Cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are characterised by increasingly frequent acute pulmonary exacerbations that reduce life quality and length. Human airways are home to a rich polymicrobial environment, including 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/strains in healthy and diseased airways. Here, we used comparative genomics to develop a real-time PCR assay to permit rapid Prevotella spp. 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 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 gene presence 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 chronic respiratory diseases and healthy lungs.

中文翻译：

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普雷沃氏菌的基因组多样性和抗菌素耐药性。从慢性肺病气道中分离

囊性纤维化 (CF) 和慢性阻塞性肺疾病 (COPD) 的特征是越来越频繁的急性肺加重，这会降低生活质量和长度。人类呼吸道拥有丰富的多种微生物环境，包括专性厌氧菌属Prevotella 的成员。尽管它们很常见，但令人惊讶的是，人们对普氏菌属物种/菌株在健康和患病气道中的流行率、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来开发实时 PCR 检测，以允许快速普氏菌属。培养物和临床标本的定量。在一组普雷沃氏菌和非Prevotella物种，然后对 CF 和 COPD 呼吸道衍生培养物进行 PCR 筛选。接下来，对 35 个 PCR 阳性分离株进行全基因组测序。在八种已识别的物种中，P. histicola、P. melaninogenica、P. nanceiensis、P . salivae和P. denticola在参与者队列之间重叠。系统发育分析揭示了相当多的宿主间但有限的宿主内多样性，表明下呼吸道中的患者特异性谱系，可能来自口腔吸入。表型 AMR 谱与 AMR 基因存在的相关性确定了tetQ存在与强力霉素敏感性降低和ermF之间的极好相关性阿奇霉素敏感性和克林霉素耐药性降低。CF 分离株的 AMR 率更高，这反映了该队列中抗生素的使用更多。所有测试的普氏菌分离株都具有妥布霉素抗性，为提高普氏菌培养物回收率提供了一种潜在的选择方法。我们将 35 个源自气道的普雷沃氏菌基因组添加到公共数据库中，这将加强持续的努力，以解开这一多样而神秘的属在慢性呼吸道疾病和健康肺部中的作用。