A Comprehensive Research on Antibiotic Resistance Genes in Microbiota of Aquatic Animals

The potential contribution of aquatic wildlife to antibiotic resistance dissemination in freshwater ecosystems: A review

Antibiotic resistance (AR) is one of the major health threats of our time. The presence of antibiotics in the environment and their continuous release from sewage treatment plants, chemical manufacturing plants and animal husbandry, agriculture and aquaculture, result in constant selection pressure on microbial organisms. This presence leads to the emergence, mobilization, horizontal gene transfer and a selection of antibiotic resistance genes, resistant bacteria and mobile genetic elements. Under these circumstances, aquatic wildlife is impacted in all compartments, including freshwater organisms with partially impermeable microbiota. In this narrative review, recent advancements in terms of occurrence of antibiotics and antibiotic resistance genes in sewage treatment plant effluents source compared to freshwater have been examined, occurrence of antibiotic resistance in wildlife, as well as experiments on antibiotic exposure. Based on this current state of knowledge, we propose the hypothesis that freshwater aquatic wildlife may play a crucial role in the dissemination of antibiotic resistance within the environment. Specifically, we suggest that organisms with high bacterial density tissues, which are partially isolated from the external environment, such as fishes and amphibians, could potentially be reservoirs and amplifiers of antibiotic resistance in the environment, potentially favoring the increase of the abundance of antibiotic resistance genes and resistant bacteria. Potential avenues for further research (trophic transfer, innovative exposure experiment) and action (biodiversity eco-engineering) are finally proposed.

Detection of Salmonella Pathogenicity Islands and Antimicrobial-Resistant Genes in Salmonella enterica Serovars Enteritidis and Typhimurium Isolated from Broiler Chickens

Rapid growth in commercial poultry production is one of the major sources of Salmonella infections that leads to human salmonellosis. The two main Salmonella enterica serovars associated with human salmonellosis are enteritidis and typhimurium. The aim of this study was to determine the prevalence of S. enterica serovars Enteritidis and S. Typhimurium as well as their Salmonella pathogenicity islands (SPI) and antibiotic resistance profiles in broiler chicken feces from slaughterhouses. A total of 480 fecal samples from broiler chickens that were grouped into 96 pooled samples were identified to have Salmonella spp. using the invA gene, whilst the Spy and sdfI genes were used to screen for the presence of S. Enteritidis and S. Typhimurium serovars, respectively, by polymerase chain reaction (PCR) assays. The isolates were also screened for the presence of Salmonella pathogenicity islands (SPIs) using PCR. The disc diffusion assay was performed to determine the antibiotic resistance profiles of the isolates. A total of 36 isolates were confirmed as Salmonella spp. through amplification of the invA gene. Out of 36 confirmed Salmonella spp. a total of 22 isolates were classified as S. Enteritidis (n = 8) and were S. Typhimurium (n = 14) serovars. All (n = 22) S. Enteritidis and S. Typhimurium isolates possessed the hilA (SPI-1), ssrB (SPI-2) and pagC (SPI-11) pathogenicity islands genes. Amongst these serovars, 50% of the isolates (n = 11/22) were resistant to tetracycline and nalidixic acid. Only 22% of the isolates, S. Typhimurium (13.6%) and S. Enteritidis (9.1%) demonstrated resistance against three or more antibiotic classes. The most detected antibiotic resistance genes were tet(K), mcr-1, sulI and strA with 13 (59.1%), 9 (40.9%), 9 (40.9%) and 7 (31.8%), respectively. The findings of this study revealed that S. Typhimurium is the most prevalent serotype detected in chicken feces. To reduce the risk to human health posed by salmonellosis, a stringent public health and food safety policy is required.

Effects of cadmium exposure on gut microbiota and antibiotic resistance genes in Haliotis diversicolor abalone

Heavy metals in soil, water, and industrial production can affect the antibiotic resistance of bacteria. Antibiotic resistance in gut microbiota has been extensively researched. The effects of cadmium (Cd) was investigated on the gut microbiota and antibiotic resistance genes (ARGs) of Haliotis diversicolor, a commercially important abalone species. By exposing H. diversicolor to four concentrations of Cd (0 μg L-1 (control), 6.5 μg L-1 (low), 42.25 μg L-1 (medium), and 274.63 μg L-1 (high)) for 30 and 60 days, 16 types of ARG (aadA-01, aadA-02, cfr, dfrA1, ermB, floR, folA, mecA, sul2, tetB-01, tetC-01, tetD-01, tetG-01, tetM-02, tetQ, vanC-01), and 1213 genus and 27 phylum microbiomes were detected. ARGs can be resistant to aminoglycoside, beta-lactamase, macrolide-lincosamide-streptogramin B, multidrug, florfenicol, macrolide, sulfonamides, tetracyclines, and vancomycin. Cadmium exposure significantly alters the abundance of tetC-01, tetB-01, tetQ, sul2, and aadA-01. About 5% (61) of genus-level microorganisms were significantly affected by Cd exposure. Microbiota alpha and beta diversities in the 60-day 42.25 μg L-1 Cd treatment differed significantly from those in other treatments. In addition, 26 pathogens were detected, and two pathogens (Vibrio and Legionella) were significantly affected by Cd exposure. Significant correlations between pathogens and ARGs increased with increased Cd concentration after 60 days of Cd exposure. Cadmium exposure may cause gut microbiota disturbance in H. diversicolor and increase the likelihood of ARG transfer to pathogens, increasing potential ecological and economic risks.

Source, transport, and toxicity of emerging contaminants in aquatic environments: A review on recent studies

Emerging contaminants (ECs) are gaining global attention owing to their widespread presence and adverse effects on human health. ECs comprise numerous composite types and pose a potential threat to the growth and functional traits of species and ecosystems. Although the occurrence and fate of ECs has been extensively studied, little is known about their long-term biological effects. This review attempts to gain insights into the unhindered connections and overlaps in aquatic ecosystems. Microplastics (MPs), one of the most representative ECs, are carriers of other pollutants because of their strong adsorption capacity. They form a complex of pollutants that can be transmitted to aquatic organisms and humans through the extended food chain, increasing the concentration of pollutants by tens of thousands of times. Adsorption, interaction and transport effects of emerging contaminants in the aquatic environment are also discussed. Furthermore, the current state of knowledge on the ecotoxicity of single- and two-pollutant models is presented. Herein, we discuss how aquatic organisms within complex food networks may be particularly vulnerable to harm from ECs in the presence of perturbations. This review provides an advanced understanding of the interactions and potential toxic effects of ECs on aquatic organisms.

Dietary Administration Effects of Exopolysaccharide Produced by Bacillus tequilensis PS21 Using Riceberry Broken Rice, and Soybean Meal on Growth Performance, Immunity, and Resistance to Streptococcus agalactiae of Nile tilapia (Oreochromis niloticus)

Overuse of antibiotics in aquaculture has generated bacterial resistance and altered the ecology. Aquacultural disease control requires an environmentally sustainable approach. Bacterial exopolysaccharides (EPSs) as bioimmunostimulants have not been extensively explored in aquaculture. This study investigated EPS produced from 5% w/v riceberry broken rice as a carbon source and 1% w/v soybean meal as a nitrogen source by Bacillus tequilensis PS21 from milk kefir grain for its immunomodulatory, antioxidant activities and resistance to pathogenic Streptococcus agalactiae in Nile tilapia (Oreochromis niloticus). The FTIR spectrum of EPS confirmed the characteristic bonds of polysaccharides, while the HPLC chromatogram of EPS displayed only the glucose monomer subunit, indicating its homopolysaccharide feature. This EPS (20 mg/mL) exhibited DPPH scavenging activity of 65.50 ± 0.31%, an FRAP value of 2.07 ± 0.04 mg FeSO4/g DW, and antimicrobial activity (14.17 ± 0.76 mm inhibition zone diameter) against S. agalactiae EW1 using the agar disc diffusion method. Five groups of Nile tilapia were fed diets (T1 (Control) = 0.0, T2 = 0.1, T3 = 0.2, T4 = 1.0, and T5 = 2.0 g EPS/kg diet) for 90 days. Results showed that EPS did not affect growth performances or body composition, but EPS (T4 + T5) significantly stimulated neutrophil levels and serum lysozyme activity. EPS (T5) significantly induced myeloperoxidase activity, catalase activity, and liver superoxide dismutase activity. EPS (T5) also significantly increased the survival of fish at 80.00 ± 5.77% at 14 days post-challenge with S. agalactiae EW1 compared to the control (T1) at 53.33 ± 10.00%. This study presents an efficient method for utilizing agro-industrial biowaste as a prospective source of value-added EPS via a microbial factory to produce a bio-circular green economy model that preserves a healthy environment while also promoting sustainable aquaculture.

Effects of Bacillus spp. Mixture on Growth, Immune Responses, Expression of Immune-Related Genes, and Resistance of Nile Tilapia Against Streptococcus agalactiae Infection

The purpose of this study was to evaluate the effect of Bacillus spp. mixture (Bacillus subtilis TISTR001, Bacillus megaterium TISTR067, and Bacillus licheniformis DF001) (1 × 10⁶ CFU/g) on growth, immune parameters, immune-related gene expression, and resistance of Nile tilapia against Streptococcus agalactiae AAHM04. Fish were fed different concentrations of Bacillus spp. 0 (control; T1), 1 (T2), 3 (T3), and 5 (T4) g/kg diets for 120 days. The results showed that weight gain, average daily gain, specific growth rate, feed conversion ratio in T3 diet were significantly higher than the control group and other tested diets (p < 0.05). Immune parameters, such as myeloperoxidase and lysozyme, were significantly higher in the T3 and T4 diets compared to the control group (p < 0.05). Similarly, IL-1β and TNF-α gene expressions in the spleen of fish fed T2, T3, and T4 diets were significantly higher than the control group (p < 0.05). However, no significant differences in survival rate, hematology, blood chemical indices, malondialdehyde (MDA) levels, body chemical composition, and organosomatic indices (p > 0.05) were noticed in all treatments. No significant differences in survival rate after the challenge test with S. agalactiae AAHM04 were found in fish fed Bacillus spp. mixture diets, except for the T3 diet. These results suggest that Bacillus spp. mixture diet at 3 g/kg diet (T3) could improve growth, immune response, and disease resistance of Nile tilapia.

Intestinal microbiota perturbations in the gastropod Trochus niloticus concurrently exposed to ocean acidification and environmentally relevant concentrations of sulfamethoxazole

Ocean acidification (OA) and antibiotic pollution pose severe threats to the fitness of keystone species in marine ecosystems. However, the combined effects of OA and antibiotic pollution on the intestinal microbiota of marine organisms are still not well known. In this study, we exposed the herbivorous gastropod Trochus niloticus, a keystone species to maintains the stability of coral reef ecosystems, to acidic seawater (pH 7.6) and/or sulfamethoxazole (SMX, 100 ng/L, 1000 ng/L) for 28 days and determined their impacts on (1) the accumulation of SMX in the intestine of T. niloticus; (2) the characteristics of the intestinal microbiota in T. niloticus; (3) the relative abundances of sulfonamide resistance genes (i.e., sul1 and sul2) and intI1 in the intestinal microbiota of T. niloticus. Our results show that OA exposure leads to dramatic microbiota dysbiosis in the intestine of T. niloticus, including changes in bacterial community diversity and structure, decreased abundances of dominant species, existences of characteristic taxa, and altered functional predictions. In addition, SMX exposure at environmentally relevant concentrations had little effect on the intestinal microbiota of T. niloticus, whether in isolation or in combination with OA. However, after exposure to the higher SMX concentration (1000 ng/L), the accumulation of SMX in the intestine of T. niloticus could induce an increase in the copies of sul2 in the intestinal microbiota. These results suggest that the intestinal health of T. niloticus might be affected by OA and SMX, which might lead to fitness loss of the keystone species in coral reef ecosystems.

One Health: a holistic approach for food safety in livestock

The food safety of livestock is a critical issue between animals and humans due to their complex interactions. Pathogens have the potential to spread at every stage of the animal food handling process, including breeding, processing, packaging, storage, transportation, marketing and consumption. In addition, application of the antibiotic usage in domestic animals is a controversial issue because, while they can combat food-borne zoonotic pathogens and promote animal growth and productivity, they can also lead to the transmission of antibiotic-resistant microorganisms and antibiotic-resistant genes across species and habitats. Coevolution of microbiomes may occur in humans and animals as well which may alter the structure of the human microbiome through animal food consumption. One Health is a holistic approach to systematically understand the complex relationships among humans, animals and environments which may provide effective countermeasures to solve food safety problems aforementioned. This paper depicts the main pathogen spectrum of livestock and animal products, summarizes the flow of antibiotic-resistant bacteria and genes between humans and livestock along the food-chain production, and the correlation of their microbiome is reviewed as well to advocate for deeper interdisciplinary communication and collaboration among researchers in medicine, epidemiology, veterinary medicine and ecology to promote One Health approaches to address the global food safety challenges.

Aquatic Environments as Hotspots of Transferable Low-Level Quinolone Resistance and Their Potential Contribution to High-Level Quinolone Resistance

The disposal of antibiotics in the aquatic environment favors the selection of bacteria exhibiting antibiotic resistance mechanisms. Quinolones are bactericidal antimicrobials extensively used in both human and animal medicine. Some of the quinolone-resistance mechanisms are encoded by different bacterial genes, whereas others are the result of mutations in the enzymes on which those antibiotics act. The worldwide occurrence of quinolone resistance genes in aquatic environments has been widely reported, particularly in areas impacted by urban discharges. The most commonly reported quinolone resistance gene, qnr, encodes for the Qnr proteins that protect DNA gyrase and topoisomerase IV from quinolone activity. It is important to note that low-level resistance usually constitutes the first step in the development of high-level resistance, because bacteria carrying these genes have an adaptive advantage compared to the highly susceptible bacterial population in environments with low concentrations of this antimicrobial group. In addition, these genes can act additively with chromosomal mutations in the sequences of the target proteins of quinolones leading to high-level quinolone resistance. The occurrence of qnr genes in aquatic environments is most probably caused by the release of bacteria carrying these genes through anthropogenic pollution and maintained by the selective activity of antimicrobial residues discharged into these environments. This increase in the levels of quinolone resistance has consequences both in clinical settings and the wider aquatic environment, where there is an increased exposure risk to the general population, representing a significant threat to the efficacy of quinolone-based human and animal therapies. In this review the potential role of aquatic environments as reservoirs of the qnr genes, their activity in reducing the susceptibility to various quinolones, and the possible ways these genes contribute to the acquisition and spread of high-level resistance to quinolones will be discussed.

Campylobacter jejuni from Slaughter Age Broiler Chickens: Genetic Characterization, Virulence, and Antimicrobial Resistance Genes

Campylobacter jejuni is a major cause of food-borne human gastroenteritis worldwide and is designated as a high priority antimicrobial-resistant pathogen by the World Health Organization (WHO). In this study, a total of 26 C. jejuni isolates from broiler chickens were screened for the presence of virulence and antimicrobial resistance genes by PCR. As a result, the study detected 11/26 (42.3%), 9/26 (34.6%), 8/26 (30.8%), 7/26 (26.9%), 6/26 (23.1%), and 6/26 (23.1%) of cdtC, pldA, cdtB, cdtA, cadF, and ciaB virulence genes, respectively, with seven of the isolates carrying more than two virulence genes. The majority of the isolates n = 25 (96.1%) were resistant to nalidixic acid, followed by n = 21 (80.7%), n = 22 (84.6%), and n = 5 (19.2%) for tetracycline, erythromycin, and ciprofloxacin, respectively. Most isolates were harboring catI (n = 16; 84.2%), catII (n = 15; 78.9%), catIII (n = 10; 52.6%), catIV (n = 2; 10.5%), floR (n = 10; 52.6%), ermB (n = 14; 73.7%), tetO (n = 13; 68.4%), tetA (n = 9; 47.4%), mcr-4 (n = 8; 42.1%), and ampC (n = 2; 10.5%). Meanwhile, mcr-1, mcr-2, mcr-3, mcr-5, tet(X), tet(P), and tet(W) genes were not detected in all isolates. Class I and Class II integrons were detected in 92.3% (n = 24) and 65.4% (n = 17) isolates, respectively. About 31% (8 of the 26 isolates) isolates were carrying more than two resistance genes. According to our knowledge, this is the first study to detect class II integrons in Campylobacter spp. (C. jejuni). The high prevalence of cdtA, cdtB, cdtC, cadF, pldA, and ciaB genes and antibiotic resistance genes in C. jejuni in this study indicates the pathogenic potential of these isolates. Majority of the isolates demonstrated resistance to nalidixic acid, tetracycline (tet), and erythromycin (ermB), which are the drugs of choice for treating Campylobacter infections. Therefore, these findings highlight the importance of implementing an efficient strategy to control Campylobacter in chickens and to reduce antimicrobial use in the poultry industry, which will help to prevent the spread of infections to humans.

Wildlife and Antibiotic Resistance

Antibiotic resistance is a major human health problem. While health care facilities are main contributors to the emergence, evolution and spread of antibiotic resistance, other ecosystems are involved in such dissemination. Wastewater, farm animals and pets have been considered important contributors to the development of antibiotic resistance. Herein, we review the impact of wildlife in such problem. Current evidence supports that the presence of antibiotic resistance genes and/or antibiotic resistant bacteria in wild animals is a sign of anthropic pollution more than of selection of resistance. However, once antibiotic resistance is present in the wild, wildlife can contribute to its transmission across different ecosystems. Further, the finding that antibiotic resistance genes, currently causing problems at hospitals, might spread through horizontal gene transfer among the bacteria present in the microbiomes of ubiquitous animals as cockroaches, fleas or rats, supports the possibility that these organisms might be bioreactors for the horizontal transfer of antibiotic resistance genes among human pathogens. The contribution of wildlife in the spread of antibiotic resistance among different hosts and ecosystems occurs at two levels. Firstly, in the case of non-migrating animals, the transfer will take place locally; a One Health problem. Paradigmatic examples are the above mentioned animals that cohabit with humans and can be reservoirs and vehicles for antibiotic resistance dissemination. Secondly, migrating animals, such as gulls, fishes or turtles may participate in the dissemination of antibiotic resistance across different geographic areas, even between different continents, which constitutes a Global Health issue.

Multi-drug resistance, integron and transposon-mediated gene transfer in heterotrophic bacteria from Penaeus vannamei and its culture environment

Multi-drug resistance (MDR) in bacteria is regarded as an emerging pollutant in different food production avenues including aquaculture. One hundred and sixty out of 2304 bacterial isolates from shrimp farm samples (n = 192) of Andhra Pradesh, India, were MDR. Based on biochemical identification and 16S rRNA sequencing, they were grouped into 35 bacterial species with the predominance of Vibrio parahaemolyticus (12.5%). The MDR isolates showed highest resistance toward oxytetracycline (89%) with more than 0.2 MAR (multiple antibiotic resistance), demonstrates a high-risk source. The most prevalent antibiotic-resistance gene (ARG) and mobile genetic element (MGE) detected were tetA (47.5%) and int1 (46.2%), respectively. In conjugation experiments, overall transfer frequency was found to be in the range of 1.1 × 10^-9 to 1.8 × 10^-3 with the transconjugants harbouring ARGs and MGEs. This study exposed the wide distribution of MDR bacteria in shrimp and its environment, which can further aggravate the already raised concerns of antibiotic residues in the absence of proper mitigation measures.

Antibiotics in mariculture systems: A review of occurrence, environmental behavior, and ecological effects

Antibiotics are widely applied to prevent and treat diseases occurred in mariculture. The often-open nature of mariculture production systems has led to antibiotic residue accumulation in the culturing and adjacent environments, which can adversely affect aquatic ecosystems, and even human. This review summarizes the occurrence, environmental behavior, and ecological effects of antibiotics in mariculture systems based on peer-reviewed papers. Forty-five different antibiotics (categorized into ten groups) have been detected in mariculture systems around the world, which is far greater than the number officially allowed. Indiscriminate use of antibiotics is relatively high among major producing countries in Asia, which highlights the need for stricter enforcement of regulations and policies and effective antibiotic removal methods. Compared with other environmental systems, some environmental characteristics of mariculture systems, such as high salinity and dissolved organic matter (DOM) content, can affect the migration and transformation processes of antibiotics. Residues of antibiotics favor the proliferation of antibiotic resistance genes (ARGs). Antibiotics and ARGs alter microbial communities and biogeochemical cycles, as well as posing threats to marine organisms and human health. This review may provide a valuable summary of the effects of antibiotics on mariculture systems.

New Sequence Types and Antimicrobial Drug-Resistant Strains of Streptococcus suis in Diseased Pigs, Italy, 2017-2019

Streptococcus suis is a pathogen associated with severe diseases in pigs and humans. Human infections have a zoonotic origin in pigs. To assess circulating strains, we characterized the serotypes, sequence types, and antimicrobial susceptibility of 78 S. suis isolates from diseased farmed pigs in Italy during 2017-2019. Almost 60% of infections were caused by serotypes 1/2 and 9. All but 1 of the serotype 2 and 1/2 isolates were confined to a single cluster, and serotype 9 isolates were distributed along the phylogenetic tree. Besides sequence type (ST) 1, the serotype 2 cluster included ST7, which caused severe human infections in China in 1998 and 2005. A large proportion of serotype 9 isolates, assigned to ST123, were resistant to penicillin. The emergence of this clone threatens the successful treatment of S. suis infection. Characterizing S. suis isolates from pigs will promote earlier detection of emerging clones.

Vertical and horizontal distributions of clinical antibiotic resistance genes and bacterial communities in Danjiangkou Reservoir, China

The Danjiangkou Reservoir is an important water source for the middle route of the South-to-North Water Diversion Project in China. The current anthropogenic pollution of this reservoir is a great public health concern. Therefore, the horizontal and vertical distributions of seven clinical antibiotic resistance genes (ARGs) and bacterial communities in the Danjiangkou Reservoir were investigated using qPCR and next-generation sequencing, respectively. The average relative abundance of ARGs was 3.01 × 10^-4 to 1.90 × 10^-3 and 4.66 × 10^-4 to 1.85 × 10^-3 in horizontal and vertical profiles, respectively. There was a significant difference in the vertical composition of ARGs, which was caused by different media (i.e. water column vs. sediment). No significant differences in the composition of ARGs were found in the horizontal profile. Proteobacteria was the most abundant phylum, followed by Actinobacteria in the Danjiangkou Reservoir. The beta diversity pattern of the microbial communities in the vertical profile was consistent with that of the ARGs. Moreover, a significant difference in the horizontal composition of the bacterial communities among these water columns was found. All of these factors have resulted in noticeably different co-occurrence patterns of ARGs and bacterial communities between water columns and surface sediment samples. ARGs were closely associated with Proteobacteria and Chloroflexi in the sediment samples, indicating potential anthropogenic pollution in the Danjiangkou Reservoir. Although there was no significant correlation between the occurrence of ARGs and 11 opportunistic pathogens, our results point to potential risks for the development of multi-resistant pathogens due to the simultaneous presence of ARGs and pathogens in the study area. These results provide a good basis for thorough ecological evaluation and remediation of the Danjiangkou Reservoir.

Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures

The shortage of wild fishery resources and the rising demand for human nutrition has driven a great expansion in aquaculture during the last decades in terms of production and economic value. As such, sustainable aquaculture production is one of the main priorities of the European Union's 2030 agenda. However, the intensification of seafood farming has resulted in higher risks of disease outbreaks and in the increased use of antimicrobials to control them. The selective pressure exerted by these drugs provides the ideal conditions for the emergence of antimicrobial resistance hotspots in aquaculture facilities. Omics technology is an umbrella term for modern technologies such as genomics, metagenomics, transcriptomics, proteomics, culturomics, and metabolomics. These techniques have received increasing recognition because of their potential to unravel novel mechanisms in biological science. Metagenomics allows the study of genomes in microbial communities contained within a certain environment. The potential uses of metagenomics in aquaculture environments include the study of microbial diversity, microbial functions, and antibiotic resistance genes. A snapshot of these high throughput technologies applied to microbial diversity and antimicrobial resistance studies in aquacultures will be presented in this review.

Tracking high-risk β-lactamase gene (bla gene) transfers in two Chinese intensive dairy farms

Extended-spectrum β-lactam antibiotics are critically important antibiotics for humans, but their use in food-animals poses a potential threat for public health. This paper addressed the occurrence of high-risk β-lactamase genes (bla genes) in intensive dairy farms, and assessed the effects of different waste treatment technologies at dairies on the propagation and dissemination of bla genes. Results showed that ESBL genes (bla_TEM-1, bla_OXA-1), ampC β-lactamase genes (bla_ampC) and carbapenemase genes (bla_GES-1, bla_NDM) were prevalent in dairy cow waste, and even prevailed through each processing stage of solid manure and dairy wastewater. Significant levels of bla genes were present in the final lagoon (from 10⁴ to 10⁶ copies/mL, representing from 10% to 151%, of raw influent levels), raising the possibility of dissemination to the receiving environment. This concern was validated by the investigation on farmland that had long-term undergone wastewater irrigation, where causing an increase in bla gene levels in soils (approximately 1-3 orders of magnitude). More troublesomely, considerable levels of certain bla genes were still observed in the bedding material (up to 10⁵ and 10⁷ copies/g), which would directly threaten the dairy cow health. Otherwise, correlation analysis showed that both bacterial community and environmental factors played important roles in the bla genes abundances in dairy farms. This study demonstrated the prevalence of high-risk bla genes in dairy farms, and also underscored that dairy waste was a non-ignored great source of multidrug resistance for their surroundings.

A Comparative Analysis of Aquatic and Polyethylene-Associated Antibiotic-Resistant Microbiota in the Mediterranean Sea

In this study, we evaluated the microbiome and the resistome profile of water and fragments of polyethylene (PE) waste collected at the same time from a stream and the seawater in a coastal area of Northwestern Sicily. Although a core microbiome was determined by sequencing of the V3-V4 region of the bacterial 16S rDNA gene, quantitative differences were found among the microbial communities on PE waste and the corresponding water samples. Our findings indicated that PE waste contains a more abundant and increased core microbiome diversity than the corresponding water samples. Moreover, PCR analysis of specific antibiotic resistance genes (ARGs) showed that PE waste harbors more ARGs than the water samples. Thus, PE waste could act as a carrier of antibiotic-resistant microbiota, representing an increased danger for the marine environment and living organisms, as well.

Occurrence and antibacterial resistance of culturable antibiotic-resistant bacteria in the Fildes Peninsula, Antarctica

Quantifying the occurrence of Antarctic antibiotic-resistant bacteria (ARB) is essential for assessing the level of pollution and assessing the "baseline" or background level of ARB in human uninhabited environments. Animal feces, soil, and sediments were sampled from Fildes Peninsula. The abundance of sulfamethazine- and ciprofloxacin-resistance bacteria and antibotic resistance genes (ARGs) within ARB were investigated. The results showed Ciprofloxacin- and Sulfamethazine-resistant bacteria isolated from samples accounted for the highest abundances of 30 CFU/g and 79.8 CFU/g, respectively. The dominant genus of Sulfamethazine-and quinolone-resistance bacteria was Pseudomonas and Arthrobacter, respectively. 106 ARGs were detected from ARB. Strong positive correlations between mobile genetic elements (MGEs) and ARGs were found, what is relatively novel observation that the mechanism is confirmed to also occur in the Antarctic. This study reveals the compositional characteristics of ARGs of strains in Antarctic, providing support for the source of Antarctic antibiotic resistance and drug resistance mechanisms.

Live Feeds Used in the Larval Culture of Red Cusk Eel, Genypterus chilensis, Carry High Levels of Antimicrobial-Resistant Bacteria and Antibiotic-Resistance Genes (ARGs)

Simple Summary

The culture of the marine fish red cusk eel Genypterus chilensis is currently considered a priority for Chilean aquaculture but low larval survival rates have prompted the need for the continuous use of antibiotics, mainly florfenicol. In this study, the role of live prey (rotifers and the brine shrimp Artemia franciscana) used to feed fish larvae as a source of antibacterial-resistant bacteria in a commercial culture of G. chilensis was investigated. Samples of live feeds were collected during the larval growth period and their bacterial contents were determined. High levels of potentially opportunistic pathogens, such as Vibrio spp., as well as florfenicol-resistant bacteria, were detected. Sixty-five florfenicol-resistant isolates were recovered from these cultures and identified as Vibrio (81.5%) and Pseudoalteromonas (15.4%), which exhibited a high incidence of co-resistance to the antibiotics streptomycin, oxytetracycline, co-trimoxazole, and kanamycin. The majority of them carried the florfenicol-resistance encoding genes floR and fexA. The high prevalence of antibiotic-resistant bacteria and the associated genetic elements in live feed administered to reared fish larvae requires the prompt implementation of efficient management strategies to prevent future therapy failures in fish larval cultures and the spread of antibiotic-resistant bacteria to associated aquatic environments.

Abstract

The culture of red cusk eel Genypterus chilensis is currently considered a priority for Chilean aquaculture but low larval survival rates have prompted the need for the continuous use of antibacterials. The main aim of this study was to evaluate the role of live feed as a source of antibacterial-resistant bacteria in a commercial culture of G. chilensis. Samples of rotifer and Artemia cultures used as live feed were collected during the larval growth period and culturable bacterial counts were performed using a spread plate method. Rotifer and Artemia cultures exhibited high levels of resistant bacteria (8.03 × 10⁴ to 1.79 × 10⁷ CFU/g and 1.47 × 10⁶ to 3.50 × 10⁸ CFU/g, respectively). Sixty-five florfenicol-resistant isolates were identified as Vibrio (81.5%) and Pseudoalteromonas (15.4%) using 16S rRNA gene sequence analysis. A high incidence of resistance to streptomycin (93.8%), oxytetracycline (89.2%), co-trimoxazole (84.6%), and kanamycin (73.8%) was exhibited by resistant isolates. A high proportion of isolates (76.9%) carried the florfenicol-resistance encoding genes floR and fexA, as well as plasmid DNA (75.0%). The high prevalence of multiresistant bacteria in live feed increases the incidence of the resistant microbiota in reared fish larvae, thus proper monitoring and management strategies for live feed cultures appear to be a priority for preventing future therapy failures in fish larval cultures.