ddPCR applied on archived Continuous Plankton Recorder samples reveals long‐term occurrence of class 1 integrons and a sulphonamide resistance gene in marine plankton communities

<jats:title>Summary</jats:title><jats:p>Antibiotic resistance is a rising threat for human health. Although in clinical settings and terrestrial environments the rise of antibiotic resistant bacteria is well documented, their dissemination and spread in the marine environment, covering almost two‐thirds of the Earth's surface, is still poorly understood. In this study, the presence and abundance of sulphonamide resistance gene (<jats:italic>sul</jats:italic>2) and class 1 integron‐integrase gene (<jats:italic>intI</jats:italic>1), used as markers for the occurrence and spread of antibiotic resistance genes since the beginning of the antibiotic era, were investigated. Twenty‐nine archived formalin‐fixed samples, collected by the Continuous Plankton Recorder (CPR) survey in the Atlantic Ocean and North Sea from 1970 to 2011, were analysed using Droplet Digital PCR (ddPCR) applied for the first time on CPR samples. The two marker genes were present in a large fraction of the samples (48% for <jats:italic>sul</jats:italic>2 and 76% for <jats:italic>intI</jats:italic>1). In contrast, results from Real‐Time PCR performed on the same samples greatly underestimate their occurrence (21% for <jats:italic>sul</jats:italic>2 and 52% for <jats:italic>intI</jats:italic>1). Overall, besides providing successful use of ddPCR for the molecular analysis of CPR samples, this study reveals long‐term occurrence and spread of <jats:italic>sul</jats:italic>2 gene and class 1 integrons in the plankton‐associated bacterial communities in the ocean.</jats:p>