Evidence map›Paper›PMID 34694881›Full record

ArticleAntimicrobial agents and chemotherapy2022

Prediction of Antimicrobial Resistance in Clinical Enterococcus faecium Isolates Using a Rules-Based Analysis of Whole-Genome Sequences.

Melis N Anahtar, Juliet T Bramante, Jiawu Xu, Lisa A Desrosiers, Jeffrey M Paer, Eric S Rosenberg, Virginia M Pierce, Douglas S Kwon

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Antimicrobial agents and chemotherapy, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
0.3field-weighted citation impact, top 38% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed, 6 citations in OpenAlex.

  1. Article
  2. Cross-Sector Antimicrobial Resistance and Virulence inAntibiotics (Basel, Switzerland) · 2026
    Article
  3. Pangenome analysis ofAntimicrobial agents and chemotherapy · 2026
    Article
  4. Genomic Epidemiology of Vancomycin-ResistantAntibiotics (Basel, Switzerland) · 2025
    Article
  5. Article
  6. Article
  7. Antimicrobial Susceptibility Testing for Enterococci.Journal of clinical microbiology · 2022
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors at 3 institutions in 1 country.

Melis N AnahtarDepartment of Pathology, Massachusetts General Hospitalgrid.32224.35 and Harvard Medical School, Boston, Massachusetts, USA.ORCID 0000-0003-0309-368X
Juliet T BramanteRagon Institute of MGH, MIT and Harvardgrid.461656.6, Cambridge, Massachusetts, USA.
Jiawu XuRagon Institute of MGH, MIT and Harvardgrid.461656.6, Cambridge, Massachusetts, USA.
Lisa A DesrosiersDepartment of Pathology, Massachusetts General Hospitalgrid.32224.35 and Harvard Medical School, Boston, Massachusetts, USA.
Jeffrey M PaerRagon Institute of MGH, MIT and Harvardgrid.461656.6, Cambridge, Massachusetts, USA.
Eric S RosenbergDepartment of Pathology, Massachusetts General Hospitalgrid.32224.35 and Harvard Medical School, Boston, Massachusetts, USA.
Virginia M Pierce *Department of Pathology, Massachusetts General Hospitalgrid.32224.35 and Harvard Medical School, Boston, Massachusetts, USA.ORCID 0000-0002-3723-1326
Douglas S Kwon *Ragon Institute of MGH, MIT and Harvardgrid.461656.6, Cambridge, Massachusetts, USA.
Harvard University · USRagon Institute of MGH, MIT and Harvard · USUniversity of Washington · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Enterococcus faecium is a major cause of clinical infections, often due to multidrug-resistant (MDR) strains. Whole-genome sequencing (WGS) is a powerful tool to study MDR bacteria and their antimicrobial resistance (AMR) mechanisms. In this study, we used WGS to characterize E. faecium clinical isolates and test the feasibility of rules-based genotypic prediction of AMR. Clinical isolates were divided into derivation and validation sets. Phenotypic susceptibility testing for ampicillin, vancomycin, high-level gentamicin, ciprofloxacin, levofloxacin, doxycycline, tetracycline, and linezolid was performed using the Vitek 2 automated system, with confirmation and discrepancy resolution by broth microdilution, disk diffusion, or gradient diffusion when needed. WGS was performed to identify isolate lineage and AMR genotype. AMR prediction rules were derived by analyzing the genotypic-phenotypic relationship in the derivation set. Phylogenetic analysis demonstrated that 88% of isolates in the collection belonged to hospital-associated clonal complex 17. Additionally, 12% of isolates had novel sequence types. When applied to the validation set, the derived prediction rules demonstrated an overall positive predictive value of 98% and negative predictive value of 99% compared to standard phenotypic methods. Most errors were falsely resistant predictions for tetracycline and doxycycline. Further analysis of genotypic-phenotypic discrepancies revealed potentially novel

Indexed as

Enterococcus faeciumGram-Positive Bacterial InfectionsAnti-Bacterial AgentsDrug Resistance, BacterialHumansMicrobial Sensitivity TestsPhylogenyAnti-Bacterial Agentsantibiotic resistanceantimicrobial agentsantimicrobial resistanceEnterococcusgenome analysisgenomicsmicrobiologypredictionvancomycin resistanceVREwhole-genome sequencing

Identifiers

PMID34694881
PMCPMC8765321
OpenAlexW3211149976

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.