Characterization of antibiotic multi-resistant bacteria and resistance genes in the effluent of an intensive shrimp farm (Long An, Viet Nam)

Emergence of antibiotic resistant (AR) bacteria and antibiotic resistance genes (ARGs) in the aquaculture industry is a growing issue for human health. Shrimp farmers in Viet Nam have free access to and make use of a wide variety of antibiotics to treat diseased animals or prevent pathogen outbreaks. However, and despite of the massive use of antibiotics, important commercial losses have crippled this industry recently. Notably, very little data are available about the effects of these substances on shrimp pathogens and on the autochtonuous bacterial communities in general. In this study, molecular analysis and microbiological cultures were carried out on samples taken from the effluent channel of a shrimp farming facility (Long An Province, Viet Nam). Results revealed a high variety of ARGs (sul1, sul2, qnrA, ermB, tetA, aac (6)lb, dfrA1, dfr12, dfrA5) among the bacterial communities, targeting at least nine different substances. Most of the resistant bacterial strains possessed from 4 to 7 different ARGs, conferring multidrug resistance capacity. A high frequency of pathogenic bacteria such as Klebsiella pneumoniae and Vibrio parahaemolyticus were found among these isolates. Real time PCR analysis revealed the presence of high copy numbers of the sul2 gene in the effluent channel of the shrimp farm, ranging from 1,000 to 7,000 copies/ml and up to 200,000 to 700,000 copies/g in the water and in the river sediments respectively. Massive sequencing of plasmids isolated from antibiotic-resistant bacteria revealed the presence of a wide diversity of ARGs, conferring resistance, for instance, to trimethoprim, rifampicin, beta-lactams as well as carbapenems. These data indicated that antibiotic usage strongly promoted the emergence of multi-resistant bacteria in the shrimps ponds that subsequently spread into the adjacent natural aquatic environment. These multi-resistant bacteria could potentially cause direct harmful effects, or serve as ARGs reservoir, spreading resistance genes to human and animal pathogens. This study is the starting point for current projects aiming at monitoring antibiotic resistance issues in the Vietnamese aquaculture industry. Long term goals involve the development of strategies aiming at favoring long-term efficiency and sustainability to the aquaculture industry.