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 in a 40-50% glycerol 985 cm -1 .En outre, l'Entérocoque faecalis a été différencié avec succès des espèces d'Entérocoque faecium en utilisant les régions spectrales spécifique 1039-1054 cm -1 and 1061-1099 cm -1 .Enfin, Staphylocoque aureus et Staphylocoque à coagulasse négative ont été séparé avec succès en utilisant la région 1057-1072 cm -1 .Ces résultats suggèrent que la spectroscopie ATR-FTIR peut être utilisée comme un outil d'identification précieux pour rapidement identifier et différencier les bactéries nosocomiales Entérocoques et Staphylocoques au niveau du genre, de l'espèce et de la sous-espèce.v Acknowledgments This journey would not have been possible without my family, mentors, professors and friends.To my family, thank you for all of your constant support and guidance throughout all my wild endeavours.I am incredibly fortunate to have my dad, Antonio Langella, my mom, Manon Leclerc, and my brother, Anthony in my life.I am also very grateful for the financial support you have been able to provide, as well as all the encouragement I needed to follow my dreams.Thank you for always believing in me and being there when I needed you most.I hope I have made you proud!First and foremost
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.003 | 0.002 |
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".