Temporal resistome and microbial community dynamics in an intensive aquaculture facility with prophylactic antimicrobial treatment

Hemant J. Patil, 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, Eddie Cytryn

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Article number1984
Pages (from-to)1-17
Number of pages17
Issue number12
StatePublished - Dec 2020

Bibliographical note

Funding Information:
This study was supported by Israeli Ministry of Science and Technology (MOST) Infrastructure grant 3-10342. HP was funded by the Planning and Budgeting Committee (PBC) postdoctoral fellowship fund.

Publisher Copyright:
© 2020 by the authors. Licensee MDPI, Basel, Switzerland.


  • Antimicrobial resistance
  • Antimicrobials
  • Aquaculture
  • Metagenome
  • Microbiome
  • Resistome

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)
  • Virology


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