Wolde Deneke, Eguale Tadesse, Medhin Girmay, Haile Aklilu Feleke, Alemayehu Haile, Mihret Adane, Pirs Mateja, Strašek Smrdel Katja, Avberšek Jana, Kušar Darja, Cerar Kišek Tjaša, Janko Tea, Steyer Andrej, Starčič Erjavec Marjanca
Department of Medical Laboratory Science, College of Medicine and Health Sciences, Wachemo University, Hossana P.O. Box 667, Ethiopia.
Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia.
Antibiotics (Basel). 2024 Sep 5;13(9):851. doi: 10.3390/antibiotics13090851.
The global spread of antimicrobial resistance genes (ARGs) in is a major public health concern. The aim of this study was to investigate the genomic characteristics of extended-spectrum β-lactamase (ESBL)-producing and third-generation cephalosporin-resistant from a previously obtained collection of 260 isolates from fecal samples of patients attending primary healthcare facilities in Addis Ababa and Hossana, Ethiopia. A total of 29 isolates (19 phenotypically confirmed ESBL-producing and 10 third-generation cephalosporin-resistant isolates) were used. Whole-genome sequencing (NextSeq 2000 system, Illumina) and bioinformatic analysis (using online available tools) were performed to identify ARGs, virulence-associated genes (VAGs), mobile genetic elements (MGEs), serotypes, sequence types (STs), phylogeny and conjugative elements harbored by these isolates. A total of 7 phylogenetic groups, 22 STs, including ST131, and 23 serotypes with different VAGs were identified. A total of 31 different acquired ARGs and 10 chromosomal mutations in quinolone resistance-determining regions (QRDRs) were detected. The isolates harbored diverse types of MGEs, with plasmids being the most prevalent (66.7%). Genetic determinants associated with conjugative transfer were identified in 75.9% of the isolates studied. In conclusion, the isolates exhibited considerable genetic diversity and showed a high potential for transferability of ARGs and VAGs. Bioinformatic analyses also revealed that the isolates exhibited substantial genetic diversity in phylogenetic groups, sequence types (ST) and serogroups and were harboring a variety of virulence-associated genes (VAGs). Thus, the studied isolates have a high potential for transferability of ARGs and VAGs.
抗菌耐药基因（ARGs）在全球范围内的传播是一个重大的公共卫生问题。本研究的目的是从先前收集的260株分离株中，调查产超广谱β-内酰胺酶（ESBL）和耐第三代头孢菌素的大肠杆菌的基因组特征，这些分离株来自埃塞俄比亚亚的斯亚贝巴和霍桑纳初级医疗保健机构患者的粪便样本。总共使用了29株分离株（19株经表型确认产ESBL和10株耐第三代头孢菌素的分离株）。进行了全基因组测序（Illumina NextSeq 2000系统）和生物信息学分析（使用在线可用工具），以鉴定这些分离株携带的ARGs、毒力相关基因（VAGs）、移动遗传元件（MGEs）、血清型、序列类型（STs）、系统发育和接合元件。共鉴定出7个系统发育组、22种STs，包括ST131，以及具有不同VAGs的23种血清型。共检测到31种不同的获得性ARGs和喹诺酮耐药决定区（QRDRs）中的10个染色体突变。这些分离株携带多种类型的MGEs，其中质粒最为普遍（66.7%）。在所研究的75.9%的分离株中鉴定出与接合转移相关的遗传决定因素。总之，这些分离株表现出相当大的遗传多样性，并显示出ARGs和VAGs具有很高的转移潜力。生物信息学分析还表明，这些分离株在系统发育组、序列类型（ST）和血清群中表现出显著的遗传多样性，并携带多种毒力相关基因（VAGs）。因此，所研究的分离株具有很高的ARGs和VAGs转移潜力。
