Comprehensive surveillance approaches are needed to assess sources, clinical relevance, and mobility of antibiotic resistance genes (ARGs) in watersheds. Here, we examined metrics derived from shotgun metagenomic sequencing and relationship to human fecal markers (HFMs; crAssphage, enterococci) and anthropogenic antibiotic resistance markers (AARMs; intI1, sul1) in three distinct Puerto Rican watersheds as a function of adjacent land use and wastewater treatment plant (WWTP) input 6 months after Hurricane Maria, a category V storm. Relative abundance and diversity of total ARGs increased markedly downstream of WWTP inputs, with ARGs unique to WWTP and WWTP-impacted river samples predominantly belonging to the aminoglycoside and β-lactam resistance classes. WWTP and other anthropogenic inputs were similarly associated with elevated resistome risk scores and mobility incidence (M%). Contig analysis indicated a wide variety of mobile β-lactam ARGs associated with pathogens downstream of WWTP discharge that were consistent with regional clinical concern, e.g., Klebsiella pneumoniae contigs containing KPC-2 within an ISKpn6-like transposase. HFMs and AARMs correlated strongly with the absolute abundance of total ARGs, but AARMs better predicted the majority of ARGs in general (85.4 versus <2%) and β-lactam ARGs in particular. This study reveals sensitive, quantitative, mobile, clinically relevant, and comprehensive targets for antibiotic resistance surveillance in watersheds.

中文翻译：

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在飓风玛丽亚后的波多黎各流域展示综合的抗生素抗性基因监测方法

需要综合的监测方法来评估流域中抗生素抗性基因（ARG）的来源，临床相关性和迁移性。在这里，我们研究了从散弹枪宏基因组测序及其与人粪便标记物（HFM； crAssphage，肠球菌）和人为抗生素耐药性标记物（AARM；int I1，sul）之间的关系得出的指标。1）在飓风“玛丽亚”（V类）袭击六个月后，根据波多黎各的三个分水岭，作为相邻土地利用和废水处理厂（WWTP）的输入。在WWTP输入的下游，总ARG的相对丰度和多样性显着增加，其中WWTP和WWTP影响的河流样本特有的ARG主要属于氨基糖苷和β-内酰胺抗性类别。污水处理厂和其他人为因素也与抵抗组风险评分和活动性发生率升高（M％）相似。Contig分析表明，与WWTP排放下游病原体相关的各种各样的移动性β-内酰胺ARGs与区域临床关注相一致，例如，ISKpn中包含KPC-2的肺炎克雷伯菌重叠群6样转座酶。HFM和AARM与总ARG的绝对丰度密切相关，但AARM更好地预测了一般的大多数ARG（分别为85.4和<2％），尤其是β-内酰胺ARG。这项研究揭示了流域抗生素耐药性监测的敏感，定量，可移动，临床相关和全面的目标。