Institute of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan.
Department of Clinical Analysis, School of Pharmaceutical Sciences, University of São Paulo, Sao Paulo, Brazil.
Environ Sci Pollut Res Int. 2021 Oct;28(38):54147-54152. doi: 10.1007/s11356-021-15437-6. Epub 2021 Aug 13.
The environment plays an important role in the dissemination of clinically relevant antimicrobial-resistant bacteria and genes. In this study, we described genomic features of a plasmid-mediated colistin-resistant mcr-1-positive Escherichia coli strains (PK-3225) isolated from a dairy farm wastewater sample. After initial isolation and PCR detection of mcr-1-positive E. coli, whole-genome sequencing was performed using Illumina Hiseq 2500 followed by in silico analysis. Genetic context surrounding the mcr-1 gene was determined and SNP-based phylogenomic analysis was performed. Furthermore, plasmid analysis and conjugation assays were performed to determine transferability of mcr-1. E. coli PK-3225 belonged to ST10 and carried a broad resistome that included colistin (mcr-1), beta-lactam (bla), tetracycline (tetB), phenicol (catA1), macrolide (mdfA), trimethoprim (dfrA17), aminoglycosides (aadA5, aph(3")-Ib, aph(6)-Id), and sulphonamide (sul2) resistance genes. The draft genome of E. coli calculated as 4.9 Mbp. Conjugation experiment showed successful transfer of the mcr-1 gene to E. coli recipient strain J53. In silico analysis showed that mcr-1 was located on IncI2 plasmid of > 59 kb in length, with the nikB-mcr-1-pap2 gene array, and lack ISApl1. The phylogenomic analysis revealed that the PK-3225 was closely related to human ST10 E. coli from Brazil and USA. To our knowledge, this is the first draft genome sequence of mcr-1 carrying E. coli isolated from the farm environment in Pakistan. Considering the high burden of colistin resistance in Pakistan, presence of pandemic high-risk E. coli clones in the environment requires strict surveillance.
环境在临床相关的抗微生物耐药菌和基因的传播中起着重要作用。在这项研究中，我们描述了从一个奶牛场废水样本中分离的一种质粒介导的粘菌素耐药 mcr-1 阳性大肠杆菌菌株（PK-3225）的基因组特征。在初步分离和 mcr-1 阳性大肠杆菌的 PCR 检测后，使用 Illumina Hiseq 2500 进行全基因组测序，然后进行计算机分析。确定 mcr-1 基因周围的遗传环境，并进行 SNP 基于的系统发育分析。此外，还进行了质粒分析和接合试验，以确定 mcr-1 的可转移性。大肠杆菌 PK-3225 属于 ST10，携带广泛的耐药基因，包括粘菌素（mcr-1）、β-内酰胺（bla）、四环素（tetB）、氯霉素（catA1）、大环内酯（mdfA）、甲氧苄啶（dfrA17）、氨基糖苷（aadA5、aph(3")-Ib、aph(6)-Id）和磺胺类（sul2）耐药基因。大肠杆菌的基因组草图计算为 490 万碱基对。接合实验显示 mcr-1 基因成功转移到大肠杆菌受体菌株 J53。计算机分析表明 mcr-1 位于长度超过 59kb 的 IncI2 质粒上，带有 nikB-mcr-1-pap2 基因阵列，且缺乏 ISApl1。系统发育分析显示，PK-3225 与巴西和美国的人源 ST10 大肠杆菌密切相关。据我们所知，这是首次从巴基斯坦农场环境中分离出携带 mcr-1 的大肠杆菌的基因组草图。考虑到巴基斯坦粘菌素耐药的负担很重，环境中存在大流行高风险的大肠杆菌克隆需要严格监测。
