Clean Isn’t the Same as Clear: What a New Study Reveals About Campylobacter in Broiler Sheds

Campylobacter is one of the leading causes of foodborne gastroenteritis worldwide, and poultry is a major source of human exposure. Most control efforts focus on processing, but stopping colonization on the farm means less Campylobacter ever reaches the plant. 

A new open-access study published in Food Microbiology put standard broiler shed cleaning and disinfection to the test. Researchers in New Zealand sampled four sheds on two commercial farms before and after cleanout, tested birds from consecutive flocks, and used whole-genome sequencing to investigate relationships among Campylobacter isolates and potential transmission pathways. 

Read the full study in Food Microbiology 

Cleanout works. Mostly. 

Cleaning and disinfection made a big difference. Before cleanout, 22% of shed samples tested positive for Campylobacter. After cleanout, just 1% did. 

But a pathogen result is only part of the picture. The team also ran ATP hygiene checks after the cleanout, and 45% of the readings exceeded the company's acceptance threshold. Floors, feed loaders, fans and nipple drinkers had the highest share of failed readings. Auditors also found dust on fans and vents, residue in feeders and biofilm in drinking water lines. 

In other words, a shed can pass a pathogen test and still carry the organic residue that gives pathogens somewhere to hide and proliferate. Hygiene monitoring and pathogen detection answer different questions, and both matter. 

Where Campylobacter hides 

Before cleaning, contamination was concentrated in a few places: 

• Nipple drinkers: the top hotspot, with 31% of samples testing as positive. Standing water and fecal contamination help Campylobacter survive and worn or scaled drinkers are harder to clean. 

• The annex: 16% of samples were positive. This entry area is meant to be a hygiene barrier, but it was often cleaned less thoroughly than the shed itself. 

• Floors, walls, fans and vents: cracks, joints and dust created protected spots that cleaning can miss. 

It's not just carryover. It's reintroduction. 

This is the study's most surprising finding. Genome sequencing showed no evidence that strains survived cleanout and infected the next flock in the same shed. Instead, identical strains turned up in different sheds on the same farm at the same time. 

That suggests the organism spread between sheds, likely through people, equipment and other on-farm routes, rather than persistence after cleaning. The authors suggest that targeting these transmission routes and high-risk interfaces such as the annex may do more to reduce Campylobacter than simply cleaning harder. 

The method you use changes what you find 

The researchers tested every shed sample three ways: culture, quantitative PCR before enrichment, and presence/absence PCR after enrichment. Together, the methods identified 74 positive samples. Culture alone only found 36 of these. 

Each method told a different part of the story. Enrichment PCR detected low levels of viable Campylobacter and may catch cells that are difficult to culture when other bacteria compete on the plate. Quantitative PCR flagged areas with heavy contamination. PCR testing in the study was run with the BAX^® System Real-Time PCR Assay for Campylobacter. 

For producers and labs, the takeaway is simple: the sampling point, the enrichment step and the detection method all shape the result.  

Looking beyond the study: Hygiena offers BAX^® System and foodproof^® PCR solutions for poultry testing programs. Explore poultry and egg testing solutions. 

What this means for your operation 

• Verify the clean, not just the look. Pair visual audits with ATP monitoring and periodic PCR testing to confirm surfaces are truly clean before restocking. 

• Prioritize high-risk interfaces. Drinkers, water lines and the annex deserve extra attention in every cleanout. 

• Close the gaps between sheds. Hand hygiene, dedicated footwear and tools and clean equipment help stop strains moving from one flock to the next. 

• Standardize and train. Cleanout results varied between events, including one cleaned by a new staff member. Consistent procedures and training reduce that variation. 

• Use the right detection method. Pathogen testing confirms what hygiene checks cannot, and the right method helps catch low-level contamination. Pair ATP and PCR testing to increase confidence in results.  

Broiler Shed Cleanout Audit Checklist 

Use this checklist after cleaning and disinfection, before litter goes down and the new flock arrives. It is adapted from the risk areas identified in the study. Adjust it to your site, procedures and local requirements. 

Water system 

• Water lines flushed according to your SOP 

• Drinking water sample checked for detritus or visible biofilm 

• Nipple drinkers and cups free of residue and scale 

• Worn, discolored or damaged drinkers flagged for replacement 

Annex 

• Floors, walls and hand-contact points (door handles, control panels) cleaned and disinfected 

• No cobwebs, insects or wild bird droppings 

• Footbath refreshed or dedicated shed boots in place 

• Hand-washing or sanitizing station stocked 

• Annex door kept closed 

Floors and walls 

• No litter or debris in cracks, expansion joints or along the base of walls 

• Damaged concrete flagged for repair 

Feed system 

• Feeders, augers and feed loaders free of residual feed 

Fans and vents 

• Inside surfaces free of dust and cobwebs 

• External fan housings clean 

External areas 

• Concrete pads free of litter, droppings, sanitizer and pests  

Verification and records 

• ATP swabs taken at high-risk sites and compared with your acceptance threshold 

• Pathogen samples collected after sanitizer has dried, using a neutralizing broth 

• Documented results/handler/cleaner or similar  

• Results trended over time to spot recurring problem areas 

Between sheds 

• Workers change footwear and wash hands between sheds 

• Catching crews and shared equipment cleaned before entering 

Want help building a testing program that covers both hygiene and pathogens? Contact us: https://www.hygiena.com/contact