Salvage microbiology: opportunities and challenges in the detection of bacterial pathogens following initiation of antimicrobial treatment

References

• Breitkopf C, Hammel D, Scheld HH, et al. Impact of a molecular approach to improve the microbiological diagnosis of infective heart valve endocarditis. Circulation 2005;111(11):1415-21
   PubMed Web of Science ®Google Scholar
• Siddiqui BK, Tariq M, Jadoon A, et al. Impact of prior antibiotic use in culture-negative endocarditis: review of 86 cases from southern Pakistan. Int J Infect Dis 2009;135:606-12
   Google Scholar
• Farrell JJ, Sampath R, Ecker DJ, Bonomo RA. ’Salvage microbiology’: detection of bacteria directly from clinical specimens following initiation of antimicrobial treatment. PLoS One 2013;8(6):e66349
   Google Scholar
• Dellit TH, Owens RC, McGowan JE, et al. Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America guidelines for developing an institutional program to enhance antimicrobial stewardship. Clin Infect Dis 2007;44(2):159-77
   PubMed Web of Science ®Google Scholar
• Forrest GN, Mehta S, Weekes E, et al. Impact of rapid in situ hybridization testing on coagulase-negative staphylococci positive blood cultures. J Antimicrob Chemother 2006;58(1):154-8
   PubMedGoogle Scholar
• Holtzman C, Whitney D, Barlam T, Miller NS. Assessment of impact of peptide nucleic acid fluorescence in situ hybridization for rapid identification of coagulase-negative Staphylococci in the absence of antimicrobial stewardship intervention. J Clin Microbiol 2011;49(4):1581-2
   PubMed Web of Science ®Google Scholar
• Davey P, Brown E, Charani E, et al. Interventions to improve antibiotic prescribing practices for hospital inpatients. Cochrane Database Syst Rev 2013;4:CD003543
   PubMed Web of Science ®Google Scholar
• Weatherall C, Paoloni R, Gottlieb T. Point-of-care urinary pneumococcal antigen test in the emergency department for community acquired pneumonia. Emerg Med J 2008;25(3):144-8
   PubMedGoogle Scholar
• Rudolph K, Bulkow L, Bruce M, et al. Molecular resistance mechanisms of macrolide-resistant invasive Streptococcus pneumoniae isolates from Alaska, 1986 to 2010. Antimicrob Agents Chemother 2013;57(11):5415-22
   PubMedGoogle Scholar
• Tenover FC, Canton R, Kop J, et al. Detection of colonization by carbapenemase-producing Gram-negative Bacilli in patients by use of the Xpert MDRO assay. J Clin Microbiol 2013;51(11):3780-7
   PubMed Web of Science ®Google Scholar
• Tsalik EL, Jones D, Nicholson B, et al. Multiplex PCR to diagnose bloodstream infections in patients admitted from the emergency department with sepsis. J Clin Microbiol 2010;48(1):26-33
   PubMed Web of Science ®Google Scholar
• Gadsby NJ, Hardie A, Claas EC, Templeton KE. Comparison of the Luminex respiratory virus panel fast assay with in-house real-time PCR for respiratory viral infection diagnosis. J Clin Microbiol 2010;48(6):2213-16
   PubMedGoogle Scholar
• Couturier MR, Barney T, Alger G, et al. Evaluation of the FilmArray® Respiratory Panel for clinical use in a large children’s hospital. J Clin Lab Anal 2013;27(2):148-54
   PubMed Web of Science ®Google Scholar
• Pierce VM, Hodinka RL. Comparison of the GenMark Diagnostics eSensor respiratory viral panel to real-time PCR for detection of respiratory viruses in children. J Clin Microbiol 2012;50(11):3458-65
   PubMed Web of Science ®Google Scholar
• Hammond SP, Gagne LS, Stock SR, et al. Respiratory virus detection in immunocompromised patients with FilmArray respiratory panel compared to conventional methods. J Clin Microbiol 2012;50(10):3216-21
   PubMed Web of Science ®Google Scholar
• Popowitch EB, O’Neill SS, Miller MB. Comparison of the Biofire FilmArray RP, Genmark eSensor RVP, Luminex xTAG RVPv1, and Luminex xTAG RVP fast multiplex assays for detection of respiratory viruses. J Clin Microbiol 2013;51(5):1528-33
   PubMed Web of Science ®Google Scholar
• Jenner L, Demeshkina N, Yusupova G, Yusupov M. Structural rearrangements of the ribosome at the tRNA proofreading step. Nat Struct Mol Biol 2010;17(9):1072-8
   PubMed Web of Science ®Google Scholar
• Harris KA, Hartley JC. Development of broad-range 16S rDNA PCR for use in the routine diagnostic clinical microbiology service. J Med Microbiol 2003;52(8):685-91
   PubMedGoogle Scholar
• Clifford RJ, Milillo M, Prestwood J, et al. Detection of Bacterial 16S rRNA and Identification of Four Clinically Important Bacteria by Real-Time PCR. PLoS One 2012;7(11):e48558
   PubMed Web of Science ®Google Scholar
• Voldstedlund M, Nørum Pedersen L, Baandrup U, et al. Broad-range PCR and sequencing in routine diagnosis of infective endocarditis. APMIS 2008;116(3):190-8
   PubMedGoogle Scholar
• Li JS, Sexton DJ, Mick N, et al. Proposed modifications to the Duke criteria for the diagnosis of infective endocarditis. Clin Infect Dis 2000;30(4):633-8
   PubMed Web of Science ®Google Scholar
• Fenollar F, Roux V, Stein A, et al. Analysis of 525 samples to determine the usefulness of PCR amplification and sequencing of the 16S rRNA gene for diagnosis of bone and joint infections. J Clin Microbiol 2006;44(3):1018-28
   PubMed Web of Science ®Google Scholar
• Rampini SK, Bloemberg GV, Keller PM, et al. Broad-range 16S rRNA gene polymerase chain reaction for diagnosis of culture-negative bacterial infections. Clin Infect Dis 2011;53(12):1245-51
   PubMed Web of Science ®Google Scholar
• Baldwin CD, Howe GB, Sampath R, et al. Usefulness of multilocus polymerase chain reaction followed by electrospray ionization mass spectrometry to identify a diverse panel of bacterial isolates. Diagn Microbiol Infect Dis 2009;63(4):403-8
   PubMed Web of Science ®Google Scholar
• Kaleta EJ, Clark AE, Johnson DR, et al. Use of PCR coupled with electrospray ionization mass spectrometry for rapid identification of bacterial and yeast bloodstream pathogens from blood culture bottles. J Clin Microbiol 2011;49(1):345-53
   PubMed Web of Science ®Google Scholar
• Brinkman CL, Vergidis P, Uhl JR, et al. PCR-electrospray ionization mass spectrometry for direct detection of pathogens and antimicrobial resistance from heart valves in patients with infective endocarditis. J Clin Microbiol 2013;51(7):2040-6
   PubMedGoogle Scholar
• Jacovides CL, Kreft R, Adeli B, et al. Successful identification of pathogens by polymerase chain reaction (PCR)-based electron spray ionization time-of-flight mass spectrometry (ESI-TOF-MS) in culture-negative periprosthetic joint infection. J Bone Joint Surg Am 2012;94(24):2247-54
   PubMedGoogle Scholar
• Farrell JJ, Tsung AJ, Flier L, et al. PCR and electrospray ionization mass spectrometry for detection of persistent Enterococcus faecalis in cerebrospinal fluid following treatment of postoperative ventriculitis. J Clin Microbiol 2013;51(10):3464-6
   PubMedGoogle Scholar
• Greenwood-Quaintance KE, Uhl JR, Hanssen AD, et al. Diagnosis of prosthetic joint infection by use of PCR-electrospray ionization mass spectrometry. J Clin Microbiol 2014;52(2):642-9
   PubMedGoogle Scholar
• Melendez DP, Uhl JR, Greenwood-Quaintance KE, et al. Detection of prosthetic joint infection by use of PCR-electrospray ionization mass spectrometry applied to synovial fluid. J Clin Microbiol 2014;52(6):2202-5
   PubMedGoogle Scholar
• Lucignano B, Ranno S, Liesenfeld O, et al. Multiplex PCR allows rapid and accurate diagnosis of bloodstream infections in newborns and children with suspected sepsis. J Clin Microbiol 2011;49(6):2252-8
   PubMed Web of Science ®Google Scholar
• Vollmer T, Piper C, Horstkotte D, et al. 23S rDNA real-time polymerase chain reaction of heart valves: a decisive tool in the diagnosis of infective endocarditis. Eur Heart J 2010;31(9):1105-13
   PubMedGoogle Scholar
• Harris KA, Yam T, Jalili S, et al. Service evaluation to establish the sensitivity, specificity and additional value of broad-range 16S rDNA PCR for the diagnosis of infective endocarditis from resected endocardial material in patients from eight UK and Ireland hospitals. Eur J Clin Microbiol Infect Dis 2014;33(11):2061-6
   PubMedGoogle Scholar
• Bacconi A, Richmond GS, Baroldi MA, et al. Improved Sensitivity for Molecular Detection of Bacteria and Candida in Blood. J Clin Microbiol 2014;52(9):3164-74
   PubMed Web of Science ®Google Scholar