Genomic and molecular identification and characterization of Enterobacteriaceae and Campylobacter spp.
Notice bibliographique
Résumé
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.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,001 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,001 |
| Bibliométrie | 0,001 | 0,001 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,001 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,001 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,002 | 0,001 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».