Johnson Lisa A, Smith Derek D N, Subasinghe Renuka M, Raap Monique R, Richter Robin, Huyben David, Lau Calvin H F, Brown Liam, Chu Jackson W F, Khomenko Olena P, Manning Anthony J, Johnson Stewart C, Hamoutene Dounia
Fisheries and Oceans Canada, 125 Marine Science Dr, St. Andrews, NB E5B 0E4, Canada.
Environment and Climate Change Canada, 335 River Road, Ottawa, ON K1V 1C7, Canada.
Can J Microbiol. 2025 Jan 1;71:1-18. doi: 10.1139/cjm-2024-0206.
Surveillance methods for antimicrobial resistance genes (ARGs) are needed to assess potential risk of antimicrobial resistance, especially in complex environmental samples with limited data on ARG distribution. This study employed target-enrichment metagenomics (bait-capture) and a Resistomap qPCR assay to assess the resistome in marine and freshwater sediments associated with active Canadian finfish aquaculture operations. Differences in resistome profiles were considered with distance to the net-pens, concentrations of three aquaculture-associated chemical residues, and microbial communities as detected with 16S rRNA gene amplicon sequencing. With bait-capture, a total of 194 ARGs and 41 replicon types were detected across the sediment samples. Differences due to aquaculture proximity were noted in the composition of the resistome, which was dominated by tetracycline resistance genes. With qPCR, 37 out of 51 ARGs targets were detected, and proximity to net-pens or region did not show changes in resistome composition. Co-occurrence networks revealed significant correlations among genera and the resistome detected with bait-capture, highlighting a potential influence of aquaculture on ARGs in the environment. This study demonstrates the utility of bait-capture and qPCR assays in detection of ARGs in both freshwater and marine sediments from aquaculture sites that will assist further ARG surveillance.
需要对抗菌素耐药基因（ARGs）的监测方法进行评估，以评估抗菌素耐药性的潜在风险，尤其是在ARG分布数据有限的复杂环境样本中。本研究采用靶向富集宏基因组学（诱饵捕获）和Resistomap qPCR检测法，评估与加拿大活跃的有鳍鱼类水产养殖作业相关的海洋和淡水沉积物中的耐药基因组。考虑了与网箱的距离、三种与水产养殖相关的化学残留物的浓度以及通过16S rRNA基因扩增子测序检测到的微生物群落，分析了耐药基因组图谱的差异。通过诱饵捕获，在沉积物样本中总共检测到194个ARGs和41种复制子类型。在耐药基因组组成方面发现了因靠近水产养殖而产生的差异，其中四环素耐药基因占主导。通过qPCR，检测到了51个ARGs靶点中的37个，靠近网箱或区域并未显示出耐药基因组组成的变化。共现网络揭示了属与通过诱饵捕获检测到的耐药基因组之间的显著相关性，突出了水产养殖对环境中ARGs的潜在影响。本研究证明了诱饵捕获和qPCR检测法在检测水产养殖场地淡水和海洋沉积物中ARGs方面的实用性，这将有助于进一步的ARG监测。
