Data_Sheet_1_Precise Species Identification and Taxonomy Update for the Genus Kluyvera With Reporting Kluyvera sichuanensis sp. nov..XLSX

Kluyvera is a genus within the family Enterobacteriaceae and can cause various human infections but remains poorly studied. A carbapenem-resistant blaNDM–1-carrying Kluyvera strain 090646T was isolated from a hospital sink in Chengdu, Sichuan province, China. Whole genome sequencing of the strain revealed that it had 28.2 to 42.3% in silico DNA-DNA hybridization (isDDH) scores and 84.15 to 90.10% average nucleotide identity (ANI) values with other Kluyvera species. Both values are well below the ≥ 70.0% isDDH and ≥ 95–96% ANI cutoffs to define bacterial species, suggesting that the strain represents a novel species of the genus Kluyvera, for which the name Kluyvera sichuanensis. nov. is proposed. Type strain of K. sichuanensis is 090646T (=GDMCC 1.1872T =KCTC 82166T). Strain 090646T can be differentiated from other Kluyvera species by its ability to utilize D-sorbitol but not β-galactosidase (ONPG), D-mannose, glycerin, raffinose, nor sucrose. There were 47 genome sequences labeled as Kluyvera in GenBank, which were curated for precise species identification. Only 33 of the 47 genomes were indeed of Kluyvera and four novel Kluyvera genomospecies were identified, highlighting that the species assignation of bacterial genomes in GenBank need to be curated. Genome sequencing for more strains is required to understand the genus Kluyvera.

Kluyvera属隶属于肠杆菌科，其可引起多种人类感染，然而其研究尚显不足。一种携带blaNDM-1耐药基因的Kluyvera菌株090646T，源自中国四川省成都市的一家医院下水道，经全基因组测序分析，该菌株与其它Kluyvera物种的DNA-DNA杂交（isDDH）评分介于28.2%至42.3%之间，平均核苷酸一致性（ANI）值介于84.15%至90.10%之间。这两个数值均低于定义细菌物种时所需的≥70.0%的isDDH和≥95-96%的ANI阈值，表明该菌株代表Kluyvera属中的一个新物种，并建议命名为Kluyvera sichuanensis nov.。K. sichuanensis的模式菌株为090646T（等于GDMCC 1.1872T = KCTC 82166T）。菌株090646T可通过其利用D-山梨醇但无法利用β-半乳糖苷酶（ONPG）、D-甘露糖、甘油、蔗糖以及 raffinose的能力与其它Kluyvera物种相区分。GenBank中标记为Kluyvera的基因组序列共有47条，经精确物种鉴定后，其中仅有33条确实属于Kluyvera，并鉴定出四种新的Kluyvera基因组物种，凸显了在GenBank中对细菌基因组物种分配的必要性。为进一步理解Kluyvera属，需要对更多菌株进行基因组测序。