Skip to main content
Log in

Update in Bloodstream Infection Diagnosis Using New Methods in Microbiology

  • New Technologies and Advances in Infection Prevention (AR Marra, Section Editor)
  • Published:
Current Treatment Options in Infectious Diseases Aims and scope Submit manuscript

Opinion statement

Bloodstream infections remain an important cause of morbidity/mortality worldwide. The diagnosis of these infections is time-consuming, even with the use of automated blood culture systems. Several systems based on molecular biology and, more recently, proteomics have been developed to allow rapid and accurate diagnosis of bloodstream infections. Here, we describe some recently technologies and commercial systems available to detect and to identify microorganisms and bacterial antimicrobial resistance-coding genes from positive blood culture bottles and whole-blood samples. Evaluation of clinical outcomes in multicenter studies and clinical trials with these new tests is warranted in conjunction with antimicrobial stewardship use and programs for interpretation of results to be provided to physicians.

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

Access this article

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

Instant access to the full article PDF.

Similar content being viewed by others

References and Recommended Reading

Papers of particular interest, published recently, have been highlighted as: • Of importance •• Of major importance

  1. Laupland KB. Incidence of bloodstream infection: a review of population-based studies. Clin Microbiol Infect. 2013;19(6):492–500.

    Article  CAS  PubMed  Google Scholar 

  2. Vardakas KZ, Anifantaki FI, Trigkidis KK, Falagas ME. Rapid molecular diagnostic tests in patients with bacteremia: evaluation of their impact on decision making and clinical outcomes. Eur J Clin Microbiol Infect Dis. 2015;34(11):2149–60.

    Article  CAS  PubMed  Google Scholar 

  3. Morrell M, Fraser VJ, Kollef MH. Delaying the empiric treatment of Candida bloodstream infection until positive blood culture results are obtained: a potential risk factor for hospital mortality. Antimicrob Agents Chemother. 2005;49(9):3640–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Mancini N, Carletti S, Ghidoli N, et al. The era of molecular and other non-culture-based methods in diagnosis of sepsis. Clin Microbiol Rev. 2010;23(1):235–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Lupetti A, Barnini S, Castagna B, et al. Rapid identification and antimicrobial susceptibility testing of Gram-positive cocci in blood cultures by direct inoculation into the BD Phoenix system. Clin Microbiol Infect. 2010;16(7):986–91.

    Article  CAS  PubMed  Google Scholar 

  6. Chen J-R, Lee S-Y, Yang B-H, Lu J-J. Rapid identification and susceptibility testing using the VITEK 2 system using culture fluids from positive BacT/ALERT blood cultures. J Microbiol Immunol Infect. 2008;41(3):259–64.

    CAS  PubMed  Google Scholar 

  7. Waites KB, Brookings ES, Moser SA, Zimmer BL. Direct susceptibility testing with positive BacT/Alert blood cultures by using MicroScan overnight and rapid panels. J Clin Microbiol. 1998;36(7):2052–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Whitcombe D, Newton CR, Little S. Advances in approaches to DNA-based diagnostics. Curr Opin Biotechnol. 1998;9(6):602–8.

    Article  CAS  PubMed  Google Scholar 

  9. Riedel S, Carroll KC. Early identification and treatment of pathogens in sepsis: molecular diagnostics and antibiotic choice. Clin Chest Med. 2016;37(2):191–207.

    Article  PubMed  Google Scholar 

  10. Menezes LC, Rocchetti TT, de Bauab CK, et al. Diagnosis by real-time polymerase chain reaction of pathogens and antimicrobial resistance genes in bone marrow transplant patients with bloodstream infections. BMC Infect Dis. 2013;13:166.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. •• Quiles MG, Menezes LC, de Bauab CK, et al. Diagnosis of bacteremia in pediatric oncologic patients by in-house real-time PCR. BMC Infect Dis. 2015;15:283. This study describes some in-house molecular tests to diagnose BSIs directly from blood culture bottles and whole-blood samples using real-time PCR

    Article  PubMed  PubMed Central  Google Scholar 

  12. Salimnia H, Fairfax MR, Lephart PR, et al. Evaluation of the FilmArray blood culture identification panel: results of a multicenter controlled trial. J Clin Microbiol. 2016;54(3):687–98.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Ledeboer NA, Lopansri BK, Dhiman N, et al. Identification of gram-negative bacteria and genetic resistance determinants from positive blood culture broths by use of the Verigene gram-negative blood culture multiplex microarray-based molecular assay. J Clin Microbiol. 2015;53(8):2460–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Stevenson M, Pandor A, Martyn-St James M, et al. Sepsis: the LightCycler SeptiFast Test MGRADE®, SepsiTestTM and IRIDICA BAC BSI assay for rapidly identifying bloodstream bacteria and fungi—a systematic review and economic evaluation. Health Technol Assess 2016: 1–246.

  15. Sitnik R, Marra AR, Petroni RC, et al. SeptiFast for diagnosis of sepsis in severely ill patients from a Brazilian hospital. Einstein. 2014;12(2):191–6.

    Article  PubMed  PubMed Central  Google Scholar 

  16. Dark P, Blackwood B, Gates S, et al. Accuracy of LightCycler SeptiFast for the detection and identification of pathogens in the blood of patients with suspected sepsis: a systematic review and meta-analysis. Intensive Care Med. 2015;41(1):21–33.

    Article  CAS  PubMed  Google Scholar 

  17. Zboromyrska Y, De La Calle C, Soto M, et al. Rapid diagnosis of staphylococcal catheter-related bacteraemia in direct blood samples by real-time PCR. Plos One 2016; 1–11.

  18. Bispo PJM, de Melo GB, Hofling-Lima AL, Pignatari ACC. Detection and gram discrimination of bacterial pathogens from aqueous and vitreous humor using real-time PCR assays. Invest Ophthalmol Vis Sci. 2011;52(2):873–81.

    Article  CAS  PubMed  Google Scholar 

  19. Loonen AJM, Bos MP, van Meerbergen B, et al. Comparison of pathogen DNA isolation methods from large volumes of whole blood to improve molecular diagnosis of bloodstream infections. PLoS One. 2013;8(8):e72349.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Ellem JA, Olma T, O’Sullivan MVN. Rapid detection of methicillin-resistant Staphylococcus aureus and methicillin-susceptible S. aureus directly from positive blood cultures by use of the BD Max StaphSR assay. J Clin Microbiol. 2015;53(12):3900–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Cosgrove SE, Li DX, Tamma PD, et al. Use of PNA FISH for blood cultures growing gram-positive cocci in chains without a concomitant antibiotic stewardship intervention does not improve time to appropriate antibiotic therapy. Diagn Microbiol Infect Dis. 2016;86(1):86–92.

    Article  PubMed  Google Scholar 

  22. • Patel R. New developments in clinical bacteriology laboratories. Mayo Clin Proc 2016. This review provides a comprehensive overview of available laboratory testing for use in clinical microbiology.

  23. Monteiro J, Inoue FM, Lobo APT, et al. Fast and reliable bacterial identification direct from positive blood culture using a new TFA sample preparation protocol and the Vitek® MS system. J Microbiol Methods. 2015;109:157–9.

    Article  CAS  PubMed  Google Scholar 

  24. Carvalhaes CG, da Silva ACR, Streling AP, et al. Detection of carbapenemase activity using VITEK MS: interplay of carbapenemase type and period of incubation. J Med Microbiol. 2015;64(8):946–7.

    Article  CAS  PubMed  Google Scholar 

  25. Jordana-Lluch E, Giménez M, Quesada MD, et al. Evaluation of the broad-range PCR/ESI-MS Technology in Blood Specimens for the molecular diagnosis of bloodstream infections. PLoS One. 2015;10(10):e0140865.

    Article  PubMed  PubMed Central  Google Scholar 

  26. Bacconi A, Richmond GS, Baroldi MA, et al. Improved sensitivity for molecular detection of bacterial and Candida infections in blood. J Clin Microbiol. 2014;52(9):3164–74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Pfaller MA, Wolk DM, Lowery TJ. T2MR and T2Candida: novel technology for the rapid diagnosis of candidemia and invasive candidiasis. Future Microbiol. 2016;11(1):103–17.

    Article  CAS  PubMed  Google Scholar 

  28. Grumaz S, Stevens P, Grumaz C, et al. Next-generation sequencing diagnostics of bacteremia in septic patients. Genome Med. 2016;8(1):73.

    Article  PubMed  PubMed Central  Google Scholar 

  29. Vlek ALM, Bonten MJM, Boel CHE. Direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry improves appropriateness of antibiotic treatment of bacteremia. PLoS One. 2012;7(3):e32589.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Clerc O, Prod’hom G, Vogne C, et al. Impact of matrix-assisted laser desorption ionization time-of-flight mass spectrometry on the clinical management of patients with Gram-negative bacteremia: a prospective observational study. Clin Infect Dis. 2013;56(8):1101–7.

    Article  CAS  PubMed  Google Scholar 

  31. Huang AM, Newton D, Kunapuli A, et al. Impact of rapid organism identification via matrix-assisted laser desorption/ionization time-of-flight combined with antimicrobial stewardship team intervention in adult patients with bacteremia and candidemia. Clin Infect Dis. 2013;57(9):1237–45.

    Article  CAS  PubMed  Google Scholar 

  32. Aitken SL, Hemmige VS, Koo HL, et al. Real-world performance of a microarray-based rapid diagnostic for Gram-positive bloodstream infections and potential utility for antimicrobial stewardship. Diagn Microbiol Infect Dis. 2015;81(1):4–8.

    Article  CAS  PubMed  Google Scholar 

  33. Bork JT, Leekha S, Heil EL, et al. Rapid testing using the Verigene Gram-negative blood culture nucleic acid test in combination with antimicrobial stewardship intervention against Gram-negative bacteremia. Antimicrob Agents Chemother. 2015;59(3):1588–95.

    Article  PubMed  PubMed Central  Google Scholar 

  34. Suzuki H, Hitomi S, Yaguchi Y, et al. Prospective intervention study with a microarray-based, multiplexed, automated molecular diagnosis instrument (Verigene system) for the rapid diagnosis of bloodstream infections, and its impact on the clinical outcomes. J Infect Chemother. 2015;21(12):849–56.

    Article  PubMed  Google Scholar 

  35. Banerjee R, Teng CB, Cunningham SA, et al. Randomized trial of rapid multiplex polymerase chain reaction-based blood culture identification and susceptibility testing. Clin Infect Dis. 2015;61(7):1071–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. •• Vincent J-L, Brealey D, Libert N, et al. Rapid diagnosis of infection in the critically ill, a multicenter study of molecular detection in bloodstream infections, pneumonia, and sterile site infections. Crit Care Med. 2015;43(11):2283–91. This multicenter study evaluated the polymerase chain reaction/electrospray ionization-mass spectrometry technology for BSIs diagnosis and affirm that these technologies can result in potentially cause of altered treatment of these infections

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. • Carlesse F, Cappellano P, Quiles MG, et al. Clinical relevance of molecular identification of microorganisms and detection of antimicrobial resistance genes in bloodstream infections of paediatric cancer patients. BMC Infect Dis. 2016;16 :–462. This study highlights the clinical relevance of using molecular tests to diagnosing BSIs in a specific population

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Antonio Carlos Campos Pignatari MD, PhD.

Ethics declarations

Conflict of Interest

Milene Quiles declares that she has no conflicts of interest.

Bruno Boettger declares that he has no conflicts of interest.

Antonio Carlos Campos Pignatari declares that he has no conflicts of interest.

Human and Animal Rights and Informed Consent

This article does not contain any studies with human or animal subjects performed by any of the authors.

Additional information

Key Points

Rapid and accurate molecular methods are required for diagnosis of BSIs and can contribute for an appropriate antimicrobial therapy institution.

Validation of new molecular methodologies and platforms in the microbiology diagnostic laboratory is essential to evaluate the accuracy and sensibility of these tests before implementation in the clinical routine.

Stewardship programs should be institutionalized for implementation and evaluation of new diagnostic tests in BSIs.

This article is part of the Topical Collection on New Technologies and Advances in Infection Prevention

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Quiles, M., Boettger, B. & Pignatari, A.C.C. Update in Bloodstream Infection Diagnosis Using New Methods in Microbiology. Curr Treat Options Infect Dis 9, 1–10 (2017). https://doi.org/10.1007/s40506-017-0104-1

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s40506-017-0104-1

Keywords

Navigation