title: Genetic antimicrobial susceptibility testing in Gram-negative sepsis - impact on time to results in a routine laboratory.
abstract: Diagnostic testing of positive blood cultures is among the most critical tasks performed by clinical microbiology laboratories, and the total analysis time from sampling to results should be kept as short as possible. By providing identification of pelleted bacteria directly from positive blood-cultures, MALDI-TOF MS opens for relatively low-complex species-adjusted genetic susceptibility testing from the same bacterial pellet. In our lab routine, we prospectively evaluated a rapid in-house real-time PCR targeting the most common aminoglycoside and cephalosporin resistance genes in Escherichia coli and Klebsiella pneumoniae and measured time to preliminary susceptibility reporting for 138 samples. The results were compared to direct phenotypic susceptibility testing with interpretation after 6 h and overnight incubation respectively. Results from the genetic susceptibility testing were available for 69.5% (96/138) of the positive blood cultures within 24 h after sample collection. No phenotypic susceptibility results were available at this time. Compared to overnight direct susceptibility testing, the average time from sample collection to preliminary susceptibility reporting was reduced with 43%, from 45 h and 5 min to 25 h and 44 min, providing an earlier adjustment of antimicrobial therapy for 12 patients. Minor logistic adjustments have the potential to save yet another 4 h.
authors.affiliation: Department of Microbiology, Haukeland University Hospital, Bergen, Norway.
authors.forename: Øyvind
authors.initials: Ø
authors.lastname: Kommedal
authors.affiliation: Department of Microbiology, Haukeland University Hospital, Bergen, Norway.|Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.
authors.forename: Johanne Lind
authors.initials: JL
authors.lastname: Aasen
authors.affiliation: Department of Microbiology, Haukeland University Hospital, Bergen, Norway.|Department of Clinical Science, University of Bergen, Bergen, Norway.
authors.forename: Paul Christoffer
authors.initials: PC
authors.lastname: Lindemann
mesh_terms: D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D060005:Genotyping Techniques / Q000379:methods*; D016905:Gram-Negative Bacterial Infections / Q000175:diagnosis / Q000382:microbiology*; D006801:Humans; D007711:Klebsiella pneumoniae / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D008826:Microbial Sensitivity Tests / Q000379:methods*; D011446:Prospective Studies; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D018805:Sepsis / Q000175:diagnosis / Q000382:microbiology*; D013997:Time Factors
keywords: CTX-M; ESBL; Genetic susceptibility testing; aac(3)-II; blood culture