Szoke Zsombor, Fauszt Peter, Mikolas Maja, David Peter, Szilagyi-Tolnai Emese, Pesti-Asboth Georgina, Homoki Judit Rita, Kovacs-Forgacs Ildiko, Gal Ferenc, Stundl Laszlo, Czegledi Levente, Stagel Aniko, Biro Sandor, Remenyik Judit, Paholcsek Melinda
Faculty of Agricultural and Food Sciences and Environmental Management, Complex Systems and Microbiome-innovations Centre, University of Debrecen, Debrecen, Hungary.
Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary.
Sci Rep. 2025 Feb 8;15(1):4673. doi: 10.1038/s41598-025-89432-z.
Antimicrobial resistance (AMR) is a global health challenge requiring cross-sector action, with research largely focused on chickens, leaving ducks underexplored. This study examines AMR dynamics in Ross 308 broilers and Cherry Valley ducks over 15 months and 15 stocking periods under consistent rearing conditions. A total of 96 pooled samples were collected: 50 from broiler farms (26 biological, 24 environmental) and 46 from duck farms (24 biological, 22 environmental). Using next-generation shotgun sequencing, 3,665 distinct AMR types were identified: 1,918 in broilers and 1,747 in ducks. Host-specific AMRs comprised 25.3% in broilers and 18% in ducks, while 56.7% were shared. AMR diversity declined across production phases, with broilers losing 641 types and ducks losing 308, yet AMR frequencies increased significantly by the finisher phase (p < 0.0001). Based on in silico data, prophylactic antibiotic use significantly reduced the prevalence of multidrug-resistant bacteria in both poultry species (p < 0.05). Hospital-acquired infection-associated AMRs were higher in broilers than in ducks at the start of production but declined significantly by the end of the rearing period (p < 0.0001). Above-average resistance markers accounted for approximately 10% of all detected resistance determinants. Tetracycline and phenicol resistances emerged as the most prevalent. 13 high-resistance carrier (HRC) species were shared between both hosts. Broiler-specific HRCs exhibited significantly higher abundances (relative frequency: 0.08) than duck-specific HRCs (relative frequency: 0.003, p = 0.035). The grower phase emerged as a critical intervention point. In farm environments 15 broiler-specific and 9 duck-specific biomarker species were identified, each strongly correlated with poultry-core HRCs (correlation coefficient > 0.7). Broiler exhibited higher abundances of key resistance genes, with tetracycline resistance predominantly associated with Bacteroides coprosuis, Pasteurella multocida, and Acinetobacter baumannii. Despite its limitations, this research provides key insights into AMR trends in two major poultry types, guiding targeted interventions and sustainable management strategies.
抗菌药物耐药性（AMR）是一项全球性的健康挑战，需要跨部门行动，目前的研究主要集中在鸡身上，而鸭的研究较少。本研究考察了在一致的饲养条件下，罗斯308肉鸡和樱桃谷鸭在15个月和15个饲养周期内的AMR动态。共收集了96份混合样本：50份来自肉鸡场（26份生物样本、24份环境样本），46份来自鸭场（24份生物样本、22份环境样本）。使用新一代鸟枪法测序，共鉴定出3665种不同的AMR类型：肉鸡中有1918种，鸭中有1747种。宿主特异性AMR在肉鸡中占25.3%，在鸭中占18%，而56.7%是共享的。在整个生产阶段，AMR多样性下降，肉鸡减少了641种，鸭减少了308种，但到育肥阶段AMR频率显著增加（p < 0.0001）。基于计算机模拟数据，预防性使用抗生素显著降低了两种家禽中多重耐药菌的流行率（p < 0.05）。在生产开始时，肉鸡中与医院获得性感染相关的AMR高于鸭，但在饲养期结束时显著下降（p < 0.0001）。高于平均水平的耐药标记约占所有检测到的耐药决定因素的10%。四环素和氯霉素耐药最为普遍。两种宿主共有13种高耐药携带者（HRC）物种。肉鸡特异性HRC的丰度（相对频率：0.08）显著高于鸭特异性HRC（相对频率：0.003，p = 0.035）。生长阶段是一个关键的干预点。在农场环境中，鉴定出15种肉鸡特异性和9种鸭特异性生物标志物物种，每种都与家禽核心HRC密切相关（相关系数 > 0.7）。肉鸡中关键耐药基因的丰度更高，四环素耐药主要与猪类杆菌、多杀巴斯德菌和鲍曼不动杆菌有关。尽管本研究存在局限性，但它为两种主要家禽类型的AMR趋势提供了关键见解，为有针对性的干预措施和可持续管理策略提供了指导。
