By SIMON COLLINS science reporter

Three out of every five popular swimming spots in New Zealand's rivers and lakes are infected by the stomach bug campylobacter.

A $1 million study, which measured 10 bugs at 25 sites every fortnight for 15 months, found campylobacter in 432 of 726 water samples.

The bug, often caught from chicken, causes stomach cramps and pain, bloody diarrhoea and fever, frequently lasting a week or more.

New Zealand has the highest rate of campylobacter illness in the developed world. It had 334 cases for every 100,000 people last year, compared with 78 per 100,000 in Australia.

Public health physician Dr Michael Baker said in July that the effluent from New Zealand's cows, sheep and other animals was equivalent to untreated sewage from 200 million people.

Yesterday, the scientist who led the water study, Graham McBride, told a microbiology conference in Auckland that about 4 per cent of campylobacter cases arose from swimming in infected rivers and lakes. Other cases stemmed from animals catching the bug from water infected by other animals' wastes.

Since the infection often did not lead to illness, Mr McBride estimated that one in every 17 people was infected by campylobacter each year.

"It doesn't get much media coverage because it very seldom occurs in outbreaks [of several cases at once]. It's sporadic," he said.

"This is the first time we've known how widespread it is. This is the biggest study of this ever done in the world."

The study's highest campylobacter rate (72 per cent) was found at four sites where the biggest environmental impact was from ducks and other birds. The sites were Lake Rotoroa in Hamilton, the Avon River in Christchurch and two other South Island rivers.

The next-highest rates were in sheep farming areas (66 per cent), rural water-supply catchments (63 per cent), dairying areas (58 per cent) and forested areas (53 per cent).

Surprisingly, the lowest rate (49 per cent) was at three sites classed as "municipal": Whangarei Falls, Lake Okareka (Rotorua) and the Tukituki River (Hawkes Bay).

Mr McBride said it was still safe to swim in rivers and lakes when the water was clear, but it was often dangerous to swim after heavy rain when waterways were full of animal effluent washed off the land.

"A lot of the time it's no risk, but there are times when it can be very risky. If the water looks murky, I wouldn't go in," he said.

A co-author of the study, Auckland University microbiologist Dr Gillian Lewis, said it was usually safer to swim in the sea, where most effluent was washed away - except in places where streams and rivers disgorged their polluted cargo.