Detection of Campylobacter spp. in broiler production using metagenomic analysis of air samples.

One of the major causes of food-borne infections in Europe are Campylobacter spp. Thus, broiler production facilities need to be closely monitored for the presence of Campylobacter using effective methods. Recently, it was indicated that sampling of the ambient air in combination with real-time PCR to detect Campylobacter in broiler houses can be highly sensitive, cost-effective and user friendly.

As part of the One Health European Joint Program project AIR-SAMPLE we tested this sampling method using metagenomics shotgun sequencing and compared it to quantitative PCR. We tested the method in two ways: 1) Using defined microbial community standards (mock communities), and 2) using real samples from two Norwegian broiler houses. In both cases we spiked gelatine membrane filters with different amounts of C. jejuni in order to determine the detection sensitivity for the two described methods.

The airfilters from the broiler houses were dominated by the genera Bacteroides, Brachybacterium, Brevibacterium, Cornybacterium, Lactobacillus and Staphylococcus spp. (Mean relative abundance 4.6 ± 1.6 % of all reads). These are known taxa from both airborne particulate matter present in broiler houses and as members of broiler fecal microbiome. This indicates that the airfilters capture host-associated microbes. Campylobacter spp. could be detected in both the broiler house and the spiked microbial community standards metagenomes. Based on the community standard metagenomes we could detect a minimum of 200 colony forming units of Campylobacter spp. with a cutoff of 80 reads.

Our results show that detection of Campylobacter is feasible using shotgun metagenomics of airfilter samples. In addition, by using mock communities we could identify a contaminant (Cupriavidus oxalaticus) present in the gelatine airfilter matrix representing around 10% of the reads of the real samples. Finally, we show that this approach can also be used to monitor AMR gene abundances in broiler production facilities.