Challenges Associated with Investigating Salmonella Enteritidis with Low Genomic Diversity in New York State: The Impact of Adjusting Analytical Methods and Correlation with Epidemiological Data.
Challenges Associated with Investigating Salmonella Enteritidis with Low Genomic Diversity in New York State: The Impact of Adjusting Analytical Methods and Correlation with Epidemiological Data.
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DOI：
10.1089/fpd.2022.0068
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发表时间：
2023-06
影响因子：
2.8
通讯作者：
中科院分区：
文献类型：
--
作者：
确定肠道沙门氏菌菌株中值得研究的基因组簇具有挑战性，因为它们具有高度克隆性。我们调查了一个集群确定的核心基因组多位点序列分型（CGMLST）组成的265株分离日期跨越两年半。该簇经历了连锁，增长到14个等位基因的范围。该集群的分离株数量和广泛的等位基因范围使得难以确定它是否代表共同来源的爆发。我们探索了基于实验室的方法来细分和细化这一集群。这些方法包括使用具有较窄等位基因范围的cgMLST、全基因组多位点序列分型（wgMLST）和高质量单核苷酸多态性（hqSNP）分析。在每个分析水平上，流行病学家追溯性地审查了暴露、地理和时间性，以寻找潜在的共性。使用cgMLST将阈值降低到0等位基因证明了改进该分析的有效方法，导致该大聚类被细分为34个较小的聚类。通过wgMLST和hqSNP的额外分析提供了增强的聚类分辨率，其中大多数聚类被进一步细化。这些分析方法结合更严格的等位基因阈值和分层的流行病学数据被证明是有用的，有助于将这个大的集群细分为可操作的亚集群。
Defining investigation-worthy genomic clusters among strains of Salmonella Enteritidis is challenging because of their highly clonal nature. We investigated a cluster identified by core genome multilocus sequence typing (cgMLST) consisting of 265 isolates with isolation dates spanning two and a half years. This cluster experienced chaining, growing to a range of 14 alleles. The volume of isolates and broad allele range of this cluster made it difficult to ascertain whether it represented a common-source outbreak. We explored laboratory-based methods to subdivide and refine this cluster. These methods included using cgMLST with a narrower allele range, whole genome multilocus sequence typing (wgMLST) and high-quality single-nucleotide polymorphism (hqSNP) analysis. At each analysis level, epidemiologists retroactively reviewed exposures, geography, and temporality for potential commonalities. Lowering the threshold to 0 alleles using cgMLST proved an effective method to refine this analysis, resulting in this large cluster being subdivided into 34 smaller clusters. Additional analysis by wgMLST and hqSNP provided enhanced cluster resolution, with the majority of clusters being further refined. These analysis methods combined with more stringent allele thresholds and layering of epidemiologic data proved useful in helping to subdivide this large cluster into actionable subclusters.
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影响因子：
2.8
作者：
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通讯作者：
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