Implementation of Fourier transform infrared spectroscopy for the rapid typing of uropathogenic Escherichia coli

  • S. E. Dawson
  • T. Gibreel
  • N. Nicolaou
  • H. AlRabiah
  • Y. Xu
  • R. Goodacre
  • M. Upton
Article
First Online:
Received:
Accepted:

Abstract

In this paper, we demonstrate that Fourier transform infrared (FT-IR) spectroscopy is able to discriminate rapidly between uropathogenic Escherichia coli (UPEC) of key lineages with only relatively simple sample preparation. A total of 95 bacteria from six different epidemiologically important multilocus sequence types (ST10, ST69, ST95, ST73, ST127 and ST131) were used in this project and principal component-discriminant function analysis (PC-DFA) of these samples produced clear separate clustering of isolates, based on the ST. Analysis of data using partial least squares-discriminant analysis (PLS-DA), incorporating cross-validation, indicated a high prediction accuracy of 91.19 % for ST131. These results suggest that FT-IR spectroscopy could be a useful method for the rapid identification of members of important UPEC STs.

Notes

Acknowledgements

TG was supported by a studentship from the Libyan government. HR thanks the Saudi Ministry of Higher Education and King Saud University for funding. RG is grateful to the EU Commonsense (http://www.fp7projectcommonsense.eu/) project (Grant 261809), financed by the European Commission under the Seventh Framework Programme for Research and Technological Development.

Conflict of interest

The authors declare that they have no conflict of interest.

References

  1. 1.
    Lau SH, Reddy S, Cheesbrough J, Bolton FJ, Willshaw G, Cheasty T, Fox AJ, Upton M (2008) Major uropathogenic Escherichia coli strain isolated in the northwest of England identified by multilocus sequence typing. J Clin Microbiol 46(3):1076–1080PubMedCentralPubMedCrossRefGoogle Scholar
  2. 2.
    Kucheria R, Dasgupta P, Sacks SH, Khan MS, Sheerin NS (2005) Urinary tract infections: new insights into a common problem. Postgrad Med J 81(952):83–86. doi:10.1136/pgmj.2004.023036 PubMedCentralPubMedCrossRefGoogle Scholar
  3. 3.
    Zhang L, Foxman B, Manning SD, Tallman P, Marrs CF (2000) Molecular epidemiologic approaches to urinary tract infection gene discovery in uropathogenic Escherichia coli. Infect Immun 68(4):2009–2015. doi:10.1128/iai.68.4.2009-2015.2000 PubMedCentralPubMedCrossRefGoogle Scholar
  4. 4.
    Cagnacci S, Gualco L, Debbia E, Schito GC, Marchese A (2008) European emergence of ciprofloxacin-resistant Escherichia coli clonal groups O25:H4-ST 131 and O15:K52:H1 causing community-acquired uncomplicated cystitis. J Clin Microbiol 46(8):2605–2612. doi:10.1128/JCM.00640-08 PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Peirano G, Pitout JD (2010) Molecular epidemiology of Escherichia coli producing CTX-M beta-lactamases: the worldwide emergence of clone ST131 O25:H4. Int J Antimicrob Agents 35(4):316–321. doi:10.1016/j.ijantimicag.2009.11.003 PubMedCrossRefGoogle Scholar
  6. 6.
    Rogers BA, Sidjabat HE, Paterson DL (2011) Escherichia coli O25b-ST131: a pandemic, multiresistant, community-associated strain. J Antimicrob Chemother 66(1):1–14. doi:10.1093/jac/dkq415 PubMedCrossRefGoogle Scholar
  7. 7.
    Johnson JR, Menard M, Johnston B, Kuskowski MA, Nichol K, Zhanel GG (2009) Epidemic clonal groups of Escherichia coli as a cause of antimicrobial-resistant urinary tract infections in Canada, 2002 to 2004. Antimicrob Agents Chemother 53(7):2733–2739. doi:10.1128/AAC.00297-09 PubMedCentralPubMedCrossRefGoogle Scholar
  8. 8.
    Köhling HL, Bittner A, Müller K-D, Buer J, Becker M, Rübben H, Rettenmeier AW, Mosel F (2012) Direct identification of bacteria in urine samples by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and relevance of defensins as interfering factors. J Med Microbiol 61(Pt 3):339–344. doi:10.1099/jmm.0.032284-0 PubMedCrossRefGoogle Scholar
  9. 9.
    Jarvis RM, Goodacre R (2004) Ultra-violet resonance Raman spectroscopy for the rapid discrimination of urinary tract infection bacteria. FEMS Microbiol Lett 232(2):127–132. doi:10.1016/s0378-1097(04)00040-0 PubMedCrossRefGoogle Scholar
  10. 10.
    Goodacre R, Timmins EM, Burton R, Kaderbhai N, Woodward AM, Kell DB, Rooney PJ (1998) Rapid identification of urinary tract infection bacteria using hyperspectral whole-organism fingerprinting and artificial neural networks. Microbiology 144:1157–1170PubMedCrossRefGoogle Scholar
  11. 11.
    AlRabiah H, Correa E, Upton M, Goodacre R (2013) High-throughput phenotyping of uropathogenic E. coli isolates with Fourier transform infrared spectroscopy. Analyst 138(5):1363–1369. doi:10.1039/c3an36517d PubMedCrossRefGoogle Scholar
  12. 12.
    Gilbert MK, Frick C, Wodowski A, Vogt F (2009) Spectroscopic imaging for detection and discrimination of different E. coli strains. Appl Spectrosc 63(1):6–13PubMedGoogle Scholar
  13. 13.
    Goodacre R, Timmins EM, Rooney PJ, Rowland JJ, Kell DB (1996) Rapid identification of Streptococcus and Enterococcus species using diffuse reflectance–absorbance Fourier transform infrared spectroscopy and artificial neural networks. FEMS Microbiol Lett 140(2–3):233–239. doi:10.1111/j.1574-6968.1996.tb08342.x PubMedCrossRefGoogle Scholar
  14. 14.
    Winder CL, Gordon SV, Dale J, Hewinson RG, Goodacre R (2006) Metabolic fingerprints of Mycobacterium bovis cluster with molecular type: implications for genotype–phenotype links. Microbiology 152(Pt 9):2757–2765. doi:10.1099/mic.0.28986-0 PubMedCrossRefGoogle Scholar
  15. 15.
    Gibreel TM, Dodgson AR, Cheesbrough J, Fox AJ, Bolton FJ, Upton M (2012) Population structure, virulence potential and antibiotic susceptibility of uropathogenic Escherichia coli from Northwest England. J Antimicrob Chemother 67(2):346–356. doi:10.1093/jac/dkr451 PubMedCrossRefGoogle Scholar
  16. 16.
    Goodacre R (2003) Explanatory analysis of spectroscopic data using machine learning of simple, interpretable rules. Vib Spectrosc 32(1):33–45. doi:10.1016/s0924-2031(03)00045-6 CrossRefGoogle Scholar
  17. 17.
    Nicolaou N, Goodacre R (2008) Rapid and quantitative detection of the microbial spoilage in milk using Fourier transform infrared spectroscopy and chemometrics. Analyst 133(10):1424–1431PubMedCrossRefGoogle Scholar
  18. 18.
    Barnes RJ, Dhanoa MS, Lister SJ (1989) Standard normal variate transformation and de-trending of near-infrared diffuse reflectance spectra. Appl Spectrosc 43:772–777CrossRefGoogle Scholar
  19. 19.
    Wang Y, Kowalski BR (1992) Calibration transfer and measurement stability of near-infrared spectrometers. Appl Spectrosc 46:764–771CrossRefGoogle Scholar
  20. 20.
    Jolliffe IT (1986) Principal component analysis. Springer-Verlag, New YorkCrossRefGoogle Scholar
  21. 21.
    Jarvis RM, Goodacre R (2004) Discrimination of bacteria using surface-enhanced Raman spectroscopy. Anal Chem 76(1):40–47. doi:10.1021/ac034689c PubMedCrossRefGoogle Scholar
  22. 22.
    Barker M, Rayens W (2003) Partial least squares for discrimination. J Chemometr 17(3):166–173. doi:10.1002/cem.785 CrossRefGoogle Scholar
  23. 23.
    Efron B (1979) Bootstrap methods: another look at the jackknife. Ann Stat 7:1–26CrossRefGoogle Scholar
  24. 24.
    Godbout-DeLasalle F, Higgins R (1986) Biotyping of clinical isolates of Escherichia coli of animal origin, using the Analytab API 20E system. Can J Vet Res 50(3):418–421PubMedCentralPubMedGoogle Scholar
  25. 25.
    Gibreel TM, Dodgson AR, Cheesbrough J, Bolton FJ, Fox AJ, Upton M (2012) High metabolic potential may contribute to the success of ST131 uropathogenic Escherichia coli. J Clin Microbiol 50(10):3202–3207. doi:10.1128/jcm.01423-12 PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • S. E. Dawson
    • 1
  • T. Gibreel
    • 1
  • N. Nicolaou
    • 2
  • H. AlRabiah
    • 2
  • Y. Xu
    • 2
  • R. Goodacre
    • 2
  • M. Upton
    • 1
    • 3
    • 4
  1. 1.Microbiology and Virology Unit, School of MedicineUniversity of ManchesterManchesterUK
  2. 2.School of Chemistry and Manchester Institute of BiotechnologyUniversity of ManchesterManchesterUK
  3. 3.School of Biomedical and Healthcare SciencesPlymouth UniversityPlymouthUK
  4. 4.Formerly: School of Medicine, Stopford BuildingUniversity of ManchesterManchesterUK

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