Antimicrobial resistance is a global public health concern, and resistance genes in Salmonella, especially those located on mobile genetic elements, are part of the problem. This study used phenotypic and genomic methods to identify antimicrobial resistance and resistance genes, as well as the plasmids that bear them, in Salmonella isolates obtained from poultry in Nigeria. Seventy-four isolates were tested for susceptibility to eleven commonly used antimicrobials. Plasmid reconstruction and identification of resistance and virulence genes were performed with a draft genome using in silico approaches in parallel with plasmid extraction. Phenotypic resistance to ciprofloxacin (50.0%), gentamicin (48.6%), nalidixic acid (79.7%), sulphonamides (71.6%) and tetracycline (59.5%) was the most observed. Antibiotic resistance genes (ARGs) detected in genomes corresponded well with these observations. Commonly observed ARGs included sul1, sul2, sul3, tet (A), tet (M), qnrS1, qnrB19 and a variety of aminoglycoside-modifying genes, in addition to point mutations in the gyrA and parC genes. Multiple ARGs were predicted to be located on IncN and IncQ1 plasmids of S. Schwarzengrund and S. Muenster, and most qnrB19 genes were carried by Col (pHAD28) plasmids. Seventy-two percent (19/24) of S. Kentucky strains carried multidrug ARGs located in two distinct variants of Salmonella genomic island I. The majority of strains carried full SPI-1 and SPI-2 islands, suggesting full virulence potential.

中文翻译：

---

尼日利亚家禽沙门氏菌血清型抗菌素耐药性和耐药质粒的基因组分析

抗生素耐药性是一个全球性的公共卫生问题，沙门氏菌中的耐药基因，尤其是位于移动遗传元件上的耐药基因，是问题的一部分。这项研究使用表型和基因组方法来鉴定从尼日利亚家禽中获得的沙门氏菌分离株中的抗菌素耐药性和耐药基因，以及携带它们的质粒。测试了 74 株分离株对 11 种常用抗菌药物的敏感性。使用计算机方法与质粒提取并行地利用基因组草图进行质粒重建以及抗性和毒力基因的鉴定。对环丙沙星（50.0%）、庆大霉素（48.6%）、萘啶酸（79.7%）、磺胺类（71.6%）和四环素（59.5%）的表型耐药性最为明显。在基因组中检测到的抗生素抗性基因（ARG）与这些观察结果非常吻合。常见的 ARG 包括sul1、sul2、sul3、tet (A)、tet (M)、qnrS1、qnrB19和各种氨基糖苷修饰基因，以及gyrA和parC基因中的点突变。预计多个 ARG 位于S. Schwarzengrund 和S. Muenster 的 IncN 和 IncQ1 质粒上，并且大多数qnrB19基因由 Col (pHAD28) 质粒携带。72% (19/24) 的肯塔基州沙门氏菌菌株携带多药 ARG，位于沙门氏菌基因组岛 I 的两个不同变体中。大多数菌株携带完整的 SPI-1 和 SPI-2 岛，表明具有完整的毒力潜力。