New technology for rapid molecular diagnosis of bloodstream infections

References

• Russell JA. Management of sepsis. N. Engl. J. Med.355(16), 1699–1713 (2006).
   PubMed Web of Science ®Google Scholar
• Kumar A, Roberts D, Wood KE et al. Duration of hypotension before initiation of effective antimicrobial therapy is the critical determinant of survival in human septic shock. Crit. Care Med.34(6), 1589–1596 (2006).
   PubMed Web of Science ®Google Scholar
• Dellinger RP, Levy MM, Carlet JM et al. Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock: 2008. Crit. Care Med.36(1), 296–327 (2008).
   PubMed Web of Science ®Google Scholar
• Fenollar F, Raoult D. Molecular diagnosis of bloodstream infections caused by non-cultivable bacteria. Int. J. Antimicrob. Agents30(Suppl. 1), S7–S15 (2007).
   PubMed Web of Science ®Google Scholar
• Miller MB, Tang YW. Basic concepts of microarrays and potential applications in clinical microbiology. Clin. Microbiol. Rev.22(4), 611–633 (2009).
   PubMed Web of Science ®Google Scholar
• Tang YW, Procop GW, Persing DH. Molecular diagnostics of infectious diseases. Clin. Chem.43(11), 2021–2038 (1997).
   PubMed Web of Science ®Google Scholar
• Yagupsky P, Nolte FS. Quantitative aspects of septicemia. Clin. Microbiol. Rev.3(3), 269–279 (1990).
   PubMed Web of Science ®Google Scholar
• Werner AS, Cobbs CG, Kaye D, Hook EW. Studies on the bacteremia of bacterial endocarditis. JAMA202(3), 199–203 (1967).
   PubMed Web of Science ®Google Scholar
• Kreger BE, Craven DE, Carling PC, McCabe WR. Gram-negative bacteremia. III. Reassessment of etiology, epidemiology and ecology in 612 patients. Am. J. Med.68(3), 332–343 (1980).
   PubMed Web of Science ®Google Scholar
• Henry NK, McLimans CA, Wright AJ, Thompson RL, Wilson WR, Washington JA 2nd. Microbiological and clinical evaluation of the isolator lysis-centrifugation blood culture tube. J. Clin. Microbiol.17(5), 864–869 (1983).
   PubMed Web of Science ®Google Scholar
• Rello J, Lisboa T, Lujan M et al. Severity of pneumococcal pneumonia associated with genomic bacterial load. Chest136(3), 832–840 (2009).
   PubMed Web of Science ®Google Scholar
• Carroll KC, Leonard RB, Newcomb-Gayman PL, Hillyard DR. Rapid detection of the staphylococcal mecA gene from BACTEC blood culture bottles by the polymerase chain reaction. Am. J. Clin. Pathol.106(5), 600–605 (1996).
   PubMed Web of Science ®Google Scholar
• Chapin K, Musgnug M. Evaluation of three rapid methods for the direct identification of Staphylococcus aureus from positive blood cultures. J. Clin. Microbiol.41(9), 4324–4327 (2003).
   PubMed Web of Science ®Google Scholar
• Davis TE, Fuller DD. Direct identification of bacterial isolates in blood cultures by using a DNA probe. J. Clin. Microbiol.29(10), 2193–2196 (1991).
   PubMed Web of Science ®Google Scholar
• Fujita S, Senda Y, Iwagami T, Hashimoto T. Rapid identification of staphylococcal strains from positive-testing blood culture bottles by internal transcribed spacer PCR followed by microchip gel electrophoresis. J. Clin. Microbiol.43(3), 1149–1157 (2005).
   PubMed Web of Science ®Google Scholar
• Kempf VA, Trebesius K, Autenrieth IB. Fluorescent in situ hybridization allows rapid identification of microorganisms in blood cultures. J. Clin. Microbiol.38(2), 830–838 (2000).
   PubMed Web of Science ®Google Scholar
• Louie L, Goodfellow J, Mathieu P, Glatt A, Louie M, Simor AE. Rapid detection of methicillin-resistant staphylococci from blood culture bottles by using a multiplex PCR assay. J. Clin. Microbiol.40(8), 2786–2790 (2002).
   PubMed Web of Science ®Google Scholar
• Oliveira K, Procop GW, Wilson D, Coull J, Stender H. Rapid identification of Staphylococcus aureus directly from blood cultures by fluorescence in situ hybridization with peptide nucleic acid probes. J. Clin. Microbiol.40(1), 247–251 (2002).
   PubMed Web of Science ®Google Scholar
• Paule SM, Pasquariello AC, Thomson RB Jr, Kaul KL, Peterson LR. Real-time PCR can rapidly detect methicillin-susceptible and methicillin-resistant Staphylococcus aureus directly from positive blood culture bottles. Am. J. Clin. Pathol.124(3), 404–407 (2005).
   PubMed Web of Science ®Google Scholar
• Shrestha NK, Tuohy MJ, Hall GS, Isada CM, Procop GW. Rapid identification of Staphylococcus aureus and the mecA gene from BacT/ALERT blood culture bottles by using the LightCycler system. J. Clin. Microbiol.40(7), 2659–2661 (2002).
   PubMed Web of Science ®Google Scholar
• Tan TY, Corden S, Barnes R, Cookson B. Rapid identification of methicillin-resistant Staphylococcus aureus from positive blood cultures by real-time fluorescence PCR. J. Clin. Microbiol.39(12), 4529–4531 (2001).
   PubMed Web of Science ®Google Scholar
• Parta M, Goebel M, Matloobi M, Stager C, Musher DM. Identification of methicillin-resistant or methicillin-susceptible Staphylococcus aureus in blood cultures and wound swabs by GeneXpert. J. Clin. Microbiol.47(5), 1609–1610 (2009).
   PubMed Web of Science ®Google Scholar
• Marlowe EM, Hogan JJ, Hindler JF, Andruszkiewicz I, Gordon P, Bruckner DA. Application of an rRNA probe matrix for rapid identification of bacteria and fungi from routine blood cultures. J. Clin. Microbiol.41(11), 5127–5133 (2003).
   PubMed Web of Science ®Google Scholar
• Oliveira K, Brecher SM, Durbin A et al. Direct identification of Staphylococcus aureus from positive blood culture bottles. J. Clin. Microbiol.41(2), 889–891 (2003).
   PubMed Web of Science ®Google Scholar
• Goldmeyer J, Li H, McCormac M et al. Identification of Staphylococcus aureus and determination of methicillin resistance directly from positive blood cultures by isothermal amplification and a disposable detection device. J. Clin. Microbiol.46(4), 1534–1536 (2008).
   PubMed Web of Science ®Google Scholar
• Stender H. PNA FISH: an intelligent stain for rapid diagnosis of infectious diseases. Expert Rev. Mol. Diagn.3(5), 649–655 (2003).
   PubMed Web of Science ®Google Scholar
• Shepard JR, Addison RM, Alexander BD et al. Multicenter evaluation of the Candida albicans/Candida glabrata peptide nucleic acid fluorescent in situ hybridization method for simultaneous dual-color identification of C. albicans and C. glabrata directly from blood culture bottles. J. Clin. Microbiol.46(1), 50–55 (2008).
   PubMed Web of Science ®Google Scholar
• Sogaard M, Stender H, Schonheyder HC. Direct identification of major blood culture pathogens, including Pseudomonas aeruginosa and Escherichia coli, by a panel of fluorescence in situ hybridization assays using peptide nucleic acid probes. J. Clin. Microbiol.43(4), 1947–1949 (2005).
   PubMed Web of Science ®Google Scholar
• Han J, Swan DC, Smith SJ et al. Simultaneous amplification and identification of 25 human papillomavirus types with Templex technology. J. Clin. Microbiol.44(11), 4157–4162 (2006).
   PubMed Web of Science ®Google Scholar
• Tang YW, Kilic A, Yang Q et al. StaphPlex system for rapid and simultaneous identification of antibiotic resistance determinants and Panton–Valentine leukocidin detection of staphylococci from positive blood cultures. J. Clin. Microbiol.45(6), 1867–1873 (2007).
   PubMed Web of Science ®Google Scholar
• La Scola B, Raoult D. Direct identification of bacteria in positive blood culture bottles by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry. PLoS ONE4(11), e8041 (2009).
   PubMed Web of Science ®Google Scholar
• Seng P, Drancourt M, Gouriet F et al. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin. Infect. Dis.49(4), 543–551 (2009).
   PubMed Web of Science ®Google Scholar
• Maes N, De Gheldre Y, De Ryck R et al. Rapid and accurate identification of Staphylococcus species by tRNA intergenic spacer length polymorphism analysis. J. Clin. Microbiol.35(10), 2477–2481 (1997).
   PubMed Web of Science ®Google Scholar
• Martineau F, Picard FJ, Ke D et al. Development of a PCR assay for identification of staphylococci at genus and species levels. J. Clin. Microbiol.39(7), 2541–2547 (2001).
   PubMed Web of Science ®Google Scholar
• Poyart C, Quesne G, Boumaila C, Trieu-Cuot P. Rapid and accurate species-level identification of coagulase-negative staphylococci by using the sodA gene as a target. J. Clin. Microbiol.39(12), 4296–4301 (2001).
   PubMed Web of Science ®Google Scholar
• Jordan JA, Durso MB. Real-time polymerase chain reaction for detecting bacterial DNA directly from blood of neonates being evaluated for sepsis. J. Mol. Diagn.7(5), 575–581 (2005).
   PubMed Web of Science ®Google Scholar
• Klouche M, Schroder U. Rapid methods for diagnosis of bloodstream infections. Clin. Chem. Lab. Med.46(7), 888–908 (2008).
   PubMed Web of Science ®Google Scholar
• Lehmann LE, Hunfeld KP, Emrich T et al. A multiplex real-time PCR assay for rapid detection and differentiation of 25 bacterial and fungal pathogens from whole blood samples. Med. Microbiol. Immunol.197(3), 313–324 (2008).
   PubMed Web of Science ®Google Scholar
• Bloos F, Hinder F, Becker K et al. A multicenter trial to compare blood culture with polymerase chain reaction in severe human sepsis. Intensive Care Med.36(2), 241–247 (2009).
   PubMed Web of Science ®Google Scholar
• Dierkes C, Ehrenstein B, Siebig S, Linde HJ, Reischl U, Salzberger B. Clinical impact of a commercially available multiplex PCR system for rapid detection of pathogens in patients with presumed sepsis. BMC Infect. Dis.9, 126 (2009).
   PubMed Web of Science ®Google Scholar
• Lehmann LE, Alvarez J, Hunfeld KP et al. Potential clinical utility of polymerase chain reaction in microbiological testing for sepsis. Crit. Care Med.37(12), 3085–3090 (2009).
   PubMed Web of Science ®Google Scholar
• Lehmann LE, Hunfeld KP, Steinbrucker M et al. Improved detection of blood stream pathogens by real-time PCR in severe sepsis. Intensive Care Med.36(1), 49–56. (2009).
   PubMed Web of Science ®Google Scholar
• Louie RF, Tang Z, Albertson TE, Cohen S, Tran NK, Kost GJ. Multiplex polymerase chain reaction detection enhancement of bacteremia and fungemia. Crit. Care Med.36(5), 1487–1492 (2008).
   PubMed Web of Science ®Google Scholar
• Tsalik EL, Jones D, Nicholson B et al. Multiplex PCR to diagnose blood stream infections in patients admitted from the emergency department with sepsis. J. Clin. Microbiol.48(1), 26–33 (2010).
   PubMed Web of Science ®Google Scholar
• von Lilienfeld-Toal M, Lehmann LE, Raadts AD et al. Utility of a commercially available multiplex real-time PCR assay to detect bacterial and fungal pathogens in febrile neutropenia. J. Clin. Microbiol.47(8), 2405–2410 (2009).
   PubMed Web of Science ®Google Scholar
• Wallet F, Nseir S, Baumann L et al. Preliminary clinical study using a multiplex real-time PCR test for the detection of bacterial and fungal DNA directly in blood. Clin. Microbiol. Infect. DOI: 10.1111/j.1469-0691.2009.02940.x (2009) (Epub ahead of print).
   PubMedGoogle Scholar
• Westh H, Lisby G, Breysse F et al. Multiplex real-time PCR and blood culture for identification of bloodstream pathogens in patients with suspected sepsis. Clin. Microbiol. Infect.15(6), 544–551 (2009).
   PubMed Web of Science ®Google Scholar
• Mancini N, Clerici D, Diotti R et al. Molecular diagnosis of sepsis in neutropenic patients with haematological malignancies. J. Med. Microbiol.57(Pt 5), 601–604 (2008).
   PubMed Web of Science ®Google Scholar
• Struelens MJ. Detection of microbial DNAemia: does it matter for sepsis management?. Intensive Care Med.36(2), 193–195 (2009).
   PubMed Web of Science ®Google Scholar
• Morata P, Queipo-Ortuno MI, de Dios Colmenero J. Strategy for optimizing DNA amplification in a peripheral blood PCR assay used for diagnosis of human brucellosis. J. Clin. Microbiol.36(9), 2443–2446 (1998).
   PubMed Web of Science ®Google Scholar
• Cogswell FB, Bantar CE, Hughes TG, Gu Y, Philipp MT. Host DNA can interfere with detection of Borrelia burgdorferi in skin biopsy specimens by PCR. J. Clin. Microbiol.34(4), 980–982 (1996).
   PubMed Web of Science ®Google Scholar
• Peters RP, van Agtmael MA, Gierveld S et al. Quantitative detection of Staphylococcus aureus and Enterococcus faecalis DNA in blood to diagnose bacteremia in patients in the intensive care unit. J. Clin. Microbiol.45(11), 3641–3646 (2007).
   PubMed Web of Science ®Google Scholar
• Handschur M, Karlic H, Hertel C, Pfeilstocker M, Haslberger AG. Preanalytic removal of human DNA eliminates false signals in general 16S rDNA PCR monitoring of bacterial pathogens in blood. Comp. Immunol. Microbiol. Infect. Dis.32(3), 207–219 (2009).
   PubMed Web of Science ®Google Scholar
• Gebert S, Siegel D, Wellinghausen N. Rapid detection of pathogens in blood culture bottles by real-time PCR in conjunction with the pre-analytic tool MolYsis. J. Infect.57(4), 307–316 (2008).
   PubMed Web of Science ®Google Scholar
• Hansen WL, Bruggeman CA, Wolffs PF. Evaluation of new preanalysis sample treatment tools and DNA isolation protocols to improve bacterial pathogen detection in whole blood. J. Clin. Microbiol.47(8), 2629–2631 (2009).
   PubMed Web of Science ®Google Scholar
• Wellinghausen N, Kochem AJ, Disque C et al. 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(9), 2759–2765 (2009).
   PubMed Web of Science ®Google Scholar
• Sachse S, Straube E, Lehmann M, Bauer M, Russwurm S, Schmidt KH. Truncated human cytidylate-phosphate-deoxyguanylate-binding protein for improved nucleic acid amplification technique-based detection of bacterial species in human samples. J. Clin. Microbiol.47(4), 1050–1057 (2009).
   PubMed Web of Science ®Google Scholar
• Hofstadler SA, Sampath R, Blyn LB et al. TIGER: the universal biosensor. Int. J. Mass Spectrom.242, 23–41 (2005).
   Web of Science ®Google Scholar
• Ecker DJ, Sampath R, Massire C et al. Ibis T5000: a universal biosensor approach for microbiology. Nat. Rev. Microbiol.6(7), 553–558 (2008).
   PubMed Web of Science ®Google Scholar
• Ecker DJ, Drader J, Gutierrez J et al. The Ibis T5000 Universal Biosensor – an automated platform for pathogen identification and strain typing. JALA11, 341–351 (2006).
   Google Scholar
• Ecker DJ, Sampath R, Blyn LB et al. Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance. Proc. Natl Acad. Sci. USA102(22), 8012–8017 (2005).
   PubMed Web of Science ®Google Scholar
• Hall TA, Sampath R, Blyn LB et al. Rapid molecular genotyping and clonal complex assignment of S. aureus isolates by PCR/ESI-MS. J. Clin. Microbiol.47(6), 1733–1741 (2009).
   PubMed Web of Science ®Google Scholar
• Wolk DM, Blyn LB, Hall TA et al. Pathogen profiling: rapid molecular characterization of Staphylococcus aureus by PCR/ESI-MS and correlation with phenotype. J. Clin. Microbiol.47(10), 3129–3137 (2009).
   PubMed Web of Science ®Google Scholar
• Ubukata K, Nonoguchi R, Matsuhashi M, Konno M. Expression and inducibility in Staphylococcus aureus of the mecA gene, which encodes a methicillin-resistant S. aureus-specific penicillin-binding protein. J. Bacteriol.171(5), 2882–2885 (1989).
   PubMed Web of Science ®Google Scholar
• Handwerger S, Perlman DC, Altarac D, McAuliffe V. Concomitant high-level vancomycin and penicillin resistance in clinical isolates of enterococci. Clin. Infect. Dis.14(3), 655–661 (1992).
   PubMed Web of Science ®Google Scholar
• Yigit H, Queenan AM, Anderson GJ et al. Novel carbapenem-hydrolyzing β-lactamase, KPC-1, from a carbapenem-resistant strain of Klebsiella pneumoniae. Antimicrob. Agents Chemother.45(4), 1151–1161 (2001).
   PubMed Web of Science ®Google Scholar
• Petti CA, Bosshard PP, Brandt ME et al. Interpretive criteria for identification of bacteria and fungi by DNA target sequencing; approved guideline. Clin. Lab. Standards Inst.28, 88 (2008).
   Google Scholar
• Eshoo MW, Crowder CD, Li H et al. Detection and identification of Ehrlichia species in blood using PCR and electrospray ionization mass spectrometry. J. Clin. Microbiol.48(2), 472–478 (2010).
   PubMed Web of Science ®Google Scholar
• Tang YW, Rys PN, Rutledge BJ, Mitchell PS, Smith TF, Persing DH. Comparative evaluation of colorimetric microtiter plate systems for detection of herpes simplex virus in cerebrospinal fluid. J. Clin. Microbiol.36(9), 2714–2717 (1998).
   PubMed Web of Science ®Google Scholar
• Thomas LD, Hongo I, Bloch KC, Tang YW, Dummer S. Human ehrlichiosis in transplant recipients. Am. J. Transplant.7(6), 1641–1647 (2007).
   PubMed Web of Science ®Google Scholar
• Paddock CD, Folk SM, Shore GM et al. Infections with Ehrlichia chaffeensis and Ehrlichia ewingii in persons coinfected with human immunodeficiency virus. Clin. Infect. Dis.33(9), 1586–1594 (2001).
   PubMed Web of Science ®Google Scholar
• Doyle CK, Labruna MB, Breitschwerdt EB et al. Detection of medically important Ehrlichia by quantitative multicolor TaqMan real-time polymerase chain reaction of the dsb gene. J. Mol. Diagn.7(4), 504–510 (2005).
   PubMed Web of Science ®Google Scholar
• Eremeeva ME, Dasch GA, Silverman DJ. Evaluation of a PCR assay for quantitation of Rickettsia rickettsii and closely related spotted fever group rickettsiae. J. Clin. Microbiol.41(12), 5466–5472 (2003).
   PubMed Web of Science ®Google Scholar
• Peters RP, Mohammadi T, Vandenbroucke-Grauls CM, Danner SA, van Agtmael MA, Savelkoul PH. Detection of bacterial DNA in blood samples from febrile patients: underestimated infection or emerging contamination?. FEMS Immunol. Med. Microbiol.42(2), 249–253 (2004).
   PubMedGoogle Scholar
• Hong T, Butler WR, Hollis F et al. Characterization of a novel rapidly growing Mycobacterium species associated with sepsis. J. Clin. Microbiol.41(12), 5650–5653 (2003).
   PubMed Web of Science ®Google Scholar
• Kilic A, Li H, Mellmann A et al.Acinetobacter septicus sp. nov. association with a nosocomial outbreak of bacteremia in a neonatal intensive care unit. J. Clin. Microbiol.46(3), 902–908 (2008).
   PubMed Web of Science ®Google Scholar
• Tang YW, Hopkins MK, Kolbert CP, Hartley PA, Severance PJ, Persing DH. Bordetella holmesii-like organisms associated with septicemia, endocarditis, and respiratory failure. Clin. Infect. Dis.26(2), 389–392 (1998).
   PubMed Web of Science ®Google Scholar