INTRODUCTION

Infectious diseases pose a major global health problem, contributing to significant morbidity and mortality, particularly in developing countries. A combination of environmental, pathogen and host genetic factors play a role in determining susceptibility to microbes and the ultimate course of infection. A constant battle rages between infectious agents and host immune systems. The knowledge of how org an isms vary to escape recognition is central to vaccine and drug design, the control of epidemics and understanding the likely evolution of organisms. Common themes are developed in the course of this text using examples of viral, bacterial and parasitological pathogens that exemplify mechanisms of infectious disease and are of particular relevance to South Africa and the region. This will include reference to HIV, tuberculosis and malaria, diseases responsible for the greatest disease burden in Africa.

Micro-organisms may inhabit the body as normal flora, opportunistic pathogens or true pathogens. Each has its own unique physiology and associated metabolic path ways. The main role of the diagnostic micro biologist is to isolate, identify and analyse the organisms that cause disease in humans. A patient usually presents with signs and symptoms (often very non-specific) suggesting an infectious disease process. Fever has been recognised as one of the most characteristic signs of infection. A multitude of other symptoms may be present depending on the causative organism and the organ system involved. The cornerstone of diagnosis is identification of the ‘bug’ or organism. In this text a brief introduction to conventional techniques will be given, but the focus will be on the application of molecular methods to identify and characterise infectious agents. Any clinical sample can be used to detect the presence of foreign, non-human DNA or RNA. Every species has a unique genome, and we are therefore not only looking for an abnormality in the genome, but a specific sequence characteristic of a particular organism.

Organisms may be classified on the basis of a number of genotypic or phenotypic characteristics. Sub-species may be based on phenotypic differences including protein, bacterio phage and chromatographic profiles, biotyping and susceptibility studies. Genotypic differences may be determined by DNA or RNA analysis, phage typing and restriction fragment length polymorphism (RFLP) analysis. Classification may also be based on cell organisation and function.