摘要
      幼崽中沙门氏菌的存在是将沙门氏菌引入家禽养殖场的唯一最重要的风险因素，耐药菌株尤其令人担忧，因为它们可能会影响因食用受污染的家禽产品而感染的人类的治疗结果。这项研究估计了沙门氏菌的流行率，确定了从尼日利亚孵化的幼崽中回收的菌株的耐药性，并确定了孵化的菌株和家禽养殖场的菌株之间的遗传相关性。在这项研究中，收集了300份粪便样本。通过培养分离沙门氏菌并通过PCR进行确认，并通过圆盘扩散法检测分离株对抗菌药物的敏感性。对菌株进行配对末端测序，并使用基因组获得血清型和抗生素耐药性基因。使用基于全基因组的系统发育分析来确定这些分离株与来自同一地理区域内先前表征的年长鸡的菌株之间的遗传相关性。13种沙门氏菌血清型的患病率为10.7%。对卡那霉素（30/32）、环丙沙星（22/32）、萘啶酸（22/32。22株（68.8%）分离株表现出多药耐药性。计算机预测确定了36个抗微生物耐药性基因。4株（12.5%）和22株（68.8%）gyrA和parC出现点突变。常见的获得性抗性基因包括sul1、sul2、sul3和tet（A）以及各种氨基糖苷类修饰基因。11个（34.4%）分离株被预测具有对磷霉素（fosA7，fosB）产生耐药性的基因。一株S.Stanleyville菌株被预测具有optrA，这赋予了对呋喃唑酮的抗性。从孵化的小鸡身上获得的肯塔基S.Kentucky、明斯特S.Muenster和门斯顿S.Menston菌株显示出密切的遗传相关性，因为它们与之前从相同来源接收孵化小鸡的农场从鸡身上回收的菌株的SNPs差异小于30。
ABSTRACT
The presence of Salmonella in hatchlings is the single most important risk factor for the introduction of Salmonella into poultry farms, and resistant strains are particularly worrisome, as they could affect treatment outcomes in humans infected through consumption of contaminated poultry products. This study estimated Salmonella prevalence, determined resistance profiles of strains recovered from hatchlings in Nigeria, and determined genetic relatedness between hatchling strains and strains from poultry farms. In this study, 300 fecal samples were collected. Salmonella was isolated by culture and confirmed by PCR, and isolates were tested for susceptibility to antimicrobials by the disk diffusion method. Strains were pair-end sequenced, and genomes were used to obtain serotypes and antibiotic resistance genes. Whole-genome based phylogenetic analysis was used to determine genetic relatedness between these isolates and strains from previously characterized older chicken within the same geographical area. A prevalence of 10.7% was obtained belonging to 13 Salmonella serovars. Resistance to kanamycin (30/32), ciprofloxacin (22/32), nalidixic acid (22/32), and sulfonamides (22/32) were the most commonly observed phenotypic resistances. Twenty-two (68.8%) isolates showed multidrug resistance. In silico predictions identified 36 antimicrobial resistance genes. Four (12.5%) and 22 (68.8%) strains showed point mutations in gyrA and parC. Commonly observed acquired resistance genes included sul1, sul2, sul3, and tet(A) as well as a variety of aminoglycoside-modifying genes. Eleven (34.4%) isolates were predicted to have genes that confer resistance to fosfomycin (fosA7, fosB). A strain of S. Stanleyville was predicted to have optrA, which confers resistance to furazolidone. Strains of S. Kentucky, S. Muenster, and S. Menston obtained from hatchlings showed close genetic relatedness by having less than 30 SNPs difference to strains recovered from chickens at farms previously receiving hatchlings from the same sources.

https://www.sciencedirect.com/science/article/pii/S0032579122007210