Extensive Within-Host Diversity in Fecally Carried Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli Isolates: Implications for Transmission Analyses.
Extensive Within-Host Diversity in Fecally Carried Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli Isolates: Implications for Transmission Analyses.
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DOI：
10.1128/jcm.00378-15
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发表时间：
2015-07
影响因子：
9.4
通讯作者：
Modernizing Medical Microbiology Informatics Group
中科院分区：
文献类型：
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作者：
Stoesser N;Sheppard AE;Moore CE;Golubchik T;Parry CM;Nget P;Saroeun M;Day NP;Giess A;Johnson JR;Peto TE;Crook DW;Walker AS;Modernizing Medical Microbiology Informatics Group
耐药大肠埃希菌（如携带超广谱β-内酰胺酶（ESBL）基因的菌株）的传播流行病学研究经常使用直肠监测拭子的选择性培养来鉴定分离株，以进行分子流行病学调查。通常情况下，只评估单个菌落，这可能低估物种多样性和传播事件。对16株E.大肠杆菌菌落的8个粪便样本（n = 127个基因组;一个失败），取自柬埔寨的不同个体，一个高产ESBL大肠杆菌的地区。大肠杆菌感染率。序列数据被用来描述E.大肠杆菌分离株及其抗性/毒力基因含量作为辅助基因组多样性的替代指标。127 E。大肠杆菌基因组代表31个不同的序列类型（ST）。8例受试者中有7例（88%）携带ESBL阳性分离株，均含有blaCTX-M变异体。多样性是实质性的，中位数为4 ST/个人（范围，1至10）和广泛的遗传分歧，在核苷酸水平内的一些ST。在2/8（25%）个体中，相同的blaCTX-M变体出现在不同的克隆中，和/或不同的blaCTX-M变体出现在相同的克隆中。其他抗性基因和常见毒力因子的模式，代表在辅助基因组的差异，也不同的克隆内和之间。ESBL阳性大肠埃希菌在人群中的分布具有多样性。大肠杆菌表明，粪便监测，特别是如果基于单菌落传代培养，可能会低估传播事件，特别是在高流行率的设置。
Studies of the transmission epidemiology of antimicrobial-resistant Escherichia coli, such as strains harboring extended-spectrum beta-lactamase (ESBL) genes, frequently use selective culture of rectal surveillance swabs to identify isolates for molecular epidemiological investigation. Typically, only single colonies are evaluated, which risks underestimating species diversity and transmission events. We sequenced the genomes of 16 E. coli colonies from each of eight fecal samples (n = 127 genomes; one failure), taken from different individuals in Cambodia, a region of high ESBL-producing E. coli prevalence. Sequence data were used to characterize both the core chromosomal diversity of E. coli isolates and their resistance/virulence gene content as a proxy measure of accessory genome diversity. The 127 E. coli genomes represented 31 distinct sequence types (STs). Seven (88%) of eight subjects carried ESBL-positive isolates, all containing blaCTX-M variants. Diversity was substantial, with a median of four STs/individual (range, 1 to 10) and wide genetic divergence at the nucleotide level within some STs. In 2/8 (25%) individuals, the same blaCTX-M variant occurred in different clones, and/or different blaCTX-M variants occurred in the same clone. Patterns of other resistance genes and common virulence factors, representing differences in the accessory genome, were also diverse within and between clones. The substantial diversity among intestinally carried ESBL-positive E. coli bacteria suggests that fecal surveillance, particularly if based on single-colony subcultures, will likely underestimate transmission events, especially in high-prevalence settings.