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

小规模家禽养殖在发展中国家的乡村社区中极为普遍。为探究小规模家禽养殖作为耐药决定因子储存库的潜在程度，研究人员对厄瓜多尔北部某乡村的两类家禽粪便样本的耐药组（resistome）进行了对比分析：一类是饲喂过抗生素的商品肉鸡，另一类是未使用过抗生素的散养家鸡。本研究采用搭载248对引物的定量PCR阵列（qPCR array）对抗生素抗性基因（Antibiotic Resistance Genes, ARGs）与可移动遗传元件（Mobile Genetic Elements, MGEs）进行定量检测，并通过16S rRNA基因测序分析微生物组结构。本次研究共检出148种抗生素抗性基因与29种可移动遗传元件。商品肉鸡的抗生素抗性基因丰富度显著高于家鸡，平均多检出15个基因（p < 0.01）。此外，商品肉鸡体内的抗生素抗性基因与可移动遗传元件丰度远高于家鸡，最高差异可达157倍。商品肉鸡样本的分类学多样性显著更低，且伽马变形菌纲（Gammaproteobacteria）、贝塔变形菌纲（Betaproteobacteria）与黄杆菌纲（Flavobacteria）的相对丰度更高。本次研究发现，小规模家禽养殖环境中抗生素抗性基因与可移动遗传元件的高丰度与高多样性，与此前大型畜禽养殖体系中的检测水平相当，这表明此类家禽可作为将抗生素抗性基因扩散至乡村社区的本地储存库。