Comparative genome analysis investigation of nosocomial and community-acquired cases of Legionnaires’ disease caused by ST2858 and ST378
Notice bibliographique
Résumé
ABSTRACT Eight cases of Legionnaires’ disease caused by Legionella pneumophila serogroup 1 sequence type (ST) ST2858 were detected within 4 years in Montréal, Canada. Most cases were associated with a single healthcare facility, and one of them presented with a co-infection, from which ST378 was isolated as well. The source of ST2858 was not identified, despite extensive environmental sampling. The goal of this study was to determine the diversity of both STs and confirm the source of each by matching clinical to environmental isolates. Comparative genome analysis was performed to investigate the genetic relatedness of the isolates. Long- and short-read hybrid assembly was used to produce high-quality closed genomes. A PCR assay, amplifying a unique gene of ST2858, was also developed. None of the 599 environmental isolates screened by PCR was ST2858. The ST2858 clinical isolates had a maximum of two single nucleotide polymorphisms in pairwise comparison, suggesting a common source. ST378 isolates had higher genomic diversity, and the isolate from the co-infection was similar to environmental ST378 from the healthcare facility’s hot water distribution system. The isolate from the co-infection harbored a plasmid conferring increased copper resistance. Understanding genomic diversity could help identify potential sources and should be considered for matching clinical with environmental isolates. Phenotypic diversity may be relevant for outbreak investigation, surveillance, and management. IMPORTANCE Legionnaires’ disease (LD) is transmitted to humans by inhalation of aerosols contaminated with Legionella . When an outbreak occurs, identification of the source allows public officials to make sure the source is controlled to prevent further cases. In this study, whole genome sequencing was used to investigate the relatedness between clinical and environmental isolates collected during the epidemiological investigation of cases of LD centered around a single healthcare facility, providing valuable information about the diversity of Legionella within water systems and similarity thresholds for matching clinical and environmental strains. The genomic data were also used to design a methodology to rapidly screen hundreds of historical isolates and DNA extracts, which could benefit source identification in other outbreaks. Furthermore, Legionella isolates may differ in their ability to resist disinfection methods and potentially acquire novel genetic determinants, and water system characteristics may select for specific Legionella strains.
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Comment cette classification a été obtenuedéplier
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 | 0,001 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
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 tête enseignante, 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 ».