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Elementary molecular biology as related to genetic epidemiology and microbiology

Genetics: Elementary molecular biology as related to genetic epidemiology and microbiology


Although infectious diseases are known to be a serious cause of both morbidity and mortality in developing countries, there is also evidence to suggest a role for infectious agents in some common diseases of the developed world; for example, the causative role of the bacterium Helicobacter pylori in stomach ulcers.

Simple environmental and behavioural measures such as improved sanitation and 'safe sex' can make a major impact on infectious disease incidence. However, genetic research can also play an important role by elucidating the molecular basis of infection and the disease process, thereby identifying potential new targets for drug therapies or vaccine development. Many important pathogens have also developed resistance to standard drug treatments; molecular analysis can identify the mechanisms of drug resistance and may suggest ways of overcoming it.

Pathogen genetics

A major thrust of the genomics initiative has been towards the sequencing of pathogen genomes. Since the first bacterial pathogen genome sequence was determined in 1995 (Haemophilus influenzae), more than 70 pathogen genomes have been sequenced, including those of the organisms implicated in such important diseases as tuberculosis, malaria, plague, leprosy, diphtheria, cholera and typhoid. Comparison of pathogenic, innocuous and drug resistant strains of the same organism helps in the identification of key factors involved in virulence and drug resistance, and how these properties are propagated between strains. This information is of value in devising new drugs, vaccines and diagnostic tools.

It will take several years for knowledge stemming from this research to be translated into validated medical applications, but genomic approaches are already flagging up potentially useful avenues for more detailed investigation. For example, research on the genome of the malaria parasite Plasmodium falciparum identified an unusual biochemical pathway for steroid synthesis that is not found in humans. The drug fosmidomycin, which targets this pathway, has shown promise in several clinical studies.

Sequencing the genomes of microbial pathogens is a relatively rapid process due to the small genome sizes. Smallest of all are the viral genomes, ranging in size from a few thousand to around 1.2 million base pairs. Some viruses (for example, poliovirus) carry their genetic information in the form of RNA rather than DNA, or alternatively have DNA genomes that require the production of an RNA intermediate during replication (such as the hepatitis B virus). All these viruses have high mutation rates, due to the absence of RNA proof-reading mechanisms to correct errors of replication, with the exception of the retroviruses. Retroviruses, of which the best-known example is HIV-1, also have RNA genomes but these are transcribed into DNA in host cells by a viral enzyme, and integrate into the host genome.

Bacterial genomes are larger, ranging from under 600,000 base pairs (600 Kbp) for the smallest intracellular mycobacteria, to around 10 million base pairs (10 Mbp) for the largest, free-living bacteria. A further complexity of bacterial genetics is that many species also possess additional, non-genomic DNA in the form of plasmids. These independently-replicating elements contain genes that may confer virulence or antibiotic resistance on host bacteria, and they can be readily exchanged between different bacteria. This is the major process that underlies the acquisition of antibiotic resistance in previously susceptible bacterial strains.

Parasite genomes frequently possess multiple genetic loci that allow rapid switching of surface proteins to avoid immune recognition by the host organism, a technique known as antigenic variation. This is typified by the pathogen Trypanosoma cruzi, which causes trypanosomiasis.

A striking recent illustration of the power of genomics in the service of communicable disease control has been the characterisation and sequencing of the coronavirus responsible for the SARS epidemic. Accurate diagnosis of SARS enables it to be distinguished from other diseases that have flu-like symptoms in their early stages, so that individuals suffering from SARS can receive intensive treatment and the disease can be more effectively contained. The avian flu virus is also under genetic surveillance in the hope that, if it mutates to a strain capable of human-to-human transmission, information about the genome sequence will aid diagnosis and perhaps also point to features that may be useful in developing an effective vaccine and/ortherapy.

'Host' genetics
The process of infection involves not just the pathogen genome but also that of the host organism. The genomes of human populations have co-evolved with those of their pathogens, and resistance or susceptibility to infection has been a strong selective pressure in human evolution. A wide range of human genes including the highly polymorphic genes of the immune system are involved in human responses to pathogens.

In some cases a single genetic variant appears to be significantly associated with susceptibility or resistance to a disease. Perhaps the best-known example concerns the autosomal recessive disease sickle-cell anaemia. Individuals who are homozygous for the mutant haemoglobin S-allele have a structural defect in their haemoglobin molecules due to this genetic variant, which makes the red blood cells form a more rigid 'sickle' shape, and to clump together in conditions of low oxygen. These deformed red blood cells occlude small blood vessels, causing ischaemia with concomitant pain and damage to internal organs (figure 16).

Sickle-cell anaemia is most common in populations of specific geographical origin, such as those with West African descent. The natural geographic distribution of the S-allele coincides remarkably closely with areas of endemic malaria caused by the Plasmodium falciparum parasite, where it confers a protective effect against malarial infection. Selective pressure over time has maintained a potentially very harmful allele within certain populations because of the selective advantage it confers on heterozygotes.

In most cases, however, susceptibility or resistance to a specific disease is likely to be associated with variation in several genes, each of which has a relatively weak effect. The search for these genes has much in common with approaches used to identify the genes implicated in susceptibility to common disease, and shares the same difficulties and pitfalls. Nevertheless, association studies on some candidate genes have met with some success. For example, a specific polymorphism in the gene encoding the cell-surface receptor molecule CCR5 has been shown to be associated with increased resistance to infection by human immunodeficiency virus (HIV). This gene was chosen for analysis because the receptor was known to be involved in entry of the virus into specific cells of the immune system. Resistant individuals are homozygous for a 32 base-pair deletion in the CCR5 gene (figure 17).

Similarly, the polymorphic proteins of the major histocompatibility complex are known to play an important role in immune responses to pathogens. Specific polymorphisms in some of these genes have been associated with resistance or susceptibility to diseases including pulmonary tuberculosis, HIV/AIDS, typhoid, leprosy and malaria.

Genome-wide association studies to search for genes involved in responses to pathogens are underway but have not yet yielded robust, validated associations. Association studies face many difficulties, including the problem of ascertaining which individuals have been exposed to the disease-causing organism. Some success has been achieved by genome-wide linkage studies, which attempt to identify alleles that are shared more often by family members with a particular disease than would be expected by chance. This approach has identified genomic regions that may harbour genes affecting susceptibility to schistosomiasis and leprosy, for example.

As well as pointing the way to new drug targets and modes of treatment that will be applicable at the whole-population level, studies on genetic determinants of responses to infection may eventually enable the development of approaches targeted at individuals with specific genotypes. For example, vaccination might be targeted at people most susceptible to infection, or intensive treatment targeted at those whose genotype indicated that their infection was likely to lead to particularly severe disease. Approaches such as these will require careful validation. Attention must also be paid to the need to protect the interests of those - perhaps minority ethnic groups - whose genotype may render them highly susceptible to infection but who constitute too small a market to be of interest to drug companies searching for new therapies.

© Public Health Genetics Unit 2006