Genetic composition, virulence factors, and antimicrobial resistance profiles of Bacillus cereus and Bacillus subtilis isolates from food vendors in Ondo State, Nigeria: implications for food safety
Bibliographic record
Abstract
Abstract Background This study investigated Bacillus cereus and Bacillus subtilis from food vendors in Ondo State, Nigeria. Methods A comprehensive whole-genome sequencing (WGS) analysis of Bacillus genomes, including genome assembly, plasmid prediction, species identification, antimicrobial resistance (AMR) gene identification, virulence gene identification, and multilocus sequencing typing, was conducted. Results The genome assembly revealed a B. cereus genome with 87 contigs, a length of 5,798,917 base pairs, and a GC content of 34.79%, whereas B. subtilis had a genome length of 4,238,143 bp and was composed of 253 contigs with a contig L50 of 24, a contig N50 of 55,053, and a GC content of 43.14904%. Plasmid prediction revealed the absence of prominent plasmids in the assembled B. cereus genome, whereas the repUS12 plasmid was recognized with an identity of less than 95.63% for the B. subtilis genome. Species identification via the average nucleotide identity (ANI) calculation confirmed that Bacillus cereus had a 98.97% ANI value, whereas a 98.39% ANI value was confirmed for B. subtilis WAUSV36. AMR genes were identified, with virulence genes such as the alo, cytK, and hbl genes also detected in B. cereus, whereas clpX, codY, purA, and purB genes were detected in B. subtilis. Multiple-locus sequence typing (MLST) revealed that B. cereus belongs to sequence type 73 with 100% identity, identifying housekeeping gene alleles, including glp_13, gmk_8, and ilv_9, whereas B. subtilis belongs to sequence type 130, with the ilvD gene showing a perfect match and the highest allele length of 471 for the housekeeping genes identified. Conclusions This detailed WGS analysis provides valuable insights into the genetic composition, potential virulence factors, and resistance profiles of B. cereus and B. subtilis, enhancing the understanding of their pathogenicity and epidemiology. The genomic analysis of B. cereus and B. subtilis revealed potential genomic applications in the context of food safety.
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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 | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 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".