Skip to main content
SpringerLink
Log in

DNA Microarray-based Detection of Bacteria in Samples Containing Antibiotics: Effect of Antibiotics on the Performance of Pathogen Detection Assays

  • Research Paper
  • Published:
Biotechnology and Bioprocess Engineering Aims and scope Submit manuscript

Abstract

In pathogen diagnostics, conventional culture-based assays remain the gold-standard; however, they are time-consuming, and shows the low positivity rate. Prior treatment with antibiotics is one of the major factors lowering the culture positivity rate. It is therefore important to evaluate the effects of prior antibiotic treatment on established detection methods and to develop sensitive and specific methods for detecting pathogens. Here, we report the detection of bacteria in samples containing antibiotics. Escherichia coli and Klebsiella pneumoniae were chosen as model and they were independently inoculated into culture flasks along with ceftriaxone (0.5× MIC, 1× MIC, 2× MIC). After 0, 2, 4, 6, 12, and 24 h, samples were collected from each flask and divided into two for evaluation using microarray or BacT/Alert culture-based systems. The newly designed probes showed a detection limit of 101 CFU for E. coli and 102 CFU for K. pneumoniae with high specificities. DNA microarray obtained true positive results at approximately 4 to 24 h after antimicrobial treatment, in which the culture-based method failed to detect the pathogenic bacteria. The DNA microarray-based assay could be useful for efficient detection of pathogenic bacteria in a clinical setting, allowing for appropriate administration of antibiotics in infected patients.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Reimer, L. G., M. L. Wilson, and M. P. Weinstein (1997) Update on detection of bacteremia and fungemia. Clin. Microbiol. Rev. 10: 444–465.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Yoo, S. M. and S. Y. Lee (2010) DNA microarray for the identification of pathogens causing bloodstream infections. Expert. Rev. Mol. Diagn. 10: 263–268.

    Article  CAS  PubMed  Google Scholar 

  3. Bouza, E., D. Sousa, M. Rodríguez-Créixems, J. G. Lechuz, and P. Muñoz (2007) Is the volume of blood cultured still a significant factor in the diagnosis of bloodstream infections? J. Clin. Microbiol. 45: 2765–2769.

    Article  PubMed  PubMed Central  Google Scholar 

  4. Lamy, B., S. Dargere, M. C. Arendrup, J. J. Parienti, and P. Tattevin (2016) How to optimize the use of blood cultures for the diagnosis of bloodstream infections? A state-of-the art. Front. Microbiol. 7: 697.

    Article  PubMed  PubMed Central  Google Scholar 

  5. Al-Mayahi, M., A. Cian, B. A. Lipsky, D. Suvà, C. Müller, C. Landelle, H. H. Miozzari, and I. Uçkay (2015) Administration of antibiotic agents before intraoperative sampling in orthopedic infections alters culture results. J. Infect. 71: 518–525.

    Article  PubMed  Google Scholar 

  6. Bidell, M. R., M. P. Opraseuth, M. Yoon, J. Mohr, and T. P. Lodise (2017) Effect of prior receipt of antibiotics on the pathogen distribution and antibiotic resistance profile of key Gram-negative pathogens among patients with hospital-onset urinary tract infections. BMC Infect. Dis. 17: 176.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  7. Kim, C. J., K. H. Song, W. B. Park, E. S. Kim, S. W. Park, H. B. Kim, M. D. Oh, and N. J. Kim (2012) Microbiologically and clinically diagnosed vertebral osteomyelitis: impact of prior antibiotic exposure. Antimicrob. Agents Chemother. 56: 2122–2124.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Shahi, A., C. Deirmengian, C. Higuera, A. Chen, C. Restrepo, B. Zmistowski, and J. Parvizi (2015) Premature therapeutic antimicrobial treatments can compromise the diagnosis of late periprosthetic joint infection. Clin. Orthop. Relat. Res. 473: 2244–2249.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Bearman, G. M. L. and R. P. Wenzel (2005) Bacteremias: a leading cause of death. Arch. Med. Res. 36: 646–659.

    Article  PubMed  Google Scholar 

  10. Peach, B. C. (2017) Implications of the new sepsis definition on research and practice. J. Crit. Care. 38: 259–262.

    Article  PubMed  Google Scholar 

  11. Singer, M., C. S. Deutschman, C. W. Seymour, M. Shankar-Hari, D. Annane, M. Bauer, R. Bellomo, G. R. Bernard, J. D. Chiche, C. M. Coopersmith, R. S. Hotchkiss, M. M. Levy, J. C. Marshall, G. S. Martin, S. M. Opal, G. D. Rubenfeld, T. van der Poll, J. L. Vincent, and D. C. Angus (2016) The third international consensus definitions for sepsis and septic shock (Sepsis-3). JAMA. 315: 801–810.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Timsit, J. F., J. F. Soubirou, G. Voiriot, S. Chemam, M. Neuville, B. Mourvillier, R. Sonneville, E. Mariotte, L. Bouadma, and M. Wolff (2014) Treatment of bloodstream infections in ICUs. BMC Infect. Dis. 14: 489.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Flayhart, D., A. P. Borek, T. Wakefield, J. Dick, and K. C. Carroll (2007) Comparison of BACTEC PLUS blood culture media to BacT/Alert FA blood culture media for detection of bacterial pathogens in samples containing therapeutic levels of antibiotics. J. Clin. Microbiol. 45: 816–821.

    Article  CAS  PubMed  Google Scholar 

  14. Kang, H. and S. Kim (2012) Clinical features associated with blood cultures according to the use of antimicrobial agents prior to blood collection. Ann. Clin. Microbiol. 15: 21–26.

    Google Scholar 

  15. Templier, V., T. Livache, S. Boisset, M. Maurin, S. Slimani, R. Mathey, and Y. Roupioz (2017) Biochips for direct detection and identification of bacteria in blood culture-like conditions. Sci. Rep. 7: 9457.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Lovern, D., B. Katzin, K. Johnson, D. Broadwell, E. Miller, A. Gates, P. Deol, K. Doing, A. van Belkum, C. Marshall, E. Mathias, and W. M. Dunne Jr. (2016) Antimicrobial binding and growth kinetics in BacT/ALERT® FA Plus and BACTEC® Aerobic/F Plus blood culture media. Eur. J. Clin. Microbiol. Infect. Dis. 35: 2033–2036.

    Article  CAS  PubMed  Google Scholar 

  17. Doern, C. D., S. Mirrett, D. Halstead, J. Abid, P. Okada, and L. B. Reller (2014) Controlled clinical comparison of new pediatric medium with adsorbent polymeric beads (PF Plus) versus charcoal-containing PF medium in the BacT/alert blood culture system. J. Clin. Microbiol. 52: 1898–1900.

    Article  PubMed  PubMed Central  Google Scholar 

  18. Rajapaksha, P., A. Elbourne, S. Gangadoo, R. Brown, D. Cozzolino, and J. Chapman (2019) A review of methods for the detection of pathogenic microorganisms. Analyst. 144: 396–411.

    Article  CAS  PubMed  Google Scholar 

  19. Opota, O., K. Jaton, and G. Greub (2015) Microbial diagnosis of bloodstream infection: towards molecular diagnosis directly from blood. Clin. Microbiol. Infect. 21: 323–331.

    Article  CAS  PubMed  Google Scholar 

  20. Anis, E., I. K. Hawkins, M. R. S. Ilha, M. W. Woldemeskel, J. T. Saliki, and R. P. Wilkes (2018) Evaluation of targeted next-generation sequencing for detection of bovine pathogens in clinical samples. J. Clin. Microbiol. 56: e00399–18.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Yoo, S. M., S. Y. Lee, K. H. Chang, S. Y. Yoo, N. C. Yoo, K. C. Keum, W. M. Yoo, J. M. Kim, and J. Y. Choi (2009) High-throughput identification of clinically important bacterial pathogens using DNA microarray. Mol. Cell. Probes. 23: 171–177.

    Article  CAS  PubMed  Google Scholar 

  22. Yoo, S. M., J. Y. Choi, J. K. Yun, J. K. Choi, S. Y. Shin, K. Lee, J. M. Kim, and S. Y. Lee (2010) DNA microarray-based identification of bacterial and fungal pathogens in bloodstream infections. Mol. Cell. Probes. 24: 44–52.

    Article  CAS  PubMed  Google Scholar 

  23. Tissari, P., A. Zumla, E. Tarkka, S. Mero, L. Savolainen, M. Vaara, A. Aittakorpi, S. Laakso, M. Lindfors, H. Piiparinen, M. Mäki, C. Carder, J. Huggett, and V. Gant (2010) Accurate and rapid identification of bacterial species from positive blood cultures with a DNA-based microarray platform: an observational study. Lancet. 375: 224–230.

    Article  CAS  PubMed  Google Scholar 

  24. Thanthrige-Don, N., O. Lung, T. Furukawa-Stoffer, C. Buchanan, T. Joseph, D. L. Godson, J. Gilleard, T. Alexander, and A. Ambagala (2018) A novel multiplex PCR-electronic microarray assay for rapid and simultaneous detection of bovine respiratory and enteric pathogens. J. Virol. Methods. 261: 51–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Yoo, S. M. and S. Y. Lee (2016) Optical biosensors for the detection of pathogenic microorganisms. Trends Biotechnol. 34: 7–25.

    Article  CAS  PubMed  Google Scholar 

  26. Knabl, L., W. Mutschlechner, and D. Orth-Höller (2016) Evaluation of a multiplex OnSpot primer-extension PCR assay in the diagnosis of sepsis. J. Microbiol. Methods. 120: 91–93.

    Article  CAS  PubMed  Google Scholar 

  27. De Angelis, G., B. Posteraro, E. De Carolis, G. Menchinelli, F. Franceschi, M. Tumbarello, G. De Pascale, T. Spanu, and M. Sanguinetti (2018) T2Bacteria magnetic resonance assay for the rapid detection of ESKAPEc pathogens directly in whole blood. J. Antimicrob. Chemother. 73: iv20–iv26.

    Article  CAS  PubMed  Google Scholar 

  28. Patch, M. E., E. Weisz, A. Cubillos, S. J. Estrada, and M. A. Pfaller (2018) Impact of rapid, culture-independent diagnosis of candidaemia and invasive candidiasis in a community health system. J. Antimicrob. Chemother. 73: iv27–iv30.

    Article  CAS  PubMed  Google Scholar 

  29. Stevenson, M., A. Pandor, M. Martyn-St James, R. Rafia, L. Uttley, J. Stevens, J. Sanderson, R. Wong, G. D. Perkins, R. McMullan, and P. Dark (2016) Sepsis: the LightCycler SeptiFast Test MGRADE®, SepsiTest™ and IRIDICA BAC BSI assay for rapidly identifying bloodstream bacteria and fungi - a systematic review and economic evaluation. Health Technol. Assess. 20: 1–246.

    PubMed  PubMed Central  Google Scholar 

  30. Pilecky, M., A. Schildberger, D. Orth-Höller, and V. Weber (2019) Pathogen enrichment from human whole blood for the diagnosis of bloodstream infection: prospects and limitations. Diagn. Microbiol. Infect. Dis. 94: 7–14.

    Article  PubMed  Google Scholar 

  31. Nguyen, Q. H. and M. I. Kim (2020) Nanomaterial-mediated paper-based biosensors for colorimetric pathogen detection. Trends Analyt. Chem. 132: 116038.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Le, T. N., T. D. Tran, and M. I. Kim (2020) A convenient colorimetric bacteria detection method utilizing chitosan-coated magnetic nanoparticles. Nanomaterials (Basel). 10: 92.

    Article  CAS  PubMed Central  Google Scholar 

  33. Keum, K. C., S. M. Yoo, S. Y. Lee, K. H. Chang, N. C. Yoo, W. M. Yoo, J. M. Kim, J. Y. Choi, J. S. Kim, and G. Lee (2006) DNA microarray-based detection of nosocomial pathogenic Pseudomonas aeruginosa and Acinetobacter baumannii. Mol. Cell. Probes. 20: 42–50.

    Article  CAS  PubMed  Google Scholar 

  34. Humphries, R. M., J. Ambler, S. L. Mitchell, M. Castanheira, T. Dingle, J. A. Hindler, L. Koeth, and K. Sei (2018) CLSI methods development and standardization working group best practices for evaluation of antimicrobial susceptibility tests. J. Clin. Microbiol. 56: e01934–17.

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Wiegand, I., K. Hilpert, and R. E. W. Hancock (2008) Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances. Nat. Protoc. 3: 163–175.

    Article  CAS  PubMed  Google Scholar 

  36. Uslan, D. Z., S. J. Crane, J. M. Steckelberg, F. R. Cockerill 3rd, J. L. St Sauver, W. R. Wilson, and L. M. Baddour (2007) Age- and sex-associated trends in bloodstream infection: a population-based study in Olmsted County, Minnesota. Arch. Intern. Med. 167: 834–839.

    Article  PubMed  Google Scholar 

  37. Li, L. and H. Huang (2017) Risk factors of mortality in bloodstream infections caused by Klebsiella pneumonia: A single-center retrospective study in China. Medicine (Baltimore). 96: e7924.

    Article  PubMed  PubMed Central  Google Scholar 

  38. Durdu, B., I. N. Hakyemez, S. Bolukcu, G. Okay, B. Gultepe, and T. Aslan (2016) Mortality markers in nosocomial Klebsiella pneumoniae bloodstream infection. Springerplus. 5: 1892.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Vardakas, K. Z., D. K. Matthaiou, M. E. Falagas, E. Antypa, A. Koteli, and E. Antoniadou (2015) Characteristics, risk factors and outcomes of carbapenem-resistant Klebsiella pneumoniae infections in the intensive care unit. J. Infect. 70: 592–599.

    Article  PubMed  Google Scholar 

  40. Schleibinger, M., C. L. Steinbach, C. Töpper, A. Kratzer, U. Liebchen, F. Kees, B. Salzberger, and M. G. Kees (2015) Protein binding characteristics and pharmacokinetics of ceftriaxone in intensive care unit patients. Br. J. Clin. Pharmacol. 80: 525–533.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Ravan, H., S. Kashanian, N. Sanadgol, A. Badoei-Dalfard, and Z. Karami (2014) Strategies for optimizing DNA hybridization on surfaces. Anal. Biochem. 444: 41–46.

    Article  CAS  PubMed  Google Scholar 

  42. Yoo, S. M., D. M. Kim, and S. Y. Lee (2015) Multispot array combined with S1 nuclease-mediated elimination of unpaired nucleotides. BioChip J. 9: 156–163.

    Article  CAS  Google Scholar 

  43. Milton, J. A., S. Patole, H. Yin, Q. Xiao, T. Brown, and T. Melvin (2013) Efficient self-assembly of DNA-functionalized fluorophores and gold nanoparticles with DNA functionalized silicon surfaces: the effect of oligomer spacers. Nucleic Acids Res. 41: e80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Wirtz, R., C. Wälti, P. Tosch, M. Pepper, A. G. Davies, W. A. Germishuizen, and A. P. J. Middelberg (2004) Influence of the thiol position on the attachment and subsequent hybridization of thiolated DNA on gold surfaces. Langmuir. 20: 1527–1530.

    Article  CAS  PubMed  Google Scholar 

  45. Wick, L. M., J. M. Rouillard, T. S. Whittam, E. Gulari, J. M. Tiedje, and S. A. Hashsham (2006) On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes. Nucleic Acids Res. 34: e26.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  46. Yilmaz, L. S., A. Loy, E. S. Wright, M. Wagner, and D. R. Noguera (2012) Modeling formamide denaturation of probetarget hybrids for improved microarray probe design in microbial diagnostics. PLoS One. 7: e43862.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Regué, M., B. Hita, N. Piqué, L. Izquierdo, S. Merino, S. Fresno, V. J. Benedí, and J. M. Tomás (2014) A gene, uge, is essential for Klebsiella pneumoniae virulence. Infect. Immun. 72: 54–61.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by an NRF grant funded by the Ministry of Science and ICT (NRF-2019R1A2C1088504) and the Chung-Ang University Research Scholarship Grants in 2019.

Author information

Authors and Affiliations

  1. Department of Infectious Diseases, Yonsei University College of Medicine, Seoul, 03722, Korea

    So Youn Shin & June Myung Kim

  2. Department of Infectious Diseases, International St. Mary Hospital, Catholic Kwandong University, Incheon, 22711, Korea

    So Youn Shin

  3. Center for Applied Life Science, Hanbat National University, Daejeon, 34158, Korea

    Dong Min Kim

  4. School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Korea

    Yeonggyu Jo & Seung Min Yoo

Authors
  1. So Youn Shin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dong Min Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yeonggyu Jo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. June Myung Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Seung Min Yoo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Seung Min Yoo.

Ethics declarations

The authors declare no conflict of interest.

Neither ethical approval nor informed consent was required for this study.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Shin, S.Y., Kim, D.M., Jo, Y. et al. DNA Microarray-based Detection of Bacteria in Samples Containing Antibiotics: Effect of Antibiotics on the Performance of Pathogen Detection Assays. Biotechnol Bioproc E 26, 447–455 (2021). https://doi.org/10.1007/s12257-020-0342-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12257-020-0342-9

Keywords

Search

Navigation