The Resistome of Farmed Fish Feces Contributes to the Enrichment of Antibiotic Resistance Genes in Sediments below Baltic Sea Fish Farms

Abstract

Our previous studies showed that particular antibiotic resistance genes (ARGs) were enriched locally in sediments below fish farms in the Northern Baltic Sea, Finland, even when the selection pressure from antibiotics was negligible. We assumed that a constant influx of farmed fish feces could be the plausible source of the ARGs enriched in the farm sediments. In the present study, we analyzed the composition of the antibiotic resistome from the intestinal contents of 20 fish from the Baltic Sea farms. We used a high-throughput method, WaferGen qPCR array with 364 primer sets to detect and quantify ARGs, mobile genetic elements (MGE), and the 16S rRNA gene. Despite a considerably wide selection of qPCR primer sets, only 28 genes were detected in the intestinal contents. The detected genes were ARGs encoding resistance to sulfonamide (sul1), trimethoprim (dfrA1), tetracycline [tet(32), tetM, tetO, tetW], aminoglycoside (aadA1, aadA2), chloramphenicol (catA1), and efflux-pumps resistance genes (emrB, matA, mefA, msrA). The detected genes also included class 1 integron-associated genes (intI1, qacEΔ1) and transposases (tnpA). Importantly, most of the detected genes were the same genes enriched in the farm sediments. This preliminary study suggests that feces from farmed fish contribute to the ARG enrichment in farm sediments despite the lack of contemporaneous antibiotic treatments at the farms. We observed that the intestinal contents of individual farmed fish had their own resistome compositions. Our result also showed that the total relative abundances of transposases and tet genes were significantly correlated (p = 0.001, R2 = 0.71). In addition, we analyzed the mucosal skin and gill filament resistomes of the farmed fish but only one multidrug-efflux resistance gene (emrB) was detected. To our knowledge, this is the first study reporting the resistome of farmed fish using a culture-independent method. Determining the possible sources of ARGs, especially mobilized ARGs, is essential for controlling the occurrence and spread of ARGs at fish farming facilities and for lowering the risk of ARG spread from the farms to surrounding environments.

Aquatic animals promote antibiotic resistance gene dissemination in water via conjugation: Role of different regions within the zebra fish intestinal tract, and impact on fish intestinal microbiota

“…Our findings also further confirmed the results published by Muziasari et al. (, ), in which they found that “a constant influx of farmed fish faeces could be the plausible source of the ARGs enriched in the farm sediments.”…”

“…Furthermore, the exchange and dissemination of ARGs from exogenous organisms to water‐indigenous microbes through horizontal gene transfer are also a potentially significant factor that contributes to ARGs dissemination (Aminov, ). Many studies have revealed that sediments of aquaculture farms are also environments in which various ARGs are concentrated (Armstrong, Hargrave, & Haya, ; Muziasari et al., , ; Zou et al., ). Additionally, a variety of antibiotic resistance bacteria (ARB) and ARGs were detected in fish intestines and faeces (Smith, Desbois, & Dyrynda, ; Sørum, Roberts, & Crosa, ; Xiong et al., ).…”

Monitoring Antimicrobial Resistance Dissemination in Aquatic Systems

“…To detect the prevalence of ARGs and vectors such as mobile genetic elements (MGE) that may facilitate horizontal gene transfer of ARGs, traditional quantitative polymerase chain reaction (qPCR), and the more recent high-throughput qPCR (HT-qPCR) platform with capabilities of detection of~200 different ARGs and mobile genetic elements (MGE), has been used to compare relative concentrations of AMR contamination across a variety of aquatic environments including water treatment plants [19][20][21][22][23][24]. OMIC approaches such as metagenomics are able to provide a holistic picture of the diversity of ARGs, MGE and vectors (e.g., integrons, plasmids) that assist horizontal gene transfer, and the overall microbial community structure (bacteria, viruses) in environmental systems and wastewaters [25][26][27][28][29].…”

Response of gut microbiota to feed-borne bacteria depends on fish growth rate: a snapshot survey of farmed juvenileTakifugu obscurus

“…As a demersal fish, fugu live on or near the bottom of water, foraging food by scraping them off the surface (30). Meanwhile, feces from farmed fugu can also play a part of bacterial enrichment in rearing water and sediment as seen in other fish species (31,32). Such dynamic reciprocal interactions might be expected to lead to a closer association between the gut of farmed fugu and its rearing environment to some extent, i.e.…”