Browse AMR Genes

Explore antimicrobial resistance genes from the literature

cfr(E)

radical S-adenosyl-l-methionine (SAM) enzyme

NCBI Pathogen Isolates

Bacterial genomes carrying this gene

NCBI Reference Gene Catalog

Known alleles and reference sequences

Protein entries specific to cfr(E)

Browse AMR rules for cfr(E)

Validation StatusConfirmed2+ DBs

Overview

Mechanism: hypermethylation of nucleotide A2503 in 23S rRNA
Validation Method: in vitro methylation assay
Drug Classes: Phenicol, Lincosamide, Oxazolidinone, Pleuromutilin, Streptogramin a, VIRGINIAMYCIN M, FLORFENICOL, CLINDAMYCIN, LINCOMYCIN, LINEZOLID, TIAMULIN, CHLORAMPHENICOL, THIAMPHENICOL, VIRGINIAMYCIN, PRISTINAMYCIN IIA, DALFOPRISTIN, LINCOSAMIDE, Linezolid
Organisms: Clostridium difficile, Clostridium sp. AF37-7, Clostridioides difficile
Geographic Location: Latin America, Mexico, USA|United Kingdom|Mexico|China
Alleles: 2
Papers: 4
Databases: Card DatabaseReference Gene CatalogResFinder DatabaseReslit

Allele Variants2

Allele	Database	Papers	Drug Classes	Organisms	Countries	Years	Sequence Accession	Protein Accession
Cfr(E)	Card DatabaseReference Gene CatalogResFinder DatabaseReslit	6	Phenicol, Lincosamide +16

Papers4

1

cfr(B), cfr(C), and a New cfr-Like Gene, cfr(E), in Clostridium difficile Strains Recovered across Latin America.

PMID 31685464 · 2019

The study identifies cfr(B), cfr(C), and a new cfr-like gene, cfr(E), in Clostridium difficile strains from Latin America, demonstrating their ability to confer resistance to multiple antibiotics through hypermethylation of 23S rRNA.

Gene Information

Gene Name: cfr(E)
Allele: Cfr(E)
Encodes: radical S-adenosyl-l-methionine (SAM) enzyme
Source Database: Reslit
Mechanism: hypermethylation of nucleotide A2503 in 23S rRNA
Confers Resistance To: PhenicolLincosamideOxazolidinonePleuromutilinStreptogramin a
Organisms Tested In: • Clostridium difficile
Geographic Location: Latin America
Validation Method: in vitro methylation assay
Sequence Accession: KM359438|CCL89685|AJ879565|MG707078|CAADRH000000000|CAADRI000000000|ERR467555

2

cfr(B), cfr(C), and a New cfr-Like Gene, cfr(E), in Clostridium difficile Strains Recovered across Latin America.

PMID 31685464 · 2019

Gene Information

Gene Name: cfr(E)
Allele: Cfr(E)
Encodes: 23S rRNA (adenine(2503)-C(8))-methyltransferase Cfr(E)
Source Database: Reference Gene Catalog
Mechanism: Target modification
Confers Resistance To: VIRGINIAMYCIN MFLORFENICOLCLINDAMYCINLINCOMYCINLINEZOLIDTIAMULINCHLORAMPHENICOLTHIAMPHENICOLVIRGINIAMYCINPRISTINAMYCIN IIADALFOPRISTINLINCOSAMIDE
Organisms Tested In: • Clostridium sp. AF37-7
Sequence Accession: QUDP01000003.1
Protein Accession: RHO92765.1
Notes: 23S rRNA methylase

3

cfr(B), cfr(C), and a New cfr-Like Gene, cfr(E), in Clostridium difficile Strains Recovered across Latin America.

PMID 31685464 · 2019

Gene Information

Gene Name: cfr(E)
Allele: Cfr(E)
Encodes: 23S rRNA (adenine(2503)-C(8))-methyltransferase Cfr(E)
Source Database: ResFinder Database
Mechanism: Target modification
Confers Resistance To: VIRGINIAMYCIN MFLORFENICOLCLINDAMYCINLINCOMYCINLINEZOLIDTIAMULINCHLORAMPHENICOLTHIAMPHENICOLVIRGINIAMYCINPRISTINAMYCIN IIADALFOPRISTINLINCOSAMIDE
Organisms Tested In: • Clostridium sp. AF37-7
Sequence Accession: QUDP01000003.1
Protein Accession: RHO92765.1
Notes: 23S rRNA methylase

4

cfr(B), cfr(C), and a New cfr-Like Gene, cfr(E), in Clostridium difficile Strains Recovered across Latin America.

PMID 31685464 · 2019

Gene Information

Gene Name: cfr(E)
Allele: Cfr(E)
Encodes: 23S rRNA (adenine(2503)-C(8))-methyltransferase Cfr(E)
Source Database: Card Database
Mechanism: Target modification
Confers Resistance To: VIRGINIAMYCIN MFLORFENICOLCLINDAMYCINLINCOMYCINLINEZOLIDTIAMULINCHLORAMPHENICOLTHIAMPHENICOLVIRGINIAMYCINPRISTINAMYCIN IIADALFOPRISTINLINCOSAMIDE
Organisms Tested In: • Clostridium sp. AF37-7
Sequence Accession: QUDP01000003.1
Protein Accession: RHO92765.1
Notes: 23S rRNA methylase

5

Molecular Epidemiology and Antimicrobial Resistance of Clostridioides difficile in Hospitalized Patients From Mexico.

PMID 35360652 · 2021

The study identified several AMR genes and mutations in C. difficile isolates from Mexico, including cfrE, ermB, aadE, aadA27, aac(6')-Ie-aph(2'')-Ia, catP, blaCDD2, blaCCD1, tetM, tetO, tetB, tetA, and cdeA, along with mutations in rpoB, rpoC, fusA, and pbp2 associated with resistance to various antibiotics.

Gene Information

Gene Name: cfr(E)
Allele: cfrE
Encodes: rRNA methyltransferase
Source Database: Reslit
Confers Resistance To: Linezolid
Organisms Tested In: • Clostridioides difficile
Geographic Location: Mexico
Validation Method: genomic analysis and correlation with phenotype
Sequence Accession: PRJNA203445

6

Genomic Characterization of Linezolid-Resistant Clostridioides difficile Harboring cfr Variants.

PMID 40558391 · 2025

The study identifies cfr gene variants (cfr(B), cfr(C), and cfr(E)) in linezolid-resistant Clostridioides difficile strains, highlighting their association with resistance and the presence of specific mutations in these genes.

Gene Information

Gene Name: cfr(E)
Allele: Cfr(E)
Encodes: ribosomal RNA large subunit methyltransferase
Source Database: Reslit
Confers Resistance To: Linezolid
Organisms Tested In: • Clostridioides difficile
Geographic Location: USA|United Kingdom|Mexico|China
Validation Method: genomic analysis and mutation analysis
Sequence Accession: CCL89685

7

PMID Unpublished

Gene Information

Gene Name: cfr(E)
Allele: Cfr(E)
Source Database: ResFinder Database
Mechanism: Target modification
Confers Resistance To: CLINDAMYCINLINCOMYCINLINEZOLIDTIAMULINCHLORAMPHENICOLFLORFENICOLPRISTINAMYCIN IIADALFOPRISTINVIRGINIAMYCIN M
Sequence Accession: 70225
Notes: 23S rRNA methylase

8

Gene Information

Gene Name: cfr(E)
Allele: cfrE
Encodes: Cfr 23S ribosomal RNA methyltransferase
Source Database: Card Database
Mechanism: antibiotic target alteration
Organisms Tested In: • Clostridium sp. AF37-7
Sequence Accession: QUDP01000003.1
Protein Accession: RHO92765.1
Notes: ARO:3005023