Vancomycin-resistant <i>Enterococcus faecium</i> harbouring <i>vanN</i> in Canada: a case and complete sequence of pEfm12493 harbouring the <i>vanN</i> operon
Notice bibliographique
Résumé
Sir, Resistance to vancomycin in Enterococcus faecium and Enterococcus faecalis is due to acquired operon structures of two types, namely the d-alanyl-d-lactate and d-alanyl-d-serine operons named for the specific ligase they harbour. The former group consists of the vanA, vanB, vanD and vanM operons and the latter group consists of the vanE, vanG, vanL and vanN operons.1–5 The d-Ala-d-Lac operons can be carried on plasmids or on the chromosome while the d-Ala-d-Ser operons are chromosomally located except for vanN, which has been found on a plasmid.5 To date vanN has only been described twice, from E. faecium isolated in 2008 from a patient in France4 and from E. faecium isolated from a chicken meat sample collected in Japan in 2011.5 The vanN operons were identical except for a single non-synonymous substitution in the vanSN gene. A 51-year-old male with tibial and femoral artery occlusion on the right ankle was scheduled for angiography with revascularization. Three weeks later the patient presented at hospital with cellulitis in the right heel and ischaemia in the right ankle wound, which on microbial sampling yielded Escherichia coli, Stenotrophomonas maltophilia and Pantoea agglomerans. Ertapenem treatment was begun and 4 days later trimethoprim/sulfamethoxazole was added. Treatment continued for a further 15 days; the patient was then admitted for revascularization, and the infection was cured successfully. At admission screening (rectal) E. faecium N12-0493 was isolated and was determined by Etest to have a vancomycin MIC of 16 mg/L and a teicoplanin MIC of 0.5 mg/L. Additional testing by Vitek 2 (AST-GP67) showed E. faecium N12-493 was resistant to vancomycin and clindamycin, had intermediate susceptibility to ciprofloxacin, quinupristin/dalfopristin and nitrofurantoin, and was susceptible to ampicillin, high-level gentamicin, levofloxacin, linezolid, tetracycline and tigecycline. No further antimicrobial therapy was started after the procedure. MLST analysis revealed a unique profile, which was assigned ST955 (www.efaecium.mlst.net). ST955 did not cluster with the classical hospital-associated strain types (formerly known as CC17). PCR analysis revealed E. faecium N12-0493 was positive for the E. faecium ddl gene and vanN genes. The putative translation product (149 residues) of the vanN amplicon sequence shared 94% identity with the VanN protein. To identify the genetic context of the complete vanN operon, the genome of E. faecium N12-0493 was completely sequenced using Illumina technology. The assembled reads and the partial vanN sequence of E. faecium N12-0493 were further assembled using the Seqman Pro module of Lasergene 10 (DNASTAR, Madison, WI, USA). In this way a single 137 817 bp circular sequence, designated pEfm12493, was assembled from five contigs, ranging from 2222 to 90 738 bp (mean = 27.6 kb), with confirmation by standard PCR and sequencing (Figure 1). A total of 127 ORFs were annotated using Prokka6 and manual BLAST analysis (http://blast.ncbi.nlm.nih.gov/Blast.cgi) and are listed in Table S1 (available as Supplementary data at JAC Online). Plasmid pEfm12493 was assigned GenBank accession number KP342511.
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 | 0,006 |
| Méta-épidémiologie (sens strict) | 0,001 | 0,001 |
| Méta-épidémiologie (sens large) | 0,001 | 0,001 |
| Bibliométrie | 0,001 | 0,001 |
| Études des sciences et des technologies | 0,003 | 0,002 |
| Communication savante | 0,002 | 0,001 |
| Science ouverte | 0,002 | 0,001 |
| Intégrité de la recherche | 0,010 | 0,007 |
| 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; 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 ».