School of medicine, College of Medicine, Chang Gung University, 333, Taoyuan, Taiwan.
Physical Education Office, Chang Gung University, 333, Taoyuan, Taiwan.
BMC Med Genomics. 2019 Sep 3;12(1):126. doi: 10.1186/s12920-019-0576-6.
Indigenous typhoid fever was continuing to be identified in Taiwan which has not been endemic for the enteric fever for more than 20 years. The source and transmission by which the local patients acquired typhoid and the population structure of the indigenous typhoid strains remain not well characterized.
During 2001 and 2014, non-duplicated clinical Salmonella enterica serovar Typhi isolates in a hospital were analyzed by whole-genome sequencing (WGS) and determined for pulsotypes. Maximum likelihood phylogeny was constructed by nucleotide alterations in core genomes and compared to the framework of global typhoid strains. Potential source and transmission were traced by correlating the phylogeny and the temporal relationship between isolates.
A total of 43 S. Typhi isolates from indigenous cases were analyzed and a majority (39, 90.7%) of them were belonged to six WGS-defined genotypes prevailing mainly in Southeast Asia. Genotype 3.4.0 and a multidrug-resistant type 4.3.1 (also known as pandemic H58 haplotype) were associated respectively with two solitary small-scale outbreaks, implying a transmission mode of importation followed by outbreak. Twelve isolates with nearly identical core genomes were belonged to genotype 3.2.1 but were categorized into three different pulsotypes. The 3.2.1 isolates were identified across 13 years and involved in three clusters and a sporadic case, indicating sustained local transmission of the same strain. The remaining indigenous isolates belonging to three genotypes (2.1, 3.1.2, and 3.0.0) were of substantial genetic diversity and isolated at different time points, indicating independent event of each case.
Indigenous typhoid in Taiwan occurred mainly with the forms of small-scale outbreaks or sporadic events likely by contracting imported strains which prevailed in Southeast Asia. Sustained local transmission of certain strain was also evident by WGS analysis, but not by conventional pulsotyping, highlighting the importance of continuing molecular surveillance of typhoid fever with adequate tools in the non-endemic region.
在台湾，本土伤寒持续被发现，而台湾已有 20 多年没有发生肠热病。当地患者感染伤寒的来源和传播途径，以及本土伤寒菌株的人群结构仍未得到很好的描述。
在 2001 年至 2014 年期间，对一家医院的非重复临床沙门氏菌血清伤寒杆菌分离株进行全基因组测序（WGS）分析，并确定脉冲类型。通过核心基因组中的核苷酸变化构建最大似然系统发育，并与全球伤寒菌株的框架进行比较。通过比较进化关系和分离株之间的时间关系来追溯潜在的来源和传播途径。
共分析了 43 株来自本土病例的伤寒分离株，其中大多数（39 株，90.7%）属于在东南亚流行的六种 WGS 定义的基因型。基因型 3.4.0 和一种多药耐药型 4.3.1（也称为大流行 H58 单倍型）分别与两个孤立的小规模暴发有关，表明传播模式是输入后暴发。12 株具有几乎相同核心基因组的分离株属于基因型 3.2.1，但分为三种不同的脉冲类型。3.2.1 分离株在 13 年内被鉴定出来，并涉及三个聚类和一个散发病例，表明同一菌株的持续本地传播。其余属于三种基因型（2.1、3.1.2 和 3.0.0）的本土分离株具有相当大的遗传多样性，并且在不同的时间点分离，表明每个病例都是独立的事件。
台湾的本土伤寒主要以小规模暴发或散发性事件的形式发生，可能是由于感染了在东南亚流行的输入菌株。通过 WGS 分析也明显存在某些菌株的持续本地传播，但通过常规脉冲类型分析则不然，这突出了在非流行地区继续使用适当工具进行伤寒监测的重要性。
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