Characterising the methylome of <i>Legionella longbeachae</i> serogroup 1 clinical isolates and assessing geo-temporal genetic diversity
Notice bibliographique
Résumé
Abstract Legionella longbeachae is an environmental bacterium that is commonly found in soil and composted plant material. In New Zealand (NZ) it is the most clinically significant Legionella species causing around two-thirds of all notified cases of Legionnaires’ disease. Here we report the sequencing and analysis of the geo-temporal genetic diversity of 54 L. longbeachae serogroup 1 (sg1) clinical isolates that were derived from cases from around NZ over a 22-year period, including one complete genome and its associated methylome. Our complete genome consisted of a 4.1 Mb chromosome and a 108 kb plasmid. The genome was highly methylated with two known epigenetic modifications, m 4 C and m 6 A, occurring in particular sequence motifs within the genome. Phylogenetic analysis demonstrated the 54 sg1 isolates belonged to two main clades that last shared a common ancestor between 108 BCE and 1608 CE. These isolates also showed diversity at the genome-structural level, with large-scale arrangements occurring in some regions of the chromosome and evidence of extensive chromosomal and plasmid recombination. This includes the presence of plasmids derived from recombination and horizontal gene transfer between various Legionella species, indicating there has been both intra-species and inter-species gene flow. However, because similar plasmids were found among isolates within each clade, plasmid recombination events may pre-empt the emergence of new L. longbeachae strains. Our high-quality reference genome and extensive genetic diversity data will serve as a platform for future work linking genetic, epigenetic and functional diversity in this globally important emerging environmental pathogen. Author Summary Legionnaires’ disease is a serious, sometimes fatal pneumonia caused by bacteria of the genus Legionella . In New Zealand, the species that causes the majority of disease is Legionella longbeachae . Although the analyses of pathogenic bacterial genomes is an important tool for unravelling evolutionary relationships and identifying genes and pathways that are associated with their disease-causing ability, until recently genomic data for L. longbeachae has been sparse. Here, we conducted a large-scale genomic analysis of 54 L. longbeachae isolates that had been obtained from people hospitalised with Legionnaires’ disease between 1993 and 2015 from 8 regions around New Zealand. Based on our genome analysis the isolates could be divided into two main groups that persisted over time and last shared a common ancestor up to 1700 years ago. Analysis of the bacterial chromosome revealed areas of high modification through the addition of methyl groups and these were associated with particular DNA sequence motifs. We also found there have been large-scale rearrangements in some regions of the chromosome, producing variability between the different L. longbeacahe strains, as well as evidence of gene-flow between the various Legionella species via the exchange of plasmid DNA.
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 | 0,000 |
| Bibliométrie | 0,001 | 0,001 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| 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) | 0,001 | 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 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 ».