Turumtay Halbay
Department of Energy System Engineering, Karadeniz Technical University, Trabzon, Turkey.
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, USA.
Adv Clin Exp Med. 2023 Jan;32(1):91-96. doi: 10.17219/acem/152704.
Urinary tract infections (UTIs) are one of the most common infectious diseases. Inappropriate and excessive administration of antibiotics has led to the increased antibiotic resistance in the pathogens that cause UTIs. This work focused on identifying genetic determinants of antibiotic resistance in a clinical isolate of UTI-causing Escherichia coli.
A clinical isolate of E. coli resistant to β-lactam, tetracycline and aminoglycoside antibiotics was analyzed using whole-genome sequencing (WGS) to identify genes that contribute to its resistance.
The clinical isolate was obtained from a urine sample of a UTI patient in Turkey and identified via 16S rDNA sequencing. Antimicrobial susceptibility test was performed for 17 antibiotics using VITEK® 2 and the results were confirmed using minimum inhibitory concentration assay. Whole-genome sequencing of the isolate was performed using Illumina sequencing and analyzed with bioinformatic tools for multilocus sequence typing, replicon types, virulence factors, and antimicrobial resistance genes.
Whole-genome datum was submitted to the National Center for Biotechnology Information (NCBI; accession No. JAKSGM000000000). The isolate was only found to be resistant to piperacillin in the β-lactam class of antibiotics. While the isolate was also resistant to aminoglycoside and tetracycline antibiotics, it was sensitive to other antibiotics tested. Ten antibiotic resistance genes were identified in the genome of the isolate: blaOXA-1, blaOXA-2, aac(6')-II, aac(6')-Ib-cr, tetB, catB3, qacE, sitABCD, mdfA, and sul-2. Clonal subtype (ST) and serotype of the isolate were identified as ST2141 and O107/H39, respectively. Plasmid replicon typing was used to identify 5 plasmid types in the genome of E. coli Rize-53 (Col(BS512), IncC, IncIA, IncFIB(AP1918), and IncFII(pRSB107)); however, none of the resistance genes were encoded on the plasmid.
Genetic determinants of resistance to tetracycline, β-lactam and aminoglycoside antibiotics were identified using WGS in a uropathogenic E. coli from ST2141 lineage and O107:H39 serotype, isolated in Turkey.
尿路感染（UTIs）是最常见的传染病之一。抗生素的不恰当和过度使用导致了引起UTIs的病原体中抗生素耐药性的增加。这项工作的重点是确定引起UTIs的大肠杆菌临床分离株中抗生素耐药性的遗传决定因素。
使用全基因组测序（WGS）分析一株对β-内酰胺类、四环素类和氨基糖苷类抗生素耐药的大肠杆菌临床分离株，以确定导致其耐药的基因。
该临床分离株取自土耳其一名UTI患者的尿液样本，并通过16S rDNA测序进行鉴定。使用VITEK® 2对17种抗生素进行药敏试验，并使用最低抑菌浓度测定法确认结果。使用Illumina测序对该分离株进行全基因组测序，并使用生物信息学工具对多位点序列分型、复制子类型、毒力因子和抗菌药物耐药基因进行分析。
全基因组数据已提交至美国国立生物技术信息中心（NCBI；登录号JAKSGM000000000）。该分离株仅对β-内酰胺类抗生素中的哌拉西林耐药。虽然该分离株也对氨基糖苷类和四环素类抗生素耐药，但对其他测试抗生素敏感。在该分离株的基因组中鉴定出10个抗生素耐药基因：blaOXA-1、blaOXA-2、aac(6')-II、aac(6')-Ib-cr、tetB、catB3、qacE、sitABCD、mdfA和sul-2。该分离株的克隆亚型（ST）和血清型分别鉴定为ST2141和O107/H39。使用质粒复制子分型法在大肠杆菌Rize-53的基因组中鉴定出5种质粒类型（Col(BS512)、IncC、IncIA、IncFIB(AP1918)和IncFII(pRSB107)）；然而，耐药基因均未在质粒上编码。
使用WGS在土耳其分离的一株来自ST2141谱系和O107:H39血清型的尿路致病性大肠杆菌中鉴定出了对四环素、β-内酰胺类和氨基糖苷类抗生素耐药的遗传决定因素。
