Highly Divergent <i>Clostridium difficile</i> Strains Isolated from the Environment

Clostridium difficile is one of the most important human and animal pathogens. However, the bacterium is ubiquitous and can be isolated from various sources. Here we report the prevalence and characterization of C. difficile in less studied environmental samples, puddle water (n = 104) and soil (n = 79). C. difficile was detected in 14.4% of puddle water and in 36.7% of soil samples. Environmental strains displayed antimicrobial resistance patterns comparable to already published data of human and animal isolates. A total of 480 isolates were grouped into 34 different PCR ribotypes. More than half of these (52.9%; 18 of 34) were already described in humans or animals. However, 14 PCR ribotypes were new in our PCR ribotype library and all but one were non-toxigenic. The multilocus sequence analysis of these new PCR ribotypes revealed that non-toxigenic environmental isolates are phylogenetically distinct and belong to three highly divergent clades, two of which have not been described before. Our data suggest that environment is a potential reservoir of genetically diverse population of C. difficile.

艰难梭菌（Clostridium difficile）是最重要的人类与动物病原菌之一。不过该菌分布广泛，可从多种来源分离得到。本研究针对此前研究较少的环境样本——积水坑水（n=104）与土壤样本（n=79），报道了其中艰难梭菌的检出率与特征。本研究中，积水坑水样本的艰难梭菌检出率为14.4%，土壤样本检出率为36.7%。环境分离株的抗菌药物耐药谱与已发表的人类、动物分离株数据相近。总计480株分离株可划分为34种不同的PCR核糖体分型（PCR ribotype）。其中超过半数（52.9%，34种中的18种）已在人类或动物样本中被报道过。但本研究的核糖体分型库中另有14种为新型分型，且除1种外均为非产毒株。对这些新型分型的多位点序列分析（multilocus sequence analysis）显示，非产毒环境分离株在系统发育上具有独特性，隶属于3个高度分化的进化枝，其中2个此前从未被报道过。本研究数据表明，环境可能是遗传多样性艰难梭菌种群的潜在储存库。