Prion diseases of humans and other animals have clinical, economic and political significance. Pre-mortem diagnosis is therefore of great importance. Clinical diagnostic criteria and the current status of the available diagnostic tests are reviewed and possible future developments discussed. Presently, most diagnostic tests are indirect, relying on findings that may not be confined to prion diseases rather than on their particular intrinsic nature. They are therefore not absolutely specific nor are they 100% sensitive. The electroencephalogram (EEG), cerebral imaging and cerebrospinal fluid (CSF) analysis are the main techniques employed. However, there is hope that useful blood tests could be developed which would be simpler and less invasive. Also, there is hope that more specific tests will become available.

Since they were first utilized, immunoassays have witnessed phenomenal growth in the range and scope of their applications. A vast array of different labels and assay strategies has been developed to meet the requirements of sensitivity, accuracy and convenience. The development of increasingly sensitive labels and detection equipment has seen a drastic improvement in the sensitivity of immunoassay systems, allowing an ever-increasing range of analytes to be measured accurately. At the same time, simple to use, inexpensive assay systems have been developed with the necessary reliability, accuracy and sensitivity to bring immunoassay technology to much more diverse areas such as home testing, near-patient monitoring, and large screening programmes in developing countries. Recent developments in molecular biology techniques have made possible the production of fusion antibody conjugates, which can lead to further improvements in sensitivity and cost of reagents, as well as possibly revolutionizing the production of monoclonal antibodies. However, dissatisfaction with various aspects of existing immunoassay technology will necessarily lead to the continued development of this already widely diverse subject.

Diseases caused by viruses are a constant and major problem for livestock production world wide. The diseases range from highly contagious acute forms with high mortality, to chronic disabling diseases with an insidious effect on production. Such diseases cannot be regarded as static in nature due to the highly mutable nature of viruses and their direct selection at the host level and indirect selection in vectors, inducing changes in pathogenicity. Considerable efforts are needed to control these diseases including accurate and rapid diagnosis using both classical and emerging technologies. The methods used are based on both serological and molecular biological based methods. The ELISA and use of monoclonal antibodies are significant in the serological field whereas the Polymerase Chain reaction (PCR) and its direct and indirect uses for identifying (sequencing) and amplification of gene products, is vital to both research and applied fields. Both areas have to be used in a complementary way in the diagnosis of virus diseases.

Schistosomiasis remains a serious world-wide public health problem with a still unfulfilled need for routine cost-effective methods of diagnosis. Such methods are required not only for people in endemic areas, but increasingly for tourists who may have become infected during visits to such places. This article reviews the wide range of immunoassays and antigenic preparations that have been shown to have potential for diagnosis of schistosomiasis by the indirect method of antibody detection. Antigens in native form derived from cercariae, adult worms and eggs are considered, as well as schistosome antigens produced by recombinant DNA technology and the schistosome cross-reactive antigen, keyhole limpet haemocyanin (KLH). Respective advantages and disadvantages of antibody detection, circulating antigen detection and parasitological methods of diagnosis are analysed. It is suggested that due to the relative insensitivity of both parasitology and antigen detection, antibody detection methods could find increasing use in situations of low infection intensity.

The filarial nematodes Wuchereria bancrofti, Brugia malayi and Onchocerca volvulus represent major public health problems in the Tropics. Effective diagnosis of infection with these parasites is required both for administration of drugs to infected individuals and for monitoring of control programs. However parasitological diagnosis is associated with a number of problems including frequently inadequate sensitivity, long pre-patency of infection and inconvenience for patients. For these reasons there has been considerable effort expended in developing other forms of diagnosis, in particular immunoassays for measuring antibody and circulating parasite antigen as well as molecular-biology-based assays for detecting parasite DNA. This article reviews the progress and achievements obtained to date. The latter include the development of ELISAs employing recombinant antigen for detection of antibody to O. volvulus which have both high sensitivity and specificity, the commercial availability of immunoassays to measure circulating antigen in W. bancrofti infection and the generation of specific DNA-based detection systems for all three parasites.

The development of molecular diagnostic methods, particularly those utilizing PCR for the detection of parasitic protozoa will contribute greatly to the identification and control of these pathogens, by increasing speed of diagnosis, specificity and sensitivity, reproducibility and ease of interpretation. PCR methods are not without their problems however, and there is a need for laboratory procedures to be refined before PCR-based assays are accepted as the tools of choice for the routine detection of protozoan parasites. The application of PCR detection to various parasites is discussed.

There is an essential requirement for highly sensitive tools that will differentiate nematode parasites of animals and plants to the species level. For studying host range, genetic variation, virulence and resistance, the availability of well defined populations is vital. Many nematode species cannot be identified with certainty using traditional morphological or morphometric techniques. This is particularly the case for the more accessible developmental stages that, depending on the particular group concerned, live as eggs and larvae in the environment or as micro-filariae that circulate in the blood or inhabit the skin. Morphological identification of these stages requires specialized expertise and is extremely time consuming. Immunological assays have their place in nematode identification but they do not discriminate between current and previous infections, an essential requirement in many epidemiological and prevalence studies. In addition to being highly sensitive, DNA-based methods of detection define present over past infection and are not dependent on the parasite stage. Many types of methodology are available for the detection and definition of nematode DNA. This paper reviews these methods citing examples that have been used with success in the laboratory as well as the field.

The importance of foodborne parasitic zoonoses remains high in many regions of the world. Although control efforts have been exerted for quite some time, overall progress has not been satisfactory, even in many well developed countries. An important drawback in control programmes for parasites such as Trichinella, Toxoplasma and Taenia has been the absence of rapid, accurate and sensitive diagnostic tests for these meatborne parasites. However, the rapid advances in the molecular biology of these organisms has yielded concomitant gains in precision of detection. This review highlights these advances and their impact or potential application to the control of foodborne parasites.

The environmental route of transmission is important for many protozoan and helminth parasites, with water, soil and food being particularly significant. Both the potential for producing large numbers of transmissive stages and their environmental robustness (with the ability to survive in moist microclimates for prolonged periods of time) pose persistent threats to public and veterinary health. Increased demands made on natural resources increase the likelihood of encountering environments and produce contaminated with parasites. In the last 30 years, endemic and epidemic waterborne and foodborne outbreaks in developed countries have led to a reappraisal of conventional isolation and detection methods. While these methods have proved invaluable in our understanding of environmental transmission routes for helminths, they have been less effective for the parasitic protozoa. Robust, efficient detection, viability and typing methods are required to assess risk and to further epidemiological understanding. Greater awareness of parasite contamination of our environment and its impact on health has precipitated the development of better detection methods. Currently, nowhere is this more apparent than with Cryptosporidium, with a broad range of immunological, microscopical and molecular methods available. The upsurge in molecular techniques, particularly the polymerase chain reaction, for determining occurrence and viability have brought with them the added benefits of increased sensitivity and specificity, yet many methods still have to be shown to address these issues consistently in the field. Rapid commercialization of reagents and standardization of methods provide consistency. The advances identified in non-destructive and destructive methods for the protozoa have application for helminths and emerging pathogens and should determine the importance of the matrices involved in the environmental transmission of parasites, further safeguarding public and veterinary health.

Isospora belli, Cyclospora cayetanensis as well as several species of microsporidia are recognized as emerging protozoan pathogens of humans. All are obligate intracellular parasites, with Isospora and the microsporidia being primarily associated with immunocompromised hosts. Cyclospora is a cause of traveller's diarrhoea, and is responsible for water-borne and food-borne outbreaks of disease. Drug treatment is available for these infections. Improved diagnostic methods including the autofluorescence of I. belli and C. cayetanensis oocysts have assisted in the routine detection of these pathogens. Since the recognition of immunosuppression due to HIV infection, microsporidia have become recognized as important human pathogens with a continuing expansion of the parasite-associated clinico-pathological spectrum. The small size, intracellular nature and poor staining properties with many histological stains result in under-reporting of microsporidial infections. Trichrome stain and optical brighteners are used to detect spores in faeces, urines, respiratory secretions and other aspirates. Electron microscopy remains an important diagnostic method but its sensitivity is relatively poor. Molecular techniques should overcome current diagnostic limitations. The ability to extract DNA and amplify by PCR directly from clinical samples has increased the usefulness of molecular methods. Restriction fragment length polymorphism analysis of amplicons can be used to determine genus, species and strain types of various microsporidia. Increased specificity is required in primer design because current primers used for amplifying non-microsporidian DNA also amplify microsporidian DNA. Diagnosis and pathogen characterisation rely increasingly on PCR-based approaches, and the sequence analysis approach becomes increasingly feasible and affordable. However, robust, reliable and sensitive methods are still required for dissecting pathogenesis, epidemiology, transmission routes and sources of infections.

In this chapter, the contribution of molecular tools in understanding the aetiology and ecology of infectious diseases is examined in the context of molecular epidemiology (ME). ME is seen as providing the ‘tools’, both laboratory and analytical, which have predictive significance in epidemiological investigations of the causation of disease. A diversity of questions can be addressed with these tools which can conveniently be viewed as particular regions of DNA and grouped according to the different hierarchical levels of specificity by which infectious agents can be characterized. These groupings and the applications of the different molecular tools are described, and consideration given to the most appropriate methods of analysing data from ME investigations.

Using microelectrode structures, various forms of electric fields, such as non-uniform, rotating and travelling wave, can be imposed on particles of sizes ranging from proteins and viruses to micro-organisms and cells. Each type of particle responds to the forces exerted on them in a unique way, allowing for their controlled and selective manipulation as well as their characterization. Moreover, particles of the same type but of different viability can be distinguished in a simple, reliable manner. This review outlines the principles that govern the way in which bioparticles respond to these various field types, and how they can be exploited. Examples of current and potential biotechnological and biomedical applications are given, along with a critical comparison of current techniques.

There has been an enormous growth in the development of biotechnological applications, where advances in the techniques of microelectronic fabrication and the technologies of miniaturization and integration in semiconductor industries are being applied to the production of Laboratory-on-a-Chip devices. The aim of this development is to create devices that will perform the same processes that are currently carried out in the laboratory in reduced timescales, at a lower cost, requiring less reagents, and with a greater resolution of detection and specificity. The expectations of this Laboratory-on-a-Chip revolution is that this technology will facilitate rapid advances in gene discovery, genetic mapping and gene expression with broader applications ranging from infectious diseases and cancer diagnostics to food quality and environmental testing. A review of the current state of development in this field reveals the scale of the ongoing revolution and serves to highlight the advances that can be perceived in the development of Laboratory-on-a-Chip technologies. Since miniaturization can be applied to such a wide range of laboratory processes, some of the sub-units that can be used as building blocks in these devices are described, with a brief description of some of the fabrication processes that can be used to create them.

Throughout the past decade much research has been directed towards identifying the occurrence, epidemiology, and risks associated with waterborne protozoa. While outbreaks are continually documented, sporadic cases of disease associated with exposure to low levels of waterborne protozoa are of increasing concern. Current methodologies may not be sensitive enough to define these low levels of disease. However, risk assessment methods may be utilised to address these low level contamination events. The purpose of this article is to provide an introduction to microbial risk assessment for waterborne protozoa. Risk assessment is a useful tool for evaluating relative risks and can be used for development of policies to decrease risks. Numerous studies have been published on risk assessment methods for pathogenic protozoa including Cryptosporidium and Giardia. One common notion prevails: microbial risk assessment presents interesting complications to the traditional chemical risk assessment paradigm. Single microbial exposures (non-threshold) are capable of causing symptomatic illness unlike traditional chemical exposures, which require a threshold to be reached. Due to the lack of efficient recovery and detection methods for protozoa, we may be underestimating the occurrence, concentration and distribution of these pathogenic micro-organisms. To better utilize the tool of microbial risk assessment for risk management practices, future research should focus in the area of exposure assessment.