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.
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References
Akova M (2016) Epidemiology of antimicrobial resistance in bloodstream infections. Virulence 7:252–266. https://doi.org/10.1080/21505594.2016.1159366
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
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
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
Candel FJ, Borges Sa M, Belda S et al (2018) Current aspects in sepsis approach. Turning things around. Rev Esp Quimioter 31:1–18
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
Corless CE, Guiver M, Borrow R et al (2000) Contamination and sensitivity issues with a real-time universal 16S rRNA PCR. J Clin Microbiol 38:1747–1752
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
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
Del Bono V, Giacobbe DR (2016) Bloodstream infections in internal medicine. Virulence 7:353–365. https://doi.org/10.1080/21505594.2016.1140296
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
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
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
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
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
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
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
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
Gauer RL (2013) Early recognition and management of sepsis in adults: the first six hours. Am Fam Physician 88:44–53
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
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
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
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
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
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
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 42:232–239
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
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
Martinez RM, Wolk DM (2016) Bloodstream Infections. Microbiol Spectr 4:1–34. https://doi.org/10.1128/microbiolspec.DMIH2-0031-2016.Correspondence
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
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 65–72
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Viscoli C (2016) Bloodstream infections: the peak of the iceberg. Virulence 7:248–251. https://doi.org/10.1080/21505594.2016.1152440
Yagupsky P, Nolte FS (1990) Quantitative aspects of septicemia. Microbiology 3:269–279
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
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
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
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Cendejas-Bueno, E., Romero-Gómez, M.P. & Mingorance, J. The challenge of molecular diagnosis of bloodstream infections. World J Microbiol Biotechnol 35, 65 (2019). https://doi.org/10.1007/s11274-019-2640-y
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DOI: https://doi.org/10.1007/s11274-019-2640-y