Evaluation of the Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry for the Identification of Cystic Fibrosis Pathogens
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
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.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 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 it