Diversity and antimicrobial resistance among bacterial isolates from finfish aquaculture in Thailand

Global aquaculture, has expanded rapidly, especially in Southeast Asia, with Thailand emerging as a leading producer. However, the sector faces economic losses from disease outbreaks and has problems with escalating antimicrobial resistance (AMR).

This study examined bacterial diversity and AMR in 695 moribund fish samples collected from regions across Thailand between 2018 and 2024, and spanning eight key finfish aquaculture species such as tilapia, Asian sea bass, snakeskin gourami, snakehead, walking catfish and carp species. Gram-negative bacteria (86.62% of isolates) were dominated by Vibrionaceae and Aeromonadaceae, while Gram-positive bacteria were primarily from Streptococcaceae, with notable species including A. veronii, V. vulnificus, S. agalactiae and S. suis. Antibiotic susceptibility testing was conducted with 29 antibiotics across nine different classes and the isolates were classified as wild-type (WT) or non-wild-type (NWT) based on their inhibition zone diameters. The results indicated high resistance levels, particularly against metronidazole, streptomycin, clindamycin, sulfonamide, and kanamycin. Multidrug resistance (MDR) was notably high in Aeromonas and Vibrio species. Antimicrobial resistance gene (ARG) analysis showed a high prevalence of beta-lactam, tetracycline, and fluoroquinolone resistance in Gram-negative bacteria, and resistance to beta-lactams, macrolides, fluoroquinolones, and peptides in Gram-positive bacteria. Antibiotic efflux was the predominant putatively detected resistance mechanism, accounting for 50-60% of ARGs. Identification of unique resistance gene families in Aeromonas spp. and V. vulnificus, including the SMR efflux pump and OXA beta-lactamase, emphasizes the adaptive strategies of these bacteria and the discovery of host-specific resistance mechanisms in S. suis, such as nutrient acquisition pathways, underscores the challenges of controlling and managing AMR in aquaculture systems. Mobile genetic elements (MGEs), particularly IS elements, were found to be widespread in all species, underscoring the significant role of horizontal gene transfer in the dissemination of resistance.

This study advocates for enhanced AMR surveillance, responsible antibiotic use, and species-specific monitoring to safeguard aquaculture and public health utilizing the one health approach.