Metagenomics analysis of the microbial communities contaminating meat and carcasses

Summary

Control of plant hygiene and the prevention of contamination of carcasses is a vital aspect of meat production.  Reduction or prevention of microbial contamination is important for public health, Market compliance, and the prevention of spoilage.  A significant burden of microbial testing is required to meet both local and international requirements.  Although it is well understood that undesirable microorganisms such as Escherichia coli O157:H7 and other pathogens that contaminate meat are derived from cattle faeces it is interesting to note that the ecology of the carcass environment remains essentially unknown.  Pathogens from faeces or other sources do not occur in isolation but instead are a small part of a diverse collection of microbes.  These collections of organisms will be present on most living (biotic) surfaces or non-living (abiotic) surfaces.  Traditionally, organisms are detected by sampling the biotic or abiotic surfaces then growing the resulting microbes in the lab.  While this cultural technique can be targeted to calculate the numbers of selected organisms it cannot provide an overview of the ecology and full range of organisms present. Therefore, this research will explore, through a proof of concept project, the application of metagenomics to examining the microbial ecology of meat production.
Metagenomics is a broad-brush term used to describe the analysis of microbial communities without culturing them, instead the genetic material from cells are sampled from either biotic or abiotic surfaces.  New high-throughput DNA analysis techniques analyze the genetic material to yield a snapshot of everything that is present.  There is no need to grow the organisms and the rapidly improving Genetics and genomics technology has developed to the point where it is capable of analyzing large numbers of samples and providing detailed descriptions of who is there. It will investigate the application of metagenomics to characterize the microbiome of carcass, hide and faeces from a single day of production at an export abattoir.  It is hoped that this work will be the first step toward goals such as unambiguous identification of the source(s) of contamination (e.g., faeces vs. hide), understanding how the microbial communities are impacted by processing treatments (e.g., hot water washes, air vs. spray chilling), improved testing/detection and potentially the manipulation of the bovine microbiome to hopefully mitigate pathogen contamination through processes like competitive exclusion.
Hides were found to be the primary source of contamination of the air samples collected from all 3 sampling sites. Source tracking analysis indicated that an average of 86 % of the bacteria in the air samples were derived from the hides. This large contribution of hide bacteria to the air samples was not limited to locations adjacent to the hide puller, it was also observed outside the slaughter floor and in the chiller. Source tracking analysis performed on the carcasses was highly variable with likely air contamination ranging from 100 % to nothing.
When averaged across all 79 samples it suggested that 25 % of the bacteria on carcasses came from the air. Approximately 25 % of carcass samples were heavily contaminated by bacteria derived from the air, including three carcass samples whose microbial profile was nearly identical to the air. For another 25 % of the carcass samples the proportions of bacteria present indicated that the air was not a likely source of direct contamination while for the remaining 50 % of samples the air contributed a low level of contamination. Interestingly, the types of bacteria present on carcasses were similar to those on hides but differences in their proportions between hides and carcasses suggests that air was not the main route by which they reached the carcass.
Careful examination of the types of bacteria present on the carcasses suggested an important source of contamination may be a mix of rumen and oral bacteria both of which would be likely to come from the mouth. One carcass was contaminated almost exclusively with a single type of common oral bacteria, Fusobacterium. Many of the abundant carcass bacteria not derived from the hide or air matched those that have been identified as ruminant oral bacteria. Therefore, it is possible droplets sprayed from the mouth and tongues of animals prior to removal of the head may be a significant source of contamination. Rapid and erratic movements of the head during hide removal may result in droplets directly reaching the carcasses or perhaps processes like floor brushing or hose spraying may mobilize these contaminants.
This work suggests that control of air movement to prevent or limit contamination of the carcasses with bacteria from the hides may be helpful. Traditional microbial analysis showed that the number of bacteria in the air near the hide puller was at least 60 times higher than elsewhere in the facility. Furthermore, control of bacteria derived from the mouth of the animal may also be beneficial. Any substantive reduction in carcass contamination should result in fewer lots of meat lost to the identification of pathogens. Ultimately, demonstrated improvements in carcass and meat hygiene could be used as evidence in the case to reduce the burden of testing or to improve access to overseas markets.