The spread of antimicrobial-resistant bacteria is a significant concern, as it can lead to increased morbidity and mortality in both humans and animals. Whole-genome sequencing (WGS) is a powerful tool that can be used to conduct a comprehensive analysis of the genetic basis of antimicrobial resistance (AMR). We compared the phenotypic and genotypic AMR profiles of 97 Salmonella isolates derived from chicken and turkey diagnostic samples. We focused AMR analysis on 5 antimicrobial classes: aminoglycoside, beta-lactam, phenicol, tetracycline, and trimethoprim. The overall sensitivity and specificity of WGS in predicting phenotypic antimicrobial resistance in the Salmonella isolates were 93.4% and 99.8%, respectively. There were 16 disagreement instances, including 15 that were phenotypically resistant but genotypically susceptible; the other instance involved phenotypic susceptibility but genotypic resistance. Of the isolates examined, 67 of 97 (69%) carried at least 1 resistance gene, with 1 isolate carrying as many as 12 resistance genes. Of the 31 AMR genes analyzed, 16 were identified as aminoglycoside-resistance genes, followed by 4 beta-lactam–resistance, 3 tetracycline-resistance, 2 sulfonamide-resistance, and 1 each of fosfomycin-, quinolone-, phenicol-, trimethoprim-, bleomycin-, and colistin-resistance genes. Most of the resistance genes found were located on plasmids.

中文翻译：

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家禽诊断标本中肠沙门氏菌分离株的基因型和表型抗菌药物耐药性比较

耐药细菌的传播是一个重大问题，因为它可能导致人类和动物的发病率和死亡率增加。全基因组测序（WGS）是一种强大的工具，可用于对抗菌素耐药性（AMR）的遗传基础进行全面分析。我们比较了来自鸡和火鸡诊断样本的 97 种沙门氏菌分离株的表型和基因型 AMR 谱。我们将 AMR 分析重点放在 5 种抗菌药物上：氨基糖苷类、β-内酰胺类、苯尼考类、四环素类和甲氧苄啶类。 WGS 预测沙门氏菌分离株表型抗菌药物耐药性的总体敏感性和特异性分别为 93.4% 和 99.8%。有16个不一致的实例，其中15个是表型耐药但基因型易感的；另一个例子涉及表型易感性但基因型抗性。在检查的分离株中，97 个分离株中的 67 个（69%）携带至少 1 个抗性基因，其中 1 个分离株携带多达 12 个抗性基因。在分析的 31 个 AMR 基因中，有 16 个被鉴定为氨基糖苷类耐药基因，其次是 4 个 β-内酰胺类耐药基因、3 个四环素类耐药基因、2 个磺胺类耐药基因，以及磷霉素类、喹诺酮类、苯尼考类、甲氧苄啶类各 1 个基因。 、博来霉素和粘菌素抗性基因。发现的大多数抗性基因位于质粒上。