Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.
Karaganda State Medical University, Karaganda, Kazakhstan.
J Antimicrob Chemother. 2018 Jul 1;73(7):1781-1785. doi: 10.1093/jac/dky109.
To discover the Escherichia coli STs and associated resistance mechanisms in the community in Islamabad, Pakistan by analysis of E. coli isolates in sewage.
One hundred and ten E. coli were isolated from sewage across the city of Islamabad without antibiotic bias and confirmed as E. coli by MALDI-TOF MS. Isolates were characterized by fumC/fimH (CH) typing and core-genome MLST. Resistance mechanisms, virulence genes, phylotypes and plasmid incompatibility types were determined in a subset of isolates by in silico analysis. The genomic position of blaCTX-M-15 was determined using S1-PFGE, probing and Nanopore MinION sequencing.
The most prevalent STs were ST394, ST10 and ST648, accounting for 39% of all isolates collected and were found at many sites across Islamabad. Carbapenemase genes were absent and only a single isolate of ST131 was found. The most prevalent resistance mechanisms were qnrS1 and blaCTX-M-15, with blaCTX-M-15 penetrating many STs and found in 31% of all collected isolates. However, the majority of the successful STs were blaCTX-M-15 negative indicating that resistance is not the main driver of prevalence. Twenty-three percent of blaCTX-M-15 genes were chromosomally encoded and large ISEcp1-mediated insertions included qnrS1 and several plasmid genes. In all chromosomally encoded isolates no plasmid copies of blaCTX-M-15 were found. The most prevalent ST (ST394) contained many enteroaggregative E. coli virulence genes and the fimH30 variant allele previously linked to the success of ST131.
通过分析伊斯兰堡污水中的大肠杆菌分离株，发现巴基斯坦伊斯兰堡社区中的大肠杆菌 ST 株及其相关耐药机制。
从无抗生素偏向的伊斯兰堡市各地污水中分离出 110 株大肠杆菌，并通过基质辅助激光解吸电离飞行时间质谱（MALDI-TOF MS）确认为大肠杆菌。通过 fumC/fimH（CH）分型和核心基因组 MLST 对分离株进行特征分析。通过计算机分析，在部分分离株中确定耐药机制、毒力基因、 phylotype 和质粒不相容类型。使用 S1-PFGE、探针和 Nanopore MinION 测序确定 blaCTX-M-15 的基因组位置。
最常见的 ST 株为 ST394、ST10 和 ST648，占所有分离株的 39%，分布在伊斯兰堡的许多地点。未发现碳青霉烯酶基因，仅发现一株 ST131。最常见的耐药机制是 qnrS1 和 blaCTX-M-15，blaCTX-M-15 渗透多个 ST 株，在所有收集的分离株中发现率为 31%。然而，大多数成功的 ST 株均不含 blaCTX-M-15，表明耐药性不是流行的主要驱动因素。23%的 blaCTX-M-15 基因位于染色体上，包含 qnrS1 和几个质粒基因的 ISEcp1 介导的大片段插入。在所有染色体编码的分离株中均未发现 blaCTX-M-15 的质粒拷贝。最常见的 ST（ST394）含有许多肠聚集性大肠杆菌毒力基因，以及先前与 ST131 成功相关的 fimH30 变体等位基因。
