Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2018

Metagenomic profile of the bacterial community structure on poultry carcasses throughout a factory processing line (#110)

Stanley H Chen 1 2 , Narelle Fegan 3 , Chawalit Kocharunchitt 2 , John P Bowman 2 , Lesley L Duffy 1
  1. Agriculture & Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Coopers Plains, Queensland, Australia
  2. Tasmanian Institute of Agriculture/School of Land and Food, University of Tasmania, Hobart, Tasmania, Australia
  3. Agriculture & Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Werribee, Victoria, Australia

Food safety issues in poultry have been gaining attention due to increasing poultry sales particularly in relation to food-borne pathogen contamination. This study aimed to examine the bacterial community structure at specific poultry processing steps, using next generation sequencing and cultural techniques. A single flock was sampled from pre-/post-scalding, pre-/post-immersion chilling and post-air chilling (10 birds per stage) as well as 10 caeca after evisceration. Total Viable Count (TVC), enumeration of Escherichia coli and Campylobacter, and determination of Salmonella prevalence was performed. The bacterial community structures were investigated by targeting the V4 region of bacterial 16S rRNA genes. Reductions of >4 log10 CFU/ml in TVC and E. coli, and >5 log10 CFU/ml in Campylobacter were recorded when comparing cultural counts of pre-scalding to post-air chilling. Salmonella was not detected in post-air chilling samples compared to 50% Salmonella prevalence in pre-scalding samples. The bacterial community data revealed the four most abundant bacterial phyla in all processing stages were Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria, which all together represented at least 97.1% of the bacterial population at each processing stage. At genera level, unclassified Lachnospiraceae, Lactobacillus and Staphylococcus were persistent bacteria in Top 10 OTUs across all sampled stages. The relative abundance of Campylobacter was consistently around 0.1% throughout processing with highest abundance at 0.5% in post-immersion chilling samples, whereas the cultural counts suggested the reduction of Campylobacter through processing. However changes of the relative abundance of E. coli was in agreement with its cultural counts, which decreased through processing with an increase of 7.5% between post-scalding and pre-immersion chilling. Interestingly Faecalibacterium and unclassified Ruminococcaceae became Top 10 OTUs after scalding and immersion chilling, suggesting there are potential contamination. Pseudomonas was the most dominant bacterium (20.3%) in post-air chilling samples, indicating its role in the downstream spoilage community. The investigation offers an understanding of the bacterial community structure on chicken carcasses, how it changes, and where the contamination may occur through processing.