Genomic and molecular identification and characterization of Enterobacteriaceae and Campylobacter spp.
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Bibliographic record
Abstract
Campylobacter spp. is the most prevalent bacterial pathogen worldwide. Despite causing mainly self-limited gastroenteritis, campylobacteriosis could also trigger neurological disorders and causes the highest number of disability adjusted life years (DALYs) globally after rotavirus. Campylobacter jejuni and C. coli have been the most recognised Campylobacter species mainly due to their asymptomatic carriage in poultry. However, in the last two decades with the advent of the next generation sequencing technologies, species other than C. jejuni/coli have emerged as potentially having a role in human disease, such as C. concisus. In addition, many novel Campylobacter species have been discovered due to increased whole-genome sequencing and genomic techniques with high resolution in discriminating closely related taxa. In public health, precise identification and discrimination of Campylobacter is important for developing control strategies to decrease human and economic burden caused by campylobacteriosis. Chapter 2 of the dissertation focused on the development of TaqMan multiplex real-time PCR assays for discrimination of 17 of the described Campylobacter species, associated with both human and animal diseases. However, despite the robust primer and probe design and rigorous in silico specificity tests, we encountered high cross-reactivity for certain Campylobacter species. To increase the diagnostic specificities of the real-time PCR assays, 2-step approaches were optimized which enhanced the discrimination between the examined taxa. The third chapter utilized bioinformatic methods for taxonogenomic and phylogenomic placement of environmental Campylobacter species collected in North America, including description of two novel Campylobacter taxa and a detection of two isolates of the recently described C. novaezeelandiae from agricultural water in Canada. Comparative genomic analysis revealed abundance of virulence genes in all examined isolates, but a low diversity of antimicrobial resistance genes. In addition, detailed analysis of the genomes of the novel Campylobacter species revealed that their small genomes are in part result of a loss of genes for amino acid biosynthesis and energy metabolism, which resembles the C. lari-like species metabolism and could be associated with occupation of marine environments. The last chapter of the dissertation focused on azithromycin as a last line critically important antimicrobial for treatment of gastrointestinal infections in Enterobacteriaceae. The objective of this chapter was to describe the occurrence and diversity of macrolide resistance genes in poultry, bovine, and swine E. coli and Salmonella isolates collected within Europe and to compare genotypic with phenotypic data. It was found that isolates harboring the mph(A) gene exhibited both wild-type and non-wild type phenotypes (MIC values of 4 to ≥64 mg/L). Comparative genomic analysis revealed the wild-type isolates lacked the mphR(A) repressor gene and had a deletion within the promoter region as compared to the non-wild-type isolates. In addition, in this chapter we described novel and emerging antimicrobial resistance genes mediating high level resistance to azithromycin, particularly the erm(42) gene which was found for the first time in E. coli in this study and the mef(C)-mph(G) genes which to date have not been described in Enterobacteriaceae. These genes were located on plasmids and carried in addition other antimicrobial resistance genes, which is a concern for co-selection and spread.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| 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 it