Uropathogenic Escherichia coli are less likely than paired fecal E. coli to have CRISPR loci

Infection, Genetics and Evolution

Volumn 19, Issue , 2013, Pages 212-218

  Dang, Trang Nguyen Doan ^a   Zhang, Lixin ^a   Zöllner, Sebastian ^a,b   Srinivasan, Usha ^a   Abbas, Khadija ^a   Marrs, Carl F ^a   Foxman, Betsy ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF MICHIGAN HEALTH SYSTEM   (United States)

Author keywords

Antibiotic resistance; Commensal; Urinary tract infection; Uropathogenic

Indexed keywords

AMIKACIN; AMPICILLIN; AZTREONAM; CEFAZOLIN; CEFEPIME; CEFTRIAXONE; CIPROFLOXACIN; COTRIMOXAZOLE; ERTAPENEM; GENTAMICIN; IMIPENEM; MEROPENEM; MOXIFLOXACIN; NITROFURANTOIN; TIGECYCLINE; TOBRAMYCIN;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; ARTICLE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; COMMENSAL ESCHERICHIA COLI; CONTROLLED STUDY; DNA STRUCTURE; NONHUMAN; PRIORITY JOURNAL; UROPATHOGENIC ESCHERICHIA COLI;

ANTIBIOTIC RESISTANCE; COMMENSAL; URINARY TRACT INFECTION; UROPATHOGENIC;

ANTI-BACTERIAL AGENTS; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; DRUG RESISTANCE, BACTERIAL; ESCHERICHIA COLI; ESCHERICHIA COLI INFECTIONS; FECES; FEMALE; HUMANS; MICROBIAL SENSITIVITY TESTS; STATISTICS, NONPARAMETRIC; URINARY TRACT INFECTIONS; UROPATHOGENIC ESCHERICHIA COLI; YOUNG ADULT;

EID: 84882621545     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2013.07.017     Document Type: Article

References (50)

1. Almendros C., Guzmán N.M., Díez-Villaseñor C., García-Martínez J., Mojica F.J. Target motifs affecting natural immunity by a constitutive CRISPR-Cas system in Escherichia coli. PLoS ONE 2012, 7:e50797.
2. Anastasi E.M., Matthews B., Stratton H.M., Katouli M. Pathogenic Escherichia coli found in sewage treatment plants and environmental waters. Appl. Environ. Microbiol. 2012, 78:5536-5541.
3. Andersson A.F., Banfield J.F. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 2008, 320:1047-1050.
4. Bentley D.R. Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 2006, 16:545-552.
5. Bergeron C.R., Prussing C., Boerlin P., Daignault D., Dutil L., Reid-Smith R.J., Zhanel G.G., Manges A.R. Chicken as reservoir for extraintestinal pathogenic Escherichia coli in humans. Can. Emerg. Infect. Dis. 2012, 18:415-421.
6. Bikard D., Hatoum-Aslan A., Mucida D., Marraffini L.A. CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection. Cell Host Microbe 2012, 12:177-186.
7. Casas V., Maloy S. Role of bacteriophage-encoded exotoxins in the evolution of bacterial pathogens. Future Microbiol. 2011, 6:1461-1473.
8. Chaudhuri R.R., Henderson I.R. The evolution of the Escherichia coli phylogeny. Infect. Genet. Evol. 2012, 12:214-226.
9. Diez-Villasenor C., Almendros C., Garcia-Martinez J., Mojica F.J. Diversity of CRISPR loci in Escherichia coli. Microbiology 2010, 156:1351-1361.
10. Dobrindt U., Agerer F., Michaelis K., Janka A., Buchrieser C., Samuelson M., Svanborg C., Gottschalk G., Karch H., Hacker J. Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays. J. Bacteriol. 2003, 185:1831-1840.
11. Fàbrega A., Madurga S., Giralt E., Vila J. Mechanism of action of and resistance to quinolones. Microb. Biotechnol. 2008, 2:40-61.
12. Foxman B. The epidemiology of urinary tract infection. Nat. Rev. Urol. 2010, 7:653-660.
13. Foxman B., Zhang L., Tallman P., Palin K., Rode C., Bloch C., Gillespie B., Marrs C.F. Virulence characteristics causing first time urinary tract infection predict risk of second infection. J. Infect. Dis. 1995, 172:1536-1541.
14. Foxman B., Zhang L., Tallman P., Andree B.C., Geiger A.M., Koopman J.S., Gillespie B., Palin K.A., Sobel J.D., Rode C.K., Bloch C.A., Marrs C.F. Transmission of uropathogens between sex partners. J. Infect. Dis. 1997, 175:989-992.
15. Foxman B., Manning S.D., Tallman P., Bauer R., Zhang L., Koopman J.S., Gillespie B., Sobel J.D., Marrs C.F. Uropathogenic Escherichia coli are more likely than commensal E. coli to be shared between heterosexual sex partners. Am. J. Epidemiol. 2002, 156:1133-1140.
16. Heidelberg J.F., Nelson W.C., Schoenfeld T., Bhaya D. Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes. PLoS ONE 2009, 4:e4169.
17. Hopkins K.L., Davies R.H., Threlfall E.J. Mechanisms of quinolone resistance in Escherichia coli and Salmonella: recent developments. Int. J. Antimicrob. Agents. 2005, 25:358-373.
18. Horvarth P., Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science 2010, 327:167-170.
19. Kass E.H. Asymptomatic infections of the urinary tract. Trans. Assoc. Am. Phys. 1956, 69:56-64.
20. Lipps G. Plasmids: Current Research and Future Trends 2008, Caister Academic Press, Norfolk, United Kingdom.
21. Louwen R., et al. A novel link between Campylobacter jejuni bacteriophage defence, virulence and Guillain-Barré syndrome. Eur. J. Clin. Microbiol. Infect. Dis. 2013, 32:207-226.
22. Makarova K.S., Grishin N.V., Shabalina S.A., Wolf Y.I., Koonin E.V. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct 2006, 1:7.
23. Makarova K.S., Haft D.H., Barrangou R., Brouns S.J., Charpentier E., Horvath P., Moineau S., Mojica F.J., Wolf Y.I., Yakunin A.F., Van der Oost J., Koonin E.V. Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 2011, 9:467-477.
24. Marraffini L.A. Impact of CRIPSR immunity on the emergence of bacterial pathogens. Future Microbiol. 2010, 5:693-695.
25. Marraffini L.A., Sontheimer E.J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 2008, 19:1843-1845.
26. Marraffini L.A., Sontheimer E.J. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat. Rev. Genet. 2010, 11:181-190.
27. Marrs C.F., Zhang L., Tallman P., Manning S.D., Somsel P., Raz P., Colodner R., Jantunen M.E., Siitonen A., Saxen H., Foxman B. Variations in 10 putative uropathogen virulence genes among urinary, faecal, and peri-urethral Escherichia coli. J. Med. Microbiol. 2002 Feb, 51(2):138-142.
28. Mayers D.L. Antimicrobial Drug Resistance: Mechanisms of Drug resistance 2009, vol. 1. Springer, New York, (pp. 259-271).
29. Mojica F.J.M., Diez-Villasenor C., Garcia-Martinez J., Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 2005, 60:174-182.
30. Molloy S.S. Bacterial genetics: hitting the CRISPR target. Nat. Rev. Microbiol. 2012, 10:376-377.
31. Performance Standards for Antimicrobial Susceptibility Testing, M100-S18 NCCLS 2008, Wayne, PA, USA. NCCLS (Ed.).
32. Oelschlaeger T.A., Dobrindt U., Hacker J. Pathogenicity islands of uropathogenic E. coli and the evolution of virulence. Int. J. Antimicrob. Agents. 2002, 19:517-521.
33. Palmer K.L., Gilmore M.S. Multidrug-resistant enterococci lack CRISPR-cas. mBio 2010, 1:e00210-e00227.
34. Pougach K., Semenova E., Bogdanova E., Datsenko K.A., Djordjevic M., Wanner B.L., Severinov K. Transcription, processing and function of CRISPR cassettes in Escherichia coli. Mol. Microbiol. 2010, 77:1367-1379.
35. Rupp M.E., Fey P.D. Extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae. Considerations for diagnosis, prevention and drug treatment. Drugs 2003, 63:353-365.
36. Sampson T.R., Saroj S.D., Llewellyn A.C., Tzeng Y.L., Weiss D.S. A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 2013, 9:254-257.
37. Simonsen C.C., Chen E.Y., Levinson A.D. Identification of the type I trimethoprim-resistant dihydrofolate reductase specified by the Escherichia coli R-plasmid R483: comparison with procaryotic and eukaryotic dihydrofolate reductases. J. Bacteriol. 1983, 155:1001-1008.
38. Sorek R., Kunin V., Hugenholtz P. CRISPR - a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat. Rev. Microbiol. 2008, 6:181-186.
39. Stamey T.A. Recurrent urinary tract infections in female patients: an overview of management and treatment. Rev. Infect. Dis. 1987, 9:195-210.
40. Tan T.Y., Ng S.Y., Teo L., Koh Y., Teok C.H. Detection of plasmid-mediated AmpC in Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis. Clin. Pathol. 2008, 61:642-644.
41. Tenaillon O., Skurnik D., Picard B., Denamur E. The population genetics of commensal Escherichia coli. Nat. Rev. Microbiol. 2010, 8:207-217.
42. Touchon M., Rocha E.P. The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS ONE 2010, 5:e11126.
43. Touchon M., Charpentier S., Clermont O., Rocha E.P.C., Denamur E., Branger C. CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection. J. Bacteriol. 2011, 193:2460-2467.
44. Touchon M., Charpentier S., Pognard D., Picard B., Arlet G., Rocha E.P., Denamur E., Branger C. Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements. Microbiology 2012, 158:2997-3004.
45. Vigil P.D., Stapleton A.E., Johnson J.R., Hooton T.M., Hodges A.P., He Y., Mobley H.L. Presence of putative repeat-in-toxin tosA in Escherichia coli predicts successful colonization of the urinary tract. MBio 2011 May 3, 2(3):e00061-e00066.
46. Westra E.R., et al. H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO. Mol. Microbiol. 2010, 77:1380-1393.
47. Westra E.R., Swarts D.C., Staals R.H.J., Jore M.M., Brouns S.J.J., Van der Oost J. The CRISPRs, they are A-Changin': how prokaryotes generate adaptive immunity. Ann. Rev. Genet. 2012, 46:311-339.
48. Xia X., Meng J., McDermott P.F., Zhao S. Escherichia coli from retail meats carry genes associated with uropathogenic Escherichia coli, but are weakly invasive in human bladder cell culture. J. Appl. Microbiol. 2011, 110:1166-1176.
49. Zhang L., Foxman B. Molecular epidemiology of Escherichia coli mediated urinary tract infections. Front. Biosci. 2003, 8:e235-e244.
50. Zhang L., Foxman B., Marrs C.F. Both urinary and fecal Escherichia coli are dominated by strains of phylogenetic group B2. J. Clin. Microbiol. 2002, 40:3951-3955.