Genome-based analyses from four clinically-isolated strains refined the taxonomy of Proteus genomosp. 6 and revealed their underestimated role in gastrointestinal diseases.

IF 4.3 3区医学 Q1 GASTROENTEROLOGY & HEPATOLOGY

Gut Pathogens Pub Date : 2025-05-15 DOI:10.1186/s13099-025-00701-8

Zhiyun Zhang, Jing He, Xueqing Liu, Linqian Huang, Zhou Zeng, Yao Peng, Xunchao Cai

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引用次数: 0

Abstract

Background: 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.

Results: 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.

Conclusion: 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.

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对四个临床分离菌株的基因组分析完善了变形杆菌基因组的分类。揭示了它们在胃肠道疾病中被低估的作用。

背景：变形杆菌在尿路感染中的作用早已被认识到，而最近的证据揭示了它们在胃肠道疾病中的作用。尽管如此，临床衍生的变形杆菌的分类，特别是那些来自胃肠道样本的分类，仍然没有得到充分的研究，而且经常被错误地分配，这限制了我们对这些物种引起的感染的理解。结果：从急性阑尾炎患者阑尾脓液中分离到4株Proteus菌株（DFP240708、LHD240705、TSJ240517和WDL240414），全基因组平均核苷酸识别（ANI）分析均为Proteus基因组。6，不同于使用自动细菌鉴定仪器（VITEK®-32）鉴定的结果。基于ANI和核心基因组系统发育树，我们发现87.5%的临床相关菌株应该被重新归类为变形杆菌基因组。6. 此外，Proteus基因组。6个基因组均携带一个或多个β -内酰胺耐药基因，但没有携带氨基糖苷耐药基因，本研究分离的4株菌株的药敏试验证实了这些发现。在分析的基因组中，只有4个（本研究中的2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。结论：我们的研究强调了临床环境下变形门属物种分类的不准确性，强调了使用基于基因组的分类分配方法的必要性。我们揭示了变形杆菌基因组的普遍性。在临床感染中的比例可能被低估了。此外，考虑到耐药基因的缺失和它们对氨基糖苷的敏感性，氨基糖苷可能成为由该物种引起的感染的一线治疗选择。

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来源期刊

Gut Pathogens GASTROENTEROLOGY & HEPATOLOGY-MICROBIOLOGY

CiteScore

7.70

自引率

2.40%

发文量

期刊介绍： Gut Pathogens is a fast publishing, inclusive and prominent international journal which recognizes the need for a publishing platform uniquely tailored to reflect the full breadth of research in the biology and medicine of pathogens, commensals and functional microbiota of the gut. The journal publishes basic, clinical and cutting-edge research on all aspects of the above mentioned organisms including probiotic bacteria and yeasts and their products. The scope also covers the related ecology, molecular genetics, physiology and epidemiology of these microbes. The journal actively invites timely reports on the novel aspects of genomics, metagenomics, microbiota profiling and systems biology. Gut Pathogens will also consider, at the discretion of the editors, descriptive studies identifying a new genome sequence of a gut microbe or a series of related microbes (such as those obtained from new hosts, niches, settings, outbreaks and epidemics) and those obtained from single or multiple hosts at one or different time points (chronological evolution).