The effects of environmental metals on the spread of antimicrobial resistance genes in the stickleback skin microbiome

抗生素耐药性（AMR）是对人类、动物和环境的主要威胁。虽然这通常与人类和牲畜为主的环境中滥用和过度使用抗生素有关，但对其更广泛的环境发生情况知之甚少。新出现的证据表明，AMR基因（ARG）经常在微生物中发现，如宿主相关和环境微生物组的成员。这构成了一个重大风险，因为耐药微生物可能成为耐药基因的储存库，这些耐药基因可以水平转移到病原体或在未来引起机会性感染。为了有效应对抗菌素耐药性，我们需要了解环境变化（例如，pH和温度）促进ARG在细菌之间的传播（即，水平基因转移（HGT）。已经表明，对金属（例如，铜、锌、铅等）和AMR通常在细菌基因组中共同选择，并与环境金属水平直接相关（CITIC等人，2017 Adv Micro Physio）。三棘鱼是一种研究充分的模式生物，原产于北方沃茨淡水。虽然各种环境因素与肠道微生物组的组成相关（Rennison et al. 2019 Proc皇家学会B），但皮肤微生物组仍未得到充分探索。鱼的皮肤是与环境直接接触的粘膜，是预防感染的重要机制，并且是微生物组研究的理想选择（Reverter等人，该项目调查了苏格兰北尤伊斯特岛金属浓度的环境变化是否导致棘鱼皮肤微生物中ARG的存在，丰度和传播（通过HGT）增加。为实现项目目标，我们将：a.对棘鱼种群的皮肤微生物组（和周围的水进行测序，以确定背景细菌污染（Krotman et al. 2020 Microbiome）），并解释基因型/环境差异b。培养微生物组并分析AMR细菌。此外，在诺丁汉水族馆，殖民gnotobiotic（即，将对来自低金属和高金属环境的皮肤微生物组（无菌）鱼类进行研究，并对皮肤微生物组进行纵向采样，以确定新的HGT事件。该研究将为环境变化如何为ARG转移提供有利条件提供有价值的见解，并提供对抗抗生素耐药性的有效策略。

Antimicrobial resistance (AMR) is a major threat to humans, animals, and our environment. Although this is often associated with the misuse and overuse of antibiotics in human and livestock-dominated environments, its wider environmental occurrence is poorly understood. Emerging evidence suggests that AMR genes (ARGs) are frequently identified in commensal organisms, such as members of host-associated and environmental microbiomes. This poses a major risk as commensal-resistant organisms might serve as a reservoir of resistance genes that can be horizontally transferred to pathogens or cause opportunistic infections in the future. To effectively combat AMR, we need to understand how environmental variation (e.g., pH and temperature) encourages the spread of ARGs between bacteria (i.e., horizontal gene transfer (HGT). It has been shown that resistance to metals (e.g., copper, zinc, lead, etc.) and AMR are often co-selected in bacterial genomes and directly correlate with environmental metal levels (Pal C et al. 2017 Adv Micro Physio). The three-spined stickleback is a well-studied model organism native to fresh and oceanic northern waters. While a variety of environmental factors have been associated with the composition of their gut microbiome (Rennison et al. 2019 Proc Royal Soc B), the skin microbiome remains under-explored. The skin of fish, a mucus membrane in direct contact with the environment, is an important mechanism in infection prevention and ideal for microbiome study (Reverter et al., 2018 Fish Sahul).This project investigates whether environmental variation in metal concentrations on the island of North Uist, Scotland, leads to increased presence, abundance, and spread (via HGT) of ARGs in stickleback skin microbiomes. To address the objective of the project, we will:a. Sequence the skin microbiome (and the surrounding water to determine background bacterial contamination (Krotman et al. 2020 Microbiome)) of stickleback populations, and account for genotype/environmental differencesb. Culture the microbiome and profile AMR bacteriac. Also, in the Nottingham aquariums, colonize gnotobiotic (i.e., germ-free) fish with a skin microbiome from low- vs. high-metal environments will be studied, and longitudinally sample the skin microbiome to identify new HGT events.The study will provide valuable insight into how environmental variations can provide favourable conditions for the transfer of ARGs and offer effective strategies to combat antibiotic resistance.