Bogaerts Bert, Winand Raf, Van Braekel Julien, Mattheus Wesley, De Keersmaecker Sigrid C J, Roosens Nancy H C, Marchal Kathleen, Vanneste Kevin, Ceyssens Pieter-Jan
Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium.
Department of Plant Biotechnology and Bioinformatics, Ghent University, 9000 Ghent, Belgium.
Microorganisms. 2021 Apr 6;9(4):767. doi: 10.3390/microorganisms9040767.
Shigellosis is an acute enteric infection caused mainly by the species and . Since surveillance of these pathogens indicated an increase in ciprofloxacin-resistant samples collected in Belgium between 2013 and 2018, a subset of 148 samples was analyzed with whole genome sequencing (WGS) to investigate their dispersion and underlying genomic features associated with ciprofloxacin resistance. A comparison between observed phenotypes and WGS-based resistance prediction to ciprofloxacin revealed perfect correspondence for all samples. Core genome multi-locus sequence typing and single nucleotide polymorphism-typing were used for phylogenomic investigation to characterize the spread of these infections within Belgium, supplemented with data from international reference collections to place the Belgian isolates within their global context. For , substantial diversity was observed with ciprofloxacin-resistant isolates assigned to several phylogenetic groups. Besides travel-related imports, several clusters of highly similar Belgian isolates could not be linked directly to international travel suggesting the presence of domestically circulating strains. For , Belgian isolates were all limited to lineage III, and could often be traced back to travel to countries in Asia and Africa, sometimes followed by domestic circulation. For both species, several clusters of isolates obtained exclusively from male patients were observed. Additionally, we illustrated the limitations of conventional serotyping of , which was impacted by serotype switching. This study contributes to a better understanding of the spread of shigellosis within Belgium and internationally, and highlights the added value of WGS for the surveillance of this pathogen.
志贺氏菌病是一种主要由志贺氏菌属物种引起的急性肠道感染。由于对这些病原体的监测表明，2013年至2018年期间在比利时采集的耐环丙沙星样本有所增加，因此对148个样本的子集进行了全基因组测序（WGS）分析，以研究它们的传播情况以及与环丙沙星耐药性相关的潜在基因组特征。观察到的表型与基于WGS的环丙沙星耐药性预测之间的比较显示，所有样本的结果完全一致。核心基因组多位点序列分型和单核苷酸多态性分型用于系统基因组学研究，以描述这些感染在比利时境内的传播特征，并补充国际参考菌株的数据，以便将比利时分离株置于全球背景下进行分析。对于宋内志贺氏菌，观察到耐环丙沙星分离株具有很大的多样性，它们被归入几个系统发育组。除了与旅行相关的输入病例外，几簇高度相似的比利时分离株无法直接与国际旅行联系起来，这表明存在国内传播的菌株。对于福氏志贺氏菌，比利时分离株均局限于谱系III，并且通常可以追溯到前往亚洲和非洲国家的旅行，有时随后在国内传播。对于这两个物种，均观察到几簇仅从男性患者获得的分离株。此外，我们还说明了宋内志贺氏菌传统血清分型的局限性，它受到血清型转换的影响。这项研究有助于更好地了解志贺氏菌病在比利时境内和国际上的传播情况，并突出了WGS在监测这种病原体方面的附加价值。
