Characterization of Listeria monocytogenes plasmids that were newly identified in whole-genome sequences of listeriosis outbreak isolates
Bibliographic record
Abstract
Listeria monocytogenes is a Gram-positive bacterium that is found ubiquitously throughout nature and is the etiologic agent of listeriosis. The majority of human listeriosis is foodborne, resulting from the consumption of unpasteurized and ready-to-eat foods that are contaminated during food processing. During the 2008 nationwide outbreak, the Gilmour laboratory performed the first real-time application of high-throughput whole-genome sequencing (WGS) of outbreak strains. Within this genomic data, the 77 kb plasmid, pLM5578, was newly identified in a clinical isolate, and additional Listeria plasmids (the 80 kb pLM5026 and the 60 kb pLM0813) were subsequently identified after WGS was completed on an expanded panel of outbreak isolates. Little was known regarding how plasmids contribute to persistence and virulence of L. monocytogenes, and to investigate these potential relationships, a panel of 147 L. monocytogenes food, environmental, and clinical isolates from Canadian public health events from the last three decades was selected for further study of the plasmids they might contain. Strain carriage of plasmids was determined using conventional PCR targeting known plasmid gene targets. Bioinformatic analyses were then used to predict the functions of individual genes encoded by each sequenced plasmid. These analyses were then used to direct experiments investigating the functions and associated phenotypes conferred by plasmid carriage. Phenotypic analyses included antimicrobial susceptibility testing, heavy metal resistance, and biofilm formation assays. Finally, WGS analyses was performed on isolates with plasmid screening patterns that indicated carriage of potential novel plasmids. Screening revealed that 75 of 147 isolates were positive for the presence of a plasmid, for which WGS analysis identified 24 unique newly identified L. monocytogenes plasmids. Phenotypically, 15 of these plasmids were found to contribute to a decreased susceptibility to the heavy metal cadmium, whereas 4 conferred resistance to the sanitizer benzalkonium chloride. Plasmid carriage was also found to affect biofilm formation. Nine plasmids correlated with stronger biofilm formation phenotypes; whereas 5 plasmids were correlated with weaker biofilm formation phenotypes. No known virulence factors or antibiotic resistance determinants were present in the DNA sequences of these 24 newly identified plasmids. Numerous coding sequences predicted to assist with survival under environmental stress were identified, and it is hypothesized that these plasmids likely contributed to persistence of L. monocytogenes within food processing environments.
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| 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 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".