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Antibiotic Resistome Associated with Small-Scale Poultry Production in Rural Ecuador

Guo, Xueping, Stedtfeld, Robert D., Hedman, Hayden, Eisenberg, Joseph N. S., Trueba, Gabriel, Yin, Daqiang, Tiedje, James M., Zhang, Lixin
Environmental science & technology 2018 v.52 no.15 pp. 8165-8172
Flavobacteria, antibiotic resistance genes, antibiotics, beta-Proteobacteria, chickens, feces, gamma-Proteobacteria, hybridization probes, interspersed repetitive sequences, microbiome, poultry production, quantitative polymerase chain reaction, ribosomal RNA, rural communities, sequence analysis, species diversity, villages, Ecuador
Small-scale poultry farming is common in rural communities across the developing world. To examine the extent to which small-scale poultry farming serves as a reservoir for resistance determinants, the resistome of fecal samples was compared between production chickens that received antibiotics and free-ranging household chickens that received no antibiotics from a rural village in northern Ecuador. A qPCR array was used to quantify antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) using 248 primer pairs; and the microbiome structure was analyzed via 16S rRNA gene sequencing. A large number of ARGs (148) and MGEs (29) were detected. The ARG richness in production chickens was significantly higher than that of household chickens with an average of 15 more genes detected (p < 0.01). Moreover, ARGs and MGEs were much more abundant in production chickens than in household chickens (up to a 157-fold difference). Production chicken samples had significantly lower taxonomic diversity and were more abundant in Gammaproteobacteria, Betaproteobacteria, and Flavobacteria. The high abundance and diversity of ARGs and MGEs found in small-scale poultry farming was comparable to the levels previously found in large scale animal production, suggesting that these chickens could act as a local reservoir for spreading ARGs into rural communities.