Abstract
Microbial contamination of beef cattle carcases and subsequent cross-contamination during processing is inevitable and virtually impossible to prevent. The understanding of microbial contamination in the beef industry is currently limited to hypotheses based on traditional microbiological tools. Additionally, the complex structural and functional responses of beef cattle microbial communities to the fragmentation in the supply chain remain unknown. This study used 16S rRNA gene sequencing in combination with traditional microbiology to monitor and compare changes in the microbiota throughout slaughter in an integrated (abattoir A) and a fragmented (abattoir B) beef abattoir in Australia. Briefly, the primary difference between an integrated and a fragmented abattoir is that fragmented abattoirs receive cattle from multiple sources, whereas integrated abattoirs typically receive cattle that has been produced using the same production system and from a limited number of sources. The composition in the bacterial communities varied between the abattoirs, though the presence of the most predominant bacterial species within the microbiota at each abattoir was similar. Lactobacillales (2.4–56.2%) and Pseudomonadales (2.4–59.4%) most notably dominated hides, carcases, and the environment in abattoir B. In abattoir A, Bacteroidales (3.9–43.8%), Lactobacillales (0.0–61.9%), and Pseudomonadales (0.5–72.1%) fluctuated but generally shared the dominance over the rest. Combined results of total viable count (TVC) and 16S rRNA gene profiling indicated that an upward hide pulling system adopted by abattoir B may lead to increased transmission of hide contaminants to post-hide pull carcases. Abattoir B had 3.2 log10CFU/cm2 reduction from hide to carcase, where abattoir A had 4.5 log10CFU/cm2 reduction. The findings from this study indicated that common beef-associated microbiota exist in varying composition in Australian abattoirs, and 16S rRNA amplicon sequencing is a powerful tool to understand in-depth movement of microbial contaminants.
Highlights
The general route of contamination involves fecally contaminated hides transferring fecal matter and contaminants onto carcases during slaughter and processing of the animals (McEvoy et al, 2000; Barkocy-Gallagher et al, 2003; Arthur et al, 2004; Bosilevac et al, 2005)
Mean total viable count (TVC) of fecal samples are reported in log10CFU/g with the hide and carcase samples reported in log10CFU/cm2
The results from this study demonstrated that common meatassociated microorganisms are found throughout slaughter regardless of the level of integration in the supply chain of beef cattle
Summary
The general route of contamination involves fecally contaminated hides transferring fecal matter and contaminants onto carcases during slaughter and processing of the animals (McEvoy et al, 2000; Barkocy-Gallagher et al, 2003; Arthur et al, 2004; Bosilevac et al, 2005). Transfer of microbial contaminants from the hide to carcase is likely to occur during hide removal resulting in the contaminated carcases becoming a vector for transmission of microorganisms including pathogens to different cuts of beef throughout the supply chain (Fegan et al, 2009; Arthur et al, 2010; Chopyk et al, 2016). Such movement and prevalence of microbial contaminants including the regulatory important pathogens in the beef supply chain are well documented in the literature (Elder et al, 2000; Collis et al, 2004; Fegan et al, 2005, 2009; Antic et al, 2010; Barlow and Mellor, 2010; Svoboda et al, 2013; Stromberg et al, 2015). One could argue that higher fragmentation in the supply chain may contribute to increase variability in the microbial composition due to beef cattle arriving from multiple different sources potentially carrying diverse endogenous microbial populations
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