Abstract：
Florfenicol resistance genes (FRGs) are widely present in livestock farms. The aim of this study was to evaluate the removal efficiencies of FRGs as well as the relationships between FRGs, mobile genetic elements (MGEs) and bacterial communities during the natural drying (ND) and anaerobic digestion (AD) processes of manure treatment in swine farms by combining bacterial isolation, quantitative PCR and metagenomic approaches. Solid manure showed a higher abundance of FRGs than fresh manure and was the main contamination source of fexA and fexB in ND farms, whilst biogas slurry displayed a lower abundance of FRGs than the wastewater in AD farms. Moreover, fresh manure and wastewater showed a high abundance of optrA, and wastewater was the main contamination source of cfr in both ND and AD farms. Both optrA/fexA-positive enterococci and cfr/fexA-positive staphylococci were mainly isolated along the farms\' treatment processes. The cfr-positive staphylococci were highly prevalent in wastewater (57.14 % - 100 %) and may be associated with nasal-derived cfr-positive porcine staphylococci. An increased abundance of Enterococcus, Jeotgalibaca and Vagococcus in the bacterial community structures may account for the high optrA abundance in wastewater and Jeotgalibaca may be another potential host of optrA. Furthermore, the abundance of FRG-related MGEs increased by 22.63 % after the ND process and decreased by 66.96 % in AD farms. A significant correlation was observed between cfr and ISEnfa4, whereas no significance was found between optrA and IS1216E, although IS1216E is the predominant insertion sequence involved in the transfer of optrA. In conclusion, manure and wastewater represented independent pollution sources of FRGs in swine farms. Associated MGEs might play a key role in the transfer and persistence of FRGs. The AD process was more efficient in the removal of FRGs than the ND method, nevertheless a longer storage of slurry may be required for a complete removal.
摘要：
氟苯尼考抗性基因(FRGs)广泛存在于养殖场中。这项研究的目的是评估FRGs的去除效率以及FRGs之间的关系，通过结合细菌分离，在猪场粪肥处理的自然干燥（ND）和厌氧消化（AD）过程中的移动遗传元件（MGEs）和细菌群落，定量PCR和宏基因组方法。固体粪肥的FRGs丰度高于新鲜粪肥，是ND农场fexA和fexB的主要污染源，而沼液的FRGs丰度低于AD农场的废水。此外，新鲜的粪便和废水显示出丰富的optrA，废水是ND和AD农场cfr的主要污染源。optrA/fexA阳性肠球菌和cfr/fexA阳性葡萄球菌主要是在农场的处理过程中分离的。cfr阳性葡萄球菌在废水中非常普遍（57.14％-100％），可能与鼻源性cfr阳性猪葡萄球菌有关。肠球菌的丰度增加，细菌群落结构中的Jeotgalibaca和Vagococus可能是废水中optrA丰度高的原因，而Jeotgalibaca可能是optrA的另一种潜在宿主。此外，与FRG相关的MGE的丰度在ND过程后增加了22.63%，在AD农场减少了66.96%。在cfr和ISEnfa4之间观察到显着的相关性，而在optrA和IS1216E之间没有发现显著性。尽管IS1216E是参与optrA转移的主要插入序列。总之,粪肥和废水是猪场FRGs的独立污染源。相关的MGE可能在FRG的转移和持久性中起关键作用。AD过程比ND方法更有效地去除FRGs，然而,为了完全去除,可能需要更长的浆料储存。
