Korean Journal of Environmental Agriculture (한국환경농학회지)

The Korean Society of Environmental Agriculture (한국환경농학회)
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Co-occurrence Analyses of Antibiotic Resistance Genes and Microbial Community in Human and Livestock Animal Feces

사람 및 가축 유래 분변 미생물 군집과 항생제 내성 유전자 간 상관 관계에 대한 연구

  • Jiwon Jeong (Molecular Biotechnology (Faculty of Biotechnology), College of Applied Life Sciences, Jeju National University) ;
  • Aprajita Bhandari (Molecular Biotechnology (Faculty of Biotechnology), College of Applied Life Sciences, Jeju National University) ;
  • Tatsuya Unno (Molecular Biotechnology (Faculty of Biotechnology), College of Applied Life Sciences, Jeju National University)
  • 정지원 (제주대학교 생명자원과학대학 분자생명공학전공(생명공학부)) ;
  • 반다리 아프라지타 (제주대학교 생명자원과학대학 분자생명공학전공(생명공학부)) ;
  • 운노 타쯔야 (제주대학교 생명자원과학대학 분자생명공학전공(생명공학부))
  • Received : 2022.12.15
  • Accepted : 2022.12.21
  • Published : 2022.12.31
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Abstract

BACKGROUND: Antibiotics used in animal husbandry for disease prevention and treatment have resulted in the rapid progression of antibiotic resistant bacteria which can be introduced into the environment through livestock feces/manure, disseminating antibiotic resistant genes (ARGs). In this study, fecal samples were collected from the livestock farms located in Jeju Island to investigate the relationship between microbial communities and ARGs. METHODS AND RESULTS: Illumina MiSeq sequencing was applied to characterize microbial communities within each fecal sample. Using quantitative PCR (qPCR), ten ARGs encoding tetracycline resistance (tetB, tetM), sulfonamide resistance (sul1, sul2), fluoroquinolone resistance (qnrD, qnrS), fluoroquinolone and aminoglycoside resistance (aac(6')-Ib), beta-lactam resistance (blaTEM, blaCTX-M), macrolide resistance (ermC), a class 1 integronsintegrase gene (intI1), and a class 2 integrons-integrase gene (intI2) were quantified. The results showed that Firmicutes and Bacteroidetes were dominant in human, cow, horse, and pig groups, while Firmicutes and Actinobacteria were dominant in chicken group. Among ARGs, tetM was detected with the highest number of copies, followed by sul1 and sul2. Most of the genera belonging to Firmicutes showed positive correlations with ARGs and integron genes. There were 97, 34, 31, 25, and 22 genera in chicken, cow, pig, human, and horse respectively which showed positive correlations with ARGs and integron genes. In network analysis, we identified diversity of microbial communities which correlated with ARGs and integron genes. CONCLUSION(S): In this study, antibiotic resistance patterns in human and livestock fecal samples were identified. The abundance of ARGs and integron genes detected in the samples were associated with the amount of antibiotics commonly used for human and livestocks. We found diverse microbial communities associated with antibiotics resistance genes in different hosts, suggesting that antibiotics resistance can disseminate across environments through various routes. Identifying the routes of ARG dissemination in the environment would be the first step to overcome the challenge of antibiotic resistance in the future.

Keywords

Acknowledgement

This research was supported by the 2022 scientific promotion program funded by Jeju National University.

References

  1. Liu B, Pop M (2009) ARDB-antibiotic resistance genes database. Nucleic Acids Research, 37(suppl_1), D443-D447. https://doi.org/10.1093/nar/gkn656.
  2. Viola C, DeVincent SJ (2006) Overview of issues pertaining to the manufacture, distribution, and use of antimicrobials in animals and other information relevant to animal antimicrobial use data collection in the United States. Preventive Veterinary Medicine, 73(2-3), 111-131. https://doi.org/10.1016/j.prevetmed.2005.09.020.
  3. O'Neill J (2014) Antimicrobial resistance: Tackling a crisis for the health and wealth of nations, Review on Antimicrobial Resistance, UK, p. 6.
  4. Van Boeckel TP, Brower C, Gilbert M, Grenfell BT, Levin SA, Robinson TP, Teillant A, Laxminarayan R (2015) Global trends in antimicrobial use in food animals. Proceedings of the National Academy of Sciences, 112(18), 5649-5654. https://doi.org/10.1073/pnas.1503141112.
  5. Chantziaras I, Boyen F, Callens B, Dewulf J (2014) Correlation between veterinary antimicrobial use and antimicrobial resistance in food-producing animals: A report on seven countries. Journal of Antimicrobial Chemotherapy, 69(3), 827-834. https://doi.org/10.1093/jac/dkt443.
  6. He L-Y, Ying G-G, Liu Y-S, Su H-C, Chen J, Liu S-S, Zhao J-L (2016) Discharge of swine wastes risks water quality and food safety: Antibiotics and antibiotic resistance genes from swine sources to the receiving environments. Environment International, 92, 210-219. https://doi.org/10.1016/j.envint.2016.03.023.
  7. Mu Q, Li J, Sun Y, Mao D, Wang Q, Luo Y (2015) Occurrence of sulfonamide-, tetracycline-, plasmidmediated quinolone-and macrolide-resistance genes in livestock feedlots in Northern China. Environmental Science and Pollution Research, 22(9), 6932-6940. https://doi.org/10.1007/s11356-014-3905-5.
  8. Pu Q, Zhao L-X, Li Y-T, Su J-Q (2020) Manure fertilization increase antibiotic resistance in soils from typical greenhouse vegetable production bases, China. Journal of Hazardous Materials, 391, 122267. https://doi.org/10.1016/j.jhazmat.2020.122267.
  9. Chee Sanford JC, Mackie RI, Koike S, Krapac IG, Lin YF, Yannarell AC, Maxwell S, Aminov RI (2009) Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste. Journal of Environmental Quality, 38(3), 1086-1108. https://doi.org/10.2134/jeq2008.0128.
  10. Forsberg KJ, Reyes A, Wang B, Selleck EM, Sommer MO, Dantas G (2012) The shared antibiotic resistome of soil bacteria and human pathogens. Science, 337(6098), 1107-1111. https://10.1126/science.1220761.
  11. Zhao Y, Yang QE, Zhou X, Wang F-H, Muurinen J, Virta MP, Brandt KK, Zhu Y-G (2021) Antibiotic resistome in the livestock and aquaculture industries: Status and solutions. Critical Reviews in Environmental Science and Technology, 51(19), 2159-2196. https://doi.org/10.1080/10643389.2020.1777815.
  12. Burch TR, Stokdyk JP, Firnstahl AD, Kieke Jr BA, Cook RM, Opelt SA, Spencer SK, Durso LM, Borchardt MA (2022) Microbial source tracking and land use associations for antibiotic resistance genes in private wells influenced by human and livestock fecal sources. Journal of Environmental Quality. https://doi.org/10.1002/jeq2.20443.
  13. Li W, Su H, Cao Y, Wang L, Hu X, Xu W, Xu Y, Li Z, Wen G (2020) Antibiotic resistance genes and bacterial community dynamics in the seawater environment of Dapeng Cove, South China. Science of The Total Environment, 723, 138027. https://doi.org/10.1016/j.scitotenv.2020.138027.
  14. An X-L, Chen Q-L, Zhu D, Zhu Y-G, Gillings MR, Su J-Q (2018) Impact of wastewater treatment on the prevalence of integrons and the genetic diversity of integron gene cassettes. Applied and Environmental Microbiology, 84(9), e02766-17. https://doi.org/10.1128/AEM.02766-17.
  15. Krauland MG, Marsh JW, Paterson DL, Harrison LH (2009) Integron-mediated multidrug resistance in a global collection of nontyphoidal Salmonella enterica isolates. Emerging Infectious Diseases, 15(3), 388. https://10.3201/eid1503.081131.
  16. Blake KS, Choi J, Dantas G (2021) Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria. Cellular and Molecular Life Sciences, 78(6), 2585-2606. https://doi.org/10.1007/s00018-020-03717-2.
  17. Yang Y, Li B, Ju F, Zhang T (2013) Exploring variation of antibiotic resistance genes in activated sludge over a four-year period through a metagenomic approach. Environmental Science & Technology, 47(18), 10197- 10205. https://doi.org/10.1021/es4017365.
  18. Crossette E, Gumm J, Langenfeld K, Raskin L, Duhaime M, Wigginton K (2021) Metagenomic quantification of genes with internal standards. MBio, 12(1), e03173-e03220. https://doi.org/10.1128/mBio.03173-20.
  19. Li B, Yang Y, Ma L, Ju F, Guo F, Tiedje J M, Zhang T (2015) Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. The ISME Journal, 9(11), 2490-2502. https://doi.org/10.1038/ismej.2015.59.
  20. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO (2012) The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Research, 41(D1), D590-D596. https://doi.org/10.1093/nar/gks1219.
  21. Rognes T, Flouri T, Nichols B, Quince C, Mahe F (2016) VSEARCH: A versatile open source tool for metagenomics. PeerJ, 4, e2584. https://doi.org/10.7717/peerj.2584.
  22. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH et al. (2009) Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75(23), 7537-7541. https://doi.org/10.1128/AEM.01541-09.
  23. Jang HM, Kim YB, Choi S, Lee Y, Shin SG, Unno T, Kim YM (2018) Prevalence of antibiotic resistance genes from effluent of coastal aquaculture, South Korea. Environmental Pollution, 233, 1049-1057. https://doi.org/10.1016/j.envpol.2017.10.006.
  24. Jechalke S, Heuer H, Siemens J, Amelung W, Smalla K (2014) Fate and effects of veterinary antibiotics in soil. Trends in Microbiology, 22(9), 536-545. https://doi.org/10.1016/j.tim.2014.05.005.
  25. Song L, Jiang G, Wang C, Ma J, Chen H (2022) Effects of antibiotics consumption on the behavior of airborne antibiotic resistance genes in chicken farms. Journal of Hazardous Materials, 129288. https://doi.org/10.1016/j.jhazmat.2022.129288.
  26. Byrne-Bailey K, Gaze W, Kay P, Boxall A, Hawkey P, Wellington E (2009) Prevalence of sulfonamide resistance genes in bacterial isolates from manured agricultural soils and pig slurry in the United Kingdom. Antimicrobial Agents and Chemotherapy, 53(2), 696-702. https://doi.org/10.1128/AAC.00652-07.
  27. Mao D, Yu S, Rysz M, Luo Y, Yang F, Li F, Hou J, Mu Q, Alvarez P (2015) Prevalence and proliferation of antibiotic resistance genes in two municipal wastewater treatment plants. Water Research, 85, 458-466. https://doi.org/10.1016/j.watres.2015.09.010.
  28. Speldooren V, Heym B, Labia R, Nicolas-Chanoine M-H (1998) Discriminatory detection of inhibitorresistant β-lactamases in Escherichia coli by singlestrand conformation polymorphism-PCR. Antimicrobial Agents and Chemotherapy, 42(4), 879-884. https://doi.org/10.1128/AAC.42.4.879.
  29. Henriques IS, Fonseca F, Alves A, Saavedra MJ, Correia A (2006) Occurrence and diversity of integrons and β-lactamase genes among ampicillin-resistant isolates from estuarine waters. Research in Microbiology, 157(10), 938-947. https://doi.org/10.1016/j.resmic.2006.09.003.
  30. Pei R, Kim S-C, Carlson KH, Pruden A (2006) Effect of river landscape on the sediment concentrations of antibiotics and corresponding antibiotic resistance genes (ARG). Water Research, 40(12), 2427-2435. https://doi.org/10.1016/j.watres.2006.04.017.
  31. Park CH, Robicsek A, Jacoby GA, Sahm D, Hooper DC (2006) Prevalence in the United States of aac(6')-Ib-cr encoding a ciprofloxacin-modifying enzyme. Antimicrobial Agents and Chemotherapy, 50(11), 3953-3955. https://doi.org/10.1128/AAC.00915-06.
  32. Knapp CW, Dolfing J, Ehlert PA, Graham DW (2010) Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940. Environmental Science & Technology, 44(2), 580-587. https://doi.org/10.1021/es901221x.
  33. Luo Y, Mao D, Rysz M, Zhou Q, Zhang H, Xu L, JJ Alvarez P (2010) Trends in antibiotic resistance genes occurrence in the Haihe River, China. Environmental Science & Technology, 44(19), 7220-7225. https://doi.org/10.1021/es100233w.
  34. Goldstein C, Lee MD, Sanchez S, Hudson C, Phillips B, Register B, Grady M, Liebert C, Summers AO, White DG (2001) Incidence of class 1 and 2 integrases in clinical and commensal bacteria from livestock, companion animals, and exotics. Antimicrobial Agents and Chemotherapy, 45(3), 723-726. https://doi.org/10.1128/AAC.45.3.723-726.2001.