Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA; Department of Pediatrics, Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia & University of Pennsylvania, Philadelphia, PA, USA.
Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
Trends Microbiol. 2017 Feb;25(2):153-166. doi: 10.1016/j.tim.2016.09.009. Epub 2016 Oct 14.
A deluge of whole-genome sequencing has begun to give insights into the patterns and processes of microbial evolution, but genome sequences have accrued in a haphazard manner, with biased sampling of natural variation that is driven largely by medical and epidemiological priorities. For instance, there is a strong bias for sequencing epidemic lineages of methicillin-resistant Staphylococcus aureus (MRSA) over sensitive isolates (methicillin-sensitive S. aureus: MSSA). As more diverse genomes are sequenced the emerging picture is of a highly subdivided species with a handful of relatively clonal groups (complexes) that, at any given moment, dominate in particular geographical regions. The establishment of hegemony of particular clones appears to be a dynamic process of successive waves of replacement of the previously dominant clone. Here we review the phylogenomic structure of a diverse range of S. aureus, including both MRSA and MSSA. We consider the utility of the concept of the 'core' genome and the impact of recombination and horizontal transfer. We argue that whole-genome surveillance of S. aureus populations could lead to better forecasting of antibiotic resistance and virulence of emerging clones, and a better understanding of the elusive biological factors that determine repeated strain replacement.
大量的全基因组测序开始为微生物进化的模式和过程提供了深入的了解，但基因组序列的积累方式是随意的，对自然变异的采样存在很大的偏向，主要受医学和流行病学优先事项的驱动。例如，对耐甲氧西林金黄色葡萄球菌 (MRSA) 的流行谱系进行测序的偏向性很强，而对敏感分离株（甲氧西林敏感金黄色葡萄球菌：MSSA）的偏向性则较弱。随着更多不同基因组的测序，新兴的图景是一个高度细分的物种，只有少数相对克隆的群体（复合体）在特定的地理区域占主导地位。特定克隆的霸权的确立似乎是一个动态过程，即先前占主导地位的克隆不断被取代。在这里，我们回顾了包括 MRSA 和 MSSA 在内的各种金黄色葡萄球菌的系统发育结构。我们考虑了“核心”基因组概念的实用性以及重组和水平转移的影响。我们认为，对金黄色葡萄球菌种群的全基因组监测可以更好地预测新出现的克隆的抗生素耐药性和毒力，并更好地理解决定反复菌株替代的难以捉摸的生物学因素。
