Hundreds of residents from the rural Mexican region that is home to the country’s earliest confirmed case of swine flu have been travelling each week to work in Mexico City.

The workers, who go to and from the Mexican capital, where thousands have been infected with the virus, come from the town of La Gloria, which sits five miles upwind from a huge, partially US-owned pig farm that residents are blaming for the outbreak.

The pig farm, the biggest in Mexico, is run by Granjas Carroll de Mexico, which is half-owned by Smithfield Foods, an American giant and the world’s biggest pork producer. Its industrial-scale production techniques, and the massive lagoons of untreated pig faeces that surround its plants, have been a source of constant criticism by environmentalists in Mexico and the US. Residents and workers in the plants have complained of poor health, chest problems and the overpowering stench.

The earliest confirmed case of swine flu in Mexico has been traced to a five-year-old boy in La Gloria, Edgar Hernández, who was given the diagnosis in early April and has since recovered. No other residents have had the virus diagnosed. Yet after a massive influenza outbreak in February and March that afflicted more than 400 of its 3,000 inhabitants – many of whom claim the pig lagoons have infected the water supply, sending great clouds of flies swarming around their homes – the town was sealed off and sprayed with insecticide.

Smithfield insists that none of its pigs or workers is infected, and that its pork is safe. UN officials have only just started inspecting the country’s pig farms, including the La Gloria site, and there is no evidence that the workers spread the virus to the capital.

The Health Minister, José Ángel Cordóva denied residents’ claims that they live in the epidemic’s ground zero. He said that of 30 mucous samples taken from flu patients there, only that of Edgar Hernández was positive. The rest had common flu.

Smithfield moved into Mexico in 1999 and residents began complaining years ago. In April some held a public protest and others made allegations of police intimidation when they voiced anger about the plant. The company says some residents have become “ag-gressive” and have even broken into the facility to take photographs.

On Monday the plant manager, Victor Ochoa, showed journalists a covered, concrete swimming pool-sized vat of pig faeces. He said all the 15,000 pigs were vaccinated and that he would be happy for any inspection.

The group has long been decried by animal rights groups, although its products are eaten globally. These lagoons, particularly in plants in North Carolina and Virginia, are full of not only faeces, but also chemicals, drugs injected into the pigs, blood and afterbirth, and they are actually pink in colour.

In a four-year period, in North Carolina, 4.7 million gallons of faecal matter was discharged into the state’s rivers, killing millions of fish. Inside the plants, sows are artificially inseminated and kept in tiny cages. They cannot turn around. There is no sunlight or fresh air. The temperature can climb to 90 degrees. The company is now phasing out the use of “sow crates” after an outcry over the practice.

Times Recommends

• A doctor, a daughter and a man called Johnny
• Mona Lisa's smile may belie ill health
• ‘Parasite economy’ lies behind Greek tragedy