Science Page: Incidence risk and incidence rate

This is our Friday rubric: every week a new Science Page from the Bob Morrison’s Swine Health Monitoring Project. The previous editions of the science page are available on our website.

This week’s Science page is a follow-up from the one presented last week and focuses on the difference between incidence rate and incidence risk. Those two epidemiological measurements are often mistaken for one another.

Key points from this week edition:

  • Incidence risk is a measure of disease occurrence over a defined period of time. It is a proportion, therefore takes values from 0 to 1 (0% to 100%).
  • Incidence rate takes into account the time an individual is at risk of disease. It is not a proportion since it defines the number of cases per animal or farm time at risk.
  • Incidence risk and Incidence rate are often confused. Incidence risk and rate are numerically the same when the period at risk does not vary across individuals being studied.

Take a look at the complete report to see an example of the difference between incidence risk and incidence rate on farms.


Metabolites, antibiotimicrobials, and gut microbiome

Salmonella Bacteria, Source: NIAID

In this article published by the National Hog Farmer, nutritionists and microbiome analysts from the University of Minnesota discuss what consequences antimicrobials can have on the gut microbiome.

What does microbiome mean?

Microbiome refers to all of the microbes present in an area. For example, gut microbiome is the entire population of microorganisms (most of the time bacteria) present in the intestinal tract.

The purpose of this research program is to study the effects antimicrobials can have on the bacterial populations present in the gut and how those changes influence the metabolites present in the pig.

What is a metabolite?

Metabolites are usually small molecules and are created by enzymatic reactions happening through the natural life of a cell or organism.

One of the effects of administering tylosin to pigs was the increased growth of bacteria producing short-chain fatty acids in the intestinal flora. The use of this antimicrobial also led to the development of Lactobacillus in the gut.

Relating changes in metabolites to the gut microbiome allows for a more complete understanding and investigation of the impact that antibiotics have in enhancing growth. Without completely understanding the mechanism of increased growth, antibiotic alternatives could be used inappropriately without much added benefit.

Link to the full paper

The latest trends in PRRSV diagnostics: less serum samples, more oral fluids, and more 1-7-4 RFLP pattern

Today, Dr. Albert Rovira from the University of Minnesota, Veterinary Diagnostic Laboratory shares with us the trends he has observed in PRRSV diagnostics over the past years. The findings can be found in the slideshow below.

  • The use of tissue samples follows a seasonal pattern and represents clinical cases with a percent of positives of 30%
  • The number of oral fluid samples is increasing. Used for monitoring positive farms and more recently for surveillance in negative farms as well:: 15% of positive samples
  • The number of blood swabs, serum samples, and semen samples, typically used for surveillance in negative farms, is decreasing. Lowest percent of positive samples: 8%
  • RFLP patterns are changing over time. In the past years, 1-7-4 > 1-3-4 or 1-8-4 or 1-4-4
Reminder: what is a RFLP pattern?

RFLP stands for Restriction Fragment Length Polymorphism and is a technique used to detect nucleotide changes in a genetic sequence. The genetic material is put in contact with restriction enzymes which are very specific to a genetic sequence. If the enzyme recognizes the sequence pattern, it will cleave the DNA or RNA fragment. After that, a type is determined based on the number of fragments and its size.

For example with PRRSV, three enzymes are used and the number of fragments each of them produces makes up the numbers of the RFLP pattern. Currently, the RFLP type is not actually performed in the lab. Instead, it is predicted based on the ORF5 RNA sequence and the knowledge of the cutting capabilities of each enzyme.

Therefore, the RFLP pattern gives us a way to cluster PRRSV strains in groups but very little indication about how similar they are to each other.

Survival of porcine coronaviruses in feed ingredients and impact of feed additives

A lot of research has been done at the University of Minnesota regarding the survival of porcine coronaviruses in the feed and how to impact their survival. We are presenting today two papers published this spring looking at this important topic. First, Trudeau et al. showed that the feed ingredient which lead to the longest porcine coronaviruses’ survivability was soybean meal. Then, Cottingim et al. showed that some feed additives could inactivate PDCoV.

Importance of porcine coronaviruses and their relationship to swine feed

Porcine coronaviruses of importance in the swine industry nowadays are Porcine Epidemic Diarrhea virus (PEDV), Transmissible Gastroentiritis virus (TGEV), and Porcine Delta Coronavirus (PDCoV). All cause enteric issues in swine and some can lead to up to 100% mortality in nursing piglets. The role of feed ingredients in spreading PEDV and causing outbreaks in Northern America in 2013 has been questioned since then.

Survival of PEDV, TGEV, and PDCoV in complete feed and feed ingredients

The first research project evaluated the persistence of PEDV, TGEV, and PDCoV in porcine feed and feed ingredients. To do so, complete feed and major feed ingredients samples (spray dried porcine plasma, meat meal, meat and bone meal, blood meal, corn,
soybean meal, and corn dried distillers grains with solubles) where inoculated with PEDV, TGEV, or PDCoV and kept for up to 56 days. Aliquots were tested 11 times between the inoculation day and the end of the trial. Time necessary to reduce the viral concentration by 1 log was recorded.

Soybean meal took the longest time to attain the reduction in concentration for all of the coronaviruses, reaching 7.5 days for PEDV, and 42 days for both PDCoV and TGEV. This study also demonstrated that there was a modest positive correlation between moisture content and persistence of TGEV and PDCoV. On the other end, there was a moderate negative correlation between ether extract content and TGEV survival, not observed with the other two viruses.

Click on the banner below to access the full article in open access.

Trudeau coronavirus feed swine survival PED

Feed additives and PDCoV survival

In this second project, the survival of PDCoV was evaluated after being put in contact with nursery feed samples containing one of six different commercial feed acids (UltraAcid P, Activate DA, KEMGEST, Acid Booster, Luprosil, and Amasil), salt, or sugar. Acids were added following the recommended concentrations in the first part of the experiment and then, were double-dosed. Feed samples were inoculated with PDCoV and kept for up to 35 days. Like in the previous article, days to achieve a reduction of virus concentration by 1 log were recorded.

At recommended values, there was no difference between viral load reduction in feed samples with or without additives. When acids were added to the feed at a double concentration, the time period to attain the reduction in viral load was decreased to 0.28 days or less for all acids except for Amasil which increased it to 4.95 days (control: 0.35 days). The difference between acidifiers may be explained by the active ingredients used in the products. Furthermore, the addition of salt decreased PDCoV survival whereas sugar increased it.

Click on the banner below to access the full article in open access.

Cottingim feed additives survival PDCoV coronavirus swine


Detection of Mycoplasma hyopneumoniae in naturally infected gilts over time

A longitudinal study to assess Mycoplasma hyopneumoniae natural infection in gilts

This study was conducted by Dr. Karine Takeuti under the supervision of Dr. Maria Pieters from the University of Minnesota, College of Veterinary Medicine. The objective was to sample replacement gilts from 20 days of age until the day before weaning to detect Mycoplasma hyopneumoniae . Laryngeal swabs, tested by PCR, were taken every 30 days at a Mycoplasma positive sow farm. Therefore, the animals were naturally infected.

Gilts were found positive at 110 days, no detection in piglets

11.4% of the gilts were found positive at 110 days whereas all the previous samples came back negative. Positive results peaked at 140 days when 36.4% of the samples were positive for Mycoplasma hyopneumoniae. 27.3% of the gilts got positive results twice or more during the sampling period but 18.2% of the animals remained negative for the duration of the study.  All of the 220 piglets samples were also negative.

Takeuti longitudinal gilt mycoplasma hyopneumoniae 2017

Mycoplasma hyopneumoniae causes a chronic respiratory infection in pigs and its transmission occurs mainly by direct contact and by vertical transmission (sow-to-piglet). The objective of this study was to assess the detection dynamics and persistence of M. hyopneumoniae natural infection in replacement gilts. Forty-four twenty-day-old gilts were selected from a M. hyopneumoniae positive farm and followed up to one day prior to their first weaning. Laryngeal swabs were collected every 30 days, starting at day 20, for M. hyopneumoniae detection by real-time PCR, resulting in 12 samplings. Piglets born to selected females were sampled via laryngeal swabs one day prior to weaning to evaluate sow-to-piglet transmission. The M. hyopneumoniae prevalence was estimated at each one of the 12 samplings in gilts and a multiple comparison test and Bonferroni correction were performed. Bacterial detection in gilts started at 110 days of age (doa) and a significant increase (p < 0.05) occurred at 140 doa. The M. hyopneumoniae prevalence remained above 20% from 140 to 230 doa, decreasing thereafter. However, it did not reach 0% at any sampling after 110 doa. In this study, M. hyopneumoniae was not detected in piglets sampled prior to weaning. The M. hyopneumoniae detection pattern showed that in natural infections, gilts were positive for M. hyopneumoniae for one to three months, but occasionally long-term detection may occur. Moreover, the lack of M. hyopneumoniae detection throughout the study in 18.2% of gilts indicated the existence of negative subpopulations in positive herds.

Link to the entire article

What does antimicrobial-resistant bacteria really mean?

Antimicrobial resistance is an expression that everyone in swine production has heard at least once but what does it really mean?  How are you as a producer or veterinarian affected?

Villalta NHF antimicrobial resistance 2017.gif

In this column for the National Hog Farmer, Dr. Carles Vilalta explains that beyond the definition of a bacterium that is not affected by an antimicrobial, there are two different approaches to think about resistance:

  • One is determined by the Minimal Inhibitory Concentration or MIC, which records the minimum medicine concentration required to stop the growth of the bacteria.
  • The other focuses on the presence of genes enabling the bacterium to counteract the effect of the antimicrobial.

These genes are usually present in a sub-population of bacteria called mutants. The video below created by Harvard Medical School shows how these mutants can develop, adapt, and survive the highest antimicrobial concentrations. (video length < 2min)



Science Page: Bob Morrison’s legacy

Bob_MorrisonThis is our Friday rubric: every week a new Science Page from the Swine Health Monitoring Project. The previous editions of the science page are available on our website.

This week, the Science Page honors Dr. Robert Morrison, the founder and leader of the Swine Health Monitoring Project.

Bob’s unique talent for creating relationships that advanced the swine industry culminated in the creation of the Swine Health Monitoring Project (SHMP), one of the initiatives that Bob carried with pride. […] As it evolved, the SHMP changed names several times but many in the industry simply refer to it as “Bob’s project”. For that reason, and to give the just recognition he deserves, we have decided to renam the project to “Dr. Bob Morrison’s SHMP” (MSHMP).