Dysbiosis and Restoration Dynamics of the Gut Microbiome Following Therapeutic Exposure to Florfenicol in Snubnose Pompano (Trachinotus blochii) to Aid in Sustainable Aquaculture Production Strategies

Understanding the transfer and persistence of antimicrobial resistance in aquaculture using a model teleost gut system

BACKGROUND

The development, progression, and dissemination of antimicrobial resistance (AMR) are determined by interlinked human, animal, and environmental drivers, which pose severe risks to human and livestock health. Conjugative plasmid transfer drives the rapid dissemination of AMR among bacteria. In addition to the judicious use and implementation of stewardship programs, mitigating the spread of antibiotic resistance requires an understanding of the dynamics of AMR transfer among microbial communities, as well as the role of various microbial taxa as potential reservoirs that promote long-term AMR persistence. Here, we employed Hi-C, a high-throughput, culture-free technique, combined with qPCR, to monitor carriage and transfer of a multidrug-resistent (MDR) plasmid within an Atlantic salmon in vitro gut model during florfenicol treatment, a benzenesulfonyl antibiotic widely deployed in fin-fish aquaculture.

RESULTS

Microbial communities from the pyloric ceaca of three healthy adult farmed salmon were inoculated into three bioreactors simulating the teleost gut, which were developed for the SalmoSim gut system. The model system was then inoculated with the Escherichia coli strain ATCC 25922 carrying the plasmid pM07-1 and treated with florfenicol at a concentration of 150 mg/L in fish feed media for 5 days prior to the washout/recovery phase. Hi-C and metagenomic sequencing identified numerous transfer events, including those involving gram-negative and gram-positive taxa, and, crucially, the transfer and persistence of the plasmid continued once florfenicol treatment was withdrawn.

CONCLUSIONS

Our findings highlight the role of the commensal teleost gut flora as a reservoir for AMR even once antimicrobial selective pressure has been withdrawn. Our system also provides a model to study how different treatment regimens and interventions may be deployed to mitigate AMR persistence.

Short-term dynamics of fecal microbiome and antibiotic resistance in juvenile rainbow trout (Oncorhynchus mykiss) following antibiotic treatment and withdrawal

BACKGROUND

In aquaculture, the secretions of cultured organisms contribute to the development of aquatic antibiotic resistance. However, the antibiotic-induced changes in fish feces remain poorly understood. This study aimed to assess the short-term dynamics of fecal microbiome and antibiotic resistance in juvenile rainbow trout (Oncorhynchus mykiss) upon antibiotic treatment and withdrawal period.

METHODS

Fish were orally administered diets supplemented with oxytetracycline (OTC) or sulfadiazine/trimethoprim (SDZ/TMP) for 10 consecutive days, followed by a 25-day withdrawal period. Fecal samples were collected before antibiotic treatment (day 0), and at 1, 3, 7, and 10 days post antibiotic administration (dpa), as well as 1, 3, 7, 14, and 25 days post antibiotic cessation (dpc). The fecal microbiome community was profiled using both culture-dependent and -independent methods. The relative abundance of antibiotic resistance genes (ARGs) and the class 1 integron-integrase gene (intI1) in the feces were quantified using real-time PCR.

RESULTS

Antibiotic treatment disrupted the fecal microbial communities, and this alteration persisted even after antibiotic cessation. Moreover, OTC treatment increased the relative abundance of tet genes, while sul and dfr genes increased in the SDZ/TMP-treated group. Notably, Flavobacterium, Pseudomonas, and Streptococcus exhibited a significant correlation with the abundance of ARGs, suggesting their potential role as carriers for ARGs.

CONCLUSION

This study demonstrates the antibiotic-induced changes in the fecal microbiome and the increase of ARGs in rainbow trout feces. These findings provide novel insights into the dynamics of microbiome recovery post-antibiotic cessation and suggest that fish feces provide a non-invasive approach to predict changes in the fish gut microbiome and resistome.

Recovery of intestinal microbial community in Penaeus vannamei after florfenicol perturbation

The concept and application of probiotic intervention for restoring intestinal microbial dysbiosis induced by antibiotics in aquaculture are still in early stages. This study aimed to investigate potential responses of various recovery strategies, including natural recovery and probiotic intervention, in restoring the growth and intestinal microbial community of Penaeus vannamei following florfenicol perturbation. The basal diet (control, CN) was supplemented with florfenicol (FC) or Lactobacillus plantarum W2 (LM) throughout the entire feeding trial. Meanwhile, the basal diet was supplemented with florfenicol for 7 days, followed by a period without florfenicol (natural recovery, FB), or with live strain W2 (probiotic recovery, FM), for a duration of 35 days. Results indicated that dietary supplementation of strain W2, whether continuous or following florfenicol perturbation, along with continuous florfenicol supplementation, significantly enhanced the growth performance of shrimp. Early natural recovery and probiotic intervention did not induce significant alterations in microbial diversity and community structure. Florfenicol perturbation resulted in a decrease in the abundance of potentially beneficial bacteria in intestinal microbial community of shrimp. However, both probiotic intervention and natural recovery strategies gradually reduced the abundance of potentially pathogenic bacteria while increasing the abundance of potentially beneficial ones. The robustness of microbial network decreased during florfenicol perturbation, showed gradual improvement during probiotic recovery, and remained relatively low during natural recovery and continuous florfenicol supplementation. Moreover, the microbial community composition in intestinal habitat significantly differed under various recovery strategies compared to the control. Notably, the microbial community composition of intestinal habitat following probiotic recovery exhibited greater similarity to that of continuous strain W2 supplementation without florfenicol perturbation. In summary, dietary supplementation of florfenicol perturbed intestinal microbial community stability of shrimp, whereas probiotic intervention and natural recovery facilitated the attainment of new stable states by altering keystone taxa. Considering intestinal microbial community stability of shrimp, the recovery of microbial community through probiotic intervention appears to be more effective than natural recovery.

Gut microbes of a high-value marine fish, Snubnose Pompano (Trachinotus blochii) are resilient to therapeutic dosing of oxytetracycline

Trachinotus blochii is a high-value tropical mariculture species. The present study evaluated the gut microbial impact of therapeutic exposure (80 mg/day/kg biomass for 10 days) to oxytetracycline, the most common aquaculture antibiotic in T. blochii. The cultivable counts, α-diversity measures of taxonomic and functional metagenomics, microbial dysbiosis (MD) index, and microbial taxon abundances showed the resilience of gut microbiota at 16-26 days of treatment. A significant reduction in bacterial abundance, diversity measures, Firmicutes and Actinobacteria and an increase in γ-Proteobacteria was recorded on the 6th and 11th day of treatment. The increased metagenomic stress signatures, decreased beneficial bacterial abundances, decreased abundance of microbial pathways on energy metabolism, and MD index indicated short-term transient stress during the initial days of therapeutic withdrawal, warranting health management measures. Therapeutic exposure reduced the abundance of fish pathogens, including Vibrio spp., kanamycin and ampicillin-resistant bacteria. Strikingly, oxytetracycline treatment did not increase tetracycline-resistant bacterial counts and the predicted abundance of tetracycline resistance encoding genes in the gut, illustrating that therapeutic application would not pose a risk in the context of antimicrobial resistance in short term. Altogether, the present study provides a foundation for oxytetracycline treatment to develop suitable risk minimization tactics in sustainable aquaculture.

Intestinal Histopathological Aberrations in Oreochromis niloticus Juveniles upon Dietary Florfenicol Administration

The aquaculture use of antibiotics can cause detrimental effects on fish organs and gut microbial dysbiosis. The impact of florfenicol (FFC) on fish intestinal histology, an approved antibiotic, remains unclear. This study aimed to investigate the effects of FFC on Oreochromis niloticus juveniles by administering FFC at 10 mg and 30 mg/kg biomass/day for 30 consecutive days to mimic long-term use. A dose-dependent reduction in feed intake, survival and biomass, with an upsurge in mortalities was observed. Even the therapeutic dose instigated mortalities on day 30 of FFC dosing (FD). Histopathological analysis revealed mild to moderate alterations, including loss of absorptive regions, epithelial degeneration, necrotized areas, intercellular enterocytic space and swollen laminar propria. Post-dosing, the observation of the detachment of lamina propria from the epithelium indicated imminent irritability. Goblet cells reduced drastically on day 30 FD, accompanied by an increase in intraepithelial lymphocytes. However, cessation of dosing for 13 days resulted in the reclamation of goblet cells and absorptive regions, indicating that the intestinal tissues underwent considerable repair after lifting antibiotic pressure. These findings suggested that O. niloticus can tolerate dietary FFC but emphasize the need for responsible use of antibiotics in aquaculture.

Effects of enrofloxacin's exposure on the gut microbiota of Tilapia fish (Oreochromis niloticus)

Enrofloxacin (ENFX) has a broad-spectrum antibiotic activity, which is widely used in aquaculture. The effect of different ENFX exposure ways on the gut microbiota of tilapia is unclear. This study was conducted to investigate the effects of ENFX exposure on the gut microbiota of tilapia fish (Oreochromis niloticus). Three methods of ENFX exposure were selected: injection (IEG), oral administration (OEG) and soaking (SEG). After 48 h of exposure period, the intestine of tilapia was collected for high-throughput sequencing. PCoA analysis revealed a distinct clustering of control group, and which was located rather far away from ENFX exposure groups. The dominant phyla in the gut microbiota of tilapia fish were Proteobacteria, Actinobacteriota, Fusobacteria and Firmicutes. Compared to the control group, phylum Fusobacteriota was increased in SEG and IEG while decreased in OEG. ENFX treatment led to a decline in Corynebacterium, Clostridium sensu stricto_3 and Bacillus in treated fish compared with control fish, accompanied by an increase in Akkermansia, Ralstonia and Romboutsia. IEG had the least effect on gut microbiota of tilapia because it retained more microbes among treatment groups. Alpha- diversity decreased the most in SEG, but retained more probiotics such as Cetobacterium and Akkermansia. We assessed the effect of enrofloxacin on tilapia by changes in intestinal flora. The result indicated that either exposure method significantly reduced the diversity of tilapia gut microbiota. It may provide basic data for the scientific use of ENFX in aquaculture.

Impacts of Oral Florfenicol Medication and Residues on the Kidney and Liver of Nile Tilapia Oreochromis niloticus (L.)

Florfenicol (FFC), an approved aquaculture antibiotic, is administered in feed at doses of 10-15 mg kg biomass^-1 day^-1 for 10 successive days. In this study, healthy Oreochromis niloticus were fed with 0-10 times the therapeutic dose of 15 mg kg biomass^-1 day^-1 for 10 days and tracked for 43 days post dosing. Assessments of residue accrual and depletion, oxidative stress, serum biochemistry, histopathology and extent of kidney and liver damages were made. FFC dosing reduced the feed intake significantly. The therapeutic dose produced no mortalities on day 10. Dose-dependent alterations in serum biochemistry were noted upon dosing. Several histopathological alterations were observed in the kidney and liver, which vindicated the toxic potentials of FFC. The residual FFC and florfenicol amine (FFA) accrual, depletion and oxidative stress responses, such as increased malondialdehyde, total nitric oxide, ferric reducing antioxidant power and reduced glutathione S-transferase activity, were documented. The dietary FFC persuaded the physiological state of O. niloticus, the effects of which normalized sparsely with time upon cessation of dosing at the higher doses. The study provided a brief outlook on the physiological responses upon oral FFC administration, which should be kept in mind during its application for fish health safety purposes.