Antimicrobial resistance is often thought of as a phenomenon that occurs in animals, herds or systems. For example, veterinarians and producers deal with antimicrobial resistance when they consider treating animals as a means of preventing, controlling or treating disease. At an even higher level, veterinarians may be interested in implementing antimicrobial stewardship programs across entire systems, as a way to mitigate antimicrobial resistance.
However, we can also view AMR as a phenomenon that occurs within the complex bacterial populations that inhabit pigs and their environments. Taken from this perspective, AMR results from billions of invisible interactions that occur as bacterial populations evolve in response to their ever-changing environment. While antimicrobial drugs are certainly an important environmental pressure that bacteria encounter, there are thousands of other pressures that can influence bacteria (and the resistance genes they carry) to perish, persist, grow and evolve.
Some of these pressures include management-related events that swine experience during their life. For example, weaning and commingling are increasingly recognized to markedly shift bacterial dynamics, in turn shifting AMR profiles. Animal disease, nutrition and metabolic status can also influence microbial interactions and evolution and thereby alter AMR profiles.
Given this complexity, our team is interested in identifying how antibiotic use interacts with these other "life events" to alter both the microbial and resistance profiles in swine (i.e., the "microbiome" and "resistome"). With funding from the National Pork Board, we have conducted a study to investigate this question in the context of growing pigs experiencing a porcine reproductive and respiratory syndrome virus challenge, with subsequent exposure to different antibiotic use protocols. We followed pigs from weaning through to market to characterize shifts in their fecal microbiome-resistome as they transitioned between various production phases, and as they confronted disease challenges and antibiotic exposures.
This study is ongoing, but some interesting trends are emerging. Not surprisingly, it seems that the weaning, transport and commingling of litters is a major event not only for the pigs, but also for their fecal microbes. As viewed through the lens of the microbiome, this phase of production corresponds with a massive shift in the fecal microbial profile of piglets.
As anticipated, these events also correspond with a significant shift in the AMR genes harbored by the fecal microbes. Perhaps less expected is that the fecal microbiome and resistome seem to shift quite substantially when pigs are challenged with PRRSV. It appears that these disease-associated changes are just as large as the changes that occur during antibiotic exposures in the same pigs.
Indeed, one unique aspect of the study is that we were able to sample the pigs after the disease process began, but before antibiotics had been initiated. This provided a rare opportunity to tease apart the impacts of host disease processes from antibiotic exposure.
In addition to generating new scientific insights into AMR, our goal with this project is to identify potential "win-win" microbial behaviors, i.e., microbial dynamics that provide dual benefit in terms of mitigating AMR while also promoting pig health and performance, particularly during disease challenges.
Of course, the ultimate goal is to understand how swine management practices can be used to promote these presumed win-win dynamics; and conversely, how these win-win microbial behaviors can be manufactured or reproduced to develop interventional or preventive protocols. There is a lot of work to be done in this regard, but fortunately all of the "ingredients" are available: the tools and technologies, the scientific know-how, and most importantly, the support and interest of the swine producer community.