Identification of Antimicrobial Resistance in Faecal Microbes from Wild Dugongs (Dugong dugon)

Estuarine and coastal waters are areas of potential concern for antimicrobial resistance because of the discharge of wastewater from sewage treatment plants and the run-off from urban and agricultural lands. Herein, we evaluate the antimicrobial resistance profiles in bacteria from dugongs (Dugong dugon), mammals that inhabit and feed in shallow coastal regions and, thus, are vulnerable to encountering water and sediment contaminated by human activities. Bacterial isolates were cultured from fresh faeces of four wild dugongs, as well as from one sediment sample from a dugong foraging ground in Queensland, Australia. Ten bacterial isolates underwent phenotypic antimicrobial susceptibility testing using disc diffusion and minimum inhibitory concentration testing, and genotypic resistance and virulence gene identification through whole genome sequencing. Four Staphylococcus warneri isolates and one Bacillus cereus isolate from dugong faeces were resistant to penicillin, with two S. warneri isolates also displaying resistance to trimethoprim. Four Escherichia coli isolates were all resistant to ampicillin. Resistance genes, including fosB, BcII, dfrC, blaZ, and mdfA, were identified in the isolates cultured from dugong faeces with two virulence genes (gad and lpfA) identified in all E. coli isolates. Lysinibacillus sphaericus cultured from the marine sediment and B. cereus from dugong faeces displayed phenotypic multidrug resistance (across categories of non-extended spectrum cephalosporins, penicillins and beta-lactamase inhibitors, and clindamycin; and for L. sphaericus, phosphonic acids). These results demonstrate the role that dugongs can play as a sentinel species for antimicrobial resistance in the coastal waters across their range, which includes both disturbed urban and rural regions.