1887

Abstract

The ecosystem is continuously exposed to a wide variety of antimicrobials through waste effluents, agricultural run-offs and animal-related and anthropogenic activities, which contribute to the spread of antibiotic resistance genes (ARGs). The contamination of ecosystems with ARGs may create increased opportunities for their transfer to naive microbes and eventually lead to entry into the human food chain. Transduction is a significant mechanism of horizontal gene transfer in natural environments, which has traditionally been underestimated as compared to transformation. We explored the presence of ARGs in environmental bacteriophages in order to recognize their contribution in the spread of ARGs in environmental settings. Bacteriophages were isolated against environmental bacterial isolates, purified and bulk cultured. They were characterized, and detection of ARG and genes including , , , , , and was carried out by PCR. This study revealed the presence of various genes [ (12.7 %), (10.9 %), (10.9 %), (9.1 %), (9.1 %) and (3.6 %)] and in a significantly higher proportion (30.9 %). , , , , , and were not detected in any of the phages. Soil phages were the most versatile in terms of ARG carriage. Also, the relative abundance of differed significantly vis-à-vis source. The phages from organized farms showed varied ARGs as compared to the unorganized sector, although ARG incidences did not differ significantly. The study reflects on the role of phages in dissemination of ARGs in environmental reservoirs, which may provide an early warning system for future clinically relevant resistance mechanisms.

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2016-12-16
2020-01-22
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References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J.. 1990; Basic local alignment search tool. J Mol Biol215:403–410 [CrossRef][PubMed]
    [Google Scholar]
  2. Anand T., Vaid R. K., Bera B. C., Singh J., Barua S., Virmani N., Rajukumar K., Yadav N. K., Nagar D. et al. 2016; Isolation of a lytic bacteriophage against virulent Aeromonas hydrophila from an organized equine farm. J Basic Microbiol56:432–437 [CrossRef][PubMed]
    [Google Scholar]
  3. Arutyunov D., Frost L. S.. 2013; F conjugation: back to the beginning. Plasmid70:18–32 [CrossRef][PubMed]
    [Google Scholar]
  4. Balcazar J. L.. 2014; Bacteriophages as vehicles for antibiotic resistance genes in the environment. PLoS Pathog10:e1004219 [CrossRef][PubMed]
    [Google Scholar]
  5. Bali E. B., Acik L., Sultan N.. 2010; Phenotypic and molecular characterization of SHV, TEM, and CTX-M extended-spectrum β-lactamase produced by Escherichia coli, Acinetobacter baumannii and Klebsiella isolates in a Turkish hospital. Afr J Microbiol Res4:650–654
    [Google Scholar]
  6. Balsalobre L. C., Dropa M., de Oliveira D. E., Lincopan N., Mamizuka E. M., Matté G. R., Matté M. H.. 2010; Presence of bla TEM-116 gene in environmental isolates of Aeromonas hydrophila and Aeromonas jandaei from Brazil. Braz J Microbiol41:718–719 [CrossRef][PubMed]
    [Google Scholar]
  7. Berglund B., Fick J., Lindgren P. E.. 2015; Urban wastewater effluent increases antibiotic resistance gene concentrations in a receiving northern European river. Environ Toxicol Chem34:192–196 [CrossRef][PubMed]
    [Google Scholar]
  8. Boucher Y., Labbate M., Koenig J. E., Stokes H. W.. 2007; Integrons: mobilizable platforms that promote genetic diversity in bacteria. Trends Microbiol15:301–309 [CrossRef][PubMed]
    [Google Scholar]
  9. Bush K., Jacoby G. A., Medeiros A. A.. 1995; A functional classification scheme for beta-lactamases and its correlation with molecular structure. Antimicrob Agents Chemother39:1211–1233 [CrossRef][PubMed]
    [Google Scholar]
  10. Bush K., Jacoby G. A.. 2010; Updated functional classification of beta-lactamases. Antimicrob Agents Chemother54:969–976 [CrossRef][PubMed]
    [Google Scholar]
  11. Calero-Cáceres W., Muniesa M.. 2016; Persistence of naturally occurring antibiotic resistance genes in the bacteria and bacteriophage fractions of wastewater. Water Res95:11–18 [CrossRef][PubMed]
    [Google Scholar]
  12. Colomer-Lluch M., Imamovic L., Jofre J., Muniesa M.. 2011a; Bacteriophages carrying antibiotic resistance genes in fecal waste from cattle, pigs, and poultry. Antimicrob Agents Chemother55:4908–4911 [CrossRef]
    [Google Scholar]
  13. Colomer-Lluch M., Jofre J., Muniesa M.. 2011b; Antibiotic resistance genes in the bacteriophage DNA fraction of environmental samples. PLoS One6:e17549 [CrossRef]
    [Google Scholar]
  14. Colomer-Lluch M., Calero-Cáceres W., Jebri S., Hmaied F., Muniesa M., Jofre J.. 2014a; Antibiotic resistance genes in bacterial and bacteriophage fractions of Tunisian and Spanish wastewaters as markers to compare the antibiotic resistance patterns in each population. Environ Int73:167–175 [CrossRef]
    [Google Scholar]
  15. Colomer-Lluch M., Jofre J., Muniesa M.. 2014b; Quinolone resistance genes (qnrA and qnrS) in bacteriophage particles from wastewater samples and the effect of inducing agents on packaged antibiotic resistance genes. J Antimicrob Chemother69:1265–1274 [CrossRef]
    [Google Scholar]
  16. Czekalski N., Sigdel R., Birtel J., Matthews B., Bürgmann H.. 2015; Does human activity impact the natural antibiotic resistance background? Abundance of antibiotic resistance genes in 21 Swiss lakes. Environ Int81:45–55 [CrossRef][PubMed]
    [Google Scholar]
  17. Daghrir R., Drogui P.. 2013; Tetracycline antibiotics in the environment: a review. Env Chem Lett11:209–227 [CrossRef]
    [Google Scholar]
  18. Dinsdale E. A., Edwards R. A., Hall D., Angly F., Breitbart M., Brulc J. M., Furlan M., Desnues C., Haynes M. et al. 2008; Functional metagenomic profiling of nine biomes. Nature452:629–632 [CrossRef]
    [Google Scholar]
  19. Economou V., Gousia P.. 2015; Agriculture and food animals as a source of antimicrobial-resistant bacteria. Infect Drug Resist8:49–61 [CrossRef][PubMed]
    [Google Scholar]
  20. Enault F., Briet A., Bouteille L., Roux S., Sullivan M. B., Petit M. A.. 2016; Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses. ISME J doi:10.1038/ismej.2016.90 [CrossRef][PubMed]
    [Google Scholar]
  21. Escudero J. A., Loot C., Nivina A., Mazel D.. 2015; The integron: adaptation on demand. Microbiol Spectr3:MDNA3-0019-2014 [CrossRef][PubMed]
    [Google Scholar]
  22. Figueroa-Bossi N., Uzzau S., Maloriol D., Bossi L.. 2001; Variable assortment of prophages provides a transferable repertoire of pathogenic determinants in Salmonella. Mol Microbiol39:260–272 [CrossRef][PubMed]
    [Google Scholar]
  23. Giowanella M., Bozza A., do Rocio Dalzoto P., Dionísio J. A., Andraus S., Guimarães E. L., Pimentel I. C.. 2015; Microbiological quality of water from the rivers of Curitiba, Paraná State, Brazil, and the susceptibility to antimicrobial drugs and pathogenicity of Escherichia coli. Environ Monit Assess187:673 [CrossRef][PubMed]
    [Google Scholar]
  24. Graham D. W., Knapp C. W., Christensen B. T., McCluskey S., Dolfing J.. 2016; Appearance of β-lactam resistance genes in agricultural soils and clinical isolates over the 20th century. Sci Rep6:21550 [CrossRef][PubMed]
    [Google Scholar]
  25. Graves A. K., Liwimbi L., Israel D. W., van Heugten E., Robinson B., Cahoon C. W., Lubbers J. F.. 2011; Distribution of ten antibiotic resistance genes in E. coli isolates from swine manure, lagoon effluent and soil collected from a lagoon waste application field. Folia Microbiol56:131–137 [CrossRef][PubMed]
    [Google Scholar]
  26. Harford N., Mergeay M.. 1973; Interspecific transformation of rifampicin resistance in the genus Bacillus. Mol Gen Genet120:151–155 [CrossRef][PubMed]
    [Google Scholar]
  27. Hodgson D. A.. 2000; Generalized transduction of serotype 1/2 and serotype 4b strains of Listeria monocytogenes. Mol Microbiol35:312–323 [CrossRef][PubMed]
    [Google Scholar]
  28. Jechalke S., Broszat M., Lang F., Siebe C., Smalla K., Grohmann E.. 2015; Effects of 100 years wastewater irrigation on resistance genes, class 1 integrons and IncP-1 plasmids in Mexican soil. Front Microbiol6:163 [CrossRef][PubMed]
    [Google Scholar]
  29. Kyselková M., Jirout J., Vrchotová N., Schmitt H., Elhottová D.. 2015; Spread of tetracycline resistance genes at a conventional dairy farm. Front Microbiol6:536 [CrossRef][PubMed]
    [Google Scholar]
  30. Ladrón N., Fernández M., Agüero J., González Zörn B., Vázquez-Boland J. A., Navas J., Zorn B. G., González B.. 2003; Rapid identification of Rhodococcus equi by a PCR assay targeting the choE gene. J Clin Microbiol41:3241–3245 [CrossRef][PubMed]
    [Google Scholar]
  31. Lahlaoui H., Dahmen S., Moussa M. B., Omrane B.. 2011; First detection of TEM-116 extended-spectrum β-lactamase in a Providencia stuartii isolate from a Tunisian hospital. Indian J Med Microbiol29:258–261 [CrossRef][PubMed]
    [Google Scholar]
  32. Lindsay J. A., Holden M. T.. 2004; Staphylococcus aureus: superbug, super genome?. Trends Microbiol12:378–385 [CrossRef][PubMed]
    [Google Scholar]
  33. Livermore D. M.. 1995; beta-Lactamases in laboratory and clinical resistance. Clin Microbiol Rev8:557–584[PubMed]
    [Google Scholar]
  34. Marti E., Jofre J., Balcazar J. L.. 2013; Prevalence of antibiotic resistance genes and bacterial community composition in a river influenced by a wastewater treatment plant. PLoS One8:e78906 [CrossRef]
    [Google Scholar]
  35. Marti E., Variatza E., Balcázar J. L.. 2014; Bacteriophages as a reservoir of extended-spectrum β-lactamase and fluoroquinolone resistance genes in the environment. Clin Microbiol Infect20:O456–O459 [CrossRef][PubMed]
    [Google Scholar]
  36. Mazaheri N. F. R., Barton M. D., Heuzenroeder M. W.. 2011; Bacteriophage-mediated transduction of antibiotic resistance in enterococci: transduction in Enterococcus spp. Lett Appl Microbiol52:559–564[CrossRef]
    [Google Scholar]
  37. Mazel D.. 2004; Integrons and the origin of antibiotic resistance gene cassettes. ASM News70:520–525
    [Google Scholar]
  38. Miranda C. D., Tello A., Keen P. L.. 2013; Mechanisms of antimicrobial resistance in finfish aquaculture environments. Front Microbiol4:233–237 [CrossRef][PubMed]
    [Google Scholar]
  39. Muniesa M., García A., Miró E., Mirelis B., Prats G., Jofre J., Navarro F.. 2004; Bacteriophages and diffusion of beta-lactamase genes. Emerg Infect Dis10:1134–1137 [CrossRef][PubMed]
    [Google Scholar]
  40. Muniesa M., Colomer-Lluch M., Jofre J.. 2013; Could bacteriophages transfer antibiotic resistance genes from environmental bacteria to human-body associated bacterial populations?. Mob Genet Elements3:e25847 [CrossRef][PubMed]
    [Google Scholar]
  41. Murugan K., Prabhakaran P., Al-Sohaibani S., Sekar K.. 2012; Identification of source of faecal pollution of Tirumanimuttar River, Tamilnadu, India using microbial source tracking. Environ Monit Assess184:6001–6012 [CrossRef][PubMed]
    [Google Scholar]
  42. Paterson D. L., Hujer K. M., Hujer A. M., Yeiser B., Bonomo M. D., Rice L. B., Bonomo R. A.. International Klebsiella Study Group 2003; Extended-spectrum β-lactamases in Klebsiella pneumoniae bloodstream isolates from seven countries: dominance and widespread prevalence of SHV- and CTX-M-type β-lactamases. Antimicrob Agents Chemother47:3554–3560 [CrossRef][PubMed]
    [Google Scholar]
  43. Pruden A., Arabi M., Storteboom H. N.. 2012; Correlation between upstream human activities and riverine antibiotic resistance genes. Environ Sci Technol46:11541–11549 [CrossRef][PubMed]
    [Google Scholar]
  44. Prudhomme M., Attaiech L., Sanchez G., Martin B., Claverys J. P.. 2006; Antibiotic stress induces genetic transformability in the human pathogen Streptococcus pneumoniae. Science313:89–92 [CrossRef][PubMed]
    [Google Scholar]
  45. Roberts M. C.. 2005; Update on acquired tetracycline resistance genes. FEMS Microbiol Lett245:195–203 [CrossRef][PubMed]
    [Google Scholar]
  46. Ross J., Topp E.. 2015; Abundance of antibiotic resistance genes in bacteriophage following soil fertilization with dairy manure or municipal biosolids, and evidence for potential transduction. Appl Environ Microbiol81:7905–7913 [CrossRef][PubMed]
    [Google Scholar]
  47. Schmieger H., Schicklmaier P.. 1999; Transduction of multiple drug resistance of Salmonella enterica serovar typhimurium DT104. FEMS Microbiol Lett170:251–256 [CrossRef][PubMed]
    [Google Scholar]
  48. Schwarz S., Kehrenberg C., Doublet B., Cloeckaert A.. 2004; Molecular basis of bacterial resistance to chloramphenicol and florfenicol. FEMS Microbiol Rev28:519–542 [CrossRef][PubMed]
    [Google Scholar]
  49. Smillie C., Garcillán-Barcia M. P., Francia M. V., Rocha E. P., de la Cruz F.. 2010; Mobility of plasmids. Microbiol Mol Biol Rev74:434–452 [CrossRef][PubMed]
    [Google Scholar]
  50. Sparling P. F.. 1966; Genetic transformation of Neisseria gonorrhoeae to streptomycin resistance. J Bacteriol92:1364–1371[PubMed]
    [Google Scholar]
  51. Speer B. S., Shoemaker N. B., Salyers A. A.. 1992; Bacterial resistance to tetracycline: mechanisms, transfer, and clinical significance. Clin Microbiol Rev5:387–399 [CrossRef]
    [Google Scholar]
  52. Su H. C., Ying G. G., Tao R., Zhang R. Q., Fogarty L. R., Kolpin D. W.. 2011; Occurrence of antibiotic resistance and characterization of resistance genes and integrons in Enterobacteriaceae isolated from integrated fish farms in South China. J Environ Monit13:3229–3236 [CrossRef][PubMed]
    [Google Scholar]
  53. Subirats J., Sànchez-Melsió A., Borrego C. M., Balcázar J. L., Simonet P.. 2016; Metagenomic analysis reveals that bacteriophages are reservoirs of antibiotic resistance genes. Int J Antimicrob Agents48:163–167 [CrossRef][PubMed]
    [Google Scholar]
  54. Vignoli R., Varela G., Mota M. I., Cordeiro N. F., Power P., Ingold E., Gadea P., Sirok A., Schelotto F. et al. 2005; Enteropathogenic Escherichia coli strains carrying genes encoding the PER-2 and TEM-116 extended-spectrum β-lactamases isolated from children with diarrhea in Uruguay. J Clin Microbiol43:2940–2943 [CrossRef][PubMed]
    [Google Scholar]
  55. Walsh T. R., Toleman M. A., Jones R. N.. 2007; Comment on: occurrence, prevalence and genetic environment of CTX-M β-lactamases in Enterobacteriaceae from Indian hospitals. J Antimicrob Chemother60:187–188[CrossRef]
    [Google Scholar]
  56. Xu J., Xu Y., Wang H., Guo C., Qiu H., He Y., Zhang Y., Li X., Meng W.. 2015; Occurrence of antibiotics and antibiotic resistance genes in a sewage treatment plant and its effluent-receiving river. Chemosphere119:1379–1385 [CrossRef][PubMed]
    [Google Scholar]
  57. Yin Q., Yue D., Peng Y., Liu Y., Xiao L.. 2013; Occurrence and distribution of antibiotic-resistant bacteria and transfer of resistance genes in Lake Taihu. Microbes Environ28:479–486 [CrossRef][PubMed]
    [Google Scholar]
  58. Zechner E. L., Lang S., Schildbach J. F.. 2012; Assembly and mechanisms of bacterial type IV secretion machines. Philos Trans R Soc Lond B Biol Sci367:1073–1087 [CrossRef][PubMed]
    [Google Scholar]
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