Anses, Laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon, Lyon, France.
Anses, Laboratoire de Ploufragan-Plouzané, Unité Génétique Virale et Biosécurité, Ploufrangan, France.
J Appl Microbiol. 2020 Dec;129(6):1577-1588. doi: 10.1111/jam.14741. Epub 2020 Jul 16.
The goal was to explore the effects of subinhibitory concentration (SIC) (0·5 MIC = 20 µg l ) of ciprofloxacin on the transcriptome of enterohaemorrhagic Escherichia coli O26:H11 isolate by 60 minutes of exposure.
We used a combination of comparative genomic and transcriptomic (RNAseq) analyses. The whole genome of the E. coli O26:H11 #30934 strain of bovine origin was sequenced and assembled. This genome was next used as reference for the differential gene expression analysis. A whole-genome-based analysis of 36 publicly available E. coli O26:H11 genomes was performed to define the core and the accessory transcriptome of E. coli O26:H11. Using RNAseq and RT-qPCR analysis we observed overexpression of the SOS response and of T3SS effectors, together with the inhibition of specific motility-associated genes. Among the large set of transposases present, only three were activated, suggesting moderate transposition of genes with low doses of ciprofloxacin. Our results illustrated that transcriptional repressors, such as the CopG family protein, belonging to the core genome of E. coli O26:H11, are altered in response to fluoroquinolone exposure. The gene ontology enrichment analysis showed SIC of ciprofloxacin induced binding functions and catalytic activities, including mostly transferase and hydrolase proteins. The amino acid pathways involved in metabolic processes were significantly enhanced after the treatment.
Although the core genome of E. coli O26:H11 constituted only 54·5% of the whole genome, we demonstrated that most differentially expressed genes were associated with the core genome of E. coli O26:H11, and that effects on the mobile genetic element, phage, and plasmid-related genes were rare.
For the first time the effect of low dose of ciprofloxacin on the core transcriptome of E. coli O26:H11 was described. The effects on the main biological functions and protein classes including transcriptional regulators were illustrated.
本研究旨在探讨在暴露 60 分钟内，环丙沙星亚抑菌浓度（SIC）（0.5 MIC=20μg/L）对肠出血性大肠杆菌 O26:H11 分离株转录组的影响。
我们采用了比较基因组学和转录组学（RNAseq）分析相结合的方法。对牛源大肠杆菌 O26:H11 菌株 #30934 的全基因组进行测序和组装。接下来，我们将该基因组用作差异基因表达分析的参考。对 36 个公开的大肠杆菌 O26:H11 基因组进行了全基因组分析，以确定大肠杆菌 O26:H11 的核心和辅助转录组。通过 RNAseq 和 RT-qPCR 分析，我们观察到 SOS 反应和 T3SS 效应物的过度表达，同时特定运动相关基因受到抑制。在存在的大量转座酶中，只有 3 个被激活，这表明低剂量环丙沙星会导致基因的中度转位。我们的结果表明，转录抑制剂，如属于大肠杆菌 O26:H11 核心基因组的 CopG 家族蛋白，会因氟喹诺酮类药物的暴露而发生改变。基因本体富集分析表明，环丙沙星的 SIC 诱导了结合功能和催化活性，包括大多数转移酶和水解酶蛋白。代谢过程中涉及的氨基酸途径在治疗后显著增强。
尽管大肠杆菌 O26:H11 的核心基因组仅占全基因组的 54.5%，但我们证明大多数差异表达基因与大肠杆菌 O26:H11 的核心基因组相关，而对移动遗传元件、噬菌体和质粒相关基因的影响则很少。
本研究首次描述了低剂量环丙沙星对大肠杆菌 O26:H11 核心转录组的影响。结果表明，它对包括转录调节因子在内的主要生物学功能和蛋白质类别的影响。
