Data_Sheet_2_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，能够引发多种人类感染，但其研究尚显不足。从中国四川省成都市一家医院的下水道中分离出一株具有碳青霉烯耐药性并携带blaNDM–1的Kluyvera菌株090646T。对该菌株的全基因组测序结果显示，其与其它Kluyvera物种的模拟DNA-DNA杂交（isDDH）评分介于28.2%至42.3%，平均核苷酸同源性（ANI）值介于84.15%至90.10%，这两个指标均低于定义细菌物种的阈值≥70.0%的isDDH和≥95–96%的ANI，这表明该菌株代表Kluyvera属的一种新物种，建议命名为Kluyvera sichuanensis nov. K. sichuanensis的模式菌株为090646T（=GDMCC 1.1872T =KCTC 82166T）。菌株090646T可通过其利用D-山梨醇的能力而区别于其他Kluyvera物种，而不能利用β-半乳糖苷酶（ONPG）、D-甘露糖、甘油、棉子糖或蔗糖。在GenBank中标记为Kluyvera的基因组序列共有47条，这些序列经过精心整理以实现精确的物种鉴定。其中仅有33条基因组序列确为Kluyvera，并鉴定出四种新的Kluyvera基因组物种，这突显了GenBank中细菌基因组物种分配的整理工作亟需进行。为了更好地理解Kluyvera属，需要对更多菌株进行基因组测序。