Genomic analysis of Salmonella Typhimurium from humans and food sources accurately predicts phenotypic multi-drug resistance.
Genomic analysis of Salmonella Typhimurium from humans and food sources accurately predicts phenotypic multi-drug resistance.
复制标题
对人类和食物来源的鼠伤寒沙门氏菌进行基因组分析可准确预测表型多重耐药性。
DOI：
10.1016/j.fm.2021.103957
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发表时间：
2022
影响因子：
5.3
通讯作者：
M'ikanatha,NkuchiaM
中科院分区：
文献类型：
--
作者：
Yin,Xin;Fu,Yezhi;Tate,Heather;Pinto,Casey;Dudley,EdwardG;M'ikanatha,NkuchiaM
鼠伤寒沙门氏菌是美国食源性疾病的主要原因，导致每年超过一百万起案件。近年来，全基因组测序（WGS）已成为常规流行病学分型的标准工具。鼠伤寒沙门氏菌分离株，2）检查历史收集的MDR和泛易感分离株的遗传相关性从retail chicken.MethodsWe使用数据onSalmonellaTyphimurium分离株在公开的NARMS国家临床和零售肉类数据集从2016年至2018年。使用Staramr（0.5.1）从提交给NCBI的基因组中鉴定AMR决定簇和预测耐药性。以表型耐药结果为参考，计算WGS方法的灵敏度和特异性。基于SNP的聚类分析被用来检查MDR耐药和泛敏感分离物从零售chicken.ResultsWGS作为临床耐药的预测的总体敏感性为96.47%，总体特异性为100.00%的遗传相关性。表型和基因型结果之间的不一致主要与链霉素有关。MDR分离株的平均差异为73.1个SNP，而泛敏感分离株的平均差异为473.1个SNP（p < 0.0001）。结论WGS能可靠地预测鼠伤寒沙门氏菌耐药性，并能揭示耐药性的遗传决定因素。
IntroductionSalmonellaTyphimurium is the leading cause of foodborne illnesses in the U.S., causing over a million cases each year. In recent years, whole-genome sequencing (WGS) has become a standard tool for routine epidemiological subtyping.ObjectivesThe objectives of this study are 1) to compare the phenotypic and genotypic antimicrobial resistance (AMR) profiles of multidrug resistant (MDR)S. Typhimurium isolates, 2) to examine the genetic relatedness of a historic collection of MDR and pan-susceptible isolates from retail chickens.MethodsWe used data onSalmonellaTyphimurium isolates in the publicly available NARMS national clinical and retail meat datasets from 2016 to 2018. Staramr (0.5.1) was used to identify AMR determinants and predictive resistance from genomes submitted to NCBI. Sensitivity and specificity of the WGS method were calculated with phenotypic resistance results as the reference. SNP-based cluster analysis was used to examine the genetic relatedness of MDR resistant and pan-susceptible isolates from retail chickens.ResultsThe overall sensitivity of WGS as a predictor of clinical resistance was 96.47% and the overall specificity was 100.00%. The disagreement between phenotypic and genotypic results were mostly related to streptomycin. The MDR isolates differed by an average of 73.1 SNPs, while the pan-susceptible isolates differed by an average of 473.1 SNPs (p < 0.0001). The nearest distance between a pan-susceptible and an MDR isolate was 547 SNPs.ConclusionWGS can reliably predict AMR inS.Typhimurium isolates and it can reveal genetic determinants to elucidate the evolution of antimicrobial resistance.