Genomic DNA Extraction and Whole-Genome Sequencing of C. jejuni

Both C. jejuni strains were grown overnight at 42°C on OMHA + blood plates under microaerobic conditions and genomic DNA was extracted using Epicentre Metagenomic DNA Isolation kits for Water (Illumina) according to the manufacturer’s instructions, as previously described (Clark et al., 2016 (link)). Briefly, quantification of DNA was performed by DeNovix QFX Fluorometer using Qubit dsDNA BR assay kit (Fisher Scientific). Sample libraries were prepared using a MiSeq Nextera^® XT DNA library preparation kit (Illumina). Whole genome sequencing was performed by 250 bp paired end read sequencing on the Illumina MiSeq sequencer using a MiSeq^® Reagent Kit V2 and 500 cycles on the Illumina MiSeq platform. Sequence reads were assembled into contigs using INNUca 2.6. Pangenomic annotations were performed by Roary (Supplementary Data S1). Raw reads can be accessed on NCBI under the reference number PRJNA903792. From pangenomic annotations, strain specificity, using the NCBI BLAST tool and conventional PCRs, was verified for many genes. Among these genes, two genes unique to G2008b (LpsA and DmsB) and two genes unique to D2008b (McrBC and RimP) were selected as candidates for qPCR/PCR targets for the quantification/identification of each strain in the samples (Supplementary Figure S1).