Emergence of antibiotic resistance is a global public health concern. The relationships between antibiotic use, the gut community composition, normal physiology and metabolism, and individual and public health are still being defined. Shifts in composition of bacteria, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) after antibiotic treatment are not well-understood. This project used next-generation sequencing, custom-built metagenomics pipeline and differential abundance analysis to study the effect of antibiotic monotherapy on resistome and taxonomic composition in the gut of Balb/c mice infected with E. coli via transurethral catheterization to investigate the evolution and emergence of antibiotic resistance. There is a longitudinal decrease of gut microbiota diversity after antibiotic treatment. Various ARGs are enriched within the gut microbiota despite an overall reduction of the diversity and total amount of bacteria after antibiotic treatment. Sometimes treatment with a specific class of antibiotics selected for ARGs that resist antibiotics of a completely different class (e.g. treatment of ciprofloxacin or fosfomycin selected for cepA that resists ampicillin). Relative abundance of some MGEs increased substantially after antibiotic treatment (e.g. transposases in the ciprofloxacin group). Antibiotic treatment caused a remarkable reduction in diversity of gut bacterial microbiota but enrichment of certain types of ARGs and MGEs. These results demonstrate an emergence of cross-resistance as well as a profound change in the gut resistome following oral treatment of antibiotics.

中文翻译：

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抗生素对肠道微生物组的影响：抗生素治疗小鼠中微生物迁移和肠道抗生素耐药性的宏基因组分析

抗生素抗性的出现是全球公共卫生关注的问题。抗生素使用，肠道菌群组成，正常生理和新陈代谢以及个人和公共健康之间的关系仍在确定中。抗生素治疗后细菌组成，抗生素抗性基因（ARGs）和移动遗传元件（MGEs）的变化尚未得到很好的理解。该项目使用下一代测序，定制的宏基因组学流水线和差异丰度分析来研究抗生素单一疗法对经大肠杆菌经尿道感染的Balb / c小鼠肠道中抵抗力组和分类学组成的影响，以研究其进化和出现抗生素耐药性。抗生素处理后肠道微生物群的纵向减少。尽管抗生素治疗后细菌的多样性和总量总体下降，但肠道菌群内仍富含各种ARG。有时，用针对完全不同类别的抗生素的ARGs选择的特定类别的抗生素进行治疗（例如，针对cepA选择的抗氨苄青霉素的环丙沙星或磷霉素的治疗）。抗生素治疗后，某些MGE的相对丰度大大提高（例如环丙沙星组中的转座酶）。抗生素治疗导致肠道细菌微生物群多样性显着减少，但某些类型的ARG和MGE富集。这些结果表明交叉抗药的出现以及口服抗生素后肠道抵抗组的深刻变化。