Editor’s note: This tip was written by Roy Williams, a member of the Dairy Calf and Heifer Association’s Leadership Class

Recently, I was asked to participate in a research project involving bacterial resistance to a common disinfectant. While that study is still on-going, and does not relate directly to calves, it did remind me about a major gap in the sanitation program at most dairies and calf farms.
While we typically assume that a disease outbreak in a livestock operation is the result of that disease being "imported" to the farm, or that a disease occurs because some cleaning protocol was not properly followed, those assumptions may not always be correct.
Many instances of high rates of specific disease incidence in (human) hospitals have been traced to disinfectants. In one well-studied case, the disease organism was found to be living inside the bottle of disinfectant that was supposed to kill the organism!
It is commonly understood among microbiologists that a population of organisms that is not completely killed by a disinfectant or antimicrobial has a chance to develop resistance. Thus, if you fail to kill all the microorganisms of a given type in a given location, the organisms that survive may reproduce, and confer to their offspring a genetic ability to resist the disinfectant. Your failure to disinfect an area completely may result in a mutation that makes the organism much harder to kill next time.
It is also known that certain types of microorganisms are highly resistant to disinfectants. Of chief concern to calf growers is the protozoan Cryptosporidium parvum, which is completely resistant to all commercial disinfectants. Even very strong bleach or acid solutions do not kill Cryptosporidium parvum.
Many disinfectant products contain "quaternary ammonium compounds" or "QACs." However, it is well known that there are many genotypes (genetic variations) of staphylococcus and pseudomonas that are very resistant to QACs. In fact, as long ago as 1998, a paper was published that reported that 30 percent of all samples of staphylococcus that were tested would grow in a QAC solution. Similar examples can be found for all commercial disinfectants and cleaning solutions.
On a commercial farm, the most practical approach is to utilize different chemicals when problems develop. Be sure you use the maximum-labeled concentration of your disinfectants, and leave them on the surface for at least as long as recommended and longer if possible. Do not mix chemicals; you could start a dangerous chemical reaction!
If you can use multiple disinfectants, do so, but use them in sequence, with complete rinsing between different chemicals (like using soap and then acid in milk lines). Again, remember that mixing two chemicals together (unless specified on the label) will probably make the two chemicals not work at all, and you may produce toxic or explosive gasses or liquids.
If you have a recurring issue with one or more specific diseases, find a testing lab that has experience with environmental pathogens to help you determine a proper disinfectant protocol for your situation.

Source:  Dairy Calf and Heifer Association