van der Putten Boas C L, Matamoros S, Mende D R, Scholl E R, Consortium Combat, Schultsz C
Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.
Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.
Int J Syst Evol Microbiol. 2021 Feb;71(2). doi: 10.1099/ijsem.0.004609.
The genus comprises five species and at least five lineages currently not assigned to any species, termed ' cryptic clades'. We isolated an strain from an international traveller and resolved the complete DNA sequence of the chromosome and an IncI multidrug resistance plasmid using Illumina and Nanopore whole-genome sequencing (WGS). Strain OPT1704 can be differentiated from existing species using biochemical (VITEK2) and genomic tests [average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH)]. Phylogenetic analysis based on alignment of 16S rRNA sequences and 682 concatenated core genes showed similar results. Our analysis further revealed that strain OPT1704 falls within cryptic clade IV and is closely related to cryptic clade III. Combining our analyses with publicly available WGS data of cryptic clades III and IV from Enterobase confirmed the close relationship between clades III and IV (>96 % interclade ANI), warranting assignment of both clades to the same novel species. We propose sp. nov. as a novel species, encompassing cryptic clades III and IV (type strain OPT1704=NCCB 100732=NCTC 14359).
该属包含五个物种以及至少五个目前未归入任何物种的谱系,称为“隐秘分支”。我们从一名国际旅行者身上分离出一株菌株,并使用Illumina和Nanopore全基因组测序(WGS)解析了该菌株染色体和一个IncI多药耐药质粒的完整DNA序列。菌株OPT1704可以通过生化(VITEK2)和基因组测试[平均核苷酸同一性(ANI)和数字DNA-DNA杂交(dDDH)]与现有的物种区分开来。基于16S rRNA序列和682个串联核心基因比对的系统发育分析显示了相似的结果。我们的分析进一步表明,菌株OPT1704属于隐秘分支IV,并且与隐秘分支III密切相关。将我们的分析与Enterobase中隐秘分支III和IV的公开可用WGS数据相结合,证实了分支III和IV之间的密切关系(分支间ANI>96%),这使得将这两个分支归入同一个新物种成为必要。我们提议将[具体名称]作为一个新物种,涵盖隐秘分支III和IV(模式菌株OPT1704=NCCB 100732=NCTC 14359)。