Surveillance for Antibiotic-Resistant E. coli in the Salish Sea Ecosystem

The anthropogenic use of antibiotics in clinical, agricultural, and community settings has contributed to the spread of antibiotic-resistant bacteria throughout the world. We characterized antibiotic-resistant E. coli in water and wildlife samples from throughout the Puget Sound, WA, USA. E. coli were isolated from marine water samples obtained in four quadrants of Puget Sound and select locations near beaches, freshwater samples from streams near marine beaches, and fecal samples from harbor porpoises (Phocoena phocoena), harbor seals (Phoca vitulina), river otters (Lontra canadensis), and English sole (Parophrys vetulus). A total of 305 E. coli isolates were assessed for phenotypic and genotypic resistance to antibiotics, using antimicrobial susceptibility typing, whole-genome sequencing, fumC, and multilocus sequence typing. Of the 305 E. coli isolates, 31 (10.2%) were resistant and 20 (6.6%) displayed intermediate resistance to =1 class of antibiotics, with 31.4% (16/51) of these non-susceptible E. coli isolates from marine mammals and 33.3% (17/51) from river otters. The proportion of non-susceptible isolates within wildlife samples (33/83) was significantly higher than that within samples taken from marine water (14/212; p < 0.0001). Among marine water samples, there was no statistical difference in the proportions of resistant and non-susceptible E. coli when comparing the four quadrants of Puget Sound. Of the 305 E. coli isolates, we identified 196 unique sequence types (STs) including 37 isolates associated with eight extraintestinal pathogenic E. coli (ExPEC) STs [ST10, ST38, ST58, ST69, ST73, ST117, ST131, and ST405]. Our study suggests that aquatic wildlife may be potential sentinels for antibiotic-resistant and ExPEC E. coli in marine ecosystems such as the Salish Sea. Future research is required to understand the exposure and carriage of antibiotic-resistant bacteria in aquatic ecosystems, which may originate from wastewater treatment plants and agriculture/aquaculture run-off, and which have potential health effects for both wildlife and human communities.