7 October 2014
Pathogen genome sequencing as a tool to monitor infectious disease agents
Emerging infectious diseases such as Ebola, MERS, and pandemic influenza have been responsible for thousands of deaths in recent years, and tackling the threat posed by these infectious diseases is one of the most pressing challenges in global health. In particular, there is a need to detect their emergence sooner, through effective global surveillance, to enable swift action to be taken to prevent their spread. The consequences of failure in this task are clearly demonstrated by the recent Ebola outbreak in West Africa.
Whole genome sequencing of pathogens promises to be a valuable epidemiological tool in the fight against the spread of emerging infectious diseases. By comparing the genome sequences of different strains of a single pathogen species, the causes and patterns of transmission of these bugs can be determined at an unprecedentedly high resolution, and the emergence of novel, potentially harmful strains can potentially be identified sooner.
Animals are the source of most human emerging infectious diseases
Approximately 70% of emerging infectious diseases are zoonotic, meaning that they are spread to humans from other animals. Examples include the infectious agents responsible for important global emergencies such as the recent Ebola, MERS, ‘bird flu, ‘swine flu’, and SARS outbreaks. Potentially dangerous bacterial or viral strains are often circulating in animal populations for many years before the transmission to humans occurs. For example, a similar virus to the one responsible for the current Ebola outbreak was probably circulating in bats for many years prior to the transmission to humans, but we know remarkably little about the dynamics and distribution of such viruses in bats. The MERS virus was probably passed from camels to humans, leading the World Health Organization to recently suggest that camels should be surveyed for the MERS virus as part of public health efforts to control MERS.
Monitoring livestock and wild animal populations could therefore be a critical component in predicting outbreaks and halting them before they cause large-scale human suffering. The regular systematic genome sequencing of pathogens from animals that live in close proximity to humans could act as an early warning system of potential threats to humans. Actions could be taken to minimise contact between humans and animals harbouring unsafe pathogens, and this would help prevent deadly outbreaks. Effective collaboration between clinicians, vets, bioinformaticians, farmers, and ecologists will, however, be required to effectively conduct such multidisciplinary work
Incorporating pathogen genomics into a One Health framework
The closer linkage of human, animal, and environmental health has been termed 'One health'. This vision of combined and comparative medicine is promoted across a range of infectious diseases by the One Health initiative . Genome sequencing provides an excellent opportunity to implement a One Health approach to the surveillance of emerging infectious diseases in human and other animal populations. A particular advantage being that genomic surveillance approaches can be applied generically to a wide range of pathogens and hosts, making them relatively straightforward to develop and implement. For example, a virus in a bat can, at least in principle, be examined using the same type of genomic techniques as a virus in human or a bacterium in a mosquito.
It is important to remember, as we in the UK consider implementing pathogen genomics for the diagnosis and surveillance of infectious disease in humans, that despite the urbanisation of our population, we remain susceptible to the influences of both our local and global natural environment. Thus, it will be vital as we move forward with this exciting new technology for health policy makers to consider not only how genome sequencing can help clinicians treat the diseases of today, but also how this technique, if applied as part of a holistic framework for monitoring emerging infectious diseases beyond human populations, could help minimise the harm caused by the as yet undetected infectious diseases of tomorrow.