Impact of intramuscular ceftiofur treatment on the gut microbiome and resistome of dairy cattle

Third-generation cephalosporins such as ceftiofur, are classified as critically important antibiotics because pathogens with resistance to these drugs contribute to high mortality rates and can be readily transmitted between individuals. Furthermore, these antibiotics are frequently administered in animals, emphasizing the crucial role they play in both human and veterinary medicine. Because metritis is a common condition requiring antibiotic treatment in dairy cattle, we sought to investigate the impact of intramuscular ceftiofur treatment on the abundance of resistant bacteria and resistance genes in the fecal microbiome. Twelve cows with metritis (cases) were enrolled and treated with ceftiofur for comparison to 12 matched untreated cows (controls). Fecal samples were collected from both groups prior to ceftiofur treatment of the cases and weekly for up to four weeks. The quantity of Gram-negative bacteria with resistance to ceftiofur, ampicillin, and tetracycline was determined using MacConkey lactose agar, while metagenomic next-generation sequencing was used to characterize the microbiome and resistome. Importantly, the treated cases had persistently higher levels of Gram-negative bacteria with resistance to ceftiofur but not to ampicillin or tetracycline. Persistently higher levels of genes encoding extended-spectrum beta-lactamase (ESBL) production were also observed in the treated cows from weeks 1-4. blaCMY-4, blaACI-1, cfxA5, and cfxA6 were the most abundant genes detected. Although no substantial changes in microbiota diversity were observed, some taxa differed in abundance post-treatment. Moreover, the abundance and diversity of plasmids and virulence genes were lower one week after treatment. Bacteroidetes and Escherichia coli were identified as the main bacterial hosts of ESBL genes, while an analysis of beta-lactamase-carrying contigs revealed the co-localization of ESBLs with plasmid and transposase genes, indicating their potential involvement in the horizontal transfer of these resistance genes. Together, these findings demonstrate the persistent effects of ceftiofur treatment on the abundance of resistant bacterial populations and ESBL genes in dairy cattle over a short time frame. Implementing strategies to limit the use of ceftiofur and other critically important antibiotics can be vital for preserving the efficacy of these antibiotics and safeguarding public and animal health.

第三代头孢菌素，如头孢噻呋，被归类为至关重要的抗生素，因为这些药物耐药的病原体会导致高死亡率，并且能够在个体间轻易传播。此外，这些抗生素在动物身上的频繁使用，凸显了它们在人类和兽医医学领域所扮演的至关角色。鉴于子宫内膜炎是奶牛常见的一种需要抗生素治疗的疾病，本研究旨在探讨肌肉注射头孢噻呋治疗对粪便微生物群中耐药细菌和耐药基因丰度的影响。纳入了12头患有子宫内膜炎的奶牛（病例组）并给予头孢噻呋治疗，以与12头匹配的未接受治疗的奶牛（对照组）进行比较。在病例组接受头孢噻呋治疗前及治疗后的每周，对两组奶牛的粪便样本进行了收集。使用麦康凯乳糖琼脂确定了对头孢噻呋、氨苄西林和四环素的耐药的革兰氏阴性细菌数量，同时采用宏基因组下一代测序技术对微生物组和耐药组进行特征分析。值得注意的是，接受治疗的病例组在头孢噻呋耐药的革兰氏阴性细菌丰度上持续较高，但并非氨苄西林或四环素耐药。在治疗后的第一至四周，编码广谱β-内酰胺酶（ESBL）产生的基因水平也持续较高。检测到的最丰富的基因包括blaCMY-4、blaACI-1、cfxA5和cfxA6。尽管未观察到微生物群多样性的显著变化，但某些类群在治疗后丰度有所不同。此外，治疗一周后，质粒和致病基因的丰度和多样性均有所降低。拟杆菌和埃希氏菌被确认为ESBL基因的主要细菌宿主，而β-内酰胺酶携带的连续片段分析揭示了ESBL与质粒和转座酶基因的共定位，表明它们可能参与了这些耐药基因的水平转移。综上所述，这些研究结果共同表明，头孢噻呋治疗在短期内对奶牛耐药细菌种群和ESBL基因丰度具有持续的效应。实施限制头孢噻呋及其他至关重要的抗生素使用的策略，对于维持这些抗生素的疗效和保障公共及动物健康至关重要。