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In the fetid atmosphere of factory farms, animals are crammed together in such close confinement they have barely room to move. Poultry spend their entire growth cycles on beds of excrement. Pigs, cattle and calves are reared on slatted floors. Their feces fall beneath them into manure pits. Ammonia fumes permeate the atmosphere and burn the animals’ respiratory tracts and weaken immune systems. With injuries and sores from pecking, biting or kicking, and suffering indigestion from unnatural, fast fattening diets, the ability of intensively reared animals to fight infection becomes ever more diminished.

In such a contaminated environment the prospect of disease is an ever-present, all-pervading threat. Only the heavy use of antibiotics keeps animals alive. It is estimated that about 70% of the world’s antibiotics are fed to farm animals: the precise amount used in agriculture is poorly recorded. But what seems sure – as the number of intensively farmed animals grows – is that their use increases too, particularly in the most intensive sectors: poultry and pigs. Even in countries where the routine feeding of antibiotics is banned (as in the EU) spot checks show considerable misuse.

If we are concerned about the over-use of antibiotics in human medicine then alarm bells should sound louder still when it comes to their use in intensive farming.

In factory farms infections spread fast. Avipoxvirus, fowl cholera and Newcastle Disease are just a few that kill poultry very quickly. But some – like the undefinable disease outbreak in chickens in Burundi in 2008 – are unrecognizable and untreatable. But it is the potential impact on human health – when a virus crosses the species barrier – that causes the greatest concern: Mad Cow Disease linked to Creutzfeld-Jacob disease in humans in 1996; the bird flu that passed from chickens to humans in Hong Kong in1997; the 2009 swine flu pandemic (believed to have originated from a 950,000 pig unit in Mexico) that killed 12,200 people. In the last hundred years the only outbreak that has reached catastrophic proportions on a global scale is the 1918 -1919 ‘Spanish Flu’ pandemic. Linked to avian and swine flu it affected 20% – 40% of the world’s population and 50 million people died. In comparison subsequent flare-ups have been relatively minor.

But where diseases run rife, viruses and bacteria thrive too, and as they do they can form into resistant strains. The changing classification of the swine flu viruses reflect the pace of mutation: H5N1, H1N1, H1N2, H2N3, H3N2v. The original H5N1 is extremely deadly but does not spread fast. H1N1 is less deadly but very contagious. If the two were to link together a pandemic would be in the making. According to the Worldwatch Institute approximately 75 percent of the new diseases that affected humans between 1999 and 2009 originated in animals or animal products. Yet we remain complacent.

In intensive farming units biosecurity is crucial to disease prevention: managing the risk of infection with disinfectants; protective clothing; vaccines to combat viruses (delivered in drinking water or sprayed into the air); and antibiotics to fight harmful bacteria. Antibiotics are fed to livestock on a routine basis but if disease breaks out that dose is upped further still. If all preventative measures fail the last-ditch remedy is to ‘cull’ the entire ‘crop’ of animals.