Pages-Monteiro Laurence, Marti Romain, Commun Carine, Alliot Nolwenn, Bardel Claire, Meugnier Helene, Perouse-de-Montclos Michele, Reix Philippe, Durieu Isabelle, Durupt Stephane, Vandenesch Francois, Freney Jean, Cournoyer Benoit, Doleans-Jordheim Anne
Equipe de Recherche, Bactéries Pathogènes Opportunistes et Environnement, UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1 & VetAgro Sup, Villeurbanne, France.
Laboratoire de Bactériologie, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon (HCL), Bron, France.
PLoS One. 2017 Mar 10;12(3):e0173022. doi: 10.1371/journal.pone.0173022. eCollection 2017.
Cystic fibrosis (CF) lungs harbor a complex community of interacting microbes, including pathogens like Pseudomonas aeruginosa. Meta-taxogenomic analysis based on V5-V6 rrs PCR products of 52 P. aeruginosa-positive (Pp) and 52 P. aeruginosa-negative (Pn) pooled DNA extracts from CF sputa suggested positive associations between P. aeruginosa and Stenotrophomonas and Prevotella, but negative ones with Haemophilus, Neisseria and Burkholderia. Internal Transcribed Spacer analyses (RISA) from individual DNA extracts identified three significant genetic structures within the CF cohorts, and indicated an impact of P. aeruginosa. RISA clusters Ip and IIIp contained CF sputa with a P. aeruginosa prevalence above 93%, and of 24.2% in cluster IIp. Clusters Ip and IIIp showed lower RISA genetic diversity and richness than IIp. Highly similar cluster IIp RISA profiles were obtained from two patients harboring isolates of a same P. aeruginosa clone, suggesting convergent evolution in the structure of their microbiota. CF patients of cluster IIp had received significantly less antibiotics than patients of clusters Ip and IIIp but harbored the most resistant P. aeruginosa strains. Patients of cluster IIIp were older than those of Ip. The effects of P. aeruginosa on the RISA structures could not be fully dissociated from the above two confounding factors but several trends in these datasets support the conclusion of a strong incidence of P. aeruginosa on the genetic structure of CF lung microbiota.
囊性纤维化（CF）患者的肺部存在一个由相互作用的微生物组成的复杂群落，其中包括铜绿假单胞菌等病原体。基于来自CF痰液的52份铜绿假单胞菌阳性（Pp）和52份铜绿假单胞菌阴性（Pn）混合DNA提取物的V5-V6 rrs PCR产物进行的宏基因组分析表明，铜绿假单胞菌与嗜麦芽窄食单胞菌和普雷沃氏菌之间存在正相关，但与嗜血杆菌、奈瑟菌和伯克霍尔德菌之间存在负相关。对个体DNA提取物进行的内转录间隔区分析（RISA）在CF队列中鉴定出三个显著的遗传结构，并表明了铜绿假单胞菌的影响。RISA聚类Ip和IIIp包含铜绿假单胞菌患病率高于93%的CF痰液，而在聚类IIp中为24.2%。聚类Ip和IIIp的RISA遗传多样性和丰富度低于IIp。从两名携带相同铜绿假单胞菌克隆分离株的患者中获得了高度相似的聚类IIp RISA图谱，表明其微生物群结构存在趋同进化。聚类IIp的CF患者接受的抗生素明显少于聚类Ip和IIIp的患者，但携带的铜绿假单胞菌菌株耐药性最强。聚类IIIp的患者比Ip的患者年龄大。铜绿假单胞菌对RISA结构的影响无法完全与上述两个混杂因素区分开来，但这些数据集中的几个趋势支持以下结论：铜绿假单胞菌对CF肺部微生物群的遗传结构有很强的影响。
