Pharmaceutical pollution is ubiquitous in aquatic environments, threatening microbial communities, the ecosystem processes they facilitate and exacerbating antimicrobial resistance (AMR). Pharmaceutical pollution arises from sources including waste water treatment plant (WWTP) effluent released into aquatic environments, usually resulting in ng L-1 concentrations. To date, the effects of pharmaceuticals on microorganisms has focused on understanding effects associated with minimum inhibitory concentrations (MICs). However, trace (sub-MIC) concentrations can build selective pressure or remove susceptible populations in aquatic environments. One response of interest is persistence, a dormancy phase during exposure to antibiotic pressure. Understanding non-lethal responses of microbiota to pharmaceutical pollution is vital for managing ecosystems to facilitate the resistance necessary for continuation of ecosystem processes and prevent maintenance and spread of clinically relevant AMR.
In this project, we aimed to investigate persistence as a response to ciprofloxacin (antibiotic) in aquatic microbiota. To achieve this we undertook a field based case study on microbial communities from the Hudson River (Kingston, New York, USA) which receives discharge from a nearby WWTP. The response of this microbial community to ciprofloxacin individually and in a mixture with eight additional pharmaceuticals (sub-MIC) was investigated through culture-based and metagenomics analysis with a particular focus on the identification of susceptible, resistant and persistent populations.
Microbial growth was observed to decrease in response to ciprofloxacin when combined in a mixture of nine pharmaceuticals. This alteration in pharmacodynamics has not been reported with microbial communities displaying susceptibility at concentrations two-fold below reported MIC (60 μg L-1 for ciprofloxacin). Persister cells were isolated within the aquatic environment in the presence of 5 ng L-1 of ciprofloxacin individually and 200 ng L-1 of ciprofloxacin in a mixture. These isolates were taxonomically identified as Aeronomas veronii. Isolate antimicrobial resistance genes (ARGs) were identified and compared to 150 A. veronii reference genomes. Our study highlights the diverse effects of pharmaceuticals on aquatic microbiota, being a concern for the development of AMR and human health.