Assessment of antimicrobial resistance genes in Caribbean corals, including those treated with amoxicillin

The decimation of reefs caused by stony coral tissue loss disease prompted the use of a topical amoxicillin treatment to prevent coral mortality. Application of this treatment led to concerns about unintentional impacts such as potential alteration of the coral microbiome and possible spread of antibiotic resistance. We used two different methodologies - microbial RNA sequencing and microbial qPCR array - to assess these concerns and to establish a baseline of antimicrobial resistance genes in coral microbes. RNA sequencing was conducted on coral mucus samples collected before and 24 hours after amoxicillin application on wild Montastraea cavernosa. While diverse antibiotic resistance genes (ARGs) were expressed, no differences were detected in ARG expression after amoxicillin treatment. Additionally, there were no notable changes in the microbial communities between the before and after samples. Microbial qPCR array was used to assess differences in ARGs over longer timescales in wild Colpophyllia natans, comparing never-treated corals with ones treated a single time seven months prior and with those treated multiple times seven months and more prior. No clinically relevant ARGs represented in the arrays were detected across any samples. A small number of above-detection reads (4 in the never-treated corals, 2 in the once-treated corals, and 0 in the multi-treated corals) may indicate weak amplification of similar environmental (non-anthropogenic) ARGs in the corals. Results indicate that the localized topical application of amoxicillin to prevent mortality of SCTLD-affected corals is neither immediately disrupting the microbiome of treated corals at the colony level nor driving the development of ARGs over immediate or longer-term time scales.