Hatchery Sanitation: Understanding (and cleaning) The Nooks and Crannies

Posted by Jones-Hamilton Co. on Jan 28, 2021
Jones-Hamilton Co.

As the earliest phase of a chicken’s life, hatchery conditions, including both incubation parameters and exposure to pathogens, set the stage for flock well-being. Environmental threats present in a hatchery have the potential to cause considerable harm or loss of future performance, especially for flocks designated to be part of a raised without antibiotics program.

“There is potential for a high degree of cross contamination within a hatchery,” said Dr. Helen Wojcinski, DVM. “You have incoming eggs from a variety of breeder flocks and supplies, such as the pads for poult boxes, that can bring in contaminants such as bacteria and mold. Personnel moving around the hatchery can easily spread contaminants from dirty to clean areas if proper biosecurity procedures are not in place.

And since organic matter can interfere with the antimicrobial activity of disinfectants,1 thorough cleaning in all areas of the facility is a critical first step.

“Each hatch should be viewed as an opportunity to start clean and eliminate any bacteria or mold from a previous hatch to infect the next one. Day old hatchlings are extremely sensitive to even low levels of bacterial or fungi” said Wojcinski. While hotspots such as hatchers and the processing room are often cleaned and monitored more frequently, it’s important to clean and monitor all areas from egg receiving to delivery vehicles. This includes hatch trays, vaccination equipment, water and humidification systems, and all parts of the ventilation system (ducts, inlets, filters, etc.). If any areas are missed, bacteria or mold in that area can proliferate and contaminate clean areas, and infect chicks from the time they begin to hatch.

Hatch Tray

Fecal spots and debris remaining on this recently washed hatch tray create an opportunity for contamination once clean eggs are placed for incubation.

Chick Health Depends on a Clean Hatching Environment

For a clean hatching environment, start by removing dust, dirt, fluff, egg shells and other visible organic matter with brooms, scrapers or vacuums. Don’t forget to clean the fluff inside ventilation ducts or on fan blades, which may contaminate incoming air. After removing loose debris, consider using foam cleaners and low-pressure spray to remove remaining debris. High-pressure spray has the potential to aerosolize the organic material allowing it to more easily be spread.

Particularly dirty areas such as the hatchers and hatch trays will require more elbow grease to clean and require more diligence. Keep in mind that “if hatch tray washing machines that recirculate wash solution are not monitored to ensure that the target levels of cleaner and disinfectant are being used, the end result will be spraying bacterial soup on those trays,” said Wojcinski.

“Clean eggs that are placed into contaminated hatch trays in a warm, humid environment for three days pose a big risk of infection for those poults.” The same applies to newly hatched poults placed into contaminated poult boxes or into a contaminated truck.

Cleaning and disinfection can be more challenging in an older hatchery due to the development of little pitted holes and hairline cracks in concrete or deterioration of rubber seals in machines. All of these areas can harbor very low levels of bacteria, but when organic material is added during hatching it results in an explosion of bacterial growth. The solution may be to seal, repair or replace in order to allow the cleaning and disinfection process to work. Whenever a new hatchery is designed and built, consideration is given equally to the layout to ensure the correct flow of eggs, people and air. It’s also important to consider using materials that are more easily cleaned. This makes it easier and quicker for people to complete the all-important task of ensuring that eggs are hatched and hatchlings serviced in a clean environment.

Wojcinski commented that visually clean is just step one. “If you’re questioning how clean something is, it’s probably not. Since labor to clean and disinfect is often in short supply, we need to investigate products or technologies that will make the process easier or quicker.”

Disinfection Processes: Things to Consider

Following a thorough cleaning process, disinfection is the final step to eliminate bacterial challenges in the hatchery. While seemingly simple compared to extensive cleaning processes, the efficacy of disinfection can easily be diminished if proper procedures are not adhered to. Keep in mind:

  • Applying disinfectants to surfaces that are not dry can impact efficacy
  • Always follow the manufacturer’s guidelines, including dilution rates, contact time and safety precautions
  • Resistance to disinfectants can occur, so monitor the efficacy of your procedures and change products when necessary

Monitor, Adjust, Train

In addition to the NPIP program, most hatcheries follow their own internal monitoring or audit programs. Microbial audits on everything from the hallways and incoming eggs to the equipment and drains are swabbed to assess bacterial populations. Air plates are often placed in a variety of areas to learn where and what type of bacteria or mold are present.

“When you do the monitoring and do it well, it shows issues you didn’t know you had. Through monitoring and QA, we’re finding surprising things that allow us to adjust procedures to help improve livability in our poults in the field.”

It’s important to not spread a problem in a hatchery. The best way to avoid cross contamination is by identifying, understanding and training personnel on critical control points. “We’re depending on people to make sure best practices are being followed, so training and education is really important.”


When hatcheries work to maintain a clean environment and reduce contamination throughout the hatch process, there is a positive impact on chick health and performance. Success depends on consistent implementation of biosecurity and sanitation procedures, ongoing monitoring and training of all personnel in the facility.





1 https://www.cdc.gov/infectioncontrol/guidelines/disinfection/efficacy.html

Topics: Poultry, SWASH


SWASH™ is owned by Jones-Hamilton Co., a leading provider of science-backed solutions to the animal agriculture industry. Led by industry veterans who understand the challenges faced by producers, the SWASH™ team is dedicated to providing reliable, high-quality chemicals backed by dependable customer service and knowledgeable technical support. Our team knows that every penny matters and works continuously to ensure value, maximize efficacy, and enhance the bottom line.


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