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Traditionally, the concerns about cyanoHABs have mainly focused on cyanotoxins in water. CyanoHABs are also hypothesized to play a role in the antibiotic resistome, but whether cyanobacteria host clinically relevant antibiotic resistant genes (ARGs) in the environment is largely unknown. To investigate this emerging issue, we examined whether cyanobacteria host ARGs within the broader microbiome context. We looked for the presence of cyanobacteria-hosted ARGs using shotgun metagenomic sequencing of drinking water source samples collected during the bloom season (summer and fall) from Lake Erie and Grand Lake St. Marys (GLSM). ARGs were annotated using DeepARG and Resistance Gene Identifier (RGI). Cyanobacteria were annotated to host genes conferring putative antibiotic resistance, including efflux pumps\n                    <jats:italic>qac\/EmrE<\/jats:italic>\n                    ,\n                    <jats:italic>vatB<\/jats:italic>\n                    ,\n                    <jats:italic>van genes<\/jats:italic>\n                    , and an OXA homolog. A maximum likelihood tree with cyanobacteria and OXA reference sequences showed OXA-like homology across multiple families of cyanobacteria. Most cyanobacteria sequences clustered in a large clade with\n                    <jats:italic>ybxI<\/jats:italic>\n                    , suggesting very limited or negligible class-D beta-lactamase activity, but a small subset formed a clade with OXA-2 and OXA-46. While those hits suggest potential resistance to clinical antibiotics, overall cyanobacteria were not found to host ARGs conferring resistance to drugs of last resort in these samples. Additionally, BLAST searches of the cyanobacteria ARG contigs and coding sequences resulted in top hits for cyanobacteria, further supporting that annotated genes are likely intrinsic rather than acquired.\n                    <jats:italic>rpoB2<\/jats:italic>\n                    and\n                    <jats:italic>arlR<\/jats:italic>\n                    ARG annotations appear to be spurious hits on housekeeping genes, which demonstrates the need to verify automated ARG annotation tool results. Selected cyanotoxins, cyanobacteria, and ARGs were also chosen for quantification. We found high levels of\n                    <jats:italic>Microcystis<\/jats:italic>\n                    in Lake Erie as well as\n                    <jats:italic>Planktothrix<\/jats:italic>\n                    and microcystin concentrations in GLSM, supporting previous trends in these water bodies. This study takes a novel approach, pairing the issues of cyanoHABs and ARGs together in two drinking water sources. In a changing climate, drinking water treatment strategies should consider the treatment and public health implications of multiple contaminants.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Graphical Abstract<\/jats:bold>\n                  <\/jats:p>","DOI":"10.1007\/s11356-026-37644-9","type":"journal-article","created":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T05:29:27Z","timestamp":1774934967000},"page":"6140-6164","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Investigation of cyanobacteria-hosted antibiotic resistance genes in cyanoHAB-impacted drinking water sources"],"prefix":"10.1007","volume":"33","author":[{"given":"Abigail","family":"Volk","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Molly","family":"Mills","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Soryong","family":"Chae","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8936-1555","authenticated-orcid":false,"given":"Jiyoung","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,3,31]]},"reference":[{"issue":"10","key":"37644_CR1","doi-asserted-by":"publisher","DOI":"10.3390\/w12102756","volume":"12","author":"T Abbas","year":"2020","unstructured":"Abbas T, Kajjumba GW, Ejjada M, Masrura SU, Marti EJ, Khan E, Jones-Lepp TL (2020) Recent advancements in the removal of cyanotoxins from water using conventional and modified adsorbents\u2014a contemporary review. 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