摘要

由肠外大肠杆菌（ExPEC）引起的感染发病率正在全球范围上升，这是一个主要的公共卫生问题。对抗生素有抗药性的ExPEC菌株与死亡率过高，住院时间延长和医疗费用较高有关。大肠杆菌ST131是全球主要的ExPEC克隆群，其质粒组成可变，并且具有一系列能够实现抗菌素耐药性（AMR）的基因。 ST131分离物经常编码AMR基因blaCTX-M-14 / 15/27，该基因通常通过移动遗传元件（MGE）进行重排，扩增和易位。短的DNA读取不能完全解析质粒上重复元件的结构，从而无法完全确定编码blaCTX-M基因的MGE结构。在这里，我们进行了长读测序，以解密从六个患者中分离出的六个大肠杆菌ST131的基因组结构。大多数长阅读的程序集将整个染色体和质粒生成为单个重叠群，而单独阅读短的程序则产生了更多的碎片程序集。长时间阅读的程序集突出了带有blaCTX-M-15，blaCTX-M-14和blaCTX-M-27基因的各种辅助基因组，分别在三种，一种和一种分离物中鉴定出。一个样品没有blaCTX-M基因。两个样本具有染色体blaCTX-M-14和blaCTX-M-15基因，后者位于三个不同的位置，可能被相邻的MGE易位：ISEcp1，IS903B和Tn2。这项研究表明，即使在克隆群（如大肠杆菌ST131）内密切相关的分离株之间，AMR基因也存在于多种不同的染色体和质粒环境中。

The incidence of infections caused by extraintestinal Escherichia coli (ExPEC) is rising globally, which is a major public health concern. ExPEC strains that are resistant to antimicrobials have been associated with excess mortality, prolonged hospital stays and higher healthcare costs. E. coli ST131 is a major ExPEC clonal group worldwide with variable plasmid composition, and has an array of genes enabling antimicrobial resistance (AMR). ST131 isolates frequently encode the AMR genes blaCTX-M-14/15/27, which are often rearranged, amplified and translocated by mobile genetic elements (MGEs). Short DNA reads do not fully resolve the architecture of repetitive elements on plasmids to allow MGE structures encoding blaCTX-M genes to be fully determined. Here, we performed long read sequencing to decipher the genome structures of six E. coli ST131 isolated from six patients. Most long read assemblies generated entire chromosomes and plasmids as single contigs, contrasting with more fragmented assemblies created with short reads alone. The long read assemblies highlighted diverse accessory genomes with blaCTX-M-15, blaCTX-M-14 and blaCTX-M-27 genes identified in three, one and one isolates, respectively. One sample had no blaCTX-M gene. Two samples had chromosomal blaCTX-M-14 and blaCTX-M-15 genes, and the latter was at three distinct locations, likely transposed by the adjacent MGEs: ISEcp1, IS903B and Tn2. This study showed that AMR genes exist in multiple different chromosomal and plasmid contexts even between closely-related isolates within a clonal group such as E. coli ST131.

https://www.biorxiv.org/content/10.1101/558635v2.abstract