UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
Microbiol Res. 2024 Nov;288:127867. doi: 10.1016/j.micres.2024.127867. Epub 2024 Aug 14.
Enterobacter species are included among the normal human gut microflora and persist in a diverse range of other environmental niches. They have become important opportunistic nosocomial pathogens known to harbour plasmid-mediated multi-class antimicrobial resistance (AMR) determinants. Global AMR surveillance of Enterobacterales isolates shows the genus is second to Klebsiella in terms of frequency of carbapenem resistance. Enterobacter taxonomy is confusing and standard species identification methods are largely inaccurate or insufficient. There are currently 27 named species and a total of 46 taxa in the genus distinguishable via average nucleotide identity (ANI) calculation between pairs of genomic sequences. Here we describe an Enterobacter strain, ECC3473, isolated from the wastewater of an Australian hospital whose species could not be determined by standard methods nor by ribosomal RNA gene multi-locus typing.
To characterise ECC3473 in terms of phenotypic and genotypic antimicrobial resistance, biochemical characteristics and taxonomy as well as to determine the global distribution of the novel species to which it belongs.
Standard broth dilution and disk diffusion were used to determine phenotypic AMR. The strain's complete genome, including plasmids, was obtained following long- and short read sequencing and a novel long/short read hybrid assembly and polishing, and the genomic basis of AMR was determined. Phylogenomic analysis and quantitative measures of relatedness (ANI, digital DNA-DNA hybridisation, and difference in G+C content) were used to study the taxonomic relationship between ECC3473 and Enterobacter type-strains. NCBI and PubMLST databases and the literature were searched for additional members of the novel species to determine its global distribution.
ECC3473 is one of 21 strains isolated globally belonging to a novel Enterobacter species for which the name, Enterobacter adelaidei sp. nov. is proposed. The novel species was found to be resilient in its capacity to persist in contaminated water and adaptable in its ability to accumulate multiple transmissible AMR determinants.
E. adelaidei sp. nov. may become increasingly important to the dissemination of AMR.
肠杆菌科物种是人类肠道微生物群的正常组成部分，存在于多种其他环境小生境中。它们已成为重要的机会性病原体，已知具有质粒介导的多类抗生素耐药性（AMR）决定因素。全球肠杆菌科分离株的 AMR 监测显示，该属在碳青霉烯类耐药方面仅次于克雷伯氏菌。肠杆菌科的分类比较混乱，标准的物种鉴定方法大多不准确或不充分。目前，该属有 27 个命名种和总共 46 个分类单元，通过基因组序列对之间的平均核苷酸同一性（ANI）计算可以区分。在这里，我们描述了一种从澳大利亚医院废水分离的肠杆菌菌株 ECC3473，其不能通过标准方法或核糖体 RNA 基因多位点分型来确定其物种。
从表型和基因型抗生素耐药性、生化特性和分类学以及确定其所属新型种的全球分布方面来描述 ECC3473。
使用标准肉汤稀释和药敏纸片扩散法来确定表型 AMR。通过长读和短读测序以及新的长/短读混合组装和抛光获得菌株的全基因组，包括质粒，并确定 AMR 的基因组基础。通过系统发育基因组分析和定量亲缘关系测量（ANI、数字 DNA-DNA 杂交和 G+C 含量差异）来研究 ECC3473 与肠杆菌型菌株之间的分类关系。在 NCBI 和 PubMLST 数据库和文献中搜索了该新型种的其他成员，以确定其全球分布。
ECC3473 是全球 21 株分离株之一，属于一种新型肠杆菌种，命名为 Enterobacter adelaidei sp. nov. 该新型种在污染水中具有很强的生存能力，并且能够积累多种可传播的 AMR 决定因素，具有很强的适应性。
E. adelaidei sp. nov. 可能会在 AMR 的传播中变得越来越重要。
