Diversity of <i>Salmonella enterica</i> phages isolated from chicken farms in Kenya
Notice bibliographique
Résumé
ABSTRACT In this study, we describe the characterization of 67 Salmonella enterica phages isolated from Kenya. Specifically, the phages were isolated from chicken feces as well as from swabs and water samples obtained from chicken farms and slaughterhouses in Nairobi and Kiambu counties. Genome sequencing and analysis revealed that 59 phage isolates were distinct and could be grouped into 17 clusters belonging to four major types of phages (MT1–4). Further taxonomic analysis showed that each MT represents one phage genus. Of the 17 selected representative genomes (one per cluster), seven phages belong to the MT1 group and to the genus Jerseyvirus . The MT2 cluster contained eight representative phages that were similar to Escherichia phage T5 and belong to the Tequintavirus genus. The unique MT3 cluster with one phage representative belongs to the Zindervirus genus, while the sole MT4 phage isolate is a member of the Dhillonvirus genus. All representative phages are siphophages, except MT3 phage which is a podophage. All genomes do not contain genes associated with lysogeny and therefore, they are considered exclusively lytic. No known virulence genes or antibiotic resistance genes were detected in any of the genomes. Phage DNA termini analyses showed that MT2 phages have a direct terminal repeat-based packaging mechanism while MT1 has a headful packaging mechanism. Host range studies showed that phages belonging to MT1 and MT3 appear to only infect Salmonella strains, while MT2 and MT4 phages were also capable of infecting Escherichia and Shigella strains. IMPORTANCE Non-typhoidal Salmonella enterica infections are one of the leading causes of diarrhoeal diseases that spread to humans from animal sources such as poultry. Hence, keeping poultry farms free of Salmonella is essential for consumer safety and for a better yield of animal products. However, the emergence of antibiotic resistance due to over usage has sped up the search for alternative biocontrol methods such as the use of bacteriophages. Isolation and characterization of novel bacteriophages are key to adapt phage-based biocontrol applications. Here, we isolated and characterized Salmonella phages from samples collected at chicken farms and slaughterhouses in Kenya. The genomic characterization of these phage isolates revealed that they belong to four ICTV (International Committee on Taxonomy of Viruses) phage genera. All these phages are lytic and possibly suitable for biocontrol applications because no lysogenic genes or virulence factors were found in their genomes. Hence, we recommend further studies on these phages for their applications in Salmonella biocontrol.
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Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,001 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,003 | 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; les deux têtes enseignantes s’accordent sur ce qui est montré ici.
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