Letter to the Editor: Comments on a Recent Article by Burgos et al
Bibliographic record
Abstract
The publication by Burgos et al., 2005Burgos J.M. Ellington B.A. Varela M.F. Presence of multidrug resistant enteric bacteria in dairy farm topsoil.J. Dairy Sci. 2005; 88: 1391-1398Abstract Full Text Full Text PDF PubMed Scopus (47) Google Scholar raises several key issues regarding the use of antimicrobial susceptibility testing that are crucial to the entire study. First, the authors indicate that the 4 antimicrobial agents tested, chloramphenicol, nalidixic acid, tetracycline, and penicillin, were selected due to their widespread use in dairy cattle. Chloramphenicol has been banned from use in food-producing animals in the United States since the early 1980s and nalidixic acid is not used therapeutically in dairy cattle. Penicillin is not particularly active, nor used therapeutically, against the gram-negative enteric bacilli that were tested in the study. Tetracycline is used on dairy farms and, of the 4 compounds tested, the only one of any clinical relevance for the isolates tested. Second, Journal of Dairy Science Instructions to Authors (http://jds.fass.org/cgi/data/88/1/DC1/1) specify that antimicrobial susceptibility testing should be performed using a reproducible, standardized method such as those described by the Clinical and Laboratory Sciences Institute (formerly National Committee for Clinical Laboratory Standards; www.clsi.org). An integral part of any test method is the incorporation of routine quality control testing. Third, interpretive criteria used to categorize isolates as susceptible or resistant are linked to both the test method and the clinical efficacy of the agent. In this paper, the authors used a nonstandard method for determining the minimum inhibitory concentrations (MIC) of isolates, appear not to have performed quality control testing, and used the interpretive criteria from another method to categorize isolates as susceptible or resistant. As such, none of the MIC data or its interpretation as it presently appears in the Burgos et al., 2005Burgos J.M. Ellington B.A. Varela M.F. Presence of multidrug resistant enteric bacteria in dairy farm topsoil.J. Dairy Sci. 2005; 88: 1391-1398Abstract Full Text Full Text PDF PubMed Scopus (47) Google Scholar article meets the Journal of Dairy Science criteria for acceptance. The issues with this paper highlight several key points to consider when performing antimicrobial susceptibility testing. The methods used should be standardized and quality control performed routinely. If interpretive criteria are applied to categorize isolates as susceptible or resistant, the source and relevance of those criteria should be plainly stated in the manuscript. Clearly, readers of the journal should interpret the data presented in the Burgos et al., 2005Burgos J.M. Ellington B.A. Varela M.F. Presence of multidrug resistant enteric bacteria in dairy farm topsoil.J. Dairy Sci. 2005; 88: 1391-1398Abstract Full Text Full Text PDF PubMed Scopus (47) Google Scholar paper carefully and consider the methodological and interpretive errors before citing it elsewhere.
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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 | 0.007 | 0.045 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.003 | 0.002 |
| Scholarly communication | 0.005 | 0.005 |
| Open science | 0.005 | 0.002 |
| Research integrity | 0.040 | 0.031 |
| Insufficient payload (model declined to judge) | 0.010 | 0.014 |
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".