Table_2_Phenotypic and genotypic survey of antibiotic resistance in Salmonella enterica isolates from dairy farms in Uruguay.DOCX

Salmonella enterica is an important zoonotic pathogen that is frequently identified in dairy farming systems. An increase in antibiotic resistance has led to inadequate results of treatments, with impacts on animal and human health. Here, the phenotypic and genotypic susceptibility patterns of Salmonella isolates from dairy cattle and dairy farm environments were evaluated and compared. A collection of 75 S. enterica isolates were evaluated, and their phenotypic susceptibility was determined. For genotypic characterization, the whole genomes of the isolates were sequenced, and geno-serotypes, sequence types (STs) and core-genome-sequence types were determined using the EnteroBase pipeline. To characterize antibiotic resistance genes and gene mutations, tools from the Center for Genomic Epidemiology were used. Salmonella Dublin (SDu), S. Typhimurium (STy), S. Anatum (SAn), S. Newport (SNe), S. Agona (Sag), S. Montevideo (SMo) and IIIb 61:i:z53 were included in the collection. A single sequence type was detected per serovar. Phenotypic non-susceptibility to streptomycin and tetracycline was very frequent in the collection, and high non-susceptibility to ciprofloxacin was also observed. Multidrug resistance (MDR) was observed in 42 isolates (56.0%), with SAn and STy presenting higher MDR than the other serovars, showing non-susceptibility to up to 6 groups of antibiotics. Genomic analysis revealed the presence of 21 genes associated with antimicrobial resistance (AMR) in Salmonella isolates. More than 60% of the isolates carried some gene associated with resistance to aminoglycosides and tetracyclines. Only one gene associated with beta-lactam resistance was found, in seven isolates. Two different mutations were identified, parC_T57S and acrB_R717Q, which confer resistance to quinolones and azithromycin, respectively. The accuracy of predicting antimicrobial resistance phenotypes based on AMR genotypes was 83.7%. The genomic approach does not replace the phenotypic assay but offers valuable information for the survey of circulating antimicrobial resistance. This work represents one of the first studies evaluating phenotypic and genotypic AMR in Salmonella from dairy cattle in South America.

肠炎沙门氏菌（Salmonella enterica）是一类重要的人畜共患病原菌，在奶业养殖体系中检出率颇高。近年来抗生素耐药性问题日益凸显，导致临床治疗效果不佳，对畜禽健康与人类公共卫生安全均造成威胁。本研究对分离自奶牛及奶场环境的沙门氏菌菌株的表型与基因型耐药模式展开评估与对比分析。
本次研究共纳入75株肠炎沙门氏菌分离株，首先完成了其表型药敏性测定；在基因型特征分析环节，对所有分离株进行了全基因组测序，并通过EnteroBase流程确定了其基因血清型、序列型（STs）以及核心基因组序列型。同时借助基因组流行病学中心（Center for Genomic Epidemiology）的分析工具，对菌株的抗菌药物耐药基因与基因突变情况进行了表征。
本次研究的菌株涵盖都柏林沙门氏菌（SDu）、鼠伤寒沙门氏菌（STy）、阿纳姆沙门氏菌（SAn）、纽波特沙门氏菌（SNe）、阿贡纳沙门氏菌（Sag）、蒙得维的亚沙门氏菌（SMo）以及IIIb 61:i:z53等血清型。分析结果显示，每个血清型仅对应一种序列型。
本研究队列中，菌株对链霉素与四环素的表型耐药现象极为普遍，同时也观察到较高比例的环丙沙星耐药菌株。共有42株菌株（占比56.0%）表现出多重耐药（MDR）特征，其中阿纳姆沙门氏菌（SAn）与鼠伤寒沙门氏菌（STy）的多重耐药率高于其他血清型，可对多达6类抗生素表现出耐药性。
基因组分析结果表明，本次沙门氏菌分离株中共携带21个与抗菌药物耐药（AMR）相关的基因；超过60%的分离株携带氨基糖苷类与四环素类耐药相关基因。仅在7株分离株中检测到1个β-内酰胺类耐药相关基因。研究共鉴定出两种独立突变：parC_T57S与acrB_R717Q，二者分别赋予菌株对喹诺酮类与阿奇霉素的耐药性。
基于抗菌药物耐药基因型预测表型耐药的准确率可达83.7%。基因组分析方法虽无法替代表型药敏实验，但可为流行抗菌药物耐药性的监测工作提供极具价值的参考信息。
本研究是南美地区首批针对奶牛源沙门氏菌的表型与基因型耐药性开展的系统性研究之一。