Pen-site sampling offers cost-effective, accurate surveillance options

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Disease surveillance is a requirement to understand the progression and status of a pathogen within a swine herd. But the challenge has always been finding a balance between the type and amount of sampling needed with the cost of achieving accurate test results.

“We need to monitor the dynamics of infection of different populations within a pig farm, because monitoring and surveillance are essential tools for decision-making,” Gerard Martin, DVM, PhD, Autonomous University of Barcelona, Spain, said in his presentation on the feasibility of pen-site surveillance during the European Symposium of Porcine Health Management 2020+1.

Nasal swabs and fecal or serological samples of individual animals are useful as diagnostic tools, he said, but they are labor intensive, expensive and require a large number of samples for surveillance. Nasal swabs and sera sampling also can present animal welfare and worker safety concerns, especially when restraining large swine.

Pooling samples reduces testing costs, but it doesn’t address the need to collect individual nasal or sera samples. “We need a cost-effective, user-friendly, more effective sampling option to gain perspective of a population’s disease status or a vaccination program’s effectiveness,” Martin said.

Oral fluids: one option

Increasingly, oral fluids are being used effectively for early disease detection and monitoring large populations of growing pigs. Introduced in 2008, oral fluid samples have been increasing since 2010 and now make up the largest share of submissions to the Iowa State University veterinary diagnostic laboratory. Oral fluids can be used for a range of viruses and bacteria, with porcine reproductive and respiratory syndrome virus (PRRSV) and swine influenza virus A (IAV) being the most frequent.

For post-weaned pigs, the process involves hanging one cotton rope per 25 pigs in a pen for the animals to chew on. After a few days, the aggregated saliva samples are collected and sent on to the diagnostic laboratory. The on-farm process is welfare friendly, uses the animal’s natural curiosity and one person can handle it.

“In the case of PRRS we see that viral shedding in oral fluids can remain for a prolonged period versus the duration of viremia,” Martin noted. “That means that the detection rate can last for a longer time in a population of animals.”

For both PRRSV and IAV, oral fluids have a high level of sensitivity, allowing a high probability of detection at a low prevalence. Martin relayed that using ropes in multiple pens over consecutive batches of pigs can present a 90% to 95% probability of detecting PRRSV at a prevalence ranging between 1% and 10%.

“If you want to test that same sensitivity [via sera], we’d have to test a lot of animals,” he added. “However, [with oral fluids] you cannot sample just one batch because there is a batch effect; the prevalence at various ages is very different, depending on the virus we are assessing.”

The prospect of using oral fluids to sample swine at abattoirs has recently been tested and shows promise as a way to evaluate disease eradication programs, as well as for early detection. For example, in the case of transboundary viruses, foot-and-mouth disease can be detected as early as 1 day post-infection (DPI); for classical swine fever it’s 5 DPI and 3 DPI for African swine fever.

However, there are some limitations, primarily with piglets less than 21 days old as they do not manipulate the ropes enough, and the oral fluid volume is scarce. Adult swine also need some previous training to ensure they interact with the ropes.

Other alternatives

One option to sample the sow and piglets younger than 21 days is to collect “family oral fluids,” which involves hanging the rope so that the sow and litter both have access. It also teaches piglets what to do. For example, family oral fluids are beneficial in sampling suckling piglets to determine if PRRSV vertical transmission is occurring or to detect the presence or absence of IAV, Martin noted.

Other pooled sampling methods for very young piglets are also gaining traction, such as processing fluids extracted from tails and testes, which allows sampling by litter or room.

In the case of PRRSV, there’s good agreement between serum and processing fluids of the litter. When both tails and testes are used, the specificity is very high — 87% to 92%. But due to restrictions in various countries on castrating male pigs, testes are not always available. If only tails are collected, Martin noted that sensitivity decreases significantly, say, from 92% to 62%. “But, if you’re talking about the population level, the use of tails can still be sensitive enough,” he added.

In the case of Mycoplasma hyopneumoniae, it’s known that the testes have a higher sensitivity rate than tails.

However, in the future, tails may not be an option in some European countries as animal welfare concerns will continue to curb painful practices such as tail-docking.

Umbilical cords offer a sampling alternative for suckling pigs, shown to be equally or more sensitive than serum in determining vertical transmission of PRRSV. “When we looked at the batch level, umbilical cords could be extremely useful, as they carry high viral loads,” Martin said. “They also can be used for risk-based sampling, for example, to monitor stillbirths and weak-born piglets.”

Collecting umbilical cords is faster than serum and is welfare friendly, but fresh tissue is required and that increases labor.

Other possible sampling alternatives being studied include collecting tongues from stillbirths, deaths during farrowing (for PRRSV) and deaths before weaning. “We know the sensitivity for these is a bit lower than serum. But it’s similar results to processing fluid from tails, so it could be an alternative to evaluate big populations,” Martin noted.

For IAV, environmental swabbing and udder wipes are sensitive for detecting the virus in a litter or room. Sow udder wipes “have been shown to have a higher detection rate than nasal swabs,” he added, “and the udder is where the piglets interact. We also know that IAV can be maintained within the unit.”

Know the limitations

Pen-site sampling techniques are extremely useful, Martin stressed: They are sensitive, cost effective and user friendly, and the application will continue to expand. However, there are limitations. “We should not use this for diagnosis of a disease; use it for monitoring and surveillance only,” Martin said.

Pen-site sampling could be useful for metagenomic analysis at population level, he added, but it will be difficult to interpret sequencing results if more than one virus is circulating on a farm. In the case of IAV, two or more viruses often can be detected on a farm; with PRRSV, a field strain and vaccine strain can complicate the clarity. “So, take care when interpreting sequencing from these types of aggregated samples. If you find two virus strains, better to sample individual animals.”

Virus isolation is possible but more difficult with pooled samples. If that’s needed, he advised sampling individual animals showing clinical signs.

Pooled samples should not be used to calculate the proportion of positive animals within a room or herd because there’s no way of knowing the contribution of any individual animal to the aggregate. “It can be used to identify positive pens or a population but not the proportion,” Martin said, adding that  long-term, pen-site sampling will continue to be very useful for farmers and veterinarians to direct management, biosecurity and disease-control and -prevention strategies.