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
Bibliographic record
Abstract
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.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.006 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.003 | 0.002 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.010 | 0.007 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".