Table_3_Shared Multidrug Resistance Patterns in Chicken-Associated Escherichia coli Identified by Association Rule Mining.xlsx

Using multiple antimicrobials in food animals may incubate genetically-linked multidrug-resistance (MDR) in enteric bacteria, which can contaminate meat at slaughter. The U.S. National Antimicrobial Resistance Monitoring System tested 21,243 chicken-associated Escherichia coli between 2004 and 2012 for resistance to 15 antimicrobials, resulting in >32,000 possible MDR patterns. We analyzed MDR patterns in this dataset with association rule mining, also called market-basket analysis. The association rules were pruned with four quality measures resulting in a <1% false-discovery rate. MDR rules were more stable across consecutive years than between slaughter and retail. Rules were decomposed into networks with antimicrobials as nodes and rules as edges. A strong subnetwork of beta-lactam resistance existed in each year and the beta-lactam resistances also had strong associations with sulfisoxazole, gentamicin, streptomycin and tetracycline resistances. The association rules concur with previously identified E. coli resistance patterns but provide significant flexibility for studying MDR in large datasets.

在食用动物中联合使用多种抗菌药物，可能会诱导肠道细菌产生遗传相关的多重耐药性（multidrug-resistance, MDR），此类细菌可在屠宰环节污染畜禽肉类产品。美国国家抗菌药物耐药性监测系统（U.S. National Antimicrobial Resistance Monitoring System）于2004至2012年间，针对21243株鸡源大肠杆菌（Escherichia coli）开展了15种抗菌药物的耐药性检测，共得到超过32000种潜在的多重耐药模式。本研究采用关联规则挖掘（association rule mining，又称市场篮分析（market-basket analysis））对该数据集的多重耐药模式进行分析。通过4项质量指标对关联规则进行剪枝，最终得到的错误发现率（false-discovery rate）低于1%。相较于屠宰环节与零售环节的样本间差异，多重耐药规则在连续年份间的稳定性更强。我们将关联规则构建为以抗菌药物为节点、以规则为边的网络结构，各年度均存在一个由β-内酰胺类（beta-lactam）耐药性构成的强子网，且β-内酰胺类耐药性与磺胺异恶唑（sulfisoxazole）、庆大霉素（gentamicin）、链霉素（streptomycin）以及四环素（tetracycline）的耐药性存在显著关联。本研究得到的关联规则与此前已探明的大肠杆菌耐药模式相符，同时为大型数据集下的多重耐药性研究提供了显著的分析灵活性。