Abdalla Shima E, Bester Linda A, Abia Akebe L K, Allam Mushal, Ismail Arshad, Essack Sabiha Y, Amoako Daniel G
Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
Antibiotics (Basel). 2025 Apr 28;14(5):446. doi: 10.3390/antibiotics14050446.
: Intensive pig farming is a critical component of food security and economic activity in South Africa; however, it also presents a risk of amplifying antimicrobial resistance (AMR). This study provides genomic insights into antibiotic-resistant () circulating across the pork production chain, using a 'farm-to-fork' approach. : A total of 417 samples were collected from various points along the production continuum, including the farm (n = 144), transport (n = 60), and abattoir (n = 213). isolates were identified using the Colilert-18 system, and their phenotypic resistance was tested against 20 antibiotics. Thirty-one isolates were selected for further characterization based on their resistance profiles and sampling sources, utilizing whole-genome sequencing and bioinformatic analysis. : The isolates exhibited varying resistance to critical antibiotics used in both human and animal health, including ampicillin (31/31, 100%), tetracycline (31/31, 100%), amoxicillin-clavulanate (29/31, 94%), chloramphenicol (25/31, 81%), and sulfamethoxazole-trimethoprim (10/31, 33%). Genetic analysis revealed the presence of resistance genes for β-lactams (, ), trimethoprim/sulfonamides (, , , , ), tetracyclines (, , , ), aminoglycosides (, , variants), and phenicols (, , ), most of which were plasmid-borne. Virulome analysis identified 24 genes, including toxins and adhesion factors. Mobile genetic elements included 24 plasmid replicons, 43 prophages, 19 insertion sequence families, and 7 class 1 integrons. The isolates belonged to a diverse range of sequence types, demonstrating significant genetic variability. Further phylogenomic analysis revealed eight major clades, with isolate clustering by sequence type alongside South African environmental and clinical strains, regardless of their sampling source. : The genetic complexity observed across the pork production continuum threatens food safety and may impact human health. These findings underscore the need for enhanced AMR monitoring in livestock systems and support the integration of AMR surveillance into food safety policy frameworks.
集约化养猪是南非粮食安全和经济活动的重要组成部分；然而，它也存在加剧抗菌药物耐药性（AMR）的风险。本研究采用“从农场到餐桌”的方法，对猪肉生产链中传播的抗生素耐药性大肠杆菌进行了基因组学分析。总共从生产连续过程中的各个点收集了417份样本，包括农场（n = 144）、运输环节（n = 60）和屠宰场（n = 213）。使用Colilert - 18系统鉴定大肠杆菌分离株，并测试它们对20种抗生素的表型耐药性。根据其耐药谱和采样来源，选择了31株分离株进行进一步表征，采用全基因组测序和生物信息学分析。这些分离株对人和动物健康中使用的关键抗生素表现出不同程度的耐药性，包括氨苄西林（31/31，100%）、四环素（31/31，100%）、阿莫西林 - 克拉维酸（29/31，94%）、氯霉素（25/31，81%）和磺胺甲恶唑 - 甲氧苄啶（10/31，33%）。遗传分析揭示了β - 内酰胺类（blaTEM、blaSHV）、甲氧苄啶/磺胺类（dfrA1、dfrA5、dfrA12、sul1、sul2）、四环素类（tetA、tetB、tetC）、氨基糖苷类（aadA1、aadA2变体）和酚类（catA1、catB1、cmlA）耐药基因的存在，其中大部分是质粒携带的。病毒基因组分析鉴定出24个基因，包括毒素和黏附因子。移动遗传元件包括24个质粒复制子、43个原噬菌体、19个插入序列家族和7个1类整合子。这些大肠杆菌分离株属于多种序列类型，显示出显著的遗传变异性。进一步的系统发育基因组学分析揭示了八个主要分支，分离株按序列类型聚类，与南非环境和临床大肠杆菌菌株一起，无论其采样来源如何。在猪肉生产连续过程中观察到的遗传复杂性威胁食品安全，并可能影响人类健康。这些发现强调了加强牲畜系统中AMR监测的必要性，并支持将AMR监测纳入食品安全政策框架。
