Martínez José Rw, Planet Paul J, Maria Spencer-Sandino, Lina Rivas, Lorena Díaz, Ana Quesille-Villalobos, Roberto Riquelme-Neira, Manuel Alcalde-Rico, Blake Hanson, Carvajal Lina P, Sandra Rincón, Jinnethe Reyes, Marusella Lam, Rafael Araos, Patricia García, Arias César A, Munita José M
bioRxiv. 2023 Feb 7:2023.02.06.526811. doi: 10.1101/2023.02.06.526811.
The global dissemination of methicillin-resistant (MRSA) is associated with the emergence and establishment of clones in specific geographic areas. The Chilean-Cordobes clone (ChC) (ST5-SCC I) has been the predominant MRSA clone in Chile since its first description in 1998, despite the report of other emerging MRSA clones in the last years. Here, we characterize the evolutionary history of MRSA from 2000 to 2016 in a Chilean tertiary healthcare center using phylogenomic analyses. We sequenced 469 MRSA isolates collected between 2000-2016 in a tertiary healthcare center in Chile. We evaluated the temporal trends of the circulating clones and performed a phylogenomic reconstruction to characterize the clonal dynamics. We found a significant increase in the diversity and richness of sequence types (STs; Spearman r=0.8748, p<0.0001) with a Shannon diversity index increasing from 0.221 in the year 2000 to 1.33 in 2016. The temporal trend analysis revealed that in the period 2000-2003 most of the isolates (94.2%; n=98) belonged to the ChC clone. However, since then, the frequency of the ChC clone has decreased over time, accounting for 52% of the collection in the 2013-2016 period. This decline was accompanied by the rise of two emerging MRSA lineages, ST105-SCC II and ST72-SCC VI. In conclusion, the ChC clone remains the most frequent MRSA lineage in Chile. However, this lineage is gradually being replaced by several emerging clones, the most important of which is clone ST105-SCC II. To the best of our knowledge, this is the largest study of MRSA clonal dynamics performed in South America.
Methicillin-resistant (MRSA) is a major public health pathogen that disseminates through the emergence of successful dominant clones in specific geographic regions. Knowledge of the dissemination and molecular epidemiology of MRSA in Latin America is scarce and is largely based on small studies or classical typing techniques with several limitations to depict an accurate description of their genomic landscape. We used whole-genome sequencing to study 469 MRSA isolates collected between 2000-2016 in Chile to provide the largest and most detailed study of clonal dynamics of MRSA carried out in South America to date. We found a significant increase in the diversity of MRSA clones circulating over the 17-year study period. Additionally, we describe the emergence of two novel clones (ST105-SCCmecII and ST72-SCCmecVI), which have been gradually increasing their frequency over time. Our results drastically improve our understanding of the dissemination and update our knowledge about MRSA in Latin America.
耐甲氧西林金黄色葡萄球菌（MRSA）在全球的传播与特定地理区域内克隆株的出现和确立有关。自1998年首次被描述以来，智利-科尔多瓦克隆株（ChC）（ST5-SCCmec I）一直是智利主要的MRSA克隆株，尽管近年来有其他新兴MRSA克隆株的报道。在此，我们利用系统基因组学分析对智利一家三级医疗中心2000年至2016年期间MRSA的进化历史进行了特征描述。我们对2000年至2016年期间在智利一家三级医疗中心收集的469株MRSA分离株进行了测序。我们评估了流行克隆株的时间趋势，并进行了系统基因组重建以描述克隆动态。我们发现序列类型（STs）的多样性和丰富度显著增加（斯皮尔曼r = 0.8748，p < 0.0001），香农多样性指数从2000年的0.221增加到2016年的1.33。时间趋势分析显示，在2000 - 2003年期间，大多数分离株（94.2%；n = 98）属于ChC克隆株。然而，从那时起，ChC克隆株的频率随时间下降，在2013 - 2016年期间占所收集菌株的52%。这种下降伴随着两个新兴MRSA谱系ST105-SCCmec II和ST72-SCCmec VI的兴起。总之，ChC克隆株仍然是智利最常见的MRSA谱系。然而，这个谱系正逐渐被几个新兴克隆株所取代，其中最重要的是克隆株ST105-SCCmec II。据我们所知，这是在南美洲进行的关于MRSA克隆动态的最大规模研究。
耐甲氧西林金黄色葡萄球菌（MRSA）是一种主要的公共卫生病原体，通过在特定地理区域出现成功的优势克隆株进行传播。关于拉丁美洲MRSA传播和分子流行病学的知识匮乏，且很大程度上基于小型研究或具有若干局限性的经典分型技术，难以准确描述其基因组格局。我们使用全基因组测序研究了2000年至2016年期间在智利收集的469株MRSA分离株，以提供迄今为止在南美洲进行的关于MRSA克隆动态的最大规模和最详细研究。我们发现在17年的研究期间，流行的MRSA克隆株多样性显著增加。此外，我们描述了两个新克隆株（ST105-SCCmecII和ST72-SCCmecVI）的出现，它们的频率随时间逐渐增加。我们的结果极大地增进了我们对传播的理解，并更新了我们关于拉丁美洲MRSA的知识。
