Comparative genomic analysis of mobile genetic elements in Histophilus somni isolates from feedlot cattle
Bibliographic record
Abstract
Organisms, including bacteria, are defined by the genes they possess. This genomic pool determines whether a bacterial species can survive or compete in a changing environment. Bacteria can acquire new genomic content through de novo mutations or through external genomic reservoirs via horizontal gene transfer. Horizontal gene transfer (HGT) is the exchange of genetic material through mobile genetic elements (MGE) between cells which have no parent-offspring relationship. The conjugation pathway is one of the main routes of HGT in bacteria and is in part mediated by plasmids or integrative and conjugative elements (ICE). ICEs can provide new genes through HGT which confer new phenotypic traits such as resistance to antibiotics and heavy metals, biofilm-formation and metabolic alterations. In this study, an ICE was identified in Histophilus somni, a Gram-negative bacterium that is one of the major bacteria involved in bovine respiratory disease (BRD). The ICE and other mobile genetic elements were identified through analysis of whole-genome sequences (WGS) of H. somni isolates collected from tissue samples from Canadian and American feedlot cattle mortalities. A variety of antimicrobial resistance genes were located within ICE sequences. AMR genes tet(H), Sul2/folP, APH(3”)-Ib, APH(6)-Id, and APH(3’’)-Ia, were identified. These genes may provide phenotypic resistance for the antimicrobial classes: tetracyclines, sulfonamides, phenicols and aminoglycosides. Plasmids were not identified in WGS files. No AMR genes were found on the chromosome other than those within ICE sequences. The ICEs in Canadian and American H. somni isolates exhibited similar genome assembly and genome content. The similarity of the ICE in Canadian and American H. somni isolates indicates that they may have moved between the two countries during import and export of cattle. The ICEs of H. somni were identified as members of the ICEHin1056 ICE-family. ICEs of the ICEHin1056 ICE-family have been identified in four bacterial species; two human-specific species, Haemophilus influenzae, and Haemophilus parainfluenzae, and the animal pathogens, H. somni, Actinobacillus pleuropneumoniae, M. haemolytica, and P. multocida.
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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 | 0.000 |
| 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 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".