinary system, the urethra, also constitutes part of the reproductive system, resulting in important functional differences from the urethra of females. Thirdly, the urethral opening in females is closer to the anus than in males and is also close to the vaginal introitus, and these heavily colonised sites provide important additional sources of potential microbial colonisers. These factors combine to generate significant differences not only in the types of microbes colonising the urinary system of males and females, but also their relative susceptibility to infection.

The urinary system of females

Anatomy and physiology

Whereas the kidneys, ureters, and bladder are normally sterile, the urethra of females is usually colonised by microbes along its whole length. Further discussion of the anatomy of the urinary system is, therefore, confined to the urethra. In females, the urethra is a short tube (approximately 3.8 cm in length) leading from the floor of the bladder to the external environment via the external urethral orifice which lies in front of the vaginal opening (Figure 5.1).

The Guiness Book of Records and the Hitch Hikers Guide to the Galaxy are both books that document many astounding facts concerning life, the universe, and everything else. However, as far as I am aware, in neither of these eminent publications is there any mention of two truly amazing observations: an adult human being consists of ten times as many microbial cells as mammalian cells, and he or she carries around approximately 1.25 kg of microbes. Knowing this, who could fail to be intrigued by the microbial component of that mammal–microbe symbiosis known to us as a “human being.” The immediate questions prompted by this knowledge are usually along the lines of: (1) Which microbes are present? (2) How do they manage to survive? (3) What are they doing there? (4) Are they dangerous? Each of these questions about our “indigenous microbiota” is addressed in this book, and some of the answers will be surprising.

The complexity of the microbial communities found at many body sites is truly astounding; it has been estimated that we provide a home for at least 1,500 different microbial taxa that collectively contain more than 200 times as many genes as the human genome. Most of these organisms have not yet been grown in the laboratory, and so we know very little about them. However, modern molecular approaches are not only enabling us to detect their presence but, thanks to gene sequencing, also to gain some idea of their physiology and virulence potential.

The first 9 months of our existence – the time we spend in our mother's womb – is the only period of our life during which we are free of microbes. Our delivery from this parasitic existence into the outside world exposes us to an enormous range of microbes from a variety of environments – our first encounter with life forms which have an anatomy, physiology, and metabolism very different from those of our own. Hence, our immediate companions on life's long journey include organisms from (1) the vagina, gastrointestinal tract (GIT), skin, oral cavity, and respiratory tract of our mother; (2) the skin, respiratory tract, and oral cavity of other individuals present at the delivery; (3) the instruments and equipment used during delivery; and (4) the immediate environment. These will include, therefore, not only microbes from other human beings, but also organisms from soil, water, and vegetation that may be present. All of the studies that have been carried out on neonates have shown that, within a very short time following delivery, microbes are detectable on most of those surfaces of the baby that are exposed to the external environment (i.e., the skin, respiratory tract, GIT, and oral cavity). Despite the fact that we are exposed to a wide variety of microbes at birth, only a limited number of species are able to permanently colonise the various body sites available, and each site is colonised predominantly by only certain microbial species (i.e., the microbes display “tissue tropism”).

The only region of the male reproductive system that is colonised by microbes is the urethra, and its indigenous microbiota has already been described in Chapter 5. This chapter, therefore, is devoted to a discussion of the indigenous microbiota of the reproductive system in females.

Anatomy and physiology of the female reproductive system

The female organs of reproduction include the ovaries, Fallopian tubes, uterus, cervix, vagina, and vulva (Figure 6.1). Of these, only the vagina, vulva, and cervix of the uterus are normally colonised by microbes. While a large number of studies have been devoted to elucidating the indigenous microbiota of the vagina and, to a lesser extent, the cervix, relatively little is known with regard to which microbes inhabit the various regions of the vulva.

The vulva is a term used to denote the external female genitalia, which include the mons pubis, labia majora and minora, clitoris, and vestibule (Figure 6.2). The vestibule is lined with a stratified squamous epithelium and located within it are the vaginal orifice, the external urethral orifice, and the openings of the mucus–secreting paraurethral and Bartholins glands. The mons pubis consists of a layer of adipose tissue covered by skin and pubic hair (Table 6.1). The labia majora are longitudinal folds of skin which contain adipose tissue, have sebaceous and sudoriferous glands, and are covered in pubic hair on their outer surfaces.

Since the publication of the first edition in 1986, the field of biodeterioration has expanded, evolved, and inevitably become more complex. New techniques in molecular biology are now routinely employed, and regulations on biocide use have been refined and made more stringent in moves towards integrated pest management and environmental protection.

Despite these changes, the aim of this book and the approach we have employed have remained constant. This book is intended as a basic introduction to biodeterioration, which is the attack on materials of economic significance by living organisms. The subject is huge, and this remains a very small book. The authors have attempted to cover most of the important areas; to this end, there are now three of us and we have enlisted the help of other specialists in certain fields. Nevertheless, some readers will find their particular interest poorly represented. The approaches to the subject of biodeterioration vary widely, depending on the specialist area. Apest-control officer will view the subject differently froma bacteriologist, a biocide manufacturer differently from a museum conservator.We hope that our approach will be of help and interest to a wide range of readers who are not yet specialists in particular aspects of the topic and also to many in areas in which biodeterioration is infrequently considered. A basic level of understanding of biological systems is assumed. Those readers who do not have such an understanding are referred to the more general texts which are included in the reading lists for each chapter.

Biodeterioration of fuels and lubricants

Fuels and lubricants are derived for the most part from naturally occurring petroleum deposits and are directly utilized by a range of oxygenrequiring microorganisms (upwards of 1000 species). Interest has recently been focused on the fate of waste oil in the environment, and a number of oil-degrading strains of bacteria have been isolated which may have biotechnological uses. Being essentially hydrophobic materials, fuels and lubricants are at risk of microbial degradation only when they are in close contact with water. The water may be present as a discrete layer beneath the hydrocarbon, as large dispersed droplets in an agitated system or as an oil-in-water or water-in-oil emulsion, where the water droplet sizes are in the range of 1–10 μm in diameter. The presence of only 10 parts per million (ppm) of water may be sufficient for bacteria or fungi to grow at the interface between the oil, or fuel, and the water, and fuels containing as much as 0.1% water will normally meet the quality standards for use. Hence even apparently water-free hydrocarbons may suffer from microbial contamination.

Some microorganisms excrete surface-active materials (biosurfactants), which allow the cells to contact the non-polar hydrocarbon molecules before the uptake and/or degradation of the latter. Figure 3.1 shows the emulsion produced between an aqueous medium and diesel oil by supernatants fromcultures of Pseudomonas isolates, demonstrating that the emulsifying agents are extracellular.

Extracellular surfactants can cause significant problems in fuel storage tanks, causing emulsion (fuel-in-water) and invert emulsion (water-infuel) formation with the water bottom.

Buildings

INTRODUCTION

The problems of biodeterioration in buildings are many and various. Some relate to the materials used and some to the environment created by the building itself, its associated services, and the uses to which the building is put. Many of the materials used in buildings are already described in other parts of this book. It is, however, impossible to consider buildings without mention of individual materials, and so there is bound to be some overlap. The main emphasis of this section, however, is on the problems of buildings as structures and not as assemblages of materials.

Traditionally, buildings to house humans and their materials have evolved in style and construction with regard to the prevailing climate and within the limits set by available materials and finance. Perhaps today, style has become more important, and it can be argued at the expense of durability and resistance to biodeterioration. It was once said to the authors that there are no biological problems with buildings, only problems of construction. This would be perhaps nearer the truth if all buildings were near perfect in design, construction, maintenance, and ventilation, but we all know, alas, that this is not true.

So what are the main biological problems? For convenience these can be listed and considered under a series of general headings:

1. Fungal and bacterial growth

1. a. affecting the structural strength

2. b. affecting decorations, paintwork, furniture – ‘fouling fungi’

3. c. health problems.

DEFINITIONS

What is biodeterioration? The word has only been in use for about 40 years, but describes processes which have affected humankind ever since we began to possess and use materials. Many branches of science and technology either do not need or do not have an accepted definition in common use. We are all happy to think we know what physics is, but we have yet to agree what exactly constitutes biotechnology. Within biodeterioration we are fortunate to have a definition which was quickly accepted when first proposed by H. J. Hueck.

Hueck (1965, 1968) defined biodeterioration as ‘any undesirable change in the properties of a material caused by the vital activities of organisms’. Another term inc ommon use is that of biodegradation. Although no formal definition has general acceptance, it may be useful to think of biodegradation as being ‘the harnessing, by man, of the decay abilities of organisms to render a waste material more useful or acceptable’. Both definitions involve humankind, in a negative or harmful way in the case of biodeterioration and in a positive or useful way in the case of biodegradation as defined here. Both definitions also involve materials. Materials are any form of matter, with the exception of living organisms, which are used by humankind. All materials (and processes) will have an intrinsic value and thus there is an important economic dimension to biodeterioration. This book seeks to introduce some of the interactions between living organisms and humankind's materials through the disciplines of environmental biology, materials science, and ecology.

The interaction among people, their materials, and living organisms has been recognized, if not fully understood, for a very long time.

The prevention and control of a biodeterioration problem require a knowledge of the product composition, process and manufacturing details, supply chain information, and the application in order to be able to recommend the most equitable solution to all parties concerned. As the materials involved have a value, there may be the need to establish or apportion responsibility for a problem, and thus a forensic approach may be necessary in some cases.

The expertise in this area has, over the past 15 years, been taken up by the manufacturers and formulators of preservative products as part of their customer service package. They have developed the methodologies, built up databanks of experience, and have been proactive in the revision of national and international standards for the evaluation of preservative efficacyandmaterialsdurability forwhichmicrobial resistance is required. In a small number of areas, such as wood, stone, and food, government agencies still exist, and there are a small number of consultancies who can provide an independent view.

There are four elements to the investigation of a biodeterioration problem:

• Determining the cause

• Assessing likely control systems

• Instituting the most appropriate control system

• Monitoring the success (or otherwise)

THE PLANT AUDIT

Many biodeterioration problems have their origins in industrial processes, and it is impossible to appreciate the full range of factors involved unless a visit is made to the site of manufacture and a full survey of the situation is carried out. In this way information can be collected regarding the raw-materials storage and handling, the configuration of the process equipment, stages in the manufacturing process, and ultimate storage or distribution systems.

The division of biodeterioration into topics is convenient but artificial. Many ‘natural’ or non-synthetic materials have specific major uses: for example,wood and stone are common building materials and are therefore considered in Chapter 4 as ‘materials in use’. Where materials, such as wood, are dealt with elsewhere, only the basic mechanisms involved in their biodeterioration are considered in this chapter.

Cellulosic materials

Cellulose is the main structural component of plant cell walls and is probably the most abundant biological compound on Earth, the total world estimate being approximately 26.5 × 1010 tonnes. Cellulose is produced in vast quantities, and the fact that it is recycled relatively quickly emphasizes both its susceptibility to attack by organisms and the range of organisms able to do so and utilize the breakdownproducts. In green plants, cellulose is the main material found in the primary cell walls, which are thickened in structural and conductive tissues. These special tissues provide many of the plant fibres used by humans. Cellulose is also found in the higher fungi and algae. It occurs alone in the fungi and algae, but in higher plant groups it is frequently associated with lignin, which is much less readily biodegraded.

Cellulose is a linear polysaccharide made up of β-(1–4) linked D-glucopyranose residues (Figure 2.1), occasionally cross-linked to other similar chains by means of hydrogen bonding to produce microfibrils.

Lignin, however, although made of the same basic chemical elements as cellulose, namely carbon, hydrogen, and oxygen, is not built of sugar, but of phenylpropane subunits, and is not a carbohydrate.

The main effort in the field of biodeterioration has been to develop, either empirically or by design, methods for preventing the biodeterioration of materials and thus preserve their value and usefulness for as long as possible. The preceding chapters have contained information on control methods specific to a particular material, product, or structure. It is useful, however, to discuss control strategies in a wider context so that they can be applied to full effect in a given situation. The phrase that an ounce of prevention is better than a pound of cure is extremely pertinent to biodeterioration. As outlined in the Introduction, preventative techniques are the main option for consideration, whereas remedial treatment is at best only a temporary solution: it does not usually completely cure the problem. However, in the construction industry, a whole subindustry has built up around remedial treatment, and this often includes the use of preservatives.

Prevention should ideally commence when the raw material has assumed a potentially susceptible state. This may be directly after the harvesting of a foodstuff or when a synthetic product is placed in an environment conducive to biological activity. The first use of preventative methods was to enable the storage of foodstuffs after harvest or hunting, and these involved physical/mechanical techniques such as heat, cold, drying, osmotic pressure, and the use of mechanical barriers. Chemical methods were first introduced as fumigants (sulfur) and then as salts of mercury, copper, and zinc in the eighteenth and nineteenth centuries for preservingtimberandother natural productsin storage. Itwasnotuntil the SecondWorldWar that the widespread use of chemical preservatives – or biocides – was seriously contemplated to prevent microbial growth on military equipment used in the tropics.

BORRELIA

The genus Borrelia comprises diverse species of spirochaetes that are associated with haematophagous arthropods (Paster et al., 1991; Paster & Dewhirst, 2000). Some Borrelia species are pathogenic for humans or for livestock. Other spirochaete groups with human pathogens are the treponemes, which include the human-restricted agent of syphilis, and the leptospires, which are mostly free-living spirochaetes that infect a wide variety of animals. The spirochaete phylum also contains a number of species that are symbionts of invertebrates, such as molluscs and termites. Borrelia spirochaetes characteristically circulate in the blood of their vertebrate hosts and are transmitted between vertebrates by ticks, with the single, epidemiologically important exception of a louse-borne species. A common strategy of Borrelia spp. for prolonging spirochaetaemia – thus increasing the probability of vector transmission – is avoidance of the immune response through antigenic variation (Barbour & Restrepo, 2000; Barbour, 2002). Most types of Borrelia infections are zoonoses, but humans are the critical reservoirs for at least one species (Barbour & Hayes, 1986; Barbour, 2004).

The number of recognized Borrelia species has more than doubled over the last two decades, in part because cultivation methods improved (Barbour, 1988; Cutler et al., 1994) and technologies like PCR allowed identification and taxonomic classification without being able to culture the organism (Anda et al., 1996; Barbour et al., 1996; Kisinza et al., 2003; Scoles et al., 2001). Table 1 is a list of accepted and tentative species designations, as of early 2004. Borrelia species have been documented in the Palaearctic, Afro-Tropical, Nearctic, Neotropical and Antarctic ecological regions, and some species that use humans or livestock as reservoirs are now cosmopolitan.

INTRODUCTION TO THE CONCEPT OF VECTOR COMPETENCE

The importance of vector-borne diseases

Infectious diseases remain the leading causes of morbidity and mortality worldwide and arthropod-borne diseases include many of the most important, especially in the tropics and developing countries. For example, malarial parasites infect an estimated 200 million people annually in Africa alone with mortality estimates of about 1 million persons, primarily children (Greenwood, 1999). Vector-borne viruses are also important human pathogens. Approximately 2500 million people (two-fifths of the world's population) are at risk from dengue with about 50 million cases each year (www.who.int/inf-fs/ en/fact117.html). Many other vector-borne pathogens cause emerging diseases that have undergone resurgence or threaten to increase in prevalence or distribution in the coming years. However, despite the importance of vector-borne diseases, the mechanisms of transmission of many vector-borne pathogens remain poorly understood.

Here, we review the various factors that contribute to the transmission of pathogens by arthropod vectors. Due to space limitations, we focus primarily on human disease, with emphasis on mosquito-borne pathogens, especially arthropod-borne viruses (arboviruses).

Mechanisms of pathogen transmission by arthropod vectors

Vector-borne pathogens of humans and other animals circulate between their arthropod vectors and vertebrate hosts. Arboviruses represent the most basic form of vector-borne transmission, and undergo horizontal transmission between vertebrate and arthropod hosts (Fig. 1). In some cases they are maintained by vertical transmission from adult arthropod to offspring. Usually a restricted invertebrate host range is observed with only one or few vectors involved in transmission. Within the infected arthropod, the virus must undergo an extrinsic incubation period of variable duration before biological transmission to a susceptible vertebrate host (Fig. 2).