Zhang Zhiyun, He Jing, Liu Xueqing, Huang Linqian, Zeng Zhou, Peng Yao, Cai Xunchao
Department of Clinical Laboratory, The Central Hospital of Yongzhou, Yongzhou, 425000, China.
Department of Clinical Laboratory, Yongzhou Hospital, University of South China, Yongzhou, 425000, China.
Gut Pathog. 2025 May 15;17(1):29. doi: 10.1186/s13099-025-00701-8.
Proteus spp. have long been recognized for their role in urinary tract infections, while recent evidence disclosed their implications in gastrointestinal diseases. Despite this, the taxonomy of clinically-derived Proteus spp., particularly those from gastrointestinal samples, remains understudied and is frequently mis-assigned, which limits our understanding of infections caused by these species.
Four Proteus strains (i.e., DFP240708, LHD240705, TSJ240517 and WDL240414) were isolated from the appendiceal pus of patients with acute appendicitis, whole-genome average nucleotide identity (ANI) analysis identified all of them as Proteus genomosp. 6, different from that identified using the automated bacterial identification instrument (VITEK-32). Based on ANI and the core-genomic phylogenetic tree, we found that 87.5% of clinically-related strains previously identified as P. columbae should be re-classified as Proteus genomosp. 6. Additionally, the Proteus genomosp. 6 genomes all carry one or more beta-lactam resistance genes, but none carry aminoglycoside resistance genes, and antibiotic susceptibility testing conducted on the four strains isolated in this study confirmed these findings. Among the genomes analyzed, only four (two from this study (TSJ240517 and WDL240414)) carried virulence genes, specifically the hlyA, hlyB, and hlyD genes encoding hemolysin.
Our study highlights inaccuracies in the taxa classification of Proteus species under clinical settings, underscoring the necessity of using genomic-based taxonomic assignment methods. We revealed that the prevalence of Proteus genomosp. 6 in clinical infections has likely been underestimated. Furthermore, given the resistance-gene absence and their sensitivity to aminoglycosides, aminoglycosides may serve as a promising first-line treatment option for infections caused by this species.
变形杆菌长期以来因在尿路感染中的作用而受到认可，而最近的证据揭示了它们在胃肠道疾病中的影响。尽管如此，临床来源的变形杆菌的分类，特别是那些来自胃肠道样本的变形杆菌，仍未得到充分研究，且经常被错误分类，这限制了我们对这些物种引起的感染的理解。
从急性阑尾炎患者的阑尾脓液中分离出四株变形杆菌菌株（即DFP240708、LHD240705、TSJ240517和WDL240414），全基因组平均核苷酸同一性（ANI）分析将它们全部鉴定为变形杆菌基因组种6，这与使用自动细菌鉴定仪器（VITEK - 32）鉴定的结果不同。基于ANI和核心基因组系统发育树，我们发现先前鉴定为鸽变形杆菌的临床相关菌株中有87.5%应重新分类为变形杆菌基因组种6。此外，变形杆菌基因组种6的基因组均携带一个或多个β - 内酰胺抗性基因，但均不携带氨基糖苷类抗性基因，对本研究中分离的四株菌株进行的抗生素敏感性测试证实了这些发现。在所分析的基因组中，只有四个（本研究中的两个（TSJ240517和WDL240414））携带毒力基因，特别是编码溶血素的hlyA、hlyB和hlyD基因。
我们的研究强调了临床环境中变形杆菌物种分类的不准确之处，强调了使用基于基因组的分类方法的必要性。我们揭示了变形杆菌基因组种6在临床感染中的流行率可能被低估了。此外，鉴于其缺乏抗性基因且对氨基糖苷类敏感，氨基糖苷类可能是该物种引起的感染的一种有前景的一线治疗选择。
