Waikato dairy farmer Chris Lewis is doing his best to turn his farm into a fortress against cattle disease invader Mycoplasma bovis.

But the challenges he's facing aren't just nasty little bacteria with no cell walls to hold antibiotic treatment.

The fundamental obstacles are of the human kind - red tape and a shortage of labour.

For Lewis, next week's long-awaited official decision on what New Zealand is going to do about M. bovis – continue the drive for eradication or learn to live with it - is almost irrelevant now.

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Whichever choice the Government and agriculture leaders make, this disease will have to be managed.

Until early this week, the sector's money was on the official decision being to live with M. bovis and manage it, maybe with a rider that eradication was the ultimate goal.

But leaks from Wellington now suggest the chosen path will be to continue aggressive eradication attempts, at least in the short to medium term. The cost of either scenario will be about equal, it's suggested: about $1 billion in lost productivity and disease response costs. We can expect much firmer cost figures on Monday, after the decision has gone to Cabinet for final approval.

Whatever path is chosen, the way cattle are farmed in New Zealand will need to change. Lewis' frustration as he tries to be pro-active signal the start of what is expected to be a highly unsettling time for farmers over the next couple of years.

To limit the spread of M. bovis, cattle movements will have to be tightly managed, and maybe even restricted.

That will be a big change for a country where livestock is regularly moved far and wide. Sharemilkers and their cows up sticks for new farms every year on June 1, the start of the new dairy season, thousands of young dairy heifers leave the home farm for grazier properties, and from June through to late spring, four-day-old calves of all breeds are sold on to rearers and cattle finishers.

More dairy calves will have to be reared at home, squeezing the space for cows and cutting milk production. Farmers will need bigger calf rearing sheds and more staff.

Lewis, dairy chairman of Federated Farmers and already gearing up for the changes, cringes at the resource consent wrangle ahead of him. Then there's the labour shortage: he's offering $22 an hour for support calf rearers from July but there are no takers.

Given the extent of the disease's creep, a decision to continue an aggressive eradication attempt by killing cattle from properties which test positive may surprise those asking questions about whether the big cull was justified.

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Geoff Gwyn, response director from the Ministry for Primary Industries (MPI), says about 15,000 dairy and beef cattle had been killed up to this week, with the final push to the target of 22,000 continuing up to June 1.

That includes 1500 sick calves which were killed earlier this year and disposed of at certified landfills, he says.

Many of the targeted 22,000 animals may have carried the organism but were perfectly healthy. In many cases they had decades of dedicated breeding behind them.

But to put the 22,000 casualties in context, that's just four animals per herd nationally, notes Federated Farmers president Katie Milne.

If the decision is to learn to live with M. bovis -- as so many other dairying countries, including Australia, have done -- simmering farmer anger about the biosecurity breach and the slaughter of those animals is likely to spill over.

Amid all the uncertainty around M. bovis, one thing is for sure: there will be a full-scale review of MPI's response and performance.

The extent of the cull is being questioned because properties identified as infected weren't the scene of disease outbreaks. This is not a plague. They were identified because MPI has been tracking animal movements from the South Island farms on which M. bovis was first diagnosed in July last year by private sector Oamaru veterinarian Merlyn Hay.

It's possible M. bovis has been here for years, and the Oamaru outbreak was due to lowered cattle immunity or stress (Dairy Australia says many affected farms there have had large herds).

Prominent agribusiness consultant and former Lincoln University professor Keith Woodford says that with hindsight, there is evidence of calves dying of M. bovis in 2014.

"We also know the disease is only moderately infective and is passed from animal to animal. The outbreak we are now seeing would tend to confirm it's been around for quite some time and MPI is only now just catching up on it," Woodford says.

MPI's Gwyn says laboratory evidence is that the introduction was in December 2015 or January 2016. How M. bovis arrived is still the subject of two investigations – one a technical study to understand the origin and the other into whether someone broke biosecurity import laws.

Gwyn says MPI is aware of the 2014 case, which involved a farm since confirmed as infected. "But we have no evidence to support [the claim]. Our belief is the risk event that arrived at his property is within the time frame I have given."

Woodford likens M. bovis to the chicken pox virus.

"It's opportunistic. Most of us have the chicken pox virus hiding away inside us. We had an attack early [in life] but never got rid of the virus. If our immunity gets low we get an attack of the shingles.

"If you can keep your cow immunity up and there are no other diseases hanging around that would put them under stress, then they are less likely to get the disease, even if they carry the organism.

"That's one of the things causing most distress – we have farmers with zero sick animals and it's only the [MPI] blood test telling them."

M. bovis is not a human food safety risk, and agriculture leaders are confident the disease won't push up meat and dairy consumer prices.

Woodford is highly critical of MPI's handling of the response, although he says in hindsight eradication was always going to be difficult because of the headstart M. bovis had.

He says the ministry focused "far too much on the belief it started recently and the initial source was South Canterbury".

"It's only now with all the backtracking they're finding it's in a lot of other places. What this has meant is that in the battle between Mycoplasma bovis and MPI, Mycoplasma bovis has had a huge start."

"It's like a stealth bomber. It comes along, drops its payload and veers off. It's travelled all over the place before you know it's there."

While people, including lifestyle blockers, who have moved livestock without recording them in the National Animal Identification Tracing scheme (Nait) have contributed to the spread of M. bovis, Woodford says Nait, for all its flaws, isn't why the disease "is out of control".

The Government this month began work to improve Nait.

M. bovis is seen as a wake-up call for what would happen if there was an outbreak of foot and mouth disease, but Woodford says the scenario is completely different. "Foot and mouth isn't a stealth bomber, it's more like a nuclear attack."

He agrees with farmers that they are the best people to manage M. bovis.

"If we have a management programme we have to have good testing facilities. There's probably a role for the Government to make sure those testing facilities are in place.

"Farmers will need to be able to get test results quickly. But that is a problem because while some diseases like foot and mouth are very easy to identify, this one is difficult because it manifests itself in so many ways."

In recent weeks the $85 million question (the amount the Budget allocated for cattle culling costs) has been why is MPI still killing cattle?

Gwyn says heavy culling was to remove "disease pressure".

"I think that holds under any scenario whether you're going to eradicate or going to long-term management. Even under long-term management, if that's the way we go – and I'm not saying it is – the less disease you have in the country, the better starting point you have for reducing spread and impact. It makes the problem smaller."

The Feds' Milne says it's been heartbreaking for farmers to see "perfectly healthy" animals sent for killing.

"This is an animal welfare issue and that's the hard part for farmers. It's not an issue about food safety. These animals may be perfectly healthy but they've been exposed and in future they might end up an animal health issue."

So has the mass kill been a terrible waste, causing needless trauma and cost?

No, say Gwyn and Milne.

It's the only way to manage M. bovis if you want to eradicate it at whole herd level, according to Gwyn.

"You can't use individual selective culling if you want to achieve eradication. However, if you were to decide to go to long-term management and live with it, then that would be a sound approach."

Milne: "As hard as it is, we are taking out a big lump of animals that have the potential to spread it."

Whatever next week's decision, M. bovis will increase farm costs and, says DairyNZ chief executive Tim Mackle, change the way the $14 billion dairy industry operates. It will also hit the $2b beef industry, which gets a big part of its herd and income from dairying.

Woodford says future outbreaks could have serious financial consequences for farmers forced to kill a large part of their herd.

"It will destroy some individuals but not the dairy industry. Everyone else in the world is managing this disease – with some pain – but it hasn't destroyed their industries and so it shouldn't here."

He says debate about why taxpayers should continue to pay towards M. bovis management is "legitimate".

"In these initial stages yes, we had to do something quickly, but as we move into a management system, then if the industry wants the taxpayer to pay, then the industry will need to answer the question why?

"Mycoplasma bovis is not a trade issue. It's not going to affect our exports so people are entitled to ask the question …"

Mycoplasma bovis

What is it? A bacterium that has no cell wall, meaning antibiotics are usually ineffective.
Where is it? 38 NZ farms to date, potentially 70.
Signs: Painful mastitis in cows. Lameness, joint swelling & pneumonia in calves. Cattle can carry organism without signs of infection.
Results: Culling, death.
Spread by: Infected milk, milking/farm equipment, cattle bodily fluids. Semen and embryos suspected by overseas experts.
Tests: Milk, swabs, blood, joint fluid. Milk tests can be unreliable.
Treatment: No effective method for lactating cows. Some antibiotics may help calves.
Outlook: Increasing resistance to antibiotics noted overseas.

Lesson learnt from Australia

Bay of Plenty's Andrew Goold. Photo / Alan Gibson
Bay of Plenty's Andrew Goold. Photo / Alan Gibson

"Blissful ignorance" is probably what saved trauma and dollars for the Bay of Plenty's Andrew Goold, when M. bovis broke out on his big dairy operation in Victoria, Australia two years ago.

"It's a non-issue in Australia and because I was ignorant, perhaps I was a bit blase. By doing what we did, which was just dealing with the issues right in front of us, we've been able to get on top of it and farm on," says Goold, a farm consultant when he's not regularly visiting the four farms he owns or co-owns in Victoria.

It was on his biggest farm, then a new 1600-cow operation, that Mycoplasma bovis broke out during spring calving.

"We had a vet consultant trying to improve animal health on this new farm which was pulling together a herd from different sources and he picked something wasn't right.

"It showed in mastitis, but more in the calves with pneumonia. About 60 died with pneumonia and quite a few had joint disease. In cows there were four or five mastitis cases we couldn't cure and some had joint disease as well.

"We were a new business and because we hadn't heard of it, it wasn't frightening for us, but the vet was very concerned. He knew what it was and he wanted us to be aggressive with culling cows. We were probably slow and slacker than he wanted us to be, but it was also because we were a new business. We couldn't afford to be [aggressive]."

Goold says pasteurising the calves' milk with heat — a measure New Zealand farmers are likely to adopt — was considered but no pasteuriser was big enough to deal with the herd's milk production.

"So we just did what we saw in front of us. Cows we recognised as not normal we culled quickly. There were no more than 20 in the end. It was the same with calves.

"We didn't do a lot of proactive things in terms of animals that weren't sick. Antibiotics don't work and culling was the only answer we were advised of."

In autumn calving this year, there were no signs of M. bovis, Goold says.

"We are testing for it again to see if we are just living with it and managing it, or whether we have actually culled it out."

The direct cost of the outbreak was about $200,000, with the loss of milk production taking the total cost to about $400,000, he says.

Goold can only assume M. bovis came in with new cows.

"We bought cows from at least 50 different farms. Every time you introduce new cows there's stress on the system and you see disease pop up. The manager reckons she would be able to pick it up now and she hasn't seen it since."

Goold's other farms, which milk about 300 cows each, have had no outbreaks.

Goold says he'd hate to be in the New Zealand decision-makers' shoes but he can't understand why cattle are still being killed.

"I can understand the first 5000 cows but not now. It's desperately sad to see some beautiful herds go which have been bred for years."

Goold has employed Mary and Sarel Potgieter, who were 22 per cent variable order sharemilkers on the South Island farm first diagnosed as having M. bovis. They did not own the cows on the affected farm.

They will manage two of the Australian farms.

"I see the mental toll on them and they didn't even own the cows. It's a shocking experience for people to go through."