At a conference this week the authors present their findings on recognising the link between animal and human diseases

When avian flu arrived in Indonesia in 2003, it found the perfect stage for a rapid, destructive spread in the country's growing poultry industry. Despite the slaughter of millions of ducks and chickens, the highly pathogenic virus established a foothold throughout the vast country, where it threatened to mutate into an easily transmissible human killer.

Indonesia is the classic example of a "hotspot", where development and rapid change surpassing the speed of the industrial revolution threaten animal and human health in ways we have never seen before. Prosperity has stimulated a raid expansion of poultry operations in Indonesia, yet the country lacks adequate veterinary health resources, rendering it vulnerable to the emerging diseases that can prosper on its farms.

An entirely different set of health problems threaten "coldspots" throughout much of Africa – areas locked in a timewarp of underdevelopment and crippled by old diseases. Here, the past three decades have seen an entrenchment of livestock diseases like cattle "lung plague", caused by a bacterium eradicated from the herds of most wealthy countries a century ago.

In contrast to these "hot" and "cold" spots, the United States, Japan and the European Union have well-established, reasonably well-regulated livestock industries that can usually get new diseases under control. In these wealthy countries, consumer outrage over the occasional appearance of tainted foods is often greater than the disease risk that those foods pose to consumers.

How diseases are managed in these three different regions – hot, cold and worried – should differ.

A new human disease emerges around every four months, usually after jumping from animals. Many of these infections are minor and of interest only to microbiologists. But as intensive agricultural production expands and populations push into uninhabited areas, epidemics of devastating diseases, like Sars and HIV, which started out as animal pathogens, are likely to become more common.

Agriculture and health are intimately linked. Many infectious, and even occupational, diseases are associated with the food chain. These diseases create an especially heavy burden in poor countries, so we need to start viewing agriculture-associated disease as intimately related to public health. This starts with incorporating the health of people, animals and the environment into agricultural research, which has traditionally ignored human health issues and focused on improving yields and productivity.

Big agriculture, whether farms of hundreds of thousands of closely packed chickens or largescale irrigation projects that create new homes for disease spreaders like the mosquito, offer unprecedented opportunities for the emergence of new illnesses.

In a world of limited financial and technical resources, it makes sense to integrate our disease-combating efforts across scientific disciplines while focusing on different priorities in different parts of the world.

Too many emerging economies fail to take into account the risks of intensified livestock operations along with the benefits. Sars – a disease that broke into the human population at the intersection of traditional "wet" markets, where live animals are sold, and globalised travel – is the classic example of such risks.

In these countries, increasing demand for meat, milk and eggs is fostering more intensive cattle and poultry farming. But the countries lack the veterinary staff, surveillance and other tools required to control diseases that come with this expansion.

At the other extreme are neglected areas, "coldspots" that lack even the most basic services and where people suffer poverty, malnutrition and powerlessness. Here, the best hope for disease control may be a technical fix that leapfrogs the conditions of underdevelopment. This is why we and other organisations are working on vaccines to combat epidemics of the deadliest livestock diseases, even as we recognise that poverty, a main cause of the diseases, must also be battled at its roots.

Our responses to disease threats are often compartmentalised. Instead of jointly assessing the trade-offs between agriculture's benefits (food) and risks (disease), those in the agriculture sector remain focused on productivity and those in the health sector on disease.

The best way to counter diseases associated with agriculture is by assessing their impact on humans and animals alike, as well as the costs of implementing interventions to control them. Using these methods, authorities in Mongolia, for example, were able to show that while brucellosis was a minor threat to people, factoring in both human and animal health benefits showed that a brucellosis vaccination campaign was a wise investment.

Understanding the multiple burdens of a disease is a first step in its rational management. Addressing agriculture-associated diseases requires systems-based thinking and new multidisciplinary approaches, which in turn will require new institutional arrangements.

Yet for all the complexity of disease outbreaks, we should never ignore the obvious. Sometimes, there can be simple solutions to fight an epidemic, which is why effective vaccines are such a powerful tool.

• John McDermott and Delia Grace are researchers at the International Livestock Research Institute. They are part of a team of international researchers tracking emerging diseases in Africa and Asia, and this week in New Delhi present findings on the links between the livestock population boom, globalisation and disease outbreaks