Evaluation of the Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry for the Identification of Cystic Fibrosis Pathogens
Bibliographic record
Abstract
Background. Accurate and timely identification of organisms recovered from respiratory specimens of cystic fibrosis (CF) patients is crucial for effective management. Identification of nonfermenting Gram-negative bacilli (NFGNB) from respiratory cultures of CF patients is challenging; traditional biochemical tests, APINE, 16S rRNA sequencing, or a combination of these methods are used for identification of these organisms. Few studies have validated the use of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of NFGNB in CF patients. Methods. Two hundred forty NFGNB were isolated from respiratory specimens of CF patients at the Hospital For Sick Children between January 2013 and June 2015. Frozen isolates were subcultured onto 5% sheep blood agar before analysis was performed using the Burker Microflex LT MS system and interpreted with the Biotyper software (version 3.1). Reference identification was by partial 16S rRNA gene amplification and sequencing. Organisms identified were as follows: Achromobacter (64), Burkholderia (Burkholderia cepacia complex [BCC] [34], Burkholderia multivorans [37], and Burkholderia gladioli [8]), Chryseobacterium (16), Cupriavidus (8), Inquilinus (18), Pseudomonas (15), and Sphingobacterium (8) species. Others were as follows: Acinetobacter (5), Bordetella (3), Comamonas (1), Delftia (1), Elizabethkingia (5), Moraxella (1), Neisseria (2), Pandoraea (4), Pantoea (1), Ralstonia (4), and Stenotrophomonas (5). Results. The MALDI-TOF MS correctly identified 100% of the NFGNB isolates to genus level. All isolates of B gladioli, Inquilinus limosus, Pseudomonas aeruginosa, Ralstonia species, Stenotrophomonas maltophilia, and Sphingobacterium species were also correctly identified to species level. Although MALDI-TOF MS provided identification to species level for some of the Achromobacter, Chryseobacterium, Elizabethkingia, and Pandoraea isolates, the accuracy of these identifications cannot be confirmed due to limitations of partial 16S rRNA sequencing. The MALDI-TOF MS accurately identified B multivorans but cannot reliably provide genomovar typing of other BCC. Conclusion. The MALDI-TOF MS accurately identified NFGNB, which are challenging to identify by conventional methods from CF respiratory specimens to the genus level. Further molecular characterization is still required to appropriately speciate certain genera. Disclosures. All authors: No reported disclosures.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.003 | 0.003 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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 source (direct Gemma or distilled Codex), 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".