Environmental Microbiology

Microbial Ecology

, Volume 59, Issue 3, pp 487-498

Molecular Ecology Of Macrolide–Lincosamide–Streptogramin B Methylases in Waste Lagoons and Subsurface Waters Associated with Swine Production

  • Satoshi KoikeAffiliated withDepartment of Animal Sciences, University of Illinois at Urbana-ChampaignResearch Faculty of Agriculture, Hokkaido University
  • , Rustam I. AminovAffiliated withRowett Institute of Nutrition and Health, University of Aberdeen
  • , A. C. YannarellAffiliated withDepartment of Animal Sciences, University of Illinois at Urbana-ChampaignInstitute for Genomic Biology, University of Illinois at Urbana-Champaign
  • , Holly D. GansAffiliated withDepartment of Animal Sciences, University of Illinois at Urbana-Champaign
  • , Ivan G. KrapacAffiliated withIllinois State Geological Survey
  • , Joanne C. Chee-SanfordAffiliated withUSDA Agricultural Research Service
  • , Roderick I. MackieAffiliated withDepartment of Animal Sciences, University of Illinois at Urbana-ChampaignInstitute for Genomic Biology, University of Illinois at Urbana-Champaign Email author 

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Abstract

RNA methylase genes are common antibiotic resistance determinants for multiple drugs of the macrolide, lincosamide, and streptogramin B (MLSB) families. We used molecular methods to investigate the diversity, distribution, and abundance of MLSB methylases in waste lagoons and groundwater wells at two swine farms with a history of tylosin (a macrolide antibiotic structurally related to erythromycin) and tetracycline usage. Phylogenetic analysis guided primer design for quantification of MLSB resistance genes found in tylosin-producing Streptomyces (tlr(B), tlr(D)) and commensal/pathogenic bacteria (erm(A), erm(B), erm(C), erm(F), erm(G), erm(Q)). The near absence of tlr genes at these sites suggested a lack of native antibiotic-producing organisms. The gene combination erm(ABCF) was found in all lagoon samples analyzed. These four genes were also detected with high frequency in wells previously found to be contaminated by lagoon leakage. A weak correlation was found between the distribution of erm genes and previously reported patterns of tetracycline resistance determinants, suggesting that dissemination of these genes into the environment is not necessarily linked. Considerations of gene origins in history (i.e., phylogeny) and gene distributions in the landscape provide a useful “molecular ecology” framework for studying environmental spread of antibiotic resistance.