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Whole-farm pathogen control starts with calves

Gene Boomer for Progressive Dairy Published on 01 March 2020

Harmful pathogens lurk everywhere on a dairy. Taking a whole-farm approach to pathogen reduction can break the cycle of infection and re-infection that may prevent your herd from performing at its best.

Although it is not possible or desirable to create a totally pathogen-free environment, dairy producers can reduce the risk of transmitting disease-causing organisms through a combination of good housing management, proper nutrition and an awareness of the specific pathogens present on the individual farm.



Pathogen control is important at all stages of life, but young calves are particularly vulnerable to them. Introduction of pathogens within the first few hours and days is typically exhibited by clinical scours within the first two weeks of life and often followed by pneumonia 10 to 15 days later. These back-to-back illnesses compromise the calf’s immunity and require substantial amounts of energy to fight the infection. This reduces growth and leaves calves more susceptible to additional pathogens and illnesses. Shedding of pathogens through manure creates additional re-infection risk for the calf and its penmates.

Many factors impact the health of newborn calves, from genetics and health of the dam to housing environment and nutrition. Good hygiene and animal comfort are the foundations of all successful programs. Dairy producers must manage all these effectively to get calves off to a healthy and productive start.

Understanding pathogen loads

Effectively controlling pathogens starts with understanding how they live and grow. It’s important to realize every operation is different, with different species of organisms existing within the environment and within the calves’ bodies.

The most common pathogens in calf-rearing environments are E. coli, salmonella, coronavirus and rotaviruses. Secondary pathogens tend to be cryptosporidiosis and coccidiosis, which can impact calves for several weeks and further limit growth potential.

In addition, clostridia bacteria are rampant on U.S. dairy operations. Between November 2015 and December 2018, Arm & Hammer researchers analyzed 1,200 fecal samples from calves up to 20 weeks old from 42 locations in seven states (Texas, Wisconsin, Pennsylvania, California, Idaho, New York and Ohio). More than 70% of the fecal samples tested positive for pathogenic Clostridium perfringens, with the highest prevalence for calves in the first three weeks of life. C. perfringens challenge was highest among 2- to 3-week-old calves, with 84% of their fecal samples testing positive.


Occurrences of clostridia scours can often be traced back to a milk delivery problem when calves are force-fed milk at higher levels than they can handle, allowing the milk to backflow into the undeveloped rumen. This leads to a lower rumen pH and a more suitable environment for C. perfringens to thrive.

Hygiene is fundamental

Fundamental to protecting calves from clostridia and other pathogen challenges is surrounding the calf with a clean environment away from adverse weather and other hazards.

The first several hours of life are critical for the lifespan of the calf and must be managed well, starting with the first feeding of colostrum. Introducing high-quality colostrum within the first eight hours of life is widely recognized as the best way to get calves off to a sound start.

Unfortunately, producers may unknowingly compromise colostrum by not following proper hygiene in its collection, storage and delivery. Allowing environmental pathogens to contaminate colostrum can compromise its effectiveness and the overall health of the newborn calf.

The first step is to follow proper hygiene in collecting colostrum from the dam, including cleaning and prepping the udder. After collection, proper storage is critical, along with cleaning and sanitizing of all items in contact with colostrum. All items used to get colostrum from the dam to the calf – milk equipment, buckets, bottles, pails – must be cleaned in hot soapy water, followed by an acid rinse, and dried thoroughly.

Proper hygiene of the housing environment also plays a big role in pathogen control. Whether in group or individual pens, make sure calves are clean, dry and comfortable. Calf housing should provide adequate ventilation without being drafty.


Supporting the immune system

Supplementing the diets of young calves with ingredients designed to allow for an optimal immune response when needed and limit the shedding of fecal pathogens can help calves overcome health challenges. Balancing the population of desirable bacteria against harmful bacteria in developing calves is critical to healthy rumen development and calf growth. Using feed additives designed to promote the growth of these beneficial bacteria while combating pathogens can help young calves meet their full genetic potential.

For example, the use of Bacillus strains to combat C. perfringens is proven to make animals more resilient against pathogens as well as reduce pathogen shedding into the environment. Through testing of fecal and manure samples, dairy producers can identify the clostridia load present in the environment and address the problem with unique strains of Bacillus designed to combat the pathogens.

Feeding refined functional carbohydrates (RFCs) is also helpful for pathogen control. RFCs bind pathogens, rendering them harmless to the animal and limiting shedding to other animals. RFCs also act as a prebiotic by feeding the beneficial bacteria of the intestine while blocking sites for attachment by pathogens. In calves, the RFCs help feed the microbiome and create a thicker mucus layer, thereby tying up the pathogens and preventing them from entering the rumen.

Research shows when milk replacers and starter feeds incorporate RFCs, calves have reduced incidence, severity and duration of cryptosporidiosis. Another study with preweaned commercial dairy calves showed reduced prevalence of salmonella and rotavirus among calves fed RFCs.

Supplementing rations with proper nutrition can help set the stage for a healthy life when used in combination with good animal care. Keeping feed equipment clean, maintaining housing and hutches, and removing manure frequently all help control pathogens and produce a healthy and thriving calf.  end mark

Watch future issues of Progressive Dairy for articles discussing pathogen control in the lactating herd, forages and manure.

References omitted but are available upon requestClick here to email an editor. 

Gene Boomer
  • Gene Boomer

  • Ruminant Technical Services Manager/Nutritionist
  • Arm & Hammer Animal and Food Production
  • Email Gene Boomer