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Control pathogens that silently steal productivity

Joel Pankowski for Progressive Dairy Published on 11 March 2020

On a dairy farm, obvious challenges surface every day, perhaps a displaced abomasum or mastitic quarter. These problems are readily diagnosed and usually treated successfully.

However, hidden challenges may be difficult to diagnose and therefore more difficult to resolve. Often these challenges manifest themselves as cows that underperform for no apparent reason. While many factors cause subclinical issues, harmful pathogens could be a primary culprit.



On a typical dairy farm, pathogens proliferate inside an animal and enter the environment when manure is spread on fields. Pathogens then reside in the soil to be taken up by the plant at harvest. While forage fermentation can kill most pathogens, those that survive re-enter the animal to start the process over again.

That’s why it’s important to take a whole-farm approach to pathogen control, addressing the pathogens present in calves, cows, manure and forages. In most instances, pathogens reside in one of those four key areas.

Common pathogens

In the lactating herd, the most common pathogens are clostridia, prevalent in feed, soil and the cow’s digestive tract. Our researchers have analyzed clostridial risk on dairies since 2015. The latest data analysis shows that more than half of nearly 15,000 fecal samples from 369 farms in 27 states fall in a high-risk category based on the levels of clostridial bacteria found in samples. Toxic strains of clostridia can lead to deadly hemorrhagic bowel syndrome (HBS). Non-toxic strains can result in cows with inconsistent manure, varied feed intakes and inconsistent production.

Salmonella is a pathogen that can cause pneumonia, diarrhea and reproductive losses. Salmonella Dublin is an especially troublesome strain. Once this strain gets into the herd, it is hard to eradicate. Antibiotic treatments may reduce infections, but animals can become persistent shedders of the disease over their lifetimes.

A third pathogen prevalent on U.S. dairy farms is pathogenic E. coli. This pathogen can be isolated from manure, water, milk and other farm environments. While most strains of E. coli reside in dairy cattle with no harmful effect on the animal, many E. coli strains cause serious illness in humans and therefore need to be contained.


There are many other pathogens that can be present on a dairy farm, though these three are the most prevalent. In order to control the pathogen challenges on your dairy, it’s important to understand which pathogens are present on your farm and where they are located.

Often, cows suffering from subclinical pathogen challenges are difficult to diagnose and treat. Cows may not show any clinical signs but just don’t perform up to expectations or the level of management focused on the lactating herd. Usually the dairy producer, nutritionist and veterinarian have tried a variety of interventions to resolve the issue to no avail. These herds are good candidates for a pathogen assessment.

Unique pathogen profiles

Every operation has its own microbial terroir – the unique population of micro-organisms that reside within the farm environment, including soil, animals and feed. The microbial environment is different for each dairy, and your dairy is probably different from even the dairy just down the road. Assessing the pathogens that affect your dairy will help identify nutrition solutions that can offset the negative effects of these pathogen challenges.

When formulating a plan of action to address these challenges, consider a complete, broad-spectrum nutritional program that breaks the pathogen life cycle starting at the cow. Begin with a feed ingredient solution that offers a wide spectrum of bacterial strains, or bacillus, that are active against the pathogens within your farm’s environment. Using diverse bacillus strains provides the coverage needed to address the specific challenges within your herd’s microbial terroir.

In addition, feeding refined functional carbohydrates (RFCs) can bind harmful organisms and prevent them from doing harm in the animal. In one study conducted in a laboratory environment, RFCs were introduced to E. coli and salmonella populations. Over the period of the study, RFCs bound between 47% and 53% of E. coli and between 80% and 98% of salmonella.

A combination of feed ingredients can both target specific pathogenic challenges and bind and remove those pathogens from the animal, breaking the pathogen cycle within the animal. This program can help resolve subclinical pathogen challenges that act as an anchor on the productivity of your herd, leading to stronger immunity and enhanced productivity.


Of course, proper nutrition can’t do the job alone. Other important pathogen-reducing interventions on the dairy include keeping the environment clean inside the barn; milking parlor, calf and heifer facilities; and other housing areas. Follow good forage management practices to avoid contamination from soil or ash and use inoculants to drive optimal forage fermentation. Watch for future articles addressing pathogen control in forages and manure. end mark

Joel Pankowski
  • Joel Pankowski

  • Manager, Field Technical Services
  • Arm & Hammer Animal and Food Production
  • Email Joel Pankowski