Reservoirs and Within-Host Dynamics of Antibiotic Resistance Associated with Small-Scale Poultry Production in Northwest Ecuador Open Access

Braykov, Nikolay Petrov (2015)

Permanent URL: https://etd.library.emory.edu/concern/etds/bc386j86f?locale=en
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Abstract

Small-scale poultry production that includes non-therapeutic use of antibiotics is becoming increasingly common in developing countries, contributing to an environmental reservoir of antibiotic-resistant (AR) bacteria and posing a threat to human health. We conducted a multifactorial experiment in a poultry farming facility to assess the effect of non-therapeutic antimicrobial use and high stocking density on the within-host dynamics of resistant and susceptible Escherichia coli in broiler chickens. To validate conclusions from the experiment, we used data from an observational study in 17 remote communities in Northwest Ecuador, which allowed to assess the potential for transmission of AR between different ecological reservoirs, including 'production birds' (broiler chickens and laying hens raised for sale), coop surfaces and soil, household soil and drinking water. In both studies we found high levels of resistance associated with production birds, and evidence suggesting that AR strains associated with poultry production have a source external to our study system. The effect of management practices on the ecology of AR in E. coli was limited.

Table of Contents

Acknowledgements. 6

Chapter I: Environmental Reservoirs of Antibiotic Resistance in 17 Village Communities - an Observational Study. 1

CHAPTER SUMMARY. 1

INTRODUCTION. 3

METHODS. 5

Study area. 5

Ethnography. 5

Household surveys. 6

Poultry feed samples. 6

Sample collection & laboratory analysis. 7

Poultry samples. 7

Environmental samples. 8

Sample processing. 9

Statistical analysis. 11

RESULTS. 14

Quantitative characterization of poultry production. 14

Qualitative characterization of poultry production. 14

Chemical analysis of commercial poultry feed. 16

Sample characterization. 16

Custom susceptibility breakpoints. 18

Antibiotic resistance in poultry samples. 21

Antibiotic resistance in environmental samples. 28

Cluster analysis of resistance patterns across all sample sources. 30

DISCUSSION. 32

Study limitations and avenues for future research. 36

Chapter II: Impact of Antibiotic Exposure and Stocking Density on the Genotype and Resistance Phenotype of E. Coli Shed by Broiler Chickens - a Factorial Experiment. 39

CHAPTER SUMMARY. 39

INTRODUCTION. 41

METHODS. 45

Study design. 45

Sample processing. 46

Antibiotic susceptibility testing. 46

Genotyping. 47

Statistical analysis. 47

RESULTS. 50

Sample characteristics. 50

Prevalence of resistance over time and treatment group, by flock. 51

Prevalence of resistance over time and stocking density, by flock. 55

Effects of pre-colonization with integrase 1 on pre-slaughter resistance. 58

Phenotypic and genotypic dynamics over time, by trial. 60

Diversity dynamics by treatment and cage density. 64

Diversity dynamics by presence of resistance genes. 65

Genotypic dissimilariy between experimental trials on different days. 67

Genotypic dissimilariy between sampling days. 67

Genotypic dissimilariy between treatment groups on different days. 67

Genotypic dissimilariy between stocking density groups on different days. 67

Genotypic dissimilarity in a multivariable model. 68

DISCUSSION. 69

References. 75

Supplementary material. 89

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