Viviers Sheldon, Richter-Mouton Loandi, Featherston Jonathan, Korsten Lise
Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0028, South Africa; Department of Science and Innovation-National Research Foundation Centre of Excellence Food Security, Pretoria 0001, South Africa.
Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0028, South Africa; Department of Science and Innovation-National Research Foundation Centre of Excellence Food Security, Pretoria 0001, South Africa.
J Food Prot. 2025 Jun 23;88(7):100543. doi: 10.1016/j.jfp.2025.100543. Epub 2025 May 16.
Antimicrobial resistance (AMR) ranks among the top ten global public health threats, with extended-spectrum β-lactamase (ESBL)-producing Enterobacterales and Pseudomonas aeruginosa emerging as multidrug-resistant (MDR) priority pathogens. This study aimed to evaluate the presence and characteristics (phenotypic and genotypic AMR profiles) of ESBL/AmpC-producing Enterobacterales and P. aeruginosa isolates obtained from the water-soil-plant nexus on smallholder fresh produce farms in South Africa. Samples of irrigation water (n = 44), soil (n = 85), and fresh produce (n = 95) were collected from six smallholder farms. Potential MDR bacteria were isolated using selective enrichment, chromogenic media, and identified with MALDI-TOF MS. Antimicrobial resistance was assessed via double-disk diffusion against 13 different antibiotic classes, while 20 selected isolates were genotypically characterized using whole-genome sequencing (WGS) (Illumina MiSeq). ESBL/AmpC-producing isolates were detected in 17% of samples (38/224), primarily from fresh produce (54%), followed by soil (31%) and water (15%). The dominant Enterobacterales species identified from all three matrices included Enterobacter spp. (26%), Klebsiella spp. (26%), Serratia spp. (17%), and Escherichia coli (9%). Phenotypically, 47% and 43% of the isolates were classified as ESBL and AmpC-producers, respectively, with resistance to beta-lactams, aminoglycosides, and glycylcyclines. Notably, WGS analysis indicated the presence of clinically significant AMR and virulence genes among isolates from the environment, particularly those associated with mobile genetic elements. The results from the study add to the limited national and international knowledge of AMR prevalence in the smallholder agricultural landscape, needed for the introduction of appropriate intervention strategies and future risk assessment of the informal supply chain.
抗菌药物耐药性（AMR）位列全球十大公共卫生威胁之中，产超广谱β-内酰胺酶（ESBL）的肠杆菌科细菌和铜绿假单胞菌成为多重耐药（MDR）重点病原体。本研究旨在评估从南非小农户新鲜农产品农场的水-土壤-植物关联系统中分离出的产ESBL/AmpC肠杆菌科细菌和铜绿假单胞菌菌株的存在情况及特征（表型和基因型AMR谱）。从六个小农户农场采集了灌溉水样本（n = 44）、土壤样本（n = 85）和新鲜农产品样本（n = 95）。使用选择性富集、显色培养基分离潜在的MDR细菌，并通过基质辅助激光解吸电离飞行时间质谱（MALDI-TOF MS）进行鉴定。通过双碟扩散法针对13种不同抗生素类别评估抗菌药物耐药性，同时使用全基因组测序（WGS）（Illumina MiSeq）对20株选定菌株进行基因型特征分析。在17%的样本（38/224）中检测到产ESBL/AmpC的菌株，主要来自新鲜农产品（54%），其次是土壤（31%）和水（15%）。从所有三种基质中鉴定出的主要肠杆菌科细菌种类包括肠杆菌属（26%）、克雷伯菌属（26%）、沙雷菌属（17%）和大肠杆菌（9%）。表型上，分别有47%和43%的菌株被分类为ESBL生产者和AmpC生产者，对β-内酰胺类、氨基糖苷类和甘氨酰环素类耐药。值得注意的是，WGS分析表明环境分离株中存在具有临床意义的AMR和毒力基因，特别是那些与可移动遗传元件相关的基因。该研究结果增加了国内和国际上关于小农户农业环境中AMR流行情况的有限知识，这对于引入适当的干预策略和未来对非正式供应链的风险评估是必要的。
