De Maayer Pieter, Green Teigra, Jordan Sara, Smits Theo H M, Coutinho Teresa A
School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2000, South Africa.
Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland.
BMC Genomics. 2025 Apr 26;26(1):408. doi: 10.1186/s12864-025-11590-1.
Enterobacter hormaechei is of increasing concern as both an opportunistic and nosocomial pathogen, exacerbated by its evolving multidrug resistance. However, its taxonomy remains contentious, and little is known about its pathogenesis and the broader context of its resistome. In this study, a comprehensive comparative genomic analysis was undertaken to address these issues.
Phylogenomic analysis revealed that E. hormaechei represents a complex, comprising three predicted species, E. hormaechei, E. hoffmannii and E. xiangfangensis, with the latter putatively comprising three distinct subspecies, namely oharae, steigerwaltii and xiangfangensis. The species and subspecies all display open and distinct pan-genomes, with diversification driven by an array of mobile genetic elements including numerous plasmid replicons and prophages, integrative conjugative elements (ICE) and transposable elements. These elements have given rise to a broad, relatively conserved set of pathogenicity determinants, but also a variable set of secretion systems. The E. hormaechei complex displays a highly mutable resistome, with most taxa being multidrug resistant.
This study addressed key issues pertaining to the taxonomy of the E. hormaechei complex, which may contribute towards more accurate identification of strains belonging to this species complex in the clinical setting. The pathogenicity determinants identified in this study could serve as a basis for a deeper understanding of E. hormaechei complex pathogenesis and virulence. The extensive nature of multidrug resistance among E. hormaechei complex strains highlights the need for responsible antibiotic stewardship to ensure effective treatment of these emerging pathogens.
随着霍氏肠杆菌（Enterobacter hormaechei）逐渐演变为多重耐药菌，它作为一种机会性病原体和医院感染病原体，日益受到关注。然而，其分类学仍存在争议，人们对其发病机制及耐药组的更广泛背景知之甚少。在本研究中，我们进行了全面的比较基因组分析以解决这些问题。
系统发育基因组分析表明，霍氏肠杆菌代表一个复合体，包含三个预测物种，即霍氏肠杆菌、霍夫曼肠杆菌（E. hoffmannii）和湘芳肠杆菌（E. xiangfangensis），其中后者可能包含三个不同的亚种，即大原亚种（oharae）、施泰格瓦尔蒂亚种（steigerwaltii）和湘芳亚种。这些物种和亚种均呈现开放且独特的泛基因组，其多样化由一系列移动遗传元件驱动，包括众多质粒复制子、前噬菌体、整合结合元件（ICE）和转座元件。这些元件产生了一组广泛且相对保守的致病性决定因素，但也有一组可变的分泌系统。霍氏肠杆菌复合体显示出高度可变的耐药组，大多数分类单元具有多重耐药性。
本研究解决了与霍氏肠杆菌复合体分类学相关的关键问题，这可能有助于在临床环境中更准确地鉴定属于该物种复合体的菌株。本研究中鉴定出的致病性决定因素可作为更深入了解霍氏肠杆菌复合体发病机制和毒力的基础。霍氏肠杆菌复合体菌株中广泛存在的多重耐药性凸显了进行合理抗生素管理以确保有效治疗这些新出现病原体的必要性。
