Genome characteristics of clinical Salmonella enterica population from a state public health laboratory, New Hampshire, USA, 2017-2020.
Genome characteristics of clinical Salmonella enterica population from a state public health laboratory, New Hampshire, USA, 2017-2020.
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DOI：
10.1186/s12864-022-08769-1
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发表时间：
2022-07-23
期刊：
影响因子：
4.4
通讯作者：
Andam, Cheryl P.
中科院分区：
文献类型：
--
作者：
Turcotte, Madison R.;Smith, Joshua T.;Li, Jinfeng;Zhang, Xinglu;Wolfe, Kristin L.;Gao, Fengxiang;Benton, Christopher S.;Andam, Cheryl P.
食源性疾病分子分型网络 PulseNet 实施的全基因组测序 (WGS) 改变了美国的监测、疫情检测和公共卫生实验室实践。 2017 年，PulseNet 成员新罕布什尔州公共卫生实验室开始使用 WGS 追踪全州的食源性病原体。我们介绍了新罕布什尔州在追踪肠沙门氏菌（一种导致非伤寒食源性感染和肠热病的细菌病原体）方面向全基因组测序（WGS）过渡的举措的一些初步结果。我们描述了 2017 年至 2020 年从新罕布什尔州人类临床病例中回收的 394 个分离株基因组的种群结构和进化历史。新罕布什尔州肠沙门氏菌种群在系统发育上具有多样性，由 78 种序列类型 (ST) 和 67 种血清型组成。六个谱系在人群中占主导地位：ST 11 血清型肠炎、ST 19 鼠伤寒、ST 32 婴儿、ST 118 纽波特、ST 22 Braenderup 和 ST 26 Thompson。每个谱系都源自系统发育中的长祖先分支，表明它们在该地区的长期存在和最近的克隆扩张。我们检测到 61 个与 14 种抗菌药物耐药性相关的基因。其中，在所有基因组中均检测到五种抗菌药物（氨基香豆素类、氨基糖苷类、氟喹诺酮类、硝基咪唑类和肽类）的独特基因。我们发现多个谱系携带独立获得的抗性决定因素的不同组合，而不是携带多个抗性基因的单个克隆在该状态下扩展。我们估计主要谱系 ST 11 血清型肠炎（126 个基因组）的最近共同祖先的时间为 1965 年（95% 最高后验密度区间：1927-1982）。其人口规模一直扩大到 1978 年，随后人口下降，直到 1990 年。此后这个谱系一直在扩大。与其他州的基因组进行比较表明，缺乏表明远距离传播的地理聚类。对现有病原体多样性的全基因组测序研究为种群和谱系进化动态以及抗菌素耐药性提供了重要的见解，这可以转化为有效的公共卫生行动和决策。我们强调需要加强努力，在州公共卫生实验室实施基于全基因组测序的监测和基因组数据分析。在线版本包含可在 10.1186/s12864-022-08769-1 获取的补充材料。
The implementation of whole genome sequencing (WGS) by PulseNet, the molecular subtyping network for foodborne diseases, has transformed surveillance, outbreak detection, and public health laboratory practices in the United States. In 2017, the New Hampshire Public Health Laboratories, a member of PulseNet, commenced the use of WGS in tracking foodborne pathogens across the state. We present some of the initial results of New Hampshire’s initiative to transition to WGS in tracking Salmonella enterica, a bacterial pathogen that is responsible for non-typhoidal foodborne infections and enteric fever. We characterize the population structure and evolutionary history of 394 genomes of isolates recovered from human clinical cases in New Hampshire from 2017 to 2020. The New Hampshire S. enterica population is phylogenetically diverse, consisting of 78 sequence types (ST) and 67 serotypes. Six lineages dominate the population: ST 11 serotype Enteritidis, ST 19 Typhimurium, ST 32 Infantis, ST 118 Newport, ST 22 Braenderup, and ST 26 Thompson. Each lineage is derived from long ancestral branches in the phylogeny, suggesting their extended presence in the region and recent clonal expansion. We detected 61 genes associated with resistance to 14 antimicrobial classes. Of these, unique genes of five antimicrobial classes (aminocoumarins, aminoglycosides, fluoroquinolones, nitroimidazoles, and peptides) were detected in all genomes. Rather than a single clone carrying multiple resistance genes expanding in the state, we found multiple lineages carrying different combinations of independently acquired resistance determinants. We estimate the time to the most recent common ancestor of the predominant lineage ST 11 serotype Enteritidis (126 genomes) to be 1965 (95% highest posterior density intervals: 1927–1982). Its population size expanded until 1978, followed by a population decline until 1990. This lineage has been expanding since then. Comparison with genomes from other states reveal lack of geographical clustering indicative of long-distance dissemination. WGS studies of standing pathogen diversity provide critical insights into the population and evolutionary dynamics of lineages and antimicrobial resistance, which can be translated to effective public health action and decision-making. We highlight the need to strengthen efforts to implement WGS-based surveillance and genomic data analyses in state public health laboratories. The online version contains supplementary material available at 10.1186/s12864-022-08769-1.
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开放式细菌种群基因组学：BIGSDB软件，pubmlst.org网站及其应用。
影响因子：
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作者：
Jolley KA;Bray JE;Maiden MCJ
通讯作者：
Maiden MCJ
影响因子：
4.6
作者：
Monte, Daniel F. .;Lincopan, Nilton;Landgraf, Mariza
通讯作者：
Landgraf, Mariza
肠道沙门氏菌：血清射手之间的生存，定殖和毒力差异。
影响因子：
--
作者：
Andino A;Hanning I
通讯作者：
Hanning I
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
5.2
作者：
McMillan, Elizabeth A.;Gupta, Sushim K.;Frye, Jonathan G.
通讯作者：
Frye, Jonathan G.