High bacteria counts in your bulk tank milk can be very frustrating to all parties involved. In today’s milk market, these higher bacteria counts can also jeopardize your milk quality premium, as many cooperatives have bundled the different tests together.

Member Programs Manager / Cayuga Marketing
Virkler paul
Senior Extension Associate / Cornell University College of Veterinary Medicine

In other words, you can have a great somatic cell count (SCC) but lose your bonus because of a high bacteria count. So how do you go about troubleshooting where the problem is coming from? What we would like to outline in this article is a more systematic approach to take when you are first notified of a high bacteria count.

Ideally, your cooperative has in place some sort of alert system that notifies you in a timely manner when the bacteria count in your bulk tank is elevated above some pre-set threshold. Depending on what tests your cooperative is performing, this might be a high standard plate count (SPC) or another test replacing this test, such as a Bactoscan count. It might also be a high preliminary incubated count (PIC) if your cooperative uses this test in addition to the SPC.

Once you receive this alert, we recommend you request laboratory pasteurized counts (LPC) on all bulk tanks from that point on. The LPC is a very helpful test to differentiate whether your high bacteria counts are from an equipment cleaning problem or some other source. Although there are different recommendations on cut-off levels for the LPC count, we typically use a value of 200 cells per milliliter as the cut-off. If the LPC is above this level on multiple tanks, it is highly suggestive of an equipment cleaning issue.

The second step is to begin taking duplicate samples on every tank. The second sample should be labeled with the tank number and date and placed in the freezer. It should be noted, the purpose of the second sample is not for official testing but to have a bank of samples to send in for additional testing if necessary. The second sample also represents what the milk was on the farm and can be used to help diagnose any issues with sampling handling from the farm to the testing laboratory.


The next step is to go out and check the detergent and acid levels to make sure the barrels are not empty and that any chemical pumps are working to put the proper amount of chemical into each wash cycle. The hot water level should also be checked and one complete wash cycle observed to determine whether there are any obvious issues present.

If no issues are detected, the fourth step is to contact your equipment dealer or chemical supplier and request they perform a wash-up analysis and provide a written report. At the very least, this initial wash-up analysis should consist of:

  1. Temperature levels at the start of the pre-rinse, main wash and acid cycle, and at the end of the main wash cycle for your milking equipment wash
  2. A check of the chlorine, alkalinity and pH at the start and end of the main wash
  3. A check of the pH at the start and end of the acid cycle
  4. A visual observation of the entire milking system wash from set-up to completion, specifically looking for any issues with set-up, water flow through units, air injector function, air leakage into the system, trapping out and drainage
  5. A check of the bulk tank washes and a visual observation of all surfaces within the tank

After the report is received from the equipment dealer or chemical supplier, any issues detected should be corrected and the counts monitored for the next week. If there is no change in the SPC or LPC counts at this point, then a team meeting should be set up. The team meeting should consist of the owner, manager, equipment dealer, chemical supplier if not the equipment dealer, the herd veterinarian and potentially an outside facilitator.

The first goal of the meeting is to review all the data collected to this point, including the SPC, PIC and LPC counts, the observations of the wash, the written report of the wash-up analysis and any other input from the team members. The second goal of the meeting is to create an action plan for who will perform what additional testing moving forward.

Our recommendation would be that the next step in testing is to perform strategic milk sampling at multiple sites in the system at multiple time points throughout milking. This is done using commercially available string sampling devices and temporarily placing them into the system. We would recommend performing at least SPC and LPC on each of these samples. This sampling can be a big help to isolate which parts of the system may be causing an issue or if there is incubation over the course of the milking. On a recent herd situation, this was a critical component of the analysis and very clearly pointed out that the in-line metering device was an issue leading to high bacteria counts. After this was set up correctly to clean properly, the bacteria counts returned to normal levels.

Our second recommendation for next steps would be to perform a complete wash-up analysis by completing the “NMC Troubleshooting Cleaning Problems in Milking Systems” form, which is available online. Using this form helps to avoid the common mistake of jumping to conclusions on what may be the problem rather than systematically evaluating the entire set-up. Ideally, the equipment dealer would perform this detailed testing, including water flow through units and a slug analysis of the milkline. If they are unable to perform this in a timely manner, then we would recommend reaching out to other organizations that can perform this type of testing. A written report of the findings from this testing is essential so everyone is on the same page.

After the strategic milk sampling results and the written report from the detailed wash-up analysis are available, we would recommend a follow-up team meeting with the same members as before. The first goal of this second team meeting is to discuss the results and determine an action plan for what needs to change going forward. A second goal of this meeting should also be to create a detailed monitoring plan so everyone is aware of who is responsible for doing what. As before, counts should be monitored after changes are implemented and, if necessary, a third meeting scheduled.

It has been our experience that this strategy has been able to solve the high bacteria counts in all situations that we have been involved in, but the timeline to get to the end has been very different on individual farms. Our hope is that by laying out this detailed plan, it will help you to accelerate the correction of a high bacteria count on your farm so you do not lose premium money and return quickly to producing high-quality milk.

Lisa Ford and Paul Virkler provided this article on behalf of the Empire State Milk Quality Council (ESMQC), a non-profit organization in New York state that focuses on helping producers achieve higher levels of milk quality.