Microbial diversity of selective and non-selective media for Campylobacter

Although Campylobacter is a foodborne pathogen commonly associated with poultry, it can be difficult to isolate because Campylobacter selective media vary in effectiveness. Therefore, using 16S rRNA gene sequencing, the relative effectiveness of selective media was determined in the current study by delineating the microbial composition of the pooled colonies on selective and non-selective media for Campylobacter isolation from poultry post-chill carcass rinsates. Samples were made by aliquoting 30 mL of post-chill rinsates to individual Whirl-Pak bags and inoculating them with 1.00 to 4.00 CFU per mL of either C. jejuni, C. coli and C. lari. After inoculation, 2x Blood free Bolton Broth were added to all inoculated samples and enriched for 20 h at 42 C under microaerophilic conditions. Following incubation, samples were spread plated on Campy-Cefex, mCCDA, and TSA plates and incubated for 48 h under the corresponding conditions. The V4 region of the 16S rDNA of the subsequent pooled colonies was sequenced using an Illumina Miseq. Microbial diversity and microbiota composition (ANCOM) were analyzed in QIIME 2.2021.11. Alpha diversity revealed main effect differences for both species and media. Under Pielous Evenness and Shannons Entropy, C. jejuni had the greatest evenness and richness, followed by C. coli then C. lari. For media, under Pielous Evenness and Shannons Entropy, TSA had the most evenly distributed taxa and most diverse taxa. There was an interaction of species and media on the beta diversity. Using Bray Curtis and Weighted Unifrac pairwise differences were seen between all species pairs. Media also impacted the beta diversity with the Bray Curtis and Weighted Unifrac of TSA and mCCDA and TSA and Campy-Cefex being different. Additionally, among the three Campylobacter spp., ANCOM revealed Campylobacter, Lachnospiraceae, and Oscillospiraceae were significantly more abundant taxa. The only significant more abundant taxa among the three media at the genus level was Staphylococcus. As a result, microbial diversity, and composition of enriched poultry rinsates appear to be affected by media used for enumeration and type of Campylobacter spp. present.