Antibiotic-resistant bacteria and gut microbiome communities associated with wild-caught shrimp from the United States versus imported farm-raised retail shrimp

In the United States, farm-raised shrimp accounts for similar to 80% of the market share. Farmed shrimp are cultivated as monoculture and are susceptible to infections. The aquaculture industry is dependent on the application of antibiotics for disease prevention, resulting in the selection of antibiotic-resistant bacteria. We aimed to characterize the prevalence of antibiotic-resistant bacteria and gut microbiome communities in commercially available shrimp. Thirty-one raw and cooked shrimp samples were purchased from supermarkets in Florida and Georgia (U.S.) between March-September 2019. The samples were processed for the isolation of antibiotic-resistant bacteria, and isolates were characterized using an array of molecular and antibiotic susceptibility tests. Aerobic plate counts of the cooked samples (n=13) varied from <25 to 6.2 log CFU/g. Isolates obtained (n=110) were spread across 18 genera, comprised of coliforms and opportunistic pathogens. Interestingly, isolates from cooked shrimp showed higher resistance towards chloramphenicol (18.6%) and tetracycline (20%), while those from raw shrimp exhibited low levels of resistance towards nalidixic acid (10%) and tetracycline (8.2%). Compared to wild-caught shrimp, the imported farm-raised shrimp harbored distinct gut microbiota communities and a higher prevalence of antibiotic-resistance genes in their gut. The presence of antibiotic-resistant strains in cooked shrimps calls for change in processing for their mitigation.

Automated summary

In the United States, the majority of the shrimp market is occupied by farm-raised shrimp, which are susceptible to infections and require antibiotics, leading to antibiotic-resistant bacteria. A study found a high prevalence of antibiotic-resistant bacteria in commercially available raw and cooked shrimp, with higher resistance in cooked samples. This calls for a change in processing to mitigate the risk of antibiotic-resistant strains in cooked shrimp.