title: "Salvage microbiology": detection of bacteria directly from clinical specimens following initiation of antimicrobial treatment.
abstract: BACKGROUND
  PCR coupled with electrospray ionization mass spectrometry (ESI-MS) is a diagnostic approach that has demonstrated the capacity to detect pathogenic organisms from culture negative clinical samples after antibiotic treatment has been initiated. [1] We describe the application of PCR/ESI-MS for detection of bacteria in original patient specimens that were obtained after administration of antibiotic treatment in an open investigation analysis.
  
  
  METHODS
  We prospectively identified cases of suspected bacterial infection in which cultures were not obtained until after the initiation of antimicrobial treatment. PCR/ESI-MS was performed on 76 clinical specimens that were submitted for conventional microbiology testing from 47 patients receiving antimicrobial treatment.
  
  
  RESULTS
  In our series, 72% (55/76) of cultures obtained following initiation of antimicrobial treatment were non-diagnostic (45 negative cultures; and 10 respiratory specimens with normal flora (5), yeast (4), or coagulase-negative staphylococcus (1)). PCR/ESR-MS detected organisms in 83% (39/47) of cases and 76% (58/76) of the specimens. Bacterial pathogens were detected by PCR/ESI-MS in 60% (27/45) of the specimens in which cultures were negative. Notably, in two cases of relapse of prosthetic knee infections in patients on chronic suppressive antibiotics, the previous organism was not recovered in tissue cultures taken during extraction of the infected knee prostheses, but was detected by PCR/ESI-MS.
  
  
  CONCLUSIONS
  Molecular methods that rely on nucleic acid amplification may offer a unique advantage in the detection of pathogens collected after initiation of antimicrobial treatment and may provide an opportunity to target antimicrobial therapy and "salvage" both individual treatment regimens as well as, in select cases, institutional antimicrobial stewardship efforts.
authors.affiliation: University of Illinois School of Medicine, Department of Medicine, Peoria, Illinois, United States of America. jjf@uic.edu
authors.forename: John J
authors.initials: JJ
authors.lastname: Farrell
authors.forename: Rangarajan
authors.initials: R
authors.lastname: Sampath
authors.forename: David J
authors.initials: DJ
authors.lastname: Ecker
authors.forename: Robert A
authors.initials: RA
authors.lastname: Bonomo
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000900:Anti-Bacterial Agents / Q000494:pharmacology* / Q000627:therapeutic use; D001419:Bacteria / Q000187:drug effects / Q000302:isolation & purification*; D001424:Bacterial Infections / Q000188:drug therapy; D015780:Carbapenems / Q000494:pharmacology; D002648:Child; D003657:Decision Making; D024881:Drug Resistance, Bacterial; D005260:Female; D006801:Humans; D008297:Male; D008828:Microbiological Techniques / Q000379:methods*; D008875:Middle Aged; D016133:Polymerase Chain Reaction; D016459:Prosthesis-Related Infections / Q000188:drug therapy; D021241:Spectrometry, Mass, Electrospray Ionization
chemical_list: D000900:Anti-Bacterial Agents; D015780:Carbapenems