Chekole Wagaw Sendeku, Potgieter Lizel, Adamu Haileeyesus, Sternberg-Lewerin Susanna, Tessema Tesfaye Sisay, Magnusson Ulf
Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia.
Front Microbiol. 2025 Jun 10;16:1597580. doi: 10.3389/fmicb.2025.1597580. eCollection 2025.
Antimicrobial resistance is a global threat causing millions of deaths annually. The study aimed to identify antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence genes (VGs) and track their dissemination among isolates. Seventy-seven isolates from calves, environments, and human sources were studied. The study involved WGS sequencing, bacterial strains characterized; pan genome, multi-locus sequence typing, and serotyping using O-, and H-typing. The ARGs, VGs, and MGEs were identified using ABRicate against selected respective databases. A maximum likelihood SNP (single nucleotide polymorphism) tree was constructed and visualized with an interactive tree of life (IToL). Descriptive statistics were used to analyze the data. Seventy-seven of the isolates were identified as , later grouped into 5 clades and four known phylogroups. ST10 and O16:H48 were most prevalent in 12 and 42 isolates, respectively. There were about 106 unique ARGs detected between 1.3% and 91.9%, with 57 detected in 40% of isolates. In terms of ARGs, the most common were (90.9%), (89.6%), (84.4%), (81.8%), (79%), (79%), (75%), and (70%). It was found that 95 percent (96/106) of ARGs came from at least two sources. The majority of detected ARGs exhibited high concordance between phenotypic resistance and ARGs profiles (JSI ≥ 0.5). In eight isolates, mutations in the and genes led to ciprofloxacin and nalidixic acid resistance. The most common co-occurrences of ARG and MGE were with (34), with (13), and (11). Meanwhile, the most frequently detected VGs ( ≥ 71 isolates) included , and . Nearly, 88.3% (128/1450) VGs were shared in isolates from at least two sources. ETEC (53.2%), EAEC (22.1%), and STEC (14.3%) were the three most frequently predicted pathotypes. Despite significant ST diversity, ARGs and VGs showed an extensive distribution among the study groups. These findings suggest limited clonal transmission of isolates. In comparison, the wide distribution of ARGs and VGs may be attributed to horizontal gene transfer driven by similar antibiotic selection pressures in the study area.
抗菌药物耐药性是一种全球威胁，每年导致数百万人死亡。该研究旨在鉴定抗生素耐药基因（ARGs）、可移动遗传元件（MGEs）和毒力基因（VGs），并追踪它们在分离株中的传播情况。对来自小牛、环境和人类来源的77株分离株进行了研究。该研究涉及全基因组测序（WGS），对细菌菌株进行特征鉴定；使用O抗原和H抗原分型进行泛基因组、多位点序列分型和血清分型。使用ABRicate针对选定的相应数据库鉴定ARGs、VGs和MGEs。构建了最大似然单核苷酸多态性（SNP）树，并使用交互式生命树（IToL）进行可视化。使用描述性统计分析数据。77株分离株被鉴定为[具体细菌名称未给出]，随后分为5个进化枝和4个已知系统发育群。ST10和O16:H48分别在12株和42株分离株中最为常见。共检测到约106个独特的ARGs，占比在1.3%至91.9%之间，其中57个在40%的分离株中被检测到。就ARGs而言，最常见的是[具体基因名称未给出]（90.9%）、[具体基因名称未给出]（89.6%）、[具体基因名称未给出]（84.4%）、[具体基因名称未给出]（81.8%）、[具体基因名称未给出]（79%）、[具体基因名称未给出]（79%）、[具体基因名称未给出]（75%）和[具体基因名称未给出]（70%）。发现95%（96/106）的ARGs来自至少两个来源。大多数检测到的ARGs在表型耐药性和ARGs谱之间表现出高度一致性（JSI≥0.5）。在8株分离株中，[具体基因名称未给出]和[具体基因名称未给出]基因的突变导致对环丙沙星和萘啶酸耐药。ARGs和MGE最常见的共现情况是[具体基因组合未给出]与[具体基因组合未给出]（34次）、[具体基因组合未给出]与[具体基因组合未给出]（13次）以及[具体基因组合未给出]（11次）。同时，最常检测到的VGs（≥71株分离株）包括[具体基因名称未给出]、[具体基因名称未给出]和[具体基因名称未给出]。近88.3%（128/1450）的VGs在来自至少两个来源的分离株中共享。肠毒素性大肠杆菌（ETEC，53.2%）、肠集聚性大肠杆菌（EAEC，22.1%）和肠出血性大肠杆菌（STEC，14.3%）是三种最常预测的致病型。尽管ST多样性显著，但ARGs和VGs在研究组中广泛分布。这些发现表明分离株的克隆传播有限。相比之下，ARGs和VGs的广泛分布可能归因于研究区域内相似抗生素选择压力驱动的水平基因转移。
