Chapter 7 : Molecular Methods for Detection of Pathogens Directly from Blood Specimens

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Sepsis is a global problem and laboratory methods must be optimized to effect rapid, positive patient outcomes. The proverbial reference standard method for diagnosis, the actual culture of blood, suffers from a variety of preanalytical issues such as sufficient blood volume, prior antimicrobial treatment, time from sampling to incubation, and analytical issues of prolonged turnaround time until final identification and availability of antimicrobial susceptibility testing results. Advancements have occurred in molecular methods to provide rapid microorganism identification and resistance gene detection (e.g., in spp.) from positive blood culture broths. In a meta-analysis of these new methods, a significant reduction in time to targeted treatment was observed ( ). However, these methods are dependent on having a positive blood culture, which is subject to the preanalytical issues described above. The ability to directly identify pathogens from blood specimens would greatly reduce the time to identification and time to optimization of therapy, as well as potentially contributing to avoiding unnecessary antimicrobials and/or discontinuation of treatment in patients with negative testing results. Direct detection methods for viruses from patient specimens have benefited from advances in molecular methods, which is largely because of the high viral loads present in those specimens. In contrast, the majority of septic patients have a paucity of bacteria or fungi per milliliter of blood, necessitating the need for larger blood volumes to increase blood culture sensitivity ( ).

Citation: Gonzalez M, Jerris R. 2017. Molecular Methods for Detection of Pathogens Directly from Blood Specimens, p 137-149. In Dunne, Jr. W, Burnham C (ed), The Dark Art of Blood Cultures. ASM Press, Washington, DC. doi: 10.1128/9781555819811.ch7
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1. Buehler SS,, Madison B,, Snyder SR,, Derzon JH,, Cornish NE,, Saubolle MA,, Weissfeld AS,, Weinstein MP,, Liebow EB,, Wolk DM . 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.
2. Hall MM,, Ilstrup DM,, Washington JA II . 1976. Effect of volume of blood cultured on detection of bacteremia. J Clin Microbiol 3 : 643 645.
3. Tenney JH,, Reller LB,, Mirrett S,, Wang WL,, Weinstein MP . 1982. Controlled evaluation of the volume of blood cultured in detection of bacteremia and fungemia. J Clin Microbiol 15 : 558 561.
4. Kaditis AG,, O’Marcaigh AS,, Rhodes KH,, Weaver AL,, Henry NK . 1996. Yield of positive blood cultures in pediatric oncology patients by a new method of blood culture collection. Pediatr Infect Dis J 15 : 615 620.
5. Chang SS,, Hsieh WH,, Liu TS,, Lee SH,, Wang CH,, Chou HC,, Yeo YH,, Tseng CP,, Lee CC . 2013. Multiplex PCR system for rapid detection of pathogens in patients with presumed sepsis - a systemic review and meta-analysis. PLoS One 8 : e62323.
6. Whiting P,, Rutjes AW,, Reitsma JB,, Bossuyt PM,, Kleijnen J . 2003. The development of QUADAS: a tool for the quality assessment of studies of diagnostic accuracy included in systematic reviews. BMC Med Res Methodol 3 : 25.
7. Warhurst G,, Maddi S,, Dunn G,, Ghrew M,, Chadwick P,, Alexander P,, Bentley A,, Moore J,, Sharman M,, Carlson GL,, Young D,, Dark P . 2015. Diagnostic accuracy of SeptiFast multi-pathogen real-time PCR in the setting of suspected healthcare-associated bloodstream infection. Intensive Care Med 41 : 86 93.
8. Markota A,, Seme K,, Golle A,, Poljak M,, Sinkovič A . 2014. SeptiFast real-time PCR for detection of bloodborne pathogens in patients with severe sepsis or septic shock. Coll Antropol 38 : 829 833.
9. Dark P,, Blackwood B,, Gates S,, McAuley D,, Perkins GD,, McMullan R,, Wilson C,, Graham D,, Timms K,, Warhurst G . 2015. 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 41 : 21 33.
10. Nieman AE,, Savelkoul PH,, Beishuizen A,, Henrich B,, Lamik B,, MacKenzie CR,, Kindgen-Milles D,, Helmers A,, Diaz C,, Sakka SG,, Schade RP . 2016. A prospective multicenter evaluation of direct molecular detection of blood stream infection from a clinical perspective. BMC Infect Dis 16 : 314.
11. Wellinghausen N,, Kochem AJ,, Disqué C,, Mühl H,, Gebert S,, Winter J,, Matten J,, Sakka SG . 2009. Diagnosis of bacteremia in whole-blood samples by use of a commercial universal 16S rRNA gene-based PCR and sequence analysis. J Clin Microbiol 47 : 2759 2765.
12. Bloos F,, Sachse S,, Schmidt K-H,, Lehmann M,, Schmitz R,, Russwurm S,, Straube E,, Reinhart K . 2008. Nucleic acid amplification-based pathogen detection in the blood of severe sepsis patients. Critical Care 12( Suppl 5) : P43.
13. Schreiber J,, Nierhaus A,, Braune SA,, de Heer G,, Kluge S . 2013. Comparison of three different commercial PCR assays for the detection of pathogens in critically ill sepsis patients. Med Klin Intensivmed Notf Med 108 : 311 318.
14. Bacconi A,, Richmond GS,, Baroldi MA,, Laffler TG,, Blyn LB,, Carolan HE,, Frinder MR,, Toleno DM,, Metzgar D,, Gutierrez JR,, Massire C,, Rounds M,, Kennel NJ,, Rothman RE,, Peterson S,, Carroll KC,, Wakefield T,, Ecker DJ,, Sampath R . 2014. Improved sensitivity for molecular detection of bacterial and Candida infections in blood. J Clin Microbiol 52 : 3164 3174.
15. Jordana-Lluch E,, Giménez M,, Quesada MD,, Rivaya B,, Marcó C,, Domínguez MJ,, Arméstar F,, Martró E,, Ausina V . 2015. Evaluation of the broad-range PCR/ESI-MS technology in blood specimens for the molecular diagnosis of bloodstream infections. PLoS One 10 : e0140865.
16. Pfaller MA,, Wolk DM,, Lowery TJ . 2016. T2MR and T2Candida: novel technology for the rapid diagnosis of candidemia and invasive candidiasis. Future Microbiol 11 : 103 117.
17. Neely LA,, Audeh M,, Phung NA,, Min M,, Suchocki A,, Plourde D,, Blanco M,, Demas V,, Skewis LR,, Anagnostou T,, Coleman JJ,, Wellman P,, Mylonakis E,, Lowery TJ . 2013. T2 magnetic resonance enables nanoparticle-mediated rapid detection of candidemia in whole blood. Sci Transl Med 5 : 182ra54.
18. Beyda ND,, Alam MJ,, Garey KW . 2013. Comparison of the T2Dx instrument with T2Candida assay and automated blood culture in the detection of Candida species using seeded blood samples. Diagn Microbiol Infect Dis 77 : 324 326.
19. Mylonakis E,, Clancy CJ,, Ostrosky-Zeichner L,, Garey KW,, Alangaden GJ,, Vazquez JA,, Groeger JS,, Judson MA,, Vinagre YM,, Heard SO,, Zervou FN,, Zacharioudakis IM,, Kontoyiannis DP,, Pappas PG . 2015. T2 magnetic resonance assay for the rapid diagnosis of candidemia in whole blood: a clinical trial. Clin Infect Dis 60 : 892 899.


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Comparison of preanalytic and analytic factors for commercially available direct-from-blood multiplex assay

Citation: Gonzalez M, Jerris R. 2017. Molecular Methods for Detection of Pathogens Directly from Blood Specimens, p 137-149. In Dunne, Jr. W, Burnham C (ed), The Dark Art of Blood Cultures. ASM Press, Washington, DC. doi: 10.1128/9781555819811.ch7
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Table 2

Comparison of targets on commercially available multiplex assays

Citation: Gonzalez M, Jerris R. 2017. Molecular Methods for Detection of Pathogens Directly from Blood Specimens, p 137-149. In Dunne, Jr. W, Burnham C (ed), The Dark Art of Blood Cultures. ASM Press, Washington, DC. doi: 10.1128/9781555819811.ch7

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