Abstract：
In response to the rapid emergence and dissemination of antimicrobial resistant bacteria (ARB) and genes (ARGs), integrated surveillance systems are needed to address antimicrobial resistance (AMR) within the One Health Era. Wastewater analyses enable biomarker monitoring at the sewershed level, offering timely insights into pathogen circulation and ARB/ARGs trends originating from different compartments. During two consecutive epidemic waves of the COVID-19 pandemic in Portugal, taxonomic and functional composition of raw urban wastewater from two wastewater treatment plants (WWTPs) representing one million in equivalent population, located in the main urban areas of the country, were profiled by shotgun metagenomics. Hospital wastewater from two central hospitals located in the WWTPs catchment areas were also sequenced. The resistome and virulome were profiled using metagenomic assemblies without taxonomic constraint, and then specifically characterized for ESKAPE pathogens. Urban and hospital wastewater exhibited specific microbiota signatures, Pseudomonadota dominated in the first and Bacteroidota in the latter. Correlation network analyses highlighted 85 (out of top 100) genera co-occurring across samples. The most frequent ARGs were classified in the multidrug, tetracyclines, and Macrolides, Lincosamides, Streptogramins (MLS) classes. Links established between AMR determinants and bacterial hosts evidenced that the diversity and abundance of ARGs is not restricted to ESKAPE, being also highly predominant among emergent enteropathogens, like Aeromonas and Aliarcobacter, or in the iron (II) oxidizer Acidovorax. The Aliarcobacter genus accumulated high abundance of sulphonamides and polymyxins ARGs, while Acinetobacter and Aeromonas hosted the highest abundance of ARGs against beta-lactams. Other bacteria (e.g. Clostridioides, Francisella, Vibrio cholerae) and genes (e.g. vanA-type vancomycin resistance) of public health interest were detected, with targeted monitoring efforts being needed to establish informative baseline data. Altogether, results highlight that wastewater monitoring is a valuable component of pathogen and AMR surveillance in healthy populations, providing a community-representative snapshot of public health trends beyond priority pathogens.
摘要：
为了应对快速出现和传播的抗菌耐药菌（ARB）和基因（ARGs），在“一个健康”时代，需要综合监测系统来解决抗菌素耐药性(AMR)问题。废水分析使生物标志物能够在污水处理厂进行监测，及时了解来自不同区室的病原体循环和ARB/ARGs趋势。在葡萄牙连续两次COVID-19大流行期间，来自两个污水处理厂（WWTP）的原始城市废水的分类学和功能组成，代表100万同等人口，位于该国主要城市地区，被猎枪宏基因组学分析。还对位于污水处理厂集水区的两家中心医院的医院废水进行了测序。在没有分类学限制的情况下，使用宏基因组组装对抗性组和病毒组进行了分析，然后专门表征ESKAPE病原体。城市和医院废水表现出特定的微生物群特征，假单胞菌在第一个中占主导地位，而在第二个中占主导地位。相关网络分析突出显示了样本中共同出现的85个(前100个)属。最常见的ARGs被归类为多种药物，四环素,和大环内酯类，Lincosamides,链球菌素（MLS）类。AMR决定簇和细菌宿主之间建立的联系表明，ARGs的多样性和丰度不仅限于ESKAPE，在紧急肠病原体中也高度占优势，比如气单胞菌和Aliarcobacter,或在铁（II）氧化剂Acidovorax中。Aliarcobacter属积累了大量的磺酰胺和多粘菌素ARGs，不动杆菌和气单胞菌对β-内酰胺的ARGs含量最高。其他细菌（如梭菌，Francisella,检测到具有公共卫生意义的霍乱弧菌）和基因（例如vanA型万古霉素抗性），需要进行有针对性的监测工作，以建立翔实的基线数据。总之,结果强调，废水监测是健康人群中病原体和AMR监测的重要组成部分，提供具有社区代表性的超越优先病原体的公共卫生趋势快照。
