SRA

Here we tested the application of shotgun metagenomics on airfilter samples from poultry houses or from artificial mock communities. Both types of samples were spiked with different quantities of two Campylobacter jejuni isolate to study the usefulness of the specific DNA extraction protocol as well as sequence depth needed to detect these species in a complex background. These analyses were performed as part of the European Joint Project - AIRSAMPLE (https://onehealthejp.eu/jrp-air-sample/). AIR-SAMPLE aims to develop and validate air sampling as a low-cost and multi-purpose alternative to fecal droppings or boot swab for surveillance, monitoring and eradication of Campylobacter in confined and biosecured broiler production. The three isolates submitted here are two Campylobacter jejuni isolates and an contaminant Staphylococcus epidermis isolate that is present in the sequence data of strain C. jenuni 927. The genomes were sequence to a depht of > 2000X with Illumina MiSeq.