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Article

Temporal Resistome and Microbial Community Dynamics in an Intensive Aquaculture Facility with Prophylactic Antimicrobial Treatment

1
Institute of Soil, Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, P.O. Box 15159, Rishon LeZion 7528809, Israel
2
Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 91905, Israel
3
Dor Aquaculture Research Station, Fisheries Department, Israel Ministry of Agriculture and Rural Development, Dor 3082000, Israel
4
The Dead Sea and Arava Science Center, Masada 86900, Israel
5
Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel
6
CosmosID Inc., Rockville, MD 20742, USA
7
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
8
Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA
*
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(12), 1984; https://doi.org/10.3390/microorganisms8121984
Received: 5 November 2020 / Revised: 9 December 2020 / Accepted: 10 December 2020 / Published: 13 December 2020
Excessive use of antimicrobials in aquaculture is concerning, given possible environmental ramifications and the potential contribution to the spread of antimicrobial resistance (AR). In this study, we explored seasonal abundance of antimicrobial resistance genes and bacterial community composition in the water column of an intensive aquaculture pond stocked with Silver Carp (Hypophthalmichthys molitrix) prophylactically treated with sulfamethoprim (25% sulfadiazine; 5% trimethoprim), relative to an adjacent unstocked reservoir. Bacterial community composition was monitored using high-throughput sequencing of 16S rRNA gene amplicons in eight sampling profiles to determine seasonal dynamics, representing principal stages in the fish fattening cycle. In tandem, qPCR was applied to assess relative abundance of selected antimicrobial resistance genes (sul1, sul2, dfrA1, tetA and blaTEM) and class-1 integrons (int1). Concomitantly, resistomes were extrapolated from shotgun metagenomes in representative profiles. Analyses revealed increased relative abundance of sulfonamide and tetracycline resistance genes in fishpond-03, relative to pre-stocking and reservoir levels, whereas no significant differences were observed for genes encoding resistance to antimicrobials that were not used in the fishpond-03. Seasons strongly dictated bacterial community composition, with high abundance of cyanobacteria in summer and increased relative abundance of Flavobacterium in the winter. Our results indicate that prophylactic use of sulfonamides in intensive aquaculture ponds facilitates resistance suggesting that prophylactic use of these antimicrobials in aquaculture should be restricted. View Full-Text
Keywords: antimicrobials; antimicrobial resistance; aquaculture; metagenome; microbiome; resistome antimicrobials; antimicrobial resistance; aquaculture; metagenome; microbiome; resistome
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MDPI and ACS Style

Patil, H.J.; Gatica, J.; Zolti, A.; Benet-Perelberg, A.; Naor, A.; Dror, B.; Al Ashhab, A.; Marman, S.; Hasan, N.A.; Colwell, R.R.; Sher, D.; Minz, D.; Cytryn, E. Temporal Resistome and Microbial Community Dynamics in an Intensive Aquaculture Facility with Prophylactic Antimicrobial Treatment. Microorganisms 2020, 8, 1984. https://doi.org/10.3390/microorganisms8121984

AMA Style

Patil HJ, Gatica J, Zolti A, Benet-Perelberg A, Naor A, Dror B, Al Ashhab A, Marman S, Hasan NA, Colwell RR, Sher D, Minz D, Cytryn E. Temporal Resistome and Microbial Community Dynamics in an Intensive Aquaculture Facility with Prophylactic Antimicrobial Treatment. Microorganisms. 2020; 8(12):1984. https://doi.org/10.3390/microorganisms8121984

Chicago/Turabian Style

Patil, Hemant J., Joao Gatica, Avihai Zolti, Ayana Benet-Perelberg, Alon Naor, Barak Dror, Ashraf Al Ashhab, Sophi Marman, Nur A. Hasan, Rita R. Colwell, Daniel Sher, Dror Minz, and Eddie Cytryn. 2020. "Temporal Resistome and Microbial Community Dynamics in an Intensive Aquaculture Facility with Prophylactic Antimicrobial Treatment" Microorganisms 8, no. 12: 1984. https://doi.org/10.3390/microorganisms8121984

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