DataSheet_1_Description of Staphylococcal Strains from Straw-Coloured Fruit Bat (Eidolon helvum) and Diamond Firetail (Stagonopleura guttata) and a Review of their Phylogenetic Relationships to Other Staphylococci.zip

The phylogenetic tree of the Staphylococcus aureus complex consists of several distinct clades and the majority of human and veterinary S. aureus isolates form one large clade. In addition, two divergent clades have recently been described as separate species. One was named Staphylococcus argenteus, due to the lack of the “golden” pigment staphyloxanthin. The second one is S. schweitzeri, found in humans and animals from Central and West Africa. In late 2021, two additional species, S. roterodami and S. singaporensis, have been described from clinical samples from Southeast Asia. In the present study, isolates and their genome sequences from wild Straw-coloured fruit bats (Eidolon helvum) and a Diamond firetail (Stagonopleura guttata, an estrildid finch) kept in a German aviary are described. The isolates possessed staphyloxanthin genes and were closer related to S. argenteus and S. schweitzeri than to S. aureus. Phylogenetic analysis revealed that they were nearly identical to both, S. roterodami and S. singaporensis. We propose considering the study isolates, the recently described S. roterodami and S. singaporensis as well as some Chinese strains with MLST profiles stored in the PubMLST database as different clonal complexes within one new species. According to the principle of priority we propose it should be named S. roterodami. This species is more widespread than previously believed, being observed in West Africa, Southeast Asia and Southern China. It has a zoonotic connection to bats and has been shown to be capable of causing skin and soft tissue infections in humans. It is positive for staphyloxanthin, and it could be mis-identified as S. aureus (or S. argenteus) using routine procedures. However, it can be identified based on distinct MLST alleles, and “S. aureus” sequence types ST2470, ST3135, ST3952, ST3960, ST3961, ST3963, ST3965, ST3980, ST4014, ST4075, ST4076, ST4185, ST4326, ST4569, ST6105, ST6106, ST6107, ST6108, ST6109, ST6999 and ST7342 belong to this species.

金黄色葡萄球菌复合群的系统发育树由多个不同的枝系构成，其中大部分人类和兽医分离的金黄色葡萄球菌菌株形成一个庞大的枝系。此外，近期还描述了两个分支差异显著的枝系，分别被命名为金黄色葡萄球菌银色变种（Staphylococcus argenteus），因其缺乏“金色”色素葡萄球菌黄素，以及来自中非地区人类和动物的S. schweitzeri。至2021年末，又从东南亚的临床样本中描述了两种新的物种，即S. roterodami和S. singaporensis。在本研究中，描述了从德国禽舍中饲养的野生稻草色果蝠（Eidolon helvum）和一种火尾鹦鹉（Stagonopleura guttata，一种鹦鹉科鸣禽）的分离菌株及其基因组序列。这些分离菌株具有葡萄球菌黄素基因，并且与S. argenteus和S. schweitzeri的亲缘关系比与金黄色葡萄球菌更近。系统发育分析显示，它们与S. roterodami和S. singaporensis几乎完全相同。我们提议将本研究中的分离菌株、最近描述的S. roterodami和S. singaporensis以及存储在PubMLST数据库中的某些具有MLST特征的中国菌株视为一个新的物种内的不同克隆复合群。根据优先原则，我们建议将其命名为S. roterodami。该物种的分布范围比先前认为的要广，在非洲西部、东南亚和华南地区均有发现。它与蝙蝠存在动物源性联系，并且已有证据表明它能够引起人类皮肤和软组织感染。该物种黄素阳性，可能会被常规程序误鉴定为金黄色葡萄球菌（或S. argenteus）。然而，可以通过独特的MLST等位基因进行鉴定，属于本物种的“金黄色葡萄球菌”序列型包括ST2470、ST3135、ST3952、ST3960、ST3961、ST3963、ST3965、ST3980、ST4014、ST4075、ST4076、ST4185、ST4326、ST4569、ST6105、ST6106、ST6107、ST6108、ST6109、ST6999和ST7342。