Don't Count Your Eggs Before They Hatch: A "One Health" Investigation of Antimicrobial Resistance at the Intersection of Small-Scale Agricultural Development and Global Health in Northwestern Ecuador

Abstract

Small-scale poultry production systems have been essential to human livelihoods among rural agricultural communities for millennia, improving diet, finances, and food security of impoverished rural populations. Poultry farming is the fastest growing agricultural sub-sector, especially among low- and middle-income countries (LMICs). Small-scale chicken farming remains a rapidly growing micro industry because of the low initial investment compared to other food animals. Although the majority of households globally continue to practice backyard poultry farming, primarily encompassing indigenous chickens or sometimes crossbred varieties, more recently, there has been a shift from subsidence farming of local free-range backyard chickens to industrial food production breeds of poultry reared in concentrated animal feeding operations (CAFOS). Often international non-governmental organizations promote commercial small-scale chicken farming as a means to promote improved food security, economic development, and gender equity. Such intervention strategy has become more common since the United Nation’s Sustainability Goals to end hunger, achieve food security and improved nutrition and promote sustainable agriculture by 2030. Despite the economic benefits of industrially animal production, such introductions can present serious risks to animal and human health. Specifically, poultry reared in CAFO environments receive high amounts of antimicrobials for growth promotion and prophylaxis, leading to increased likelihood of zoonotic

spillover events of antimicrobial-resistant commensal organisms and pathogens into surrounding human populations. Globally, industrialization of agriculture is expected to exponentially increase along with the concentration of antimicrobials used in animal agriculture. Consequently, this dissertation applies a “One Health” cross disciplinary approach towards studying the confluence of small-scale agricultural development and global health within rural northwestern Ecuador. In chapter two, I present a cross-sectional study examining the impacts of a synchronous introduction of broiler farming within one community. I then enrolled 10 households to monitor the change in backyard chicken E. coli resistance levels after the introduction of broiler chickens. I found phenotypic and genotypic evidence supporting the spillover of cefotaxime resistance from broiler chickens to backyard chickens and potentially to children. In chapter three, I present a longitudinal field study to better understand the spatial relationship of antimicrobial resistance in communities that conduct small-scale farming in northwestern Ecuador. I analyzed phenotypic resistance of E. coli sampled from humans and backyard chicken to 12 antibiotics in relation to the distance to the nearest small-scale farming operation. I did not find any statistical significance when testing the relationship between the distance of a household to small-scale farming and backyard chicken or human susceptibility to antibiotics associated with that household. I also monitored the movement of backyard chickens. The null results of antimicrobial resistance spatial analysis can be supported by the observation of the extensive home range of free-ranging backyard chickens. Chapter 4 uses the same dataset from chapter 3 to examine antimicrobial resistance carriage. Between sample period 1 and 2, I observed significant increases in 6 of the 12 antibiotics in humans and 4 of the 12 antibiotics in backyard chickens. These findings suggest that the recent rebound in farming activity after a regional collapse in farming, and the observed increase of AMR in the one-day old broilers was likely the cause of the observed increase in AMR in backyard chickens and children. This dissertation provides evidence that small-scale poultry farming activity causes the emergence, spread, and persistence of antimicrobial resistance in low- and middle-income countries.