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The challenge of molecular diagnosis of bloodstream infections

  • Emilio Cendejas-Bueno
  • María Pilar Romero-Gómez
  • Jesús MingoranceEmail author
Review
  • 113 Downloads

Abstract

Early detection and identification of pathogens in bloodstream infections (BSI) is important to initiate or adjust antibiotic therapy as soon as possible. The current gold standard for diagnostic of BSI infection is the blood culture, that has a turnaround time of one to few days. Molecular tests performed directly in blood samples have promised faster diagnostics, with response times of a few hours, but their implementation into the clinical routine has been hampered by critical technical and procedural problems. Assay integration into laboratory workflows with random-access loading mode and minimal hands-on time is essential to meet rapid response times. Decreasing assay costs will favor fair clinical evaluations and might increase the applicability of the assays. Control of background contamination with bacterial DNA is one of the most difficult problems and might be avoided with pathogen-specific real-time PCR designs oriented to particular patient groups, or perhaps by quantitative, next-generation sequencing approaches.

Keywords

Bloodstream infection Sepsis Molecular assays 

Notes

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

References

  1. Akova M (2016) Epidemiology of antimicrobial resistance in bloodstream infections. Virulence 7:252–266.  https://doi.org/10.1080/21505594.2016.1159366 CrossRefPubMedPubMedCentralGoogle Scholar
  2. Alguacil-Guillen M, Ramos-Ruperto L, Ramos Ramos JC et al (2019) MALDI-TOF MS for rapid diagnosis of Anaerobiospirillum succiniciproducens, an unusual causative agent of bacteraemia in humans. Two case reports and literature review. Anaerobe 55:130–135.  https://doi.org/10.1016/j.anaerobe.2018.12.003 CrossRefPubMedGoogle Scholar
  3. Bassetti M, Righi E, Carnelutti A (2016) Bloodstream infections in the Intensive Care Unit. Virulence 7:267–279.  https://doi.org/10.1080/21505594.2015.1134072 CrossRefPubMedPubMedCentralGoogle Scholar
  4. Buehler SS, Madison B, Snyder SR et al (2016) Effectiveness of practices to increase timeliness of providing targeted therapy for inpatients with bloodstream infections: a laboratory medicine best practices systematic review and meta-analysis. Clin Microbiol Rev 29:59–103.  https://doi.org/10.1128/CMR.00053-14 CrossRefPubMedGoogle Scholar
  5. Candel FJ, Borges Sa M, Belda S et al (2018) Current aspects in sepsis approach. Turning things around. Rev Esp Quimioter 31:1–18PubMedGoogle Scholar
  6. Chandrasekaran S, Abbott A, Campeau S et al (2018) Direct-from-blood-culture disk diffusion to determine antimicrobial susceptibility of gram-negative bacteria: preliminary report from the clinical and Laboratory Standards Institute Methods Development and Standardization Working Group. J Clin Microbiol 56:1–10.  https://doi.org/10.1128/JCM.01678-17 CrossRefGoogle Scholar
  7. Corless CE, Guiver M, Borrow R et al (2000) Contamination and sensitivity issues with a real-time universal 16S rRNA PCR. J Clin Microbiol 38:1747–1752PubMedPubMedCentralGoogle Scholar
  8. Czurda S, Smelik S, Preuner-Stix S et al (2016) Occurrence of fungal DNA contamination in PCR reagents: approaches to control and decontamination. J Clin Microbiol 54:148–152.  https://doi.org/10.1128/JCM.02112-15 CrossRefPubMedGoogle Scholar
  9. Dark P, Wilson C, Blackwood B et al (2012) Accuracy of LightCycler(R) SeptiFast for the detection and identification of pathogens in the blood of patients with suspected sepsis: a systematic review protocol. BMJ Open 2:e000392.  https://doi.org/10.1136/bmjopen-2011-000392 CrossRefPubMedPubMedCentralGoogle Scholar
  10. Del Bono V, Giacobbe DR (2016) Bloodstream infections in internal medicine. Virulence 7:353–365.  https://doi.org/10.1080/21505594.2016.1140296 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Eisenhofer R, Minich JJ, Marotz C et al (2019) Contamination in low microbial biomass microbiome studies: issues and recommendations. Trends Microbiol 27:105–117.  https://doi.org/10.1016/j.tim.2018.11.003 CrossRefPubMedGoogle Scholar
  12. Falces-Romero I, Cendejas-Bueno E, Laplaza-González M et al (2018a) T2Candida®to guide antifungal and lengh of treatment of candidemia in a pediatric multivisceral transplant recipient. Med Mycol Case Rep 21:66–68.  https://doi.org/10.1016/j.mmcr.2018.05.006 CrossRefPubMedPubMedCentralGoogle Scholar
  13. Falces-Romero I, Cendejas-Bueno E, Romero-Gómez MP, García-Rodríguez J (2018b) Isolation of Rhodotorula mucilaginosa from blood cultures in a tertiary care hospital. Mycoses 61:35–39.  https://doi.org/10.1111/myc.12703 CrossRefPubMedGoogle Scholar
  14. Faron ML, Buchan BW, Ledeboer NA (2017) Matrix-assisted laser desorption ionization-time of flight mass spectrometry for use with positive blood cultures: methodology, performance, and optimization. J Clin Microbiol 55:3328–3338.  https://doi.org/10.1128/JCM.00868-17 CrossRefPubMedPubMedCentralGoogle Scholar
  15. Fenollar F, Raoult D (2007) Molecular diagnosis of bloodstream infections caused by non-cultivable bacteria. Int J Antimicrob Agents 30:7–15.  https://doi.org/10.1016/j.ijantimicag.2007.06.024 CrossRefGoogle Scholar
  16. Fernández-Cruz A, Marín M, Kestler M et al (2013) The value of combining blood culture and SeptiFast data for predicting complicated bloodstream infections caused by Gram-positive bacteria or Candida species. J Clin Microbiol 51:1130–1136.  https://doi.org/10.1128/JCM.02882-12 CrossRefPubMedPubMedCentralGoogle Scholar
  17. Fernández-Romero N, Quiles I, Jiménez C et al (2014) Use of multiplex PCR in diagnosis of bloodstream infections in kidney patients. Diagn Microbiol Infect Dis 80:93–96.  https://doi.org/10.1016/j.diagmicrobio.2014.07.001 CrossRefPubMedGoogle Scholar
  18. Florio W, Morici P, Ghelardi E et al (2018) Recent advances in the microbiological diagnosis of bloodstream infections. Crit Rev Microbiol 44:351–370.  https://doi.org/10.1080/1040841X.2017.1407745 CrossRefPubMedGoogle Scholar
  19. Gauer RL (2013) Early recognition and management of sepsis in adults: the first six hours. Am Fam Physician 88:44–53PubMedGoogle Scholar
  20. Ginn AN, Halliday CL, Douglas AP, Chen SC-A (2017) PCR-based tests for the early diagnosis of sepsis. Where do we stand? Curr Opin Infect Dis 30:565–572.  https://doi.org/10.1097/QCO.0000000000000407 CrossRefPubMedGoogle Scholar
  21. Gross I, Gordon O, Abu Ahmad W et al (2018) Yield of anaerobic blood cultures in pediatric emergency department patients. Pediatr Infect Dis J 37:281–286.  https://doi.org/10.1097/INF.0000000000001751 CrossRefPubMedGoogle Scholar
  22. Grumaz S, Stevens P, Grumaz C et al (2016) Next-generation sequencing diagnostics of bacteremia in septic patients. Genome Med 8:73.  https://doi.org/10.1186/s13073-016-0326-8 CrossRefPubMedPubMedCentralGoogle Scholar
  23. Herne V, Nelovkov A, Kütt M, Ivanova M (2013) Diagnostic performance and therapeutic impact of LightCycler SeptiFast assay in patients with suspected sepsis. Eur J Microbiol Immunol (Bp) 3:68–76.  https://doi.org/10.1556/EuJMI.3.2013.1.10 CrossRefGoogle Scholar
  24. Hewitt FC, Guertin SL, Ternus KL, et al (2018) Toward rapid sequenced-based detection and characterization of causative agents of bacteremia. bioRxiv.  https://doi.org/10.1101/162735
  25. Hong DK, Blauwkamp TA, Kertesz M et al (2018) Liquid biopsy for infectious diseases: sequencing of cell-free plasma to detect pathogen DNA in patients with invasive fungal disease. Diagn Microbiol Infect Dis 92:210–213.  https://doi.org/10.1016/j.diagmicrobio.2018.06.009 CrossRefPubMedGoogle Scholar
  26. Kuzniewicz MW, Walsh EM, Li S et al (2016) Development and implementation of an early-onset sepsis calculator to guide antibiotic management in late preterm and term neonates. Jt Comm J Qual patient Saf 42:232–239CrossRefGoogle Scholar
  27. Lamy B, Dargère S, Arendrup MC et al (2016) How to optimize the use of blood cultures for the diagnosis of bloodstream infections? A State-of-the Art. Front Microbiol 7:697.  https://doi.org/10.3389/fmicb.2016.00697 CrossRefPubMedPubMedCentralGoogle Scholar
  28. Liu CM, Kachur S, Dwan MG et al (2012) FungiQuant: a broad-coverage fungal quantitative real-time PCR assay. BMC Microbiol 12:255.  https://doi.org/10.1186/1471-2180-12-255 CrossRefPubMedPubMedCentralGoogle Scholar
  29. Martinez RM, Wolk DM (2016) Bloodstream Infections. Microbiol Spectr 4:1–34.  https://doi.org/10.1128/microbiolspec.DMIH2-0031-2016.Correspondence CrossRefGoogle Scholar
  30. McAdam AJ (2018) Shotgun metagenomic detection of pathogens: a micro-comic strip. J Clin Microbiol 56:8–9.  https://doi.org/10.1128/JCM.00799-18 CrossRefGoogle Scholar
  31. Morinaga Y, Yanagihara K (2015) Broad-range PCR in the identification of bacterial and fungal pathogens from positive blood culture bottles: a sequencing approach. In: Mancini N (ed) Sepsis: diagnostic methods and protocols (methods in molecular biology). Humana Press, New York, pp 65–72Google Scholar
  32. Opota O, Jaton K, Greub G (2015) Microbial diagnosis of bloodstream infection: towards molecular diagnosis directly from blood. Clin Microbiol Infect 21:323–331.  https://doi.org/10.1016/j.cmi.2015.02.005 CrossRefPubMedGoogle Scholar
  33. Peker N, Couto N, Sinha B, Rossen JW (2018) Diagnosis of bloodstream infections from positive blood cultures and directly from blood samples: recent developments in molecular approaches. Clin Microbiol Infect 24:944–955.  https://doi.org/10.1016/j.cmi.2018.05.007 CrossRefPubMedGoogle Scholar
  34. Périllaud C, Pilmis B, Diep J et al (2018) Prospective evaluation of rapid antimicrobial susceptibility testing by disk diffusion on Mueller-Hinton rapid-SIR directly on blood cultures. Diagn Microbiol Infect Dis 93:14–21.  https://doi.org/10.1016/j.diagmicrobio.2018.07.016 CrossRefPubMedGoogle Scholar
  35. Philipp S, Huemer HP, Irschick EU, Gassner C (2010) Obstacles of multiplex real-time PCR for bacterial 16S rDNA: primer specifity and DNA decontamination of Taq polymerase. Transfus Med Hemother 37:21–28.  https://doi.org/10.1159/000265571 CrossRefPubMedPubMedCentralGoogle Scholar
  36. Pilecky M, Schildberger A, Orth-Höller D, Weber V (2018) Pathogen enrichment from human whole blood for the diagnosis of bloodstream infection: prospects and limitations. Diagn Microbiol Infect Dis 1:1–10.  https://doi.org/10.1016/j.diagmicrobio.2018.11.015 CrossRefGoogle Scholar
  37. Prucha M, Bellingan G, Zazula R (2015) Sepsis biomarkers. Clin Chim Acta 440:97–103.  https://doi.org/10.1016/j.cca.2014.11.012 CrossRefPubMedGoogle Scholar
  38. Ramanan P, Bryson AL, Binnicker MJ et al (2017) Syndromic panel-based testing in clinical microbiology. Clin Microbiol Rev 31:1–28.  https://doi.org/10.1128/CMR.00024-17 CrossRefGoogle Scholar
  39. Reigadas E, Rodríguez-Créixems M, Sánchez-Carrillo C et al (2015) Uncommon aetiological agents of catheter-related bloodstream infections. Epidemiol Infect 143:741–744.  https://doi.org/10.1017/S0950268814001435 CrossRefPubMedGoogle Scholar
  40. Romero-Gómez M-P, Gómez-Gil R, Paño-Pardo JR, Mingorance J (2012) Identification and susceptibility testing of microorganism by direct inoculation from positive blood culture bottles by combining MALDI-TOF and Vitek-2 Compact is rapid and effective. J Infect 65:513–520.  https://doi.org/10.1016/j.jinf.2012.08.013 CrossRefPubMedGoogle Scholar
  41. Shane AL, Sánchez PJ, Stoll BJ (2017) Neonatal sepsis. Lancet (London, England) 390:1770–1780.  https://doi.org/10.1016/S0140-6736(17)31002-4 CrossRefGoogle Scholar
  42. Sharara SL, Tayyar R, Kanafani ZA, Kanj SS (2016) HACEK endocarditis: a review. Expert Rev Anti Infect Ther 14:539–545.  https://doi.org/10.1080/14787210.2016.1184085 CrossRefPubMedGoogle Scholar
  43. Sinha M, Jupe J, Mack H et al (2018) Emerging technologies for molecular diagnosis of sepsis. Clin Microbiol Rev 31:1–26.  https://doi.org/10.1128/CMR.00089-17 CrossRefGoogle Scholar
  44. Suzuki T, Kawada JI, Okuno Y et al (2017) Comprehensive detection of viruses in pediatric patients with acute liver failure using next-generation sequencing. J Clin Virol 96:67–72.  https://doi.org/10.1016/j.jcv.2017.10.001 CrossRefPubMedGoogle Scholar
  45. Tabak YP, Vankeepuram L, Ye G et al (2018) Blood culture turnaround time in U.S. acute care hospitals and implications for laboratory process optimization. J Clin Microbiol 56:1–8.  https://doi.org/10.1128/JCM.00500-18 CrossRefGoogle Scholar
  46. Timbrook TT, Morton JB, Mcconeghy KW et al (2017) The effect of molecular rapid diagnostic testing on clinical outcomes in bloodstream infections: a systematic review and meta-analysis. Clin Infect Dis 64:15–23.  https://doi.org/10.1093/cid/ciw649 CrossRefPubMedGoogle Scholar
  47. van der Geest PJ, Mohseni M, Linssen J et al (2016) The intensive care infection score—a novel marker for the prediction of infection and its severity. Crit Care 20:180.  https://doi.org/10.1186/s13054-016-1366-6 CrossRefPubMedPubMedCentralGoogle Scholar
  48. Viscoli C (2016) Bloodstream infections: the peak of the iceberg. Virulence 7:248–251.  https://doi.org/10.1080/21505594.2016.1152440 CrossRefPubMedPubMedCentralGoogle Scholar
  49. Yagupsky P, Nolte FS (1990) Quantitative aspects of septicemia. Microbiology 3:269–279Google Scholar
  50. Yahav D, Eliakim-Raz N, Leibovici L, Paul M (2016) Bloodstream infections in older patients. Virulence 7:341–352.  https://doi.org/10.1080/21505594.2015.1132142 CrossRefPubMedGoogle Scholar
  51. Zacharioudakis I, Zervou F, Mylonakis E (2018) T2 magnetic resonance assay: overview of available data and clinical implications. J Fungi 4:45.  https://doi.org/10.3390/jof4020045 CrossRefGoogle Scholar
  52. Ziegler I, Josefson P, Olcén P et al (2014) Quantitative data from the SeptiFast real-time PCR is associated with disease severity in patients with sepsis. BMC Infect Dis 14:155.  https://doi.org/10.1186/1471-2334-14-155 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZMadridSpain

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