Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways.
Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways.
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DOI：
10.1099/mgen.0.000754
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发表时间：
2022-03
影响因子：
3.9
通讯作者：
Price EP
中科院分区：
文献类型：
--
作者：
Webb KA;Olagoke O;Baird T;Neill J;Pham A;Wells TJ;Ramsay KA;Bell SC;Sarovich DS;Price EP
囊性纤维化（CF）和慢性阻塞性肺疾病（COPD）的特点是急性肺恶化日益频繁，降低了生活质量和寿命。人类的呼吸道是一个丰富的多微生物环境的家园，其中包括专门厌氧普氏菌属的成员。尽管普雷沃氏菌很常见，但令人惊讶的是，人们对健康和患病呼吸道中普雷沃氏菌种类和菌株的患病率、作用、基因组多样性和抗菌素耐药性（AMR）潜力知之甚少。在这里，我们使用比较基因组学开发了一种实时PCR检测方法，允许从培养物和临床标本中快速鉴定和定量普氏菌种类。在一组普雷沃氏菌和非普雷沃氏菌中验证了检测的特异性，随后对CF和COPD呼吸源培养物进行了PCR筛选。接下来，对35株pcr阳性分离株进行全基因组测序。在已确定的8种普雷沃氏菌中，历史普雷沃氏菌、黑色素普雷沃氏菌、南氏普雷沃氏菌、唾液普雷沃氏菌和齿状普雷沃氏菌在参与者队列中存在重叠。系统基因组学分析显示宿主间有相当大的多样性，但宿主内的多样性有限，这表明下呼吸道的患者特异性谱系可能来自口腔分泌物。AMR表型与AMR基因的相关性发现，tetQ的存在与多西环素敏感性降低之间存在良好的相关性，ermF的存在与阿奇霉素敏感性和克林霉素耐药性降低之间存在良好的相关性。CF分离株的AMR率较高，反映了该队列中抗生素使用较多。所有检测的普雷沃氏菌分离株均对妥布霉素耐药，为提高普雷沃氏菌培养回收率提供了一种潜在的选择方法。我们将35个来自气道的普雷沃氏菌基因组添加到公共数据库中，将加强正在进行的努力，以揭示这种多样化和神秘的属在患病和健康肺部中的作用。
Cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are characterized by increasingly frequent acute pulmonary exacerbations that reduce life quality and length. Human airways are home to a rich polymicrobial environment, which includes members of the obligately anaerobic genus Prevotella . Despite their commonness, surprisingly little is known about the prevalence, role, genomic diversity and antimicrobial resistance (AMR) potential of Prevotella species and strains in healthy and diseased airways. Here, we used comparative genomics to develop a real-time PCR assay to permit rapid Prevotella species identification and quantification from cultures and clinical specimens. Assay specificity was validated across a panel of Prevotella and non- Prevotella species, followed by PCR screening of CF and COPD respiratory-derived cultures. Next, 35 PCR-positive isolates were subjected to whole-genome sequencing. Of eight identified Prevotella species, P. histicola , P. melaninogenica , P. nanceiensis , P. salivae and P. denticola overlapped between participant cohorts. Phylogenomic analysis revealed considerable interhost but limited intrahost diversity, suggesting patient-specific lineages in the lower airways, probably from oral cavity aspirations. Correlation of phenotypic AMR profiles with AMR genes identified excellent correlation between tetQ presence and decreased doxycycline susceptibility, and ermF presence and decreased azithromycin susceptibility and clindamycin resistance. AMR rates were higher in the CF isolates, reflecting greater antibiotic use in this cohort. All tested Prevotella isolates were tobramycin-resistant, providing a potential selection method to improve Prevotella culture retrieval rates. Our addition of 35 airway-derived Prevotella genomes to public databases will enhance ongoing efforts to unravel the role of this diverse and enigmatic genus in both diseased and healthy lungs.
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DOI：
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发表时间：
2021-04
期刊：
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影响因子：
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