Rapid identification and classification of «Enterococcus» and «Staphylococcus» by attenuated total reflectance - Fourier transform infrared spectroscopy
Bibliographic record
Abstract
Attenuated total reflectance Fourier transform infrared (ATR-FTIR) is a proposed method for in-depth identification and discrimination of the bacterial microorganisms. Comparing this method with other clinically available identification methods such as polymerase chain reaction (PCR), pulsed field gel electrophoresis (PFGE) and automated systems including the Vitek II identification system, ATR-FTIR requires little to no sample preparation, rapid acquisition times, no reagent needed, cost effective, and identification can be performed at various taxonomic levels ranging all the way down to the pathotype level. Enterococcus faecalis, Enterococcus faecium, Staphylococcus aureus and coagulase negative staphylococci (CoNS) are some of the most prevalent pathogens causing both nosocomial and lethal hospital-acquired infections. ATR-FTIR was the method chosen for the research due to its incredible specificity to overcome the challenge which arises when differentiating between Enterococcus and Staphylococcus species due to their high degree of genetic similarity. A total of 837 isolates, composed of Enterococcus faecalis (n=142), Enterococcus faecium (n=200), Staphylococcus aureus (n=392) and Coagulase-negative Staphylococcus (n=103) of fecal and blood origin were obtained from the McGill University Health Center (MUHC), Laboratoire de Santé Publique du Québec (LSPQ), Health Canada (HC), Centre Hospitalier Universitaire Sainte-Justine, New Brunswick (NB) and Nova Scotia (NS). Each bacterial culture analyzed was initially frozen, then was plated on 5% Columbia blood agar and incubated at 37C for 18-24 h. A sub-culture was taken once the initial incubation time was completed and a second incubation period with identical parameters followed. Sub-culturing was done for the purpose of isolating pure bacterial colonies for analysis. Once the sub-culturing incubation time was complete, a single bacterial colony was collected and smeared onto the ATR crystal of the ATR-FTIR instrument to acquire a spectrum. Each bacterial strain was collected in triplicates and the spectral data was then analyzed by using principal component analysis (PCA) and hierarchical cluster analysis (HCA) of the ATR-FTIR spectral data. Enterococcus was successfully discriminated from Staphylococcus based on their whole region of selection 1480-980 cm-1 and more specifically the regions 1600-1160 cm-1 and 1064-985 cm-1. Furthermore, E. faecalis was successfully discriminated from E. faecium by using the precise spectral regions of 1039-1054 cm-1 and 1061-1099 cm-1. Finally, Staphylococcus aureus and Coagulase-negative Staphylococcus were successfully separated using the region of 1057-1072 cm-1. These results suggest that ATR-FTIR spectroscopy can be used as a valuable tool for rapidly identifying and discriminating the nosocomial bacteria Enterococcus and Staphylococcus at the species and sub-species level.
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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 | 0.000 |
| 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 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".