Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café s/n - Monte Alegre, Ribeirão Preto, SP, 14040-903, Brasil.
Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café s/n - Monte Alegre, Ribeirão Preto, SP, 14040-903, Brasil.
J Glob Antimicrob Resist. 2019 Jun;17:321-322. doi: 10.1016/j.jgar.2019.05.018. Epub 2019 May 22.
This study reports the draft genome sequence of a multidrug-resistant Escherichia coli isolate obtained from a Brazilian soil sample.
The E. coli genome was sequenced using an Illumina MiSeq platform. De novo genome assembly was performed using SPAdes v.3.9. The draft genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). The resistome, virulome and mobilome were identified using tools available from the Center for Genomic Epidemiology.
The genome presented 5613 protein-coding sequences and a GC content of 50.3%. Resistome analysis showed antimicrobial resistance genes to β-lactams (bla), tetracyclines [tet(A) and tet(34)], aminoglycosides (aadA1, aadA5 and aadA24), phenicols (floR), sulfonamides (sul2 and sul3), trimethoprim (dfrA17) and macrolides [mdf(A)]. For quinolone resistance, mutations in the quinolone resistance-determining regions of GyrA (Ser83Leu; Asp87Tyr) and ParC (Ser80Ile; Glu62Lys) were detected. Plasmid incompatibility (Inc) groups were detected, including ColpVC, IncN3, IncP1 and IncF [F113:A8:B20], with IncF113 being a new allele. The isolate belongs to ST189 (CC165), serotype O80:H26-fimH54 and presents some virulence genes (lpfA, iss and gad).
This is the first draft genome sequence of an E. coli ST189 isolate of serotype O80:H26-fimH54 obtained from soil. This draft genome sequence can be used to compare antimicrobial-resistant E. coli isolates obtained from different sources.
本研究报告了从巴西土壤样本中分离出的一株多药耐药大肠杆菌的基因组草图序列。
使用 Illumina MiSeq 平台对大肠杆菌基因组进行测序。使用 SPAdes v.3.9 进行从头基因组组装。使用 NCBI 原核基因组注释管道（PGAP）对草案基因组序列进行注释。使用来自基因组流行病学中心的可用工具鉴定抗药性组、毒力组和可移动组。
该基因组包含 5613 个蛋白质编码序列和 50.3%的 GC 含量。抗药性组分析显示，该菌株对β-内酰胺类（bla）、四环素类（tet(A)和 tet(34)）、氨基糖苷类（aadA1、aadA5 和 aadA24）、酚类（floR）、磺胺类（sul2 和 sul3）、甲氧苄啶（dfrA17）和大环内酯类（mdf(A)）具有耐药性。针对喹诺酮类耐药性，检测到 GyrA（Ser83Leu；Asp87Tyr）和 ParC（Ser80Ile；Glu62Lys）喹诺酮耐药决定区的突变。检测到质粒不相容性（Inc）组，包括 ColpVC、IncN3、IncP1 和 IncF [F113:A8:B20]，其中 IncF113 是一个新的等位基因。该分离株属于 ST189（CC165），血清型 O80:H26-fimH54，具有一些毒力基因（lpfA、iss 和 gad）。
这是从土壤中分离出的 O80:H26-fimH54 血清型 ST189 大肠杆菌的首个基因组草图序列。该基因组草图序列可用于比较来自不同来源的抗药性大肠杆菌分离株。
