Detection of Campylobacter in air samples from poultry houses using shot-gun metagenomics – a pilot study

Background Foodborne pathogens such as Campylobacter jejuni are responsible for a large fraction of the gastrointestinal infections worldwide associated with poultry meat. Campylobacter spp. can be found in the chicken fecal microbiome and can contaminate poultry meat during the slaughter process. The current standard methods to detect these pathogens at poultry farms use fecal dropping or boot swaps in combination with cultivation / PCR. In this study, we have used air filters in combination with shotgun metagenomics for the detection of Campylobacter in poultry houses and MOCK communities to test the applicability of this approach for the detection of foodborne pathogens.

Results The spiked MOCK communities showed that we could detect as little as 200 CFU Campylobacter per sample using our protocols. Since we were interested in detecting Campylobacter, a DNA extraction protocol for Gram negative bacteria was chosen, and as expected, we found that the DNA extraction protocol created a substantial bias affecting the community composition of the MOCK communities. It can be expected that the same bias is present for poultry house samples analyzed. We observed significant amounts of Campylobacter on the air filters using both real-time PCR as well as shotgun metagenomics, irrespective of the amount of spiked in Campylobacter cells, suggesting that the flocks in both houses harboured Campylobacter spp.. Interestingly, in both houses we find diverse microbial communities present in the indoor air. In addition, have we tested the Campylobacter detection rate using shotgun metagenomics by spiking with different levels of C. jejuni cells in both the mock and the house samples. This showed that even with limited sequencing Campylobacter is detectable in samples with low abundance.

Conclusions These results show that air sampling of poultry houses in combination with shotgun metagenomics can detect and identify Campylobacter spp. present at low levels. This is important since early detection of Campylobacter in food production can help to decrease the number of food-borne infections.