Davis Richard W, Brannen Andrew D, Hossain Mohammad J, Monsma Scott, Bock Paul E, Nahrendorf Matthias, Mead David, Lodes Michael, Liles Mark R, Panizzi Peter
Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, 4306 Walker Building, Auburn, AL, 36849, USA.
Department of Biological Sciences, Auburn University, 101 Rouse Life Science Building, Auburn, AL, 36849, USA.
BMC Genomics. 2016 Mar 3;17:179. doi: 10.1186/s12864-016-2433-8.
Staphylococcus aureus (S. aureus) infections range in severity due to expression of certain virulence factors encoded on mobile genetic elements (MGE). As such, characterization of these MGE, as well as single nucleotide polymorphisms, is of high clinical and microbiological importance. To understand the evolution of these dangerous pathogens, it is paramount to define reference strains that may predate MGE acquisition. One such candidate is S. aureus Tager 104, a previously uncharacterized strain isolated from a patient with impetigo in 1947.
We show here that S. aureus Tager 104 can survive in the bloodstream and infect naïve organs. We also demonstrate a procedure to construct and validate the assembly of S. aureus genomes, using Tager 104 as a proof-of-concept. In so doing, we bridged confounding gap regions that limited our initial attempts to close this 2.82 Mb genome, through integration of data from Illumina Nextera paired-end, PacBio RS, and Lucigen NxSeq mate-pair libraries. Furthermore, we provide independent confirmation of our segmental arrangement of the Tager 104 genome by the sole use of Lucigen NxSeq libraries filled by paired-end MiSeq reads and alignment with SPAdes software. Genomic analysis of Tager 104 revealed limited MGE, and a νSaβ island configuration that is reminiscent of other hospital acquired S. aureus genomes.
Tager 104 represents an early-branching ancestor of certain hospital-acquired strains. Combined with its earlier isolation date and limited content of MGE, Tager 104 can serve as a viable reference for future comparative genome studies.
金黄色葡萄球菌（S. aureus）感染的严重程度因移动遗传元件（MGE）上编码的某些毒力因子的表达而异。因此，对这些MGE以及单核苷酸多态性进行表征具有很高的临床和微生物学重要性。为了了解这些危险病原体的进化，定义可能早于MGE获得的参考菌株至关重要。其中一个候选菌株是金黄色葡萄球菌Tager 104，这是一株1947年从脓疱病患者中分离出的此前未被表征的菌株。
我们在此表明，金黄色葡萄球菌Tager 104能够在血液中存活并感染未接触过病原体的器官。我们还展示了一种构建和验证金黄色葡萄球菌基因组组装的程序，以Tager 104作为概念验证。通过整合来自Illumina Nextera双末端、PacBio RS和Lucigen NxSeq配对末端文库的数据，我们弥合了限制我们最初封闭这个2.82 Mb基因组尝试的混杂间隙区域。此外，我们仅通过使用由双末端MiSeq读取填充的Lucigen NxSeq文库并与SPAdes软件进行比对，对Tager 104基因组的片段排列进行了独立确认。对Tager 104的基因组分析显示其MGE有限，并且其νSaβ岛构型让人联想到其他医院获得性金黄色葡萄球菌基因组。
Tager 104代表了某些医院获得性菌株的早期分支祖先。结合其较早的分离日期和有限的MGE含量来看，Tager 104可以作为未来比较基因组研究的一个可行参考。
