Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA.
Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA.
J Bacteriol. 2019 Mar 13;201(7). doi: 10.1128/JB.00478-18. Print 2019 Apr 1.
The airway fluids of cystic fibrosis (CF) patients contain local pH gradients and are more acidic than those of healthy individuals. pH is a critical factor that is often overlooked in studies seeking to recapitulate the infection microenvironment. We sought to determine the impact of pH on the physiology of a ubiqituous yet understudied microbe, Phylogenomics was first used to reconstruct evolutionary relationships between 74 strains of (59 from CF patients). Neither the core genome (2,158 genes) nor the accessory genome (11,978 genes) distinguish the CF and non-CF isolates; however, strains from similar isolation sources grouped into the same subclades. We grew two human and six CF isolates from different subclades at a range of pH values and observed impaired growth and altered antibiotic tolerances at pH 5. Transcriptomes revealed increased expression of both antibiotic resistance and DNA repair genes in acidic conditions. Although the gene expression profiles of in lab cultures and CF sputum were distinct, we found that the same genes associated with low pH were also expressed during infection, and the higher pH cultures were more similar to sputum metatranscriptomes. Our findings suggest that is not well adapted to acidity and may cope with low pH by expressing stress response genes and colonizing less acidic microenvironments. As a whole, our study underlines the impact of microenvironments on bacterial colonization and adaptation in CF infections. Understanding bacterial responses to physiological conditions is an important priority for combating opportunistic infections. The majority of CF patients succumb to inflammation and necrosis in the airways, arising from chronic infection due to ineffective mucociliary clearance. Steep pH gradients characterize the CF airways but are not often incorporated in standard microbiology culture conditions. is a prevalent CF opportunistic pathogen also found in many disparate environments, yet this bacterium's contribution to CF lung damage and its response to changing environmental factors remain largely understudied. Here, we show that pH impacts the physiology and antibiotic susceptibility of , with implications for the development of relevant models and assessment of antibiotic sensitivity.
囊性纤维化（CF）患者的气道液含有局部 pH 梯度，比健康个体的气道液更酸性。pH 是一个经常被忽视的关键因素，在试图重现感染微环境的研究中。我们试图确定 pH 对一种普遍存在但研究不足的微生物的生理学的影响，使用系统发育基因组学首先重建了 74 株 （59 株来自 CF 患者）之间的进化关系。核心基因组（2158 个基因）和辅助基因组（11978 个基因）都不能区分 CF 和非 CF 分离株；然而，来自相似分离源的菌株分为相同的亚分支。我们在一系列 pH 值下培养了两个人类和六个 CF 分离株，观察到在 pH5 时生长受到抑制和抗生素耐受性改变。转录组显示在酸性条件下抗生素耐药性和 DNA 修复基因的表达增加。尽管实验室培养物和 CF 痰液中的 基因表达谱不同，但我们发现与低 pH 相关的相同基因也在感染过程中表达，并且较高 pH 的培养物与痰液宏转录组更相似。我们的研究结果表明， 不能很好地适应酸性环境，可能通过表达应激反应基因和定殖在酸性较低的微环境中来应对低 pH。总的来说，我们的研究强调了微环境对 CF 感染中细菌定植和适应的影响。了解细菌对生理条件的反应是对抗机会性感染的重要优先事项。大多数 CF 患者因无效的黏液纤毛清除而导致气道炎症和坏死，从而死于气道慢性感染。陡峭的 pH 梯度是 CF 气道的特征，但在标准微生物培养条件中并不常见。 是一种普遍存在的 CF 机会性病原体，也存在于许多不同的环境中，但这种细菌对 CF 肺部损伤的贡献及其对环境因素变化的反应在很大程度上仍未得到充分研究。在这里，我们表明 pH 影响 的生理学和抗生素敏感性，这对相关 的发展和抗生素敏感性评估具有重要意义。
