匈牙利历史犬耳炎相关铜绿假单胞菌中保守的毒力骨架和异质性III型分泌效应蛋白谱

文献信息

中文摘要

背景： 犬外耳炎提供了一个慢性、炎症且频繁接触抗菌药物的生态位，铜绿假单胞菌可通过协调的黏附、生物膜、铁获取、分泌和毒素系统在此持续存在。
方法： 我们对2010年和2017年从犬耳炎病例中获得的历史匈牙利菌株集合的毒力相关基因组结构进行了表征。在名义范围70-139的70个分离株标识符中，60个具有对应的长读长组装和关联的VFDB筛选记录。基于基因组的分类学验证显示一个组装不符合铜绿假单胞菌的种级标准，因此将其排除。
结果： 主要缺失敏感分析仅限于52个符合预设CheckM标准（完整性≥95%，污染≤5%）的基因组确认的铜绿假单胞菌组装，而另外7个不符合主要CheckM标准的基因组确认的铜绿假单胞菌组装仅保留用于描述性背景分析，并被排除在流行率分母和缺失敏感分析之外。主要队列包含242个不同的毒力相关基因，每个分离株中位数为230.5个基因。其中，217个（89.7%）为类核心基因，出现在至少95%的基因组中。藻酸盐、IV型菌毛、鞭毛、铁载体、吩嗪、群体感应、II型、III型和VI型分泌骨架广泛保守。相比之下，III型效应蛋白内容具有异质性：exoT出现在52/52个分离株中，exoY在50/52中，exoS在49/52中，exoU在4/52中；一个分离株在组装水平上共检测到exoS和exoU同源序列。全毒力组组成在2010年和2017年之间未检测到差异（平方根Jaccard PERMANOVA，R2 = 0.0134，p = 0.6083），并且在错误发现率校正后，没有单个基因与采集年份保持关联。
结论： 这些数据定义了一个保守的历史毒力相关基因组骨架，并伴有分离株水平的效应蛋白和表面结构变异。检测到的基因被解释为基因组同源物和谱系特征，而非其表达或对致病性功能贡献的证据。

英文摘要

BACKGROUND: Canine otitis externa provides a chronic, inflamed and frequently antimicrobial-exposed niche in which Pseudomonas aeruginosa can persist through a coordinated repertoire of adhesion, biofilm, iron-acquisition, secretion and toxin systems.
METHODS: We characterized the virulence-associated genomic architecture of a historical Hungarian collection obtained from canine otitis cases in 2010 and 2017. Of the 70 isolate identifiers in the nominal range 70-139, 60 had corresponding long-read assemblies and linked VFDB screening records. One assembly was excluded after genome-based taxonomic validation showed that it did not meet the species-level criterion for P. aeruginosa.
RESULTS: Primary absence-sensitive analyses were restricted to 52 genome-confirmed P. aeruginosa assemblies meeting prespecified CheckM criteria (completeness ≥95%, contamination ≤5%), while seven additional genome-confirmed P. aeruginosa assemblies that did not meet the primary CheckM criteria were retained only for descriptive contextualization and were excluded from prevalence denominators and absence-sensitive analyses. The primary cohort contained 242 distinct virulence-associated genes, with a median of 230.5 genes per isolate. Of these, 217 (89.7%) were core-like, occurring in at least 95% of genomes. Alginate, type IV pilus, flagellar, siderophore, phenazine, quorum-sensing, type II, type III and type VI secretion backbones were broadly conserved. In contrast, type III effector content was heterogeneous: exoT occurred in 52/52 isolates, exoY in 50/52, exoS in 49/52 and exoU in 4/52; one isolate showed assembly-level co-detection of exoS and an exoU-homologous sequence. Whole-virulome composition did not differ detectably between 2010 and 2017 (square-root Jaccard PERMANOVA, R2 = 0.0134, p = 0.6083), and no individual gene remained associated with collection year after false-discovery-rate correction.
CONCLUSION: These data define a conserved historical virulence-associated genomic backbone punctuated by isolate-level effector and surface-structure variation. The detected genes are interpreted as genomic homologues and repertoire features rather than as evidence of their expression or functional contribution to pathogenicity.