Developing Management Options for Staph aureus on Organic Dairies

Final report for FNE20-965

Project Type: Farmer
Funds awarded in 2020: $13,149.00
Projected End Date: 05/31/2021
Grant Recipient: Reed Farm
Region: Northeast
State: Maine
Project Leader:
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Project Information


Staph aureus is a common contagious mastitis organism worldwide, causing significant economic losses on both organic and conventional dairy farms. Decades of research have developed extensive knowledge about this antibiotic resistant organism, but successful treatment and prevention through vaccination remains low, and the challenge remains for farmers. Management of the problem relies heavily on culling infected cows and on cultural practices to prevent new infections of healthy cows. In the summer of 2018, we experienced an outbreak of Staph aureus on our organic dairy. About one third of our herd tested positive, including several young cows, making it cost prohibitive to cull all the infected cows. This proposal sought to test recommendations from New Zealand that may help prevent new infections, and that show potential to help cows overcome existing cases. For this study, we adopted rigorous milking hygiene and cattle management practices as part of our day to day operations. However, due to challenges during the Covid-19 lockdown, we were not able to transport frozen milk samples to the lab in adherence to our frequent testing schedule to sample Staph aureus positive and negative cows to evaluate the efficacy of the experimental dry cow treatments and management approaches, nor trial new mid-lactation treatments. It is questionable as to whether we achieved our goal of 100% prevention of new cases in mid-lactation cattle during the study period, but we did achieve higher milk quality and a higher pay price for our milk. We will share our findings electronically through frequently used online dairy forums, and one-on-one with other farms in our community. Plans for public presentations at Wolfe's Neck Center’s Organic Dairy Farmer Training Program in Freeport, ME, and at a milk quality workshop held in cooperation with the Maine Organic Milk Producers and UMaine Cooperative Extension, remain on hold at present.

Project Objectives:

In a second year of study testing staph aureus management in the practical setting of a working organic dairy, our research would seek to:

1) Test the effectiveness of milking hygiene and preventative management protocols from the US and New Zealand. We will monitor staph aureus negative cows to determine if the adoption of the recommended practices results in zero new infections—100% prevention—during the one year study period.

2) Trial Manuka honey therapy as (a) a dry cow treatment, and (b) a mid-lactation mastitis treatment; this would be approved under the National Organic Standards to replace antibiotic treatments typically used in conventional production. The mid-lactation treatment a new study question for the 2020 study.

3) Trial long dry periods (105+ days) as suggested by experts in New Zealand, that may allow a staph aureus infected cow to “self cure”.

4) Trial dry-off strategies. Cold-turkey dry-off and New Zealand once-a-day dry-off will be compared for staph aureus negative cows to see if one strategy is preferable for preventing new mastitis infections.


Staph aureus is a common mastitis organism affecting dairy herds worldwide, causing losses in cattle health, reduced milk quality, and therefore lower pay prices on both organic and conventional dairy farms.

Decades of research have developed a vast body of knowledge about the organism. S. aureus bacteria inhabit the exterior teat skin of cattle, especially if the skin is rough, chapped, or unclean, and inhabit unclean areas in cattle barns and yards, such as wet alleys, muddy pasture lanes, and maternity pens if not properly cleaned.  Also highly contagious, lactating cattle are vulnerable to contracting new infections from herd mates during routine milking, via droplets of milk left inside the milking unit, or on staff’s hands. Cattle also commonly contract S. aureus mastitis at dry-off and freshening if hygiene is not optimal (communications with our technical advisor, Rick Kersbergen).

Perhaps in part through failure to adopt effective preventative management, conventional and organic farms alike continue to struggle with Staph aureus. Some conventional farms in our area have 100% positive tests for S.aureus in their herds (communications with our co-op’s field rep). A major challenge is that in conventional dairy systems, S. aureus has developed antibiotic resistance; research indicates that worldwide, the rate of cured cases is between 10%-30% for conventional (antibiotic) therapies [1].  For the rare cases when S. aureus has been seen to clear, it is typically young cattle, early in lactation, with a S.aureus infection that has not yet become chronic (communication with our technical advisor, Dr. Townsend). Vaccines have been developed, but a low 30% effective rate seen in the US [2]. Therefore, farms rely heavily on culling infected cattle (moving them to the beef market) to prevent new infections. The loss of milk price for lower milk quality and the heavy pressure to cull infected cattle cause significant economic losses for farms.

In early 2018, at our farm, bulk tank cultures intermittently indicated staph aureus in our herd. Our technical advisor recommended that we test cattle whose SCCs rise beyond a certain level and display S. aureus’ telltale patterns of rise fall. Twelve out of 33 lactating cows in our herd (about 1/3) were found staph aureus positive, making culling of infected animals an economic impossibility for our small farm. Through conversations with Rick Kersbergen, we became aware that we are not the only farm facing this challenge.

Rick provided us resources from New Zealand on Staph aureus that are oriented toward the organic producer and offer interesting differences from what is recommended in the US. Articles describe excellent preventative management as well as promising all-natural dry cow treatments including Manuka honey and long dry periods. We developed the New Zealand recommendations into a SARE Farmer grant which was funded in 2019.  We have some exciting preliminary results from our study, suggesting that S. aureus can be sequestered within a herd and existing infections may be successfully treated with medical grade UMF 10+ Manuka honey as a dry cow treatment.  This 2020 proposal adds a greater focus on Manuka honey treatment of mid-lactation SA+ cattle, in order to further explore the potential of Manuka honey intermammary treatment.

During a chance late-night emergency vet call with Dr. Townsend, we began discussing our 2019 SARE Farmer grant, and he expressed interest in learning more about our research questions. We shared our proposal with him and our primary technical advisor, Rick Kersbergen, suggested we invite Dr. Townsend on board as a co-technical advisor for our 2020 proposal, to lend his veterinary expertise to questions such as, how do you know when a chronic S. aureus infection is 100% cured, since the organism can encyst in the udder and maintain dormancy for some time.

While the number of conventional and organic dairy farms in the US is steadily shrinking since 2012, the number of organic dairy farms was around 2,500 nationwide in 2016.  All dairy farms could benefit from our research if we are successful at managing the Staph aureus organism to maintain milk quality, treating the organism with organic-approved medical grade Manuka honey and/or long dry periods, and sharing our results with a wide audience. Any lessons that we can learn with successes or failures in this study can help the organic dairy producer become aware of alternative approaches, and encourage adoption of preventative practices. Healthier, more productive cows, lower cell count milk, and higher milk quality premiums will help move dairies in a direction of greater financial stability.


Click linked name(s) to expand/collapse or show everyone's info
  • Richard Kersbergen
  • Dr. Matthew Townsend, DVM


Materials and methods:


In 2019 we received a SARE Farmer Grant with a one year trial period, in theory encompassing one freshening and one dry-off period for each cow in the herd.  At Carol Delaney’s suggestion, we are applying for a second year of study, in order to follow cows through complete gestation cycles (including the dry period), since S. aureus outbreaks often occur during stressful times such as calving and early lactation.

For the study, our herd is divided into two groups, cattle who test Staph aureus negative (SA-) and those who have tested positive (SA+).

The Milking Hygiene and Preventative Management Protocols as used in the 2019 study will remain unchanged during the 2020 study:
• Milk wearing nitrile gloves
• Pre-dip using IBA Bac Stop (iodine) teat dip
• Wipe teats with single service paper towels
• Post dip using IBA Genesis Barrier teat dip
• Milk SA- cows and SA+ cows separately, by marking milking units with orange flagging tape for milking SA+ cows
• Sanitize milking clusters by dipping first in warm water, then a bucket of IBA FS-100 sanitizer for 10 seconds (100ppm) between each cow. Concentration will be monitored with chlorine test strips
• Ensure cows dry-off and calve in a clean, dry environment.

Each cow will receive one dry-off method (either the “cold-turkey” or “once-a-day” dry-off) management. Additionally, SA+ cows will receive one trial treatment (long dry period or Manuka honey). This is illustrated in Attachment 3 to clarify how this design will allow testing of multiple treatments while still providing a basis for comparison. The following dry-off methods will be tested to evaluate if dry-off procedures influence new infections during dry-off and then at freshening. We will randomly assign all cows into one of three dry-off treatment protocols:

Dry-off Methods:
1) Cold-turkey dry-off. This is the method that is often used with intermammary antibiotic therapy. Cows will be provided with lesser quality dry hay instead of high quality baleage to reduce the nutrient density thereby discouraging milk production. They will be milked until a desired point and then not milked again until after calving. Dry cows will be post-dipped with Genesis Barrier post dip twice daily for 7 days following dry off.
2) New Zealand once a day method. We will reduce ration quality as above, and milk the cow once each afternoon for 3-5 days before stopping milking. Dry cows will be post-dipped with Genesis Barrier post dip twice daily for 7 days following dry-off.

Dry Cow treatments to be tested on SA+ cows:
1) Manuka honey. Just prior to the last milking for cows to be dried off, 5ml of UMF 10+ medical grade Manuka honey will be warmed and dosed intermammary into an SA infected quarter using a single use sterile syringe and massaged in thoroughly.
2) Long dry period. SA+ cows with sufficiently long breeding intervals are candidates to be dried off 105-120 days prior to their due date, rather than the standard 50-60 days.

Mid-lactation SA+ treatment: This is new for 2020. During a period of elevated SCC indicating S. aureus is active, mid-lactation SA+ cattle will be dosed intermammary with 5ml of UMF 10+ Manuka honey as a treatment of the infection, once daily, for 7 days.  Milk from treated cows will be discarded and not enter the bulk tank for human consumption.  These cows will be cultured immediately before, and for several months after, the Manuka honey treatment to detect if S. aureus is still present after treatment.

Milk sample collection will be performed by Katie and Nate during routine milking chores, according to the description in the project Timetable. We will collect samples for culturing monthly for: (a) SA- mid-lactation cows whose SCCs rise above their normal levels, to monitor the effectiveness of our milking hygiene protocols; (b) transitioning cattle (those about to calve or to dry off in preparation for calving), as a point of reference just before the dry-off event and just after freshening, to test dry-off methods and dry cow treatments; and (c) any other cattle of interest, such as those who have received Manuka honey treatment, to monitor for success of the treatment.

When sampling, udders will be prepped as for milking. Samples will be taken following Clean Milk Sampling protocols [Attachment 2]. Composite samples (a combination of milk from all quarters) will be used for routine screening of SA- cows. Samples will be collected and frozen for 5-6 consecutive days, then combined as a composite, to increase the likelihood of catching the intermittent shedding of the staph aureus organism, reducing the chances of false negative results. If a SA- cow is found SA+, we will re-test culturing samples from each teat to learn where the infection is. Individual teat samples will be taken from identified and suspect SA+ cows to allow us to isolate infected milk and to monitor for change.

Monthly milk testing will be conducted on the whole herd using Dairy One services to monitor somatic cell counts as an indicator of cow health and to screen for potential new mastitis infections. We will also test using a CMT paddle between monthly Dairy One testing if new infections might be suspected.

Our veterinarian suggested vaccination for S. aureus to help prevent new infections. We will vaccinate all members of the herd down to age 4 months using Lysigin (Boehringer Ingelhiem), recording this in cattle health records.

Milk culture data will be recorded in a spreadsheet on a per-cow basis for SA- cows and per-teat basis for SA+ cows in chronology, in effort to correlate any changes in SA status of individual cows with events such as dry off and freshening, as well as changes in SCC that could be used as indicators of staph aureus flare ups or new infections.

Statistical analyses of our data are not planned, however if our findings appear to indicate trends, statistical analyses will be performed in cooperation with technical advisors to determine if statements can be made about cause and effect.

Research results and discussion:

This study planned for monthly milk testing with Dairy one to monitor somatic cell counts of individual cows, as well as submission of frozen milk samples to the UMaine Diagnostic Lab for identification of the types of mastitis organisms affecting our herd.  However, due to changes as the Covid-19 lockdown began, we lost the route via which we had been reliably and regularly sending samples.  During the study period, with great effort, milk samples were successfully submitted for the months of June, July, September, and November 2020.  We were able to successfully test the somatic cell counts monthly for individual cows in the herd using Dairy One milk testing services, which allowed us to monitor how severely affected the S. aureus positive cows might become, and for identifying suspected new cases.

In July of 2020, we confirmed that one young first calf heifer in our herd, Prudy, had contracted a positive case of S. aureus mastitis. It appeared to be a new infection, which may have resulted from an incidental breakdown in our daily milking hygiene protocols (e.g. someone used an incorrect or unsanitized milking unit for milking Prudy); may have been contracted from the environment (e.g. soil), or, less likely, Prudy may have had an existing infection that was previously undetected.  In theory, because this animal was young and the infection appeared new, therefore cysts may not have yet developed inside the udder, Prudy may have been a candidate for the experimental mid-lactation Manuka honey therapy protocol that the study intended to develop.  However, at that time in 2020, so many stresses faced our family that I did not have the capacity to take on the development of the administration of the treatment in a timely manner, work that would have been done in consultation with our second advisor, Dr. Matthew Townsend, DVM.  As we continued to monitor Prudy’s somatic cell counts on a monthly basis, we saw her counts climb very high, indicating the infection rapidly became severe. We isolated this animal from the milking herd, unfortunately eventually culling the individual.

Because lactation cycles for cows often last more than 12 months, there was one cow, Hattie, who received an experimental dry cow treatment using Manuka Honey during the first year study, and who then freshened in June 2020.  We found this individual remained S. aureus positive after calving as her next lactation began.  Her case of S. aureus mastitis was long standing and suggests the organism encysted and is well established in the udder. With continuous milk quality monitoring, Hattie remains in our herd.  Her cell counts are usually low, however her milk is kept out of the bulk tank whenever her counts rise.

The large gaps in the mastitis diagnostic test data that resulted from irregular lab sample submissions leaves us with an incomplete data set to analyze.  It is clear that in addition to monthly somatic cell count monitoring, routine diagnostic testing of suspect cows is absolutely necessary for a farmer to maintain certain knowledge of which cows within a herd are S. aureus positive, therefore allowing those cows to be milked completely separately, and to have confidence that the hygiene protocols are effectively preventing new cases.  Irregular testing is insufficient, especially in light of the S. aureus organism's ability to encyst in response to a strong cow’s immune system, resulting in intermittent shedding, making it difficult to detect in certain cows.  Even now in the post-study period, there is some question as to whether there may be new, undetected cases of S. aureus in our herd.


Research conclusions:

This study sought to test whether milking hygiene and animal management SOPs would allow the maintenance of a S. aureus positive group of cattle within an organic dairy herd while preventing the spread of the organism to healthy cattle. It also sought to trial Manuka honey therapy for dry and mid-lactation cattle, to see if this material is a viable way for organic farmers to approach the rare curative scenario for new mild mastitis infections with the S. aureus organism.

During the study period, successful adherence to the daily milking protocols and SCC monitoring resulted in dramatic improvement over our levels of milk quality from the pre-study period, and even over the first year study period.  However, we did not successfully meet our objectives in the mid-lactation Manuka honey treatment trials. Essentially Katie as the project lead was overwhelmed by the stresses of running our farm and our household under Covid-19 lockdown conditions.  Transportation of frozen milk samples in adherence with our testing schedule was a challenge that we did not overcome, and opportunities to develop experimental mid-lactation treatment protocols for candidate animals in the herd regrettably were missed. 

Although there is some question as to S. aureus status regarding to undetected cases in our herd in the post-study period, due to irregular lab monitoring of suspect and transitioning herd members, after two years of adherence to the Daily Milking protocols, we still have a high degree of confidence in this protecting our healthy cows from new infections. By the end of the second year, our milk quality was extremely high.  The Reed Farm received a Gold Quality award from our milk company, Organic Valley, for the 2020 calendar year. This was achieved primarily through adherence to our milking sanitation protocols, and through continuous SCC monitoring, both as described under Methods.

Participation Summary
1 Farmers participating in research

Education & Outreach Activities and Participation Summary

1 Consultations

Participation Summary:

1 Farmers participated
Education/outreach description:

Following the sharing of information from our first year study, Katie has been contacted by an organic dairy farmer in a neighboring town who is dealing with the question of how to isolate S. aureus mastitis infected cows in his small herd. Through answering his questions, we have provided him information about our daily milking protocols developed with our Advisor, Rick Kersbergen.  We also shared our Somatic Cell Count data and the dramatic improvement in milk quality that we have been able to achieve since the beginning of the first year study. The farmer found this encouraging. We plan to have ongoing phone conversations to share further details regarding the study and answer any further questions.

We had planned to speak and present our study at the 2020 Maine Organic Milk Producers field day, however the event was postponed due to the pandemic. We may have another opportunity to speak at the 2021 event.

Learning Outcomes

1 Farmers reported changes in knowledge, attitudes, skills and/or awareness as a result of their participation
Key areas in which farmers reported changes in knowledge, attitude, skills and/or awareness:

Continuing the research into the second year for Developing Management Options for Staph aureus on Organic Dairies posed unique challenges during the 2020 Covid-19 lockdown.  Part of our challenges related to transport of frozen milk samples to the lab, and part related to our personal resilience during the stresses of adapting to the changes in our lives.  In reflection, the importance of commitment to the Daily milking protocols is very clear, because they allowed us to maintain control of the spread of the highly infectious organism that we are studying. The first year of our study was the first time that we had regular results from diagnostic lab submissions, which gave us a high degree of confidence that our protocols were working. When in the second year we were unable to get the samples to the lab on a regular and frequent schedule, the resulting lack of information really highlighted the importance of routine diagnostic testing results to let us know how we are performing and to inform our decisions. We are now looking for new, reliable avenues to transport samples up to the lab. Looking forward, I anticipate an ongoing relationship with the lab to maintain a steady stream of diagnostic data that I did not fully appreciate previous to the period of the lockdown.

Project Outcomes

1 Farmers changed or adopted a practice
Project outcomes:

We are now 3 years past the discovery of the outbreak of S. aureus in the milking herd at our farm, and 2-1/4 years past the start of the first year 2019 study Developing Management Options for Staph aureus on Organic Dairies.  We are still using the practices described in Materials and Methods, with a few minor modifications.

As the number of S.aureus positive cattle has dwindled in the herd (rather than increased) we have changed from marking a specific milking unit for use on the S. aureus positive cows, over to milking the positive cows last, after all healthy udders have been milked. Both methods work well to prevent spread of the organism via residual milk in the milking unit. But, one approach or the other was found to be more efficient depending on whether a large or small percent of the herd is being isolated.

We have continued to routinely screen suspect cattle for S. aureus, meaning those who have a high somatic cell count, cattle whose somatic cell counts rise and fall periodically, and cows at freshening including first-calf heifers.  However, we have not kept up the ambitious testing schedule timelines as outlined for the purposes of the study.

After the conclusion of the 2020 study period, Katie has developed a sensitivity to the nitrile gloves, and had to discontinue using these. We have not yet found a suitable substitute. She is practicing bare hand milking and frequent hand washing, a less convenient but still viable approach during milking.

There are fewer S. aureus cows in our herd now, only 5 as compared to 13 at the start of the 2019 study.  We have largely controlled the spread of the organism to healthy cows, while slowly culling the infected cattle over time as secondary health issues arose for those individuals. Fewer infected cattle in the herd reduces the chances of spreading the organism, and also reduces the chances of any particular cow experiencing a periodic flare-up that would significantly increase somatic cell counts in our bulk tank milk and damage our milk quality.  In 2020, we received a Gold Quality Award from Organic Valley, our milk co-op. The difference in pay price that the increase in milk quality we achieved is about $1.44 per hundredweight.  This equates to around $8,600 per year for a farm our size.  We feel that this is an indication that an organic dairy can overcome challenges with S. aureus and achieve excellent milk quality, with focused attention to the challenge and 100% dedication to the practices in the Daily Milking Protocols.

Assessment of Project Approach and Areas of Further Study:

The sampling schedule described in the Timetable, and therefore the resulting data set achieved in the 2019 study, were highly ambitious and allowed us to evaluate the effectiveness SSOPs and experimental treatments being tested in this study to a degree where we may be able to hypothesize about causation for new cases of Staph Aureus mastitis contracted during the study period (e.g. was the case contracted before the dry period, during the dry period, after freshening, or mid-lactation through contact with infected milk of a herd mate, etc.).

However, as 2020 unfolded, the Covid-19 pandemic and lockdowns limited our ability to keep with our intended Timetable in submitting lab samples.  During the 2019 study, Katie had worked one day a week in a town where one of the UMaine Orono Diagnostic Lab directors lives, and therefore we had a reliable method of transportation of frozen milk samples to the lab in a timely manner for our study. After the lockdown, this connection was no longer available. We received help transporting samples from regional DFA field staff and our State dairy inspector, but their services were not regular enough to allow us to adhere to our study Timetable. Over time, the delays in sample submission led to a smaller and less complete data set on the mastitis status of our herd in 2020.  

We attempted to work with our Advisors to revise the study questions to work with the very modest sample submission rate that we could achieve, however the study lost rigor with the reduced data set. During the stresses of 2020 pandemic, we also found that we culled more of the S. aureus positive cattle from our herd, since maintaining S. aureus cattle in a milking herd requires extra effort and attention on an ongoing basis. Generally, the study lost momentum under the stresses of the pandemic year.  We feel that the original study proposal would be viable to attempt again, especially the development of therapeutic protocols for this tricky mastitis organism, in conditions where many of the logistical challenges surrounding pandemic-related changes could become normalized.  Through continuing literature research surrounding non-antibiotic treatment of S. aureus and MRSA, we have developed an interest in additional non-synthetic treatment options for therapeutic trials, including a tincture preparation made using a combination of alliums. 

It should be noted that the 2020 study work, (as with the 2019 study,) was reliant upon strict adoption of the same set of milking hygiene protocols designed for the first year study, as well as regular testing of individual cattle with Dairy One milk testing services.  Throughout the the 2020 research period, even though we were not successful in completing the planned experimental therapeutic trials, we did continue with regular monthly milk testing, and we did remain dedicated to the Milking Protocols during our daily work. In fact, we have found the Daily Milking Protocols so helpful and effective, while remaining practical, that I anticipate that we will use both these Protocols and the Dairy One services indefinitely as long as we are milking cows.

Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.