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Chapter 11 : Processing Positive Cultures

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Abstract:

It can be said that the diagnosis of bloodstream infections is one of the most important roles of the clinical microbiology laboratory; the mortality rate associated with bloodstream infection ranges from 25 to 80% ( ). There are a number of factors that contribute to the mortality rate subsequent to bloodstream infection, with time to appropriate antimicrobial therapy frequently cited as one of the most important variables correlating with clinical outcome ( ). Herein, we describe procedures for optimization of positive blood culture specimens and describe current and future methodologies to augment blood culture to diagnose bloodstream infection.

Citation: Faron M, Ledeboer N. 2017. Processing Positive Cultures, p 207-244. In Dunne, Jr. W, Burnham C (ed), The Dark Art of Blood Cultures. ASM Press, Washington, DC. doi: 10.1128/9781555819811.ch11
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Figures

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Figure 1

Example of blood culture Gram stains with multiple morphologies to illustrate size differences of various organisms. Image was acquired by adding cells from each organism with the contents of a negative blood culture. Based on size, large to small pink/brown erythrocytes can be observed throughout the Gram stain (red arrow). cells are much larger than bacterial cells and stain GP (green arrow). Smaller bacteria are observed throughout the stain with GN rods (pink arrow) and GPC (purple arrows).

Citation: Faron M, Ledeboer N. 2017. Processing Positive Cultures, p 207-244. In Dunne, Jr. W, Burnham C (ed), The Dark Art of Blood Cultures. ASM Press, Washington, DC. doi: 10.1128/9781555819811.ch11
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Image of Figure 2
Figure 2

Representative image of several Gram stain morphologies that can be observed from blood culture. Most commonly observed are Gram-negative rods (GNR) and Gram-positive cocci (GPC) ( ; ). Larger budding yeasts are less common but may yield better growth when plated to Sabouraud agar ( ). Gram-positive rods (GPR) are also less frequent and many not require unique agar to grow ( spp.), but boxy poor staining GPR may indicate spp. which grow optimally at anaerobic conditions ( ). spp. are thin GN spirochetes often growing wavelike or “gull shaped” and may require growth at 42°C on specific agar depending upon the species ( ). Finally, morphologies that may require caution because of being highly infectious agents are small GN coccobacillus , beaded branching GP rods , or bipolar staining “safety pin” ; however, many other organisms can be observed with these morphologies, and restrictions can be lifted after colony morphologies and testing rule out biological safety agents (morphology represented by ; ; ).

Citation: Faron M, Ledeboer N. 2017. Processing Positive Cultures, p 207-244. In Dunne, Jr. W, Burnham C (ed), The Dark Art of Blood Cultures. ASM Press, Washington, DC. doi: 10.1128/9781555819811.ch11
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FIGURE 3

Various approaches to structuring laboratory policy of positive blood cultures. With the variety of assays available to identify organisms growing in blood cultures, laboratories can customize workflow to fit various criteria affecting turnaround time, cost, and complexity. Potential workflow approaches for laboratories are as follows. The traditional method should not be used alone, because results are too delayed and several viable rapid options are available; however, plating should be applied to all rapid testing where the * is placed to confirm results and check for polymicrobial cultures. For ease of workflow, a single molecular device can be used for all positive bottles. This is best done using a large panel that covers the most common blood pathogens. To reduce cost or improve patient care, a multifaceted approach can be implemented where the rapid assay used changes based on the Gram stain result. For instance, using cheaper methicillin-resistant (MRSA) assays for Gram-positive cocci in clusters (GPCCL) and a panel for all other testing. Although it is labor intensive to bring on matrix-assisted laser desorption ionization–time of flight mass spectroscopy (MALDI-TOF MS) or use antimicrobial susceptibility testing (AST), panels of product that insert these assays likely have the shortest TAT for reporting susceptibilities. Combinations of these approaches can be used to fit the laboratories’ needs and abilities.

Citation: Faron M, Ledeboer N. 2017. Processing Positive Cultures, p 207-244. In Dunne, Jr. W, Burnham C (ed), The Dark Art of Blood Cultures. ASM Press, Washington, DC. doi: 10.1128/9781555819811.ch11
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References

/content/book/10.1128/9781555819828.chap11
1. Levy MM,, Rhodes A,, Phillips GS,, Townsend SR,, Schorr CA,, Beale R,, Osborn T,, Lemeshow S,, Chiche JD,, Artigas A,, Dellinger RP. 2014. Surviving Sepsis Campaign: association between performance metrics and outcomes in a 7.5-year study. Intensive Care Med 40:16231633.
2. Angus DC,, Wax RS. 2001. Epidemiology of sepsis: an update. Crit Care Med 29(Suppl):S109S116.
3. Kumar A,, Roberts D,, Wood KE,, Light B,, Parrillo JE,, Sharma S,, Suppes R,, Feinstein D,, Zanotti S,, Taiberg L,, Gurka D,, Kumar A,, Cheang M. 2006. Duration of hypotension before initiation of effective antimicrobial therapy is the critical determinant of survival in human septic shock. Crit Care Med 34:15891596.
4. Ibrahim EH,, Sherman G,, Ward S,, Fraser VJ,, Kollef MH. 2000. The influence of inadequate antimicrobial treatment of bloodstream infections on patient outcomes in the ICU setting. Chest 118:146155.
5. Shorr AF,, Micek ST,, Welch EC,, Doherty JA,, Reichley RM,, Kollef MH. 2011. Inappropriate antibiotic therapy in Gram-negative sepsis increases hospital length of stay. Crit Care Med 39:4651.
6. Kerremans JJ,, van der Bij AK,, Goessens W,, Verbrugh HA,, Vos MC. 2009. Needle-to-incubator transport time: logistic factors influencing transport time for blood culture specimens. J Clin Microbiol 47:819822.
7. Sautter RL,, Bills AR,, Lang DL,, Ruschell G,, Heiter BJ,, Bourbeau PP. 2006. Effects of delayed-entry conditions on the recovery and detection of microorganisms from BacT/ALERT and BACTEC blood culture bottles. J Clin Microbiol 44:12451249.
8. Buetti N,, Marschall J,, Atkinson A,, Kronenberg A, Swiss Centre for Antibiotic Resistance. 2016. National Bloodstream Infection Surveillance in Switzerland 2008-2014: different patterns and trends for university and community hospitals. Infect Control Hosp Epidemiol 37:10601067. doi:10.1017/ice.2016.137.
9. Cockerill FR III,, Reed GS,, Hughes JG,, Torgerson CA,, Vetter EA,, Harmsen WS,, Dale JC,, Roberts GD,, Ilstrup DM,, Henry NK. 1997. Clinical comparison of BACTEC 9240 plus aerobic/F resin bottles and the isolator aerobic culture system for detection of bloodstream infections. J Clin Microbiol 35:14691472.
10. Karahan ZC,, Mumcuoglu I,, Guriz H,, Tamer D,, Balaban N,, Aysev D,, Akar N. 2006. PCR evaluation of false-positive signals from two automated blood-culture systems. J Med Microbiol 55:5357.
11. Ziegler R,, Johnscher I,, Martus P,, Lenhardt D,, Just HM. 1998. Controlled clinical laboratory comparison of two supplemented aerobic and anaerobic media used in automated blood culture systems to detect bloodstream infections. J Clin Microbiol 36:657661.
12. Durtschi JD,, Erali M,, Bromley LK,, Herrmann MG,, Petti CA,, Smith RE,, Voelkerding KV. 2005. Increased sensitivity of bacterial detection in cerebrospinal fluid by fluorescent staining on low-fluorescence membrane filters. J Med Microbiol 54:843850.
13. Lauer BA,, Reller LB,, Mirrett S. 1981. Comparison of acridine orange and Gram stains for detection of microorganisms in cerebrospinal fluid and other clinical specimens. J Clin Microbiol 14:201205.
14. Qian Q,, Tang YW,, Kolbert CP,, Torgerson CA,, Hughes JG,, Vetter EA,, Harmsen WS,, Montgomery SO,, Cockerill FR III,, Persing DH. 2001. Direct identification of bacteria from positive blood cultures by amplification and sequencing of the 16S rRNA gene: evaluation of BACTEC 9240 instrument true-positive and false-positive results. J Clin Microbiol 39:35783582.
15. Winn WC,, Koneman EW. 2006. Koneman’s Color Atlas and Textbook of Diagnostic Microbiology, 6th ed. Lippincott Williams & Wilkins, Philadelphia, PA.
16. MacArthur RD,, Miller M,, Albertson T,, Panacek E,, Johnson D,, Teoh L,, Barchuk W. 2004. Adequacy of early empiric antibiotic treatment and survival in severe sepsis: experience from the MONARCS trial. Clin Infect Dis 38:284288.
17. Miano TA,, Powell E,, Schweickert WD,, Morgan S,, Binkley S,, Sarani B. 2012. Effect of an antibiotic algorithm on the adequacy of empiric antibiotic therapy given by a medical emergency team. J Crit Care 27:4550.
18. Wang MC,, Lin WH,, Yan JJ,, Fang HY,, Kuo TH,, Tseng CC,, Wu JJ. 2015. Early identification of microorganisms in blood culture prior to the detection of a positive signal in the BACTEC FX system using matrix-assisted laser desorption/ionization-time of flight mass spectrometry. J Microbiol Immunol Infect 48:419424.
19. Al-Soud WA,, Rådström P. 2001. Purification and characterization of PCR-inhibitory components in blood cells. J Clin Microbiol 39:485493.
20. Clark AE,, Kaleta EJ,, Arora A,, Wolk DM. 2013. Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev 26:547603.
21. Angeletti S. 2017. Matrix assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology. J Microbiol Methods 138:2029. doi:10.1016/j.mimet.2016.09.003.
22. Ferreira L,, Sánchez-Juanes F,, González-Avila M,, Cembrero-Fuciños D,, Herrero-Hernández A,, González-Buitrago JM,, Muñoz-Bellido JL. 2010. Direct identification of urinary tract pathogens from urine samples by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 48:21102115.
23. Hsieh SY,, Tseng CL,, Lee YS,, Kuo AJ,, Sun CF,, Lin YH,, Chen JK. 2008. Highly efficient classification and identification of human pathogenic bacteria by MALDI-TOF MS. Mol Cell Proteomics 7:448456.
24. La Scola B,, Raoult D. 2009. Direct identification of bacteria in positive blood culture bottles by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry. PLoS One 4:e8041.
25. Prod’hom G,, Bizzini A,, Durussel C,, Bille J,, Greub G. 2010. Matrix-assisted laser desorption ionization-time of flight mass spectrometry for direct bacterial identification from positive blood culture pellets. J Clin Microbiol 48:14811483.
26. Moussaoui W,, Jaulhac B,, Hoffmann AM,, Ludes B,, Kostrzewa M,, Riegel P,, Prévost G. 2010. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry identifies 90% of bacteria directly from blood culture vials. Clin Microbiol Infect 16:16311638.
27. Bazzi AM,, Rabaan AA,, El Edaily Z,, John S,, Fawarah MM,, Al-Tawfiq JA. 2017. Comparison among four proposed direct blood culture microbial identification methods using MALDI-TOF MS. J Infect Public Health 10:308315. doi:10.1016/j.jiph.2016.05.011.
28. Verroken A,, Defourny L,, Lechgar L,, Magnette A,, Delmée M,, Glupczynski Y. 2015. Reducing time to identification of positive blood cultures with MALDI-TOF MS analysis after a 5-h subculture. Eur J Clin Microbiol Infect Dis 34:405413.
29. Gonzalez MD,, Weber CJ,, Burnham CA. 2016. Rapid identification of microorganisms from positive blood cultures by testing early growth on solid media using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Diagn Microbiol Infect Dis 85:133135.
30. Nonnemann B,, Tvede M,, Bjarnsholt T. 2013. Identification of pathogenic microorganisms directly from positive blood vials by matrix-assisted laser desorption/ionization time of flight mass spectrometry. APMIS 121:871877.
31. Hazelton B,, Thomas LC,, Olma T,, Kok J,, O’Sullivan M,, Chen SC,, Iredell JR. 2014. Rapid and accurate direct antibiotic susceptibility testing of blood culture broths using MALDI Sepsityper combined with the BD Phoenix automated system. J Med Microbiol 63:15901594.
32. Morgenthaler NG,, Kostrzewa M. 2015. Rapid identification of pathogens in positive blood culture of patients with sepsis: review and meta-analysis of the performance of the sepsityper kit. Int J Microbiol 2015:827416.
33. Yan Y,, He Y,, Maier T,, Quinn C,, Shi G,, Li H,, Stratton CW,, Kostrzewa M,, Tang YW. 2011. Improved identification of yeast species directly from positive blood culture media by combining Sepsityper specimen processing and Microflex analysis with the matrix-assisted laser desorption ionization Biotyper system. J Clin Microbiol 49:25282532.
34. Spanu T,, Posteraro B,, Fiori B,, D’Inzeo T,, Campoli S,, Ruggeri A,, Tumbarello M,, Canu G,, Trecarichi EM,, Parisi G,, Tronci M,, Sanguinetti M,, Fadda G. 2012. Direct MALDI-TOF mass spectrometry assay of blood culture broths for rapid identification of Candida species causing bloodstream infections: an observational study in two large microbiology laboratories. J Clin Microbiol 50:176179.
35. Rychert J,, Burnham CA,, Bythrow M,, Garner OB,, Ginocchio CC,, Jennemann R,, Lewinski MA,, Manji R,, Mochon AB,, Procop GW,, Richter SS,, Sercia L,, Westblade LF,, Ferraro MJ,, Branda JA. 2013. Multicenter evaluation of the Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of Gram-positive aerobic bacteria. J Clin Microbiol 51:22252231.
36. Wang XH,, Zhang G,, Fan YY,, Yang X,, Sui WJ,, Lu XX. 2013. Direct identification of bacteria causing urinary tract infections by combining matrix-assisted laser desorption ionization-time of flight mass spectrometry with UF-1000i urine flow cytometry. J Microbiol Methods 92:231235.
37. Loonen AJ,, Jansz AR,, Stalpers J,, Wolffs PF,, van den Brule AJ. 2012. An evaluation of three processing methods and the effect of reduced culture times for faster direct identification of pathogens from BacT/ALERT blood cultures by MALDI-TOF MS. Eur J Clin Microbiol Infect Dis 31:15751583.
38. Meex C,, Neuville F,, Descy J,, Huynen P,, Hayette MP,, De Mol P,, Melin P. 2012. Direct identification of bacteria from BacT/ALERT anaerobic positive blood cultures by MALDI-TOF MS: MALDI Sepsityper kit versus an in-house saponin method for bacterial extraction. J Med Microbiol 61:15111516.
39. Almuhayawi M,, Altun O,, Abdulmajeed AD,, Ullberg M,, Özenci V. 2015. The performance of the four anaerobic blood culture bottles BacT/ALERT-FN, -FN Plus, BACTEC-Plus and -Lytic in detection of anaerobic bacteria and identification by direct MALDI-TOF MS. PLoS One 10:e0142398.
40. Schubert S,, Weinert K,, Wagner C,, Gunzl B,, Wieser A,, Maier T,, Kostrzewa M. 2011. Novel, improved sample preparation for rapid, direct identification from positive blood cultures using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. J Mol Diagn 13:701706.
41. Buchan BW,, Riebe KM,, Ledeboer NA. 2012. Comparison of the MALDI Biotyper system using Sepsityper specimen processing to routine microbiological methods for identification of bacteria from positive blood culture bottles. J Clin Microbiol 50:346352.
42. Randazzo A,, Simon M,, Goffinet P,, Classen JF,, Hougardy N,, Pierre P,, Kinzinger P,, Mauel E,, Goffinet JS. 2016. Optimal turnaround time for direct identification of microorganisms by mass spectrometry in blood culture. J Microbiol Methods 130:15.
43. Hrabák J,, Chudácková E,, Walková R. 2013. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry for detection of antibiotic resistance mechanisms: from research to routine diagnosis. Clin Microbiol Rev 26:103114.
44. Ghebremedhin B,, Halstenbach A,, Smiljanic M,, Kaase M,, Ahmad-Nejad P. 2016. MALDI-TOF MS based carbapenemase detection from culture isolates and from positive blood culture vials. Ann Clin Microbiol Antimicrob 15:5.
45. Kim JS,, Kang GE,, Kim HS,, Kim HS,, Song W,, Lee KM. 2016. Evaluation of Verigene blood culture test systems for rapid identification of positive blood cultures. BioMed Res Int 2016:1081536.
46. Uno N,, Suzuki H,, Yamakawa H,, Yamada M,, Yaguchi Y,, Notake S,, Tamai K,, Yanagisawa H,, Misawa S,, Yanagihara K. 2015. Multicenter evaluation of the Verigene Gram-negative blood culture nucleic acid test for rapid detection of bacteria and resistance determinants in positive blood cultures. Diagn Microbiol Infect Dis 83:344348.
47. Ledeboer NA,, Lopansri BK,, Dhiman N,, Cavagnolo R,, Carroll KC,, Granato P,, Thomson R Jr,, Butler-Wu SM,, Berger H,, Samuel L,, Pancholi P,, Swyers L,, Hansen GT,, Tran NK,, Polage CR,, Thomson KS,, Hanson ND,, Winegar R,, Buchan BW. 2015. 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 53:24602472.
48. Buchan BW,, Ginocchio CC,, Manii R,, Cavagnolo R,, Pancholi P,, Swyers L,, Thomson RB Jr,, Anderson C,, Kaul K,, Ledeboer NA. 2013. Multiplex identification of gram-positive bacteria and resistance determinants directly from positive blood culture broths: evaluation of an automated microarray-based nucleic acid test. PLoS Med 10:e1001478.
49. Maatallah M,, Vading M,, Kabir MH,, Bakhrouf A,, Kalin M,, Nauclér P,, Brisse S,, Giske CG. 2014. Klebsiella variicola is a frequent cause of bloodstream infection in the Stockholm area, and associated with higher mortality compared to K. pneumoniae. PLoS One 9:e113539.
50. Walker T,, Dumadag S,, Lee CJ,, Lee SH,, Bender JM,, Cupo Abbott J,, She RC. 2016. Clinical impact of laboratory implementation of Verigene BC-GN microarray-based assay for detection of Gram-negative bacteria in positive blood cultures. J Clin Microbiol 54:17891796.
51. Boom R,, Sol CJ,, Salimans MM,, Jansen CL,, Wertheim-van Dillen PM,, van der Noordaa J. 1990. Rapid and simple method for purification of nucleic acids. J Clin Microbiol 28:495503.
52. Altun O,, Almuhayawi M,, Ullberg M,, Ozenci V. 2013. Clinical evaluation of the FilmArray blood culture identification panel in identification of bacteria and yeasts from positive blood culture bottles. J Clin Microbiol 51:41304136.
53. Salimnia H,, Fairfax MR,, Lephart PR,, Schreckenberger P,, DesJarlais SM,, Johnson JK,, Robinson G,, Carroll KC,, Greer A,, Morgan M,, Chan R,, Loeffelholz M,, Valencia-Shelton F,, Jenkins S,, Schuetz AN,, Daly JA,, Barney T,, Hemmert A,, Kanack KJ. 2016. Evaluation of the FilmArray blood culture identification panel: results of a multicenter controlled trial. J Clin Microbiol 54:687698.
54. McCoy MH,, Relich RF,, Davis TE,, Schmitt BH. 2016. Performance of the FilmArray® blood culture identification panel utilized by non-expert staff compared with conventional microbial identification and antimicrobial resistance gene detection from positive blood cultures. J Med Microbiol 65:619625.
55. Southern TR,, VanSchooneveld TC,, Bannister DL,, Brown TL,, Crismon AS,, Buss SN,, Iwen PC,, Fey PD. 2015. Implementation and performance of the BioFire FilmArray® Blood Culture Identification panel with antimicrobial treatment recommendations for bloodstream infections at a midwestern academic tertiary hospital. Diagn Microbiol Infect Dis 81:96101.
56. Ward C,, Stocker K,, Begum J,, Wade P,, Ebrahimsa U,, Goldenberg SD. 2015. Performance evaluation of the Verigene® (Nanosphere) and FilmArray® (BioFire®) molecular assays for identification of causative organisms in bacterial bloodstream infections. Eur J Clin Microbiol Infect Dis 34:487496.
57. Messacar K,, Hurst AL,, Child J,, Campbell K,, Palmer C,, Hamilton S,, Dowell E,, Robinson CC,, Parker SK,, Dominguez SR. 19 August 2016. Clinical impact and provider acceptability of real-time antimicrobial stewardship decision support for rapid diagnostics in children with positive blood culture results. J Pediatric Infect Dis Soc doi:10.1093/jpids/piw047.
58. Dodémont M,, De Mendonça R,, Nonhoff C,, Roisin S,, Denis O. 2015. Evaluation of Verigene Gram-Positive Blood Culture Assay performance for bacteremic patients. Eur J Clin Microbiol Infect Dis 34:473477.
59. Buchan BW,, Reymann GC,, Granato PA,, Alkins BR,, Jim P,, Young S. 2015. Preliminary evaluation of the research-use-only (RUO) iCubate iC-GPC assay for identification of select Gram-positive bacteria and their resistance determinants in blood culture broths. J Clin Microbiol 53:39313934.
60. Hensley DM,, Tapia R,, Encina Y. 2009. An evaluation of the advandx Staphylococcus aureus/CNS PNA FISH assay. Clin Lab Sci 22:3033.
61. Chapin K,, Musgnug M. 2003. Evaluation of three rapid methods for the direct identification of Staphylococcus aureus from positive blood cultures. J Clin Microbiol 41:43244327.
62. Aydemir G,, Koç AN,, Atalay MA. 2016. [Evaluation of peptide nucleic acid fluorescent in situ hybridization (PNA FISH) method in the identification of Candida species isolated from blood cultures]. Mikrobiyol Bul 50:293299.
63. Faron ML, CC, Buchan BW,, Guralnik M,, LaBombardi VJ,, Ledeboer NA. 2016. Multicenter evaluation of the Miacom HemoFISH for bacterial identification from positive blood cultures. Poster presentation at American Society for Microbiology Microbe 2016.
64. Vincent JL,, Guralnik M,, Faron ML,, Buchan BW,, Ledeboer NA. 2016. Evaluation of the Miacom HemoFISH Assay for positive blood cultures. Poster presentation at European Congress of Clinical Microbiology and Infectious Diseases 2016.
65. Lob SH,, Biedenbach DJ,, Badal RE,, Kazmierczak KM,, Sahm DF. 2016. Discrepancy between genotypic and phenotypic extended-spectrum β-lactamase rates in Escherichia coli from intra-abdominal infections in the USA. J Med Microbiol 65:905909.
66. Burnham CA,, Frobel RA,, Herrera ML,, Wickes BL. 2014. Rapid ertapenem susceptibility testing and Klebsiella pneumoniae carbapenemase phenotype detection in Klebsiella pneumoniae isolates by use of automated microscopy of immobilized live bacterial cells. J Clin Microbiol 52:982986.
67. Metzger S,, Frobel RA,, Dunne WM Jr. 2014. Rapid simultaneous identification and quantitation of Staphylococcus aureus and Pseudomonas aeruginosa directly from bronchoalveolar lavage specimens using automated microscopy. Diagn Microbiol Infect Dis 79:160165.
68. Lisby GKS,, Knudsen JD,, Turng B,, Metzger S,, Littauer P. 2015. Performance of the new Accelerate ID/AAST System in highly resistant Acinetobacter baumannii bloodstream infection isolates, compared to routine laboratory testing. Poster presentation at European Congress of Clinical Microbiology and Infectious Diseases, 2015.
69. Price CDI,, Tuttle E,, Shorr A,, Mensack M,, Bessesen M,, Miquirray S,, Overdier K,, Duarte N,, Shamsheyeva A,, Gamage D,, Allers E,, Hance K,, Michel C,, Turng B,, Metzger S. 2015. Rapid identification and antimicrobial susceptibility testing of bacteria in bloodstream infections using the Accelerate ID/AST Technology. Poster presentation at European Congress of Clinical Microbiology and Infectious Diseases, 2015.
70. Diekema DJ,, Beekmann SE,, Chapin KC,, Morel KA,, Munson E,, Doern GV. 2003. Epidemiology and outcome of nosocomial and community-onset bloodstream infection. J Clin Microbiol 41:36553660.
71. Bauer KA,, West JE,, Balada-Llasat JM,, Pancholi P,, Stevenson KB,, Goff DA. 2010. An antimicrobial stewardship program’s impact with rapid polymerase chain reaction methicillin-resistant Staphylococcus aureus/S. aureus blood culture test in patients with S. aureus bacteremia. Clin Infect Dis 51:10741080.
72. Ruimy R,, Dos-Santos M,, Raskine L,, Bert F,, Masson R,, Elbaz S,, Bonnal C,, Lucet JC,, Lefort A,, Fantin B,, Wolff M,, Hornstein M,, Andremont A. 2008. Accuracy and potential usefulness of triplex real-time PCR for improving antibiotic treatment of patients with blood cultures showing clustered gram-positive cocci on direct smears. J Clin Microbiol 46:20452051.
73. Nguyen DT,, Yeh E,, Perry S,, Luo RF,, Pinsky BA,, Lee BP,, Sisodiya D,, Baron EJ,, Banaei N. 2010. Real-time PCR testing for mecA reduces vancomycin usage and length of hospitalization for patients infected with methicillin-sensitive staphylococci. J Clin Microbiol 48:785790.
74. Snyder JW,, Munier GK,, Heckman SA,, Camp P,, Overman TL. 2009. Failure of the BD GeneOhm StaphSR assay for direct detection of methicillin-resistant and methicillin-susceptible Staphylococcus aureus isolates in positive blood cultures collected in the United States. J Clin Microbiol 47:37473748.
75. Stamper PD,, Cai M,, Howard T,, Speser S,, Carroll KC. 2007. Clinical validation of the molecular BD GeneOhm StaphSR assay for direct detection of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus in positive blood cultures. J Clin Microbiol 45:21912196.
76. Wolk DM,, Struelens MJ,, Pancholi P,, Davis T,, Della-Latta P,, Fuller D,, Picton E,, Dickenson R,, Denis O,, Johnson D,, Chapin K. 2009. Rapid detection of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) in wound specimens and blood cultures: multicenter preclinical evaluation of the Cepheid Xpert MRSA/SA skin and soft tissue and blood culture assays. J Clin Microbiol 47:823826.
77. Bartels MD,, Boye K,, Rohde SM,, Larsen AR,, Torfs H,, Bouchy P,, Skov R,, Westh H. 2009. A common variant of staphylococcal cassette chromosome mec type IVa in isolates from Copenhagen, Denmark, is not detected by the BD GeneOhm methicillin-resistant Staphylococcus aureus assay. J Clin Microbiol 47:15241527.
78. Buchan BW,, Allen S,, Burnham CA,, McElvania TeKippe E,, Davis T,, Levi M,, Mayne D,, Pancholi P,, Relich RF,, Thomson R,, Ledeboer NA. 2015. Comparison of the next-generation Xpert MRSA/SA BC assay and the GeneOhm StaphSR assay to routine culture for identification of Staphylococcus aureus and methicillin-resistant S. aureus in positive-blood-culture broths. J Clin Microbiol 53:804809.
79. Peacock SJ,, Paterson GK. 2015. Mechanisms of methicillin resistance in Staphylococcus aureus. Annu Rev Biochem 84:577601.
80. Heraud S,, Freydiere AM,, Doleans-Jordheim A,, Bes M,, Tristan A,, Vandenesch F,, Laurent F,, Dauwalder O. 2015. Direct Identification of Staphylococcus aureus and determination of methicillin susceptibility from positive blood-culture bottles in a Bact/ALERT system using Binax Now S. aureus and PBP2a tests. Ann Lab Med 35:454457.
81. Romero-Gómez MP,, Quiles-Melero I,, Navarro C,, Paño-Pardo JR,, Gómez-Gil R,, Mingorance J. 2012. Evaluation of the BinaxNOW PBP2a assay for the direct detection of methicillin resistance in Staphylococcus aureus from positive blood culture bottles. Diagn Microbiol Infect Dis 72:282284.
82. Yossepowitch O,, Dan M,, Kutchinsky A,, Gottesman T,, Schwartz-Harari O. 2014. A cost-saving algorithm for rapid diagnosis of Staphylococcus aureus and susceptibility to oxacillin directly from positive blood culture bottles by combined testing with BinaxNOW® S. aureus and Xpert MRSA/SA Assay. Diagn Microbiol Infect Dis 78:352355.
83. Manickam K,, Walkty A,, Lagacé-Wiens PRS,, Adam H,, Swan B,, McAdam B,, Pieroni P,, Alfa M,, Karlowsky JA. 2013. Evaluation of MRSASelect (™) chromogenic medium for the early detection of methicillin-resistant Staphylococcus aureus from blood cultures. Can J Infect Dis Med Microbiol 24:e113e116.
84. Harriau P,, Ruffel F,, Lardy JB. 2006. [Use of BioRad plating agar MRSASelect for the daily detection of methicillin resistant staphylococci isolated from samples taken from blood culture bottles]. Pathol Biol (Paris) 54:506509.
85. Menon V,, Lahanas S,, Janto C,, Lee A. 2016. Utility of direct susceptibility testing on blood cultures: is it still worthwhile? J Med Microbiol 65:501509.
86. Stokkou S,, Geginat G,, Schlüter D,, Tammer I. 2015. Direct disk diffusion test using European Clinical Antimicrobial Susceptibility Testing breakpoints provides reliable results compared with the standard method. Eur J Microbiol Immunol (Bp) 5:103111.
87. Hong T,, Ndamukong J,, Millett W,, Kish A,, Win KK,, Choi YJ. 1996. Direct application of Etest to gram-positive cocci from blood cultures: quick and reliable minimum inhibitory concentration data. Diagn Microbiol Infect Dis 25:2125.
88. Funke G,, Funke-Kissling P. 2004. Use of the BD PHOENIX automated identification and susceptibility testing positive blood cultures in a microbiology system for direct of gram-negative rods from three-phase trial. J Clin Microbiol 42:14661470.
89. Lupetti A,, Barnini S,, Castagna B,, Nibbering PH,, Campa M. 2010. Rapid identification and antimicrobial susceptibility testing of Gram-positive cocci in blood cultures by direct inoculation into the BD Phoenix system. Clin Microbiol Infect 16:986991.
90. Hazelton B,, Thomas LC,, Olma T,, Kok J,, O’Sullivan M,, Chen SCA,, Iredell JR. 2014. Rapid and accurate direct antibiotic susceptibility testing of blood culture broths using MALDI Sepsityper combined with the BD Phoenix automated system. J Med Microbiol 63:15901594.
91. Gherardi G,, Angeletti S,, Panitti M,, Pompilio A,, Di Bonaventura G,, Crea F,, Avola A,, Fico L,, Palazzo C,, Sapia GF,, Visaggio D,, Dicuonzo G. 2012. Comparative evaluation of the Vitek-2 Compact and Phoenix systems for rapid identification and antibiotic susceptibility testing directly from blood cultures of Gram-negative and Gram-positive isolates. Diagn Microbiol Infect Dis 72:2031.
92. Carey JR,, Suslick KS,, Hulkower KI,, Imlay JA,, Imlay KR,, Ingison CK,, Ponder JB,, Sen A,, Wittrig AE. 2011. Rapid identification of bacteria with a disposable colorimetric sensing array. J Am Chem Soc 133:75717576.
93. Rakow NA,, Suslick KS. 2000. A colorimetric sensor array for odour visualization. Nature 406:710713.
94. Lonsdale CL,, Taba B,, Queralto N,, Lukaszewski RA,, Martino RA,, Rhodes PA,, Lim SH. 2013. The use of colorimetric sensor arrays to discriminate between pathogenic bacteria. PLoS One 8:e62726.
95. Lim SH,, Mix S,, Anikst V,, Budvytiene I,, Eiden M,, Churi Y,, Queralto N,, Berliner A,, Martino RA,, Rhodes PA,, Banaei N. 2016. Bacterial culture detection and identification in blood agar plates with an optoelectronic nose. Analyst (Lond) 141:918925.
96. Lim SH,, Mix S,, Xu Z,, Taba B,, Budvytiene I,, Berliner AN,, Queralto N,, Churi YS,, Huang RS,, Eiden M,, Martino RA,, Rhodes P,, Banaei N,, Land GA. 2014. Colorimetric sensor array allows fast detection and simultaneous identification of sepsis-causing bacteria in spiked blood culture. J Clin Microbiol 52:592598.
97. Lavrik NV,, Sepaniak MJ,, Datskos PG. 2004. Cantilever transducers as a platform for chemical and biological sensors. Rev Sci Instrum 75:22292253.
98. Longo G,, Alonso-Sarduy L,, Rio LM,, Bizzini A,, Trampuz A,, Notz J,, Dietler G,, Kasas S. 2013. Rapid detection of bacterial resistance to antibiotics using AFM cantilevers as nanomechanical sensors. Nat Nanotechnol 8:522526.
99. Gfeller KY,, Nugaeva N,, Hegner M. 2005. Micromechanical oscillators as rapid biosensor for the detection of active growth of Escherichia coli. Biosens Bioelectron 21:528533.
100. Nugaeva N,, Gfeller KY,, Backmann N,, Lang HP,, Düggelin M,, Hegner M. 2005. Micromechanical cantilever array sensors for selective fungal immobilization and fast growth detection. Biosens Bioelectron 21:849856.
101. Gfeller KY,, Nugaeva N,, Hegner M. 2005. Rapid biosensor for detection of antibiotic-selective growth of Escherichia coli. Appl Environ Microbiol 71:26262631.
102. Maquelin K,, Kirschner C,, Choo-Smith LP,, Ngo-Thi NA,, van Vreeswijk T,, Stämmler M,, Endtz HP,, Bruining HA,, Naumann D,, Puppels GJ. 2003. Prospective study of the performance of vibrational spectroscopies for rapid identification of bacterial and fungal pathogens recovered from blood cultures. J Clin Microbiol 41:324329.
103. Walsh JD,, Hyman JM,, Borzhemskaya L,, Bowen A,, McKellar C,, Ullery M,, Mathias E,, Ronsick C,, Link J,, Wilson M,, Clay B,, Robinson R,, Thorpe T,, van Belkum A,, Dunne WM Jr. 2013. Rapid intrinsic fluorescence method for direct identification of pathogens in blood cultures. MBio 4:e00865-13.
104. Patel JB. 2001. 16S rRNA gene sequencing for bacterial pathogen identification in the clinical laboratory. Mol Diagn 6:313321.
105. Hassan RM,, El Enany MG,, Rizk HH. 2014. Evaluation of broad-range 16S rRNA PCR for the diagnosis of bloodstream infections: two years of experience. J Infect Dev Ctries 8:12521258.
106. Grumaz S,, Stevens P,, Grumaz C,, Decker SO,, Weigand MA,, Hofer S,, Brenner T,, von Haeseler A,, Sohn K. 2016. Next-generation sequencing diagnostics of bacteremia in septic patients. Genome Med 8:73.
107. Salter SJ,, Cox MJ,, Turek EM,, Calus ST,, Cookson WO,, Moffatt MF,, Turner P,, Parkhill J,, Loman NJ,, Walker AW. 2014. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 12:87.
108. Goldberg B,, Sichtig H,, Geyer C,, Ledeboer N,, Weinstock GM. 2015. Making the leap from research laboratory to clinic: challenges and opportunities for next-generation sequencing in infectious disease diagnostics. MBio 6:e01888-15.
109. Motoshima M,, Yanagihara K,, Morinaga Y,, Matsuda J,, Hasegawa H,, Kohno S,, Kamihira S. 2012. Identification of bacteria directly from positive blood culture samples by DNA pyrosequencing of the 16S rRNA gene. J Med Microbiol 61:15561562.
110. Quiles-Melero I,, García-Rodriguez J,, Romero-Gómez MP,, Gómez-Sánchez P,, Mingorance J. 2011. Rapid identification of yeasts from positive blood culture bottles by pyrosequencing. Eur J Clin Microbiol Infect Dis 30:2124.
111. Bosshard PP,, Zbinden R,, Abels S,, Böddinghaus B,, Altwegg M,, Böttger EC. 2006. 16S rRNA gene sequencing versus the API 20 NE system and the VITEK 2 ID-GNB card for identification of nonfermenting Gram-negative bacteria in the clinical laboratory. J Clin Microbiol 44:13591366.
112. Timbrook TT,, Morton JB,, McConeghy KW,, Caffrey AR,, Mylonakis E,, LaPlante KL. 2017. The Effect of molecular rapid diagnostic testing on clinical outcomes in bloodstream infections: a systematic review and meta-analysis. Clin Infect Dis 64:1523.

Tables

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Table 1

Comparison of rapid identification assays for blood culture

Citation: Faron M, Ledeboer N. 2017. Processing Positive Cultures, p 207-244. In Dunne, Jr. W, Burnham C (ed), The Dark Art of Blood Cultures. ASM Press, Washington, DC. doi: 10.1128/9781555819811.ch11

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