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. 2024 Aug 30;13(9):825.
doi: 10.3390/antibiotics13090825.

Analysis of Antibiotic Resistance Genes (ARGs) across Diverse Bacterial Species in Shrimp Aquaculture

Tilden M Mitchell  1 , Tin Ho  1 , Liseth Salinas  2 , Thomas VanderYacht  1 , Nikolina Walas  1 , Gabriel Trueba  2 , Jay P Graham  1
Affiliations

Analysis of Antibiotic Resistance Genes (ARGs) across Diverse Bacterial Species in Shrimp Aquaculture

Tilden M Mitchell et al. Antibiotics (Basel). .

Abstract

There is little information available on antibiotic resistance (ABR) within shrimp aquaculture environments. The aim of this study was to investigate the presence of antibiotic resistance genes (ARGs) in shrimp farming operations in Atacames, Ecuador. Water samples (n = 162) and shrimp samples (n = 54) were collected from three shrimp farming operations. Samples were cultured and a subset of isolates that grew in the presence of ceftriaxone, a third-generation cephalosporin, were analyzed using whole-genome sequencing (WGS). Among the sequenced isolates (n = 44), 73% of the isolates contained at least one ARG and the average number of ARGs per isolate was two, with a median of 3.5 ARGs. Antibiotic resistance genes that confer resistance to the β-lactam class of antibiotics were observed in 65% of the sequenced isolates from water (20/31) and 54% of the isolates from shrimp (7/13). We identified 61 different ARGs across the 44 sequenced isolates, which conferred resistance to nine antibiotic classes. Over half of all sequenced isolates (59%, n = 26) carried ARGs that confer resistance to more than one class of antibiotics. ARGs for certain antibiotic classes were more common, including beta-lactams (26 ARGs); aminoglycosides (11 ARGs); chloramphenicol (three ARGs); and trimethoprim (four ARGs). Sequenced isolates consisted of a diverse array of bacterial orders and species, including Escherichia coli (48%), Klebsiella pneumoniae (7%), Aeromonadales (7%), Pseudomonadales (16%), Enterobacter cloacae (2%), and Citrobacter freundii (2%). Many ARGs were shared across diverse species, underscoring the risk of horizontal gene transfer in these environments. This study indicated the widespread presence of extended-spectrum β-lactamase (ESBL) genes in shrimp aquaculture, including blaCTX-M, blaSHV, and blaTEM genes. Increased antibiotic resistance surveillance of shrimp farms and identification of aquaculture operation-level risk factors, such as antibiotic use, will likely be important for mitigating the spread of ARGs of clinical significance.

Keywords: 3GCR; AMR; E. coli; aquaculture; ceftriaxone antibiotic resistance; genomic analysis; multi-drug resistance; public health; shrimp.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Study sampling locations in Atacames, Ecuador, located in the northwestern province of Esmeraldas. Three sampling locations were included that all connect to the Atacames River.
Figure 2
Figure 2
Prevalence of antibiotic resistance genes by antibiotic class for isolates detected in water samples (n = 31 isolates) and shrimp samples (n = 13 isolates) in shrimp farms.
Figure 3
Figure 3
Bacterial species identified in water (n = 31) and shrimp samples (n = 13) from shrimp aquaculture farms in Ecuador.
Figure 4
Figure 4
Type (y-axis) and number (x-axis) of antibiotic resistance genes (ARGs) among sequenced isolates (n = 44).
Figure 5
Figure 5
Venn diagram showing ARGs identified among different bacterial species from shrimp farms.
See this image and copyright information in PMC

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