Lysis Centrifugation Method for the Direct Identification of Positive Blood Cultures Using MALDI-TOF MS
Bibliographic record
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) bacterial identification has revolutionized clinical microbiology. Typically, bacteria must be first cultured prior to identification; however, several techniques have emerged that allow the identification of bacteria directly from certain specimen types, including blood cultures. The aim of this study was to compare a direct MALDI-TOF MS identification technique of positive blood cultures with those having at least 4–6 hours of sufficient growth Only blood cultures flagged overnight as positive by the BD Bactec® were included for study. A one ml aliquot was drawn and immediately processed using a lysis centrifugation technique and analyzed using MALDI-TOF (bioMérieux). Positive blood culture samples were also sub-cultured onto agar plates as per standard laboratory practice, incubated for 4–6 hours and if sufficient growth was present, processed using MALDI-TOF. Cultures with insufficient growth are incubated overnight. Direct identifications were compared with those where sufficient growth was achieved Between June 2015 to February 2016, 300 positive blood cultures were included for study. Of these there were 156 Gram-positive cocci, 112 Gram-negative bacilli, 15 anaerobic organisms, 11 Gram-positive bacilli and 6 yeast. Using a confidence threshold of 99.9%, 69% of all organisms were correctly identified using the direct identification method. The identification of any organism with a confidence threshold <99.9% was not accepted. Approximately 81% of Gram-negative bacilli were correctly identified compared with 64% of Gram-positive cocci 36% of Gram-positive bacilli. The lysis-centrifugation direct identification method is a relatively inexpensive ($1.00) and rapid technique that will allow clinicians to receive the identification of organisms from approximately 70% of bacteremic patients 6 to 24 hours early than waiting for sufficient growth. This should allow clinicians to make better informed empiric antimicrobial choices to manage their patients. All authors: No reported disclosures.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".