Antibiotic Resistance Mediated by Escherichia coli in Kuwait Marine Environment as Revealed through Genomic Analysis

Antibiotic-resistance gene elements (ARGEs) such as antibiotic-resistance genes (ARGs), integrons, and plasmids are key to the spread of antimicrobial resistance (AMR) in marine environments. Kuwait's marine area is vulnerable to sewage contaminants introduced by numerous storm outlets and indiscriminate waste disposal near recreational beaches. Therefore, it has become a significant public health issue and warrants immediate investigation. Coliforms, especially Gram-negative <i>Escherichia coli</i>, have been regarded as significant indicators of recent fecal pollution and carriers of ARGEs. In this study, we applied a genome-based approach to identify ARGs' prevalence in <i>E. coli</i> isolated from mollusks and coastal water samples collected in a previous study. In addition, we investigated the plasmids and <i>intl1</i> (class 1 integron) genes coupled with the ARGs, mediating their spread within the Kuwait marine area. Whole-genome sequencing (WGS) identified genes resistant to the drug classes of beta-lactams (<i>bla_CMY-150</i>, <i>bla_CMY-42</i>, <i>bla_CTX-M-15</i>, <i>bla_DHA-1</i>, <i>bla_MIR-1</i>, <i>bla_OKP-B-15</i>, <i>bla_OXA-1</i>, <i>bla_OXA-48</i>, <i>bla_TEM-1B</i>, <i>bla_TEM-35</i>), trimethoprim (<i>dfrA14</i>, <i>dfrA15</i>, <i>dfrA16</i>, <i>dfrA1</i>, <i>dfrA5</i>, <i>dfrA7</i>), fluroquinolone (<i>oqxA</i>, <i>oqxB</i>, <i>qnrB38</i>, <i>qnrB4</i>, <i>qnrS1</i>), aminoglycoside (<i>aadA2</i>, <i>ant(3'')-Ia</i>, <i>aph(3'')-Ib</i>, <i>aph(3')-Ia</i>, <i>aph(6)-Id</i>), fosfomycin (<i>fosA7</i>, <i>fosA_6</i>, <i>fosA</i>, <i>fosB1</i>), sulfonamide (<i>sul1</i>, <i>sul2</i>, <i>sul3</i>), tetracycline (<i>tet-A</i>, <i>tet-B</i>), and macrolide (<i>mph-A</i>). The MFS-type drug efflux gene <i>mdf-A</i> is also quite common in <i>E. coli</i> isolates (80%). The plasmid <i>ColRNAI</i> was also found to be prevalent in <i>E. coli.</i> The integron gene <i>intI1</i> and gene cassettes (GC) were reported to be in 36% and 33%, respectively, of total <i>E. coli</i> isolates. A positive and significant (<i>p</i> < 0.001) correlation was observed between phenotypic AMR-<i>intl1</i> (r = 0.311) and phenotypic AMR-GC (r = 0.188). These findings are useful for the surveillance of horizontal gene transfer of AMR in the marine environments of Kuwait.