Context matters - the complex interplay between resistome genotypes and resistance phenotypes

Current Opinion in Microbiology

Volumn 15, Issue 5, 2012, Pages 577-582

  Dantas, Gautam ^a   Sommer, Morten OA ^b,c  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^c Chalmers University of Technology   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

BETA LACTAMASE; CEPHALOSPORIN; GENOMIC DNA; VANCOMYCIN;

ANTIBIOTIC BIOSYNTHESIS; ANTIBIOTIC RESISTANCE; DISEASE CARRIER; DNA EXTRACTION; ECOLOGICAL NICHE; ENZYMATIC DEGRADATION; ESCHERICHIA COLI; EXPRESSION VECTOR; GENE CLUSTER; GENE OVEREXPRESSION; GENOTYPE; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; HORIZONTAL GENE TRANSFER; KLUYVERA; LUNG INFECTION; MICROBIAL COMMUNITY; NONHUMAN; OCHROBACTRUM ANTHROPI; PHENOTYPE; PRECURSOR; PSEUDOMONAS FLUORESCENS; REVIEW; SILENT GENE; STREPTOMYCETACEAE;

ANIMALS; ANTI-BACTERIAL AGENTS; BACTERIA; BACTERIAL INFECTIONS; ENVIRONMENTAL MICROBIOLOGY; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; GENOTYPE; HUMANS; PHENOTYPE;

BACTERIA (MICROORGANISMS);

EID: 84868152309     PISSN: 13695274     EISSN: 18790364     Source Type: Journal    
DOI: 10.1016/j.mib.2012.07.004     Document Type: Review

References (61)

1. Allen H.K., Donato J., Wang H.H., Cloud-Hansen K.A., Davies J., Handelsman J. Call of the wild: antibiotic resistance genes in natural environments. Nat Rev Microbiol 2010, 8:251-259.
2. Lester C.H., Frimodt-Moller N., Sorensen T.L., Monnet D.L., Hammerum A.M. In vivo transfer of the vanA resistance gene from an Enterococcus faecium isolate of animal origin to an E. faecium isolate of human origin in the intestines of human volunteers. Antimicrob Agents Chemother 2006, 50:596-599.
3. Shoemaker N.B., Vlamakis H., Hayes K., Salyers A.A. Evidence for extensive resistance gene transfer among Bacteroides spp. and among Bacteroides and other genera in the human colon. Appl Environ Microbiol 2001, 67:561-568.
4. de la Cruz F., Davies J. Horizontal gene transfer and the origin of species: lessons from bacteria. Trends Microbiol 2000, 8:128-133.
5. Salyers A.A., Shoemaker N.B., Stevens A.M., Li L.Y. Conjugative transposons - an unusual and diverse set of integrated gene-transfer elements. Microbiol Rev 1995, 59:579.
6. Sommer M.O., Dantas G. Antibiotics and the resistant microbiome. Curr Opin Microbiol 2011, 14:556-563.
7. Sommer M.O., Dantas G., Church G.M. Functional characterization of the antibiotic resistance reservoir in the human microflora. Science 2009, 325:1128-1131.
8. Moore A.M., Munck C., Sommer M.O.A., Dantas G. Functional metagenomic investigations of the human intestinal microbiota. Front Microb 2011, 2.
9. Vignaroli C., Zandri G., Aquilanti L., Pasquaroli S., Biavasco F. Multidrug-resistant enterococci in animal meat and faeces and co-transfer of resistance from an Enterococcus durans to a human Enterococcus faecium. Curr Microbiol 2011, 62:1438-1447.
10. Martinez J.L. Antibiotics and antibiotic resistance genes in natural environments. Science 2008, 321:365-367.
11. Baquero F., Martinez J.L., Canton R. Antibiotics and antibiotic resistance in water environments. Curr Opin Biotechnol 2008, 19:260-265.
12. Davies J., Davies D. Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 2010, 74:417-433.
13. Allen H.K., Moe L.A., Rodbumrer J., Gaarder A., Handelsman J. Functional metagenomics reveals diverse beta-lactamases in a remote Alaskan soil. ISME J 2009, 3:243-251.
14. Walsh C. Antibiotics: Actions, Origins Resistance 2003, ASM Press, Washington, DC.
15. Arthur M., Courvalin P. Genetics and mechanisms of glycopeptide resistance in enterococci. Antimicrob Agents Chemother 1993, 37:1563-1571.
16. Wang P., Brobey R.K., Horii T., Sims P.F., Hyde J.E. Utilization of exogenous folate in the human malaria parasite Plasmodium falciparum and its critical role in antifolate drug synergy. Mol Microbiol 1999, 32:1254-1262.
17. Stewart P.S., Costerton J.W. Antibiotic resistance of bacteria in biofilms. Lancet 2001, 358:135-138.
18. Poirel L., Bonnin R.A., Nordmann P. Analysis of the resistome of a multidrug-resistant NDM-1-producing Escherichia coli strain by high-throughput genome sequencing. Antimicrob Agents Chemother 2011, 55:4224-4229.
19. Goodman A.L., Kallstrom G., Faith J.J., Reyes A., Moore A., Dantas G., Gordon J.I. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc Natl Acad Sci U S A 2011, 108:6252-6257.
20. Riesenfeld C.S., Goodman R.M., Handelsman J. Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ Microbiol 2004, 6:981-989.
21. Jacoby G.A. AmpC beta-lactamases. Clin Microbiol Rev 2009, 22:161-182. (Table of contents).
22. Perez-Perez F.J., Hanson N.D. Detection of plasmid-mediated AmpC beta-lactamase genes in clinical isolates by using multiplex PCR. J Clin Microbiol 2002, 40:2153-2162.
23. Reisbig M.D., Hanson N.D. Promoter sequences necessary for high-level expression of the plasmid-associated ampC beta-lactamase gene blaMIR-1. Antimicrob Agents Chemother 2004, 48:4177-4182.
24. Karami N., Martner A., Enne V.I., Swerkersson S., Adlerberth I., Wold A.E. Transfer of an ampicillin resistance gene between two Escherichia coli strains in the bowel microbiota of an infant treated with antibiotics. J Antimicrob Chemother 2007, 60:1142-1145.
25. D'Costa V.M., King C.E., Kalan L., Morar M., Sung W.W., Schwarz C., Froese D., Zazula G., Calmels F., Debruyne R., et al. Antibiotic resistance is ancient. Nature 2011, 477:457-461.
26. Benveniste R., Davies J. Aminoglycoside antibiotic-inactivating enzymes in actinomycetes similar to those present in clinical isolates of antibiotic-resistant bacteria. Proc Natl Acad Sci U S A 1973, 70:2276-2280.
27. Dantas G., Sommer M.O., Oluwasegun R.D., Church G.M. Bacteria subsisting on antibiotics. Science 2008, 320:100-103.
28. Blodgett J.A., Oh D.C., Cao S., Currie C.R., Kolter R., Clardy J. Common biosynthetic origins for polycyclic tetramate macrolactams from phylogenetically diverse bacteria. Proc Natl Acad Sci U S A 2010, 107:11692-11697.
29. D'Costa V.M., McGrann K.M., Hughes D.W., Wright G.D. Sampling the antibiotic resistome. Science 2006, 311:374-377.
30. D'Costa V.M., Griffiths E., Wright G.D. Expanding the soil antibiotic resistome: exploring environmental diversity. Curr Opin Microbiol 2007, 10:481-489.
31. Schnappinger D., Hillen W. Tetracyclines: antibiotic action, uptake, and resistance mechanisms. Arch Microbiol 1996, 165:359-369.
32. Thaker M., Spanogiannopoulos P., Wright G.D. The tetracycline resistome. Cell Mol Life Sci 2010, 67:419-431.
33. Palmer A.C., Angelino E., Kishony R. Chemical decay of an antibiotic inverts selection for resistance. Nat Chem Biol 2010, 6:244.
34. Rodriguez-Martinez J.M., Velasco C., Garcia I., Cano M.E., Martinez-Martinez L., Pascual A. Characterisation of integrons containing the plasmid-mediated quinolone resistance gene qnrA1 in Klebsiella pneumoniae. Int J Antimicrob Agents 2007, 29:705-709.
35. Hall R.M., Collis C.M. Mobile gene cassettes and integrons: capture and spread of genes by site-specific recombination. Mol Microbiol 1995, 15:593-600.
36. Kristiansson E., Fick J., Janzon A., Grabic R., Rutgersson C., Weijdegard B., Soderstrom H., Larsson D.G. Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements. PLoS One 2011, 6:e17038.
37. Levings R.S., Lightfoot D., Partridge S.R., Hall R.M., Djordjevic S.P. The genomic island SGI1, containing the multiple antibiotic resistance region of Salmonella enterica serovar typhimurium DT104 or variants of it, is widely distributed in other S-enterica serovars. J Bacteriol 2005, 187:4401-4409.
38. Partridge S.R., Recchia G.D., Stokes H.W., Hall R.M. Family of class 1 integrons related to In4 from Tn1696. Antimicrob Agents Chemother 2001, 45:3014-3020.
39. Piddock L.J. Multidrug-resistance efflux pumps - not just for resistance. Nat Rev Microbiol 2006, 4:629-636.
40. Webber M.A., Piddock L.J. The importance of efflux pumps in bacterial antibiotic resistance. J Antimicrob Chemother 2003, 51:9-11.
41. Canton R., Coque T.M. The CTX-M beta-lactamase pandemic. Curr Opin Microbiol 2006, 9:466-475.
42. Humeniuk C., Arlet G., Gautier V., Grimont P., Labia R., Philippon A. Beta-lactamases of Kluyvera ascorbata, probable progenitors of some plasmid-encoded CTX-M types. Antimicrob Agents Chemother 2002, 46:3045-3049.
43. Poirel L., Kampfer P., Nordmann P. Chromosome-encoded Ambler class A beta-lactamase of Kluyvera georgiana, a probable progenitor of a subgroup of CTX-M extended-spectrum beta-lactamases. Antimicrob Agents Chemother 2002, 46:4038-4040.
44. Martinez-Martinez L., Pascual A., Jacoby G.A. Quinolone resistance from a transferable plasmid. Lancet 1998, 351:797-799.
45. Poirel L., Rodriguez-Martinez J.M., Mammeri H., Liard A., Nordmann P. Origin of plasmid-mediated quinolone resistance determinant QnrA. Antimicrob Agents Chemother 2005, 49:3523-3525.
46. Poirel L., Liard A., Rodriguez-Martinez J.M., Nordmann P. Vibrionaceae as a possible source of Qnr-like quinolone resistance determinants. J Antimicrob Chemother 2005, 56:1118-1121.
47. Bonemann G., Stiens M., Puhler A., Schluter A. Mobilizable IncQ-related plasmid carrying a new quinolone resistance gene, qnrS2, isolated from the bacterial community of a wastewater treatment plant. Antimicrob Agents Chemother 2006, 50:3075-3080.
48. Aminov R.I., Mackie R.I. Evolution and ecology of antibiotic resistance genes. FEMS Microbiol Lett 2007, 271:147-161.
49. Keen P.L., Montforts M.H.M.M. Antimicrobial Resistance in the Environment 2012, Wiley-Blackwell.
50. Heuer H., Schmitt H., Smalla K. Antibiotic resistance gene spread due to manure application on agricultural fields. Curr Opin Microbiol 2011, 14:236-243.
51. Walsh T.R., Weeks J., Livermore D.M., Toleman M.A. Dissemination of NDM-1 positive bacteria in the New Delhi environment and its implications for human health: an environmental point prevalence study. Lancet Infect Dis 2011, 11:355-362.
52. Auerbach E.A., Seyfried E.E., McMahon K.D. Tetracycline resistance genes in activated sludge wastewater treatment plants. Water Res 2007, 41:1143-1151.
53. Smith M.S., Yang R.K., Knapp C.W., Niu Y., Peak N., Hanfelt M.M., Galland J.C., Graham D.W. Quantification of tetracycline resistance genes in feedlot lagoons by real-time PCR. Appl Environ Microbiol 2004, 70:7372-7377.
54. Marshall B.M., Levy S.B. Food animals and antimicrobials: impacts on human health. Clin Microbiol Rev 2011, 24:718-733.
55. McManus P.S., Stockwell V.O., Sundin G.W., Jones A.L. Antibiotic use in plant agriculture. Annu Rev Phytopathol 2002, 40:443-465.
56. Knapp C.W., Dolfing J., Ehlert P.A., Graham D.W. Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940. Environ Sci Technol 2010, 44:580-587.
57. Ochman H., Lawrence J.G., Groisman E.A. Lateral gene transfer and the nature of bacterial innovation. Nature 2000, 405:299-304.
58. Elshahed M.S., Youssef N.H., Spain A.M., Sheik C., Najar F.Z., Sukharnikov L.O., Roe B.A., Davis J.P., Schloss P.D., Bailey V.L., et al. Novelty and uniqueness patterns of rare members of the soil biosphere. Appl Environ Microbiol 2008, 74:5422-5428.
59. Daniel R. The metagenomics of soil. Nat Rev Microbiol 2005, 3:470-478.
60. Sommer M.O., Church G.M., Dantas G. A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion. Mol Syst Biol 2010, 6:360.
61. Forsberg K.J., Reyes A., Wang B., Selleck E.M., Sommer M.O.A., Dantas G. The shared antibiotic resistome of soil bacteria and human pathogens. Science 2012, 10.1126/science.1220761.