Studies on changes in the intestinal flora of chickens during enrofloxacin treatment of drug-resistant Salmonella

Fluoroquinolones are the first-line drugs for the treatment of Salmonella infections, but the irrational use of this drug has led to increasing fluoroquinolone resistance. Currently, there is no clear information about the conditions and patterns of changes in drug resistance genes in the intestinal tract of chickens under the action of different doses of enrofloxacin. This study was conducted to elucidate the conditions and patterns of resistance gene transfer in the intestine under the selective pressure of different concentrations of enrofloxacin. Our results showed that the level of colonisation of resistant Salmonella and the number of copies of resistance genes carried by them showed a decreasing trend in the control, prophylactic dose (3.03 mg/kg b.w.) and therapeutic dose groups (10 mg/kg b.w.), and an overall decreasing followed by an increasing and then decreasing trend in the subinhibitory dose group (1 mg/kg b.w.). Macrogenomic analysis revealed a significant reduction in the diversity of bacterial communities in the gut in the presence of enrofloxacin (p<0.001) and a significant positive correlation between gut bacterial communities and resistance genes (p<0.001). The relative abundance of macrolide resistance genes macB and oleC, mycopeptide resistance gene bcrA, tetracycline resistance gene tet(58) and multidrug resistance gene msbA were relatively high in each group, in which the concentration of enrofloxacin had a positive correlation with the macB gene and a negative correlation with the bcrA, tet(58), msbA and oleC genes. Correlation network analysis showed that 9 of the top 20 genera in terms of relative abundance had significant positive correlations with 22 MGEs; 16 of the top 20 ARGs in terms of relative abundance had significant positive correlations with 20 MGEs, suggesting that ARGs can be transmitted between genera through MGEs. analysis of the contribution of ARGs to species showed that qnrS1, tet(A) and arr-2 were mainly contributed by Klebsiella pneumoniae, and APH(3'')-Ib, aadA5 and dfrA14 were mainly contributed by E. coli. It suggests that the resistance genes carried by the plasmid can be transferred in other genera in the organism's intestinal tract. This study provides a theoretical basis for guiding the clinical use of fluoroquinolones and reducing the transmission and prevalence of resistance genes.

氟喹诺酮类（Fluoroquinolones）是治疗沙门氏菌（Salmonella）感染的一线用药，但该类药物的不合理使用导致氟喹诺酮类耐药性问题日益严峻。目前，关于不同剂量恩诺沙星（enrofloxacin）作用下鸡肠道内耐药基因的变化条件与模式，尚缺乏明确的研究数据。本研究旨在阐明不同浓度恩诺沙星选择性压力下，肠道内耐药基因的转移条件与模式。我们的研究结果显示，在对照组、预防剂量组（3.03 mg/kg 体重）与治疗剂量组（10 mg/kg 体重）中，耐药沙门氏菌的定植水平及其携带的耐药基因拷贝数均呈下降趋势；而在亚抑菌剂量组（1 mg/kg 体重）中，该指标整体呈现先下降、后上升、再下降的动态变化趋势。宏基因组学（macrogenomic）分析结果表明，恩诺沙星存在时，肠道细菌群落多样性显著降低（p<0.001），且肠道细菌群落与耐药基因之间呈显著正相关（p<0.001）。各组中，大环内酯类耐药基因macB与oleC、霉菌肽类耐药基因bcrA、四环素类耐药基因tet(58)以及多重耐药基因msbA的相对丰度均较高；其中恩诺沙星浓度与macB基因呈正相关，与bcrA、tet(58)、msbA及oleC基因呈负相关。相关性网络分析显示，相对丰度排名前20的菌属中有9个与22种可移动遗传元件（Mobile Genetic Elements, MGEs）存在显著正相关；相对丰度排名前20的抗生素耐药基因（Antibiotic Resistance Genes, ARGs）中有16个与20种MGEs存在显著正相关，这表明耐药基因可通过可移动遗传元件在不同菌属间进行传播。对抗生素耐药基因的宿主物种贡献分析表明，qnrS1、tet(A)与arr-2主要由肺炎克雷伯菌（Klebsiella pneumoniae）贡献，而APH(3'')-Ib、aadA5与dfrA14主要由大肠杆菌（E. coli）贡献。该结果提示，质粒携带的耐药基因可在机体肠道内的其他菌属中进行转移。本研究为指导氟喹诺酮类药物的临床合理使用、降低耐药基因的传播与流行提供了理论依据。