Massot Méril, Couffignal Camille, Clermont Olivier, D'Humières Camille, Chatel Jérémie, Plault Nicolas, Andremont Antoine, Caron Alexandre, Mentré France, Denamur Erick
IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
AP-HP, Service de Biostatistique, Hôpital Bichat-Claude Bernard, Paris, France.
Appl Environ Microbiol. 2017 Jun 16;83(13). doi: 10.1128/AEM.00659-17. Print 2017 Jul 1.
To get insights into the temporal pattern of commensal populations, we sampled the feces of four healthy cows from the same herd in the Hwange District of Zimbabwe daily over 25 days. The cows had not received antibiotic treatment during the previous 3 months. We performed viable counts and characterized the 326 isolates originating from the 98 stool samples at a clonal level, screened them for and genes, and tested them for their antibiotic susceptibilities. We observed that counts and dominant clones were different among cows, and very few clones were shared. No clone was shared by three or four cows. Clone richness and evenness were not different between cows. Within each host, the variability in the count was evidenced between days, and no clone was found to be dominant during the entire sampling period, suggesting the existence of clonal interference. Dominant clones tended to persist longer than subdominant ones and were mainly from phylogenetic groups A and B1. Five clones were found to contain both the and genes, representing 6.3% of the studied isolates. All cows harbored at least one Shiga toxin-producing (STEC) strain. Resistance to tetracycline, penicillins, trimethoprim, and sulfonamides was rare and observed in three clones that were shed at low levels in two cows. This study highlights the fact that the commensal population, including the STEC population, is host specific, is highly dynamic over a short time frame, and rarely carries antibiotic resistance determinants in the absence of antibiotic treatment. The literature about the dynamics of commensal populations is very scarce. Over 25 days, we followed the total counts daily and characterized the sampled clones in the feces of four cows from the same herd living in the Hwange District of Zimbabwe. This study deals with the day-to-day dynamics of both quantitative and qualitative aspects of commensal populations, with a focus on both Shiga toxin-producing and antibiotic-resistant strains. We show that the structure of these commensal populations was highly specific to the host, even though the cows ate and roamed together, and was highly dynamic between days. Such data are of importance to understand the ecological forces that drive the dynamics of the emergence of clones of particular interest within the gastrointestinal tract and their transmission between hosts.
为深入了解共生菌群的时间模式，我们在津巴布韦万基区同一牛群中，对4头健康奶牛的粪便进行了为期25天的每日采样。这些奶牛在过去3个月内未接受过抗生素治疗。我们进行了活菌计数，并在克隆水平上对源自98份粪便样本的326株分离株进行了特征分析，筛选了它们的stx和eae基因，并检测了它们的抗生素敏感性。我们观察到，不同奶牛之间的活菌计数和优势克隆不同，很少有克隆是共享的。没有克隆被三头或四头奶牛共享。奶牛之间的克隆丰富度和均匀度没有差异。在每个宿主内，活菌计数在不同天数之间存在差异，并且在整个采样期间没有发现优势克隆，这表明存在克隆干扰。优势克隆往往比次优势克隆持续时间更长，并且主要来自系统发育组A和B1。发现有5个大肠杆菌克隆同时含有stx和eae基因，占所研究分离株的6.3%。所有奶牛都至少携带一株产志贺毒素大肠杆菌（STEC）菌株。对四环素、青霉素、甲氧苄啶和磺胺类药物的耐药性很少见，在两头奶牛中低水平排出的三个克隆中观察到。这项研究突出了这样一个事实，即共生大肠杆菌群体（包括STEC群体）具有宿主特异性，在短时间内高度动态变化，并且在没有抗生素治疗的情况下很少携带抗生素耐药决定簇。关于共生大肠杆菌群体动态的文献非常稀少。在25天的时间里，我们每天跟踪总活菌计数，并对来自津巴布韦万基区同一牛群的4头奶牛粪便中的采样克隆进行了特征分析。本研究探讨了共生大肠杆菌群体数量和质量方面的日常动态，重点关注产志贺毒素大肠杆菌和耐抗生素大肠杆菌菌株。我们表明，即使奶牛一起进食和活动，这些共生群体的结构对宿主也具有高度特异性，并且在不同天数之间高度动态变化。这些数据对于理解驱动胃肠道内特定感兴趣的大肠杆菌克隆出现及其在宿主之间传播的生态力量非常重要。
