---
title: "Integrative conjugative element in Streptococcus pyogenes carries a cfr-like gene linked to linezo"
id: "pubmed-42627159"
canonical_url: "https://medichelpline.com/clinical-feed/pubmed-42627159"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "PubMed / NCBI"
source_url: "https://pubmed.ncbi.nlm.nih.gov/42627159/"
doi: "10.1128/msphere.00277-26"
published_at: "2026-08-21T00:00:00.000Z"
evidence_level: "Journal Article"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Integrative conjugative element in Streptococcus pyogenes carries a cfr-like gene linked to linezo
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/pubmed-42627159
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** PubMed / NCBI
- **Source URL:** [Original Journal Publication](https://pubmed.ncbi.nlm.nih.gov/42627159/)
- **DOI:** [10.1128/msphere.00277-26](https://doi.org/10.1128%2Fmsphere.00277-26)
- **Published At:** 2026-08-21T00:00:00.000Z
- **Evidence Rating:** Journal Article
## Executive GIST (TL;DR)
- This report describes a clinical pharyngeal isolate of **Streptococcus pyogenes** (GAS-390756) recovered from a child with pharyngitis in the United States. - Whole-genome sequencing identified the isolate as **emm** type 89 and revealed an integrative and conjugative element (ICE Spy 390756) carrying the macrolide/lincosamide resistance gene **erm(B)** and a **cfr**-like gene denoted **cfr(C)**. - The **cfr(C)** gene in other species is known to confer the PhLOPSA resistance phenotype (phenicol, lincosamide, oxazolidinone, pleuromutilin, and streptogramin A), including resistance to **linezolid**, but functional activity depends on intact regulatory elements. - Phenotypic antimicrobial testing of GAS-390756 showed resistance to erythromycin and clindamycin but susceptibility to linezolid, consistent with expression of **erm(B)** and lack of detectable **cfr(C)**-mediated resistance. - Comparative genomic analysis suggested the promoter sequence upstream of **cfr(C)** may have been lost during acquisition by ICE Spy 390756, offering a likely explanation for the absence of a **cfr(C)** resistance phenotype in this isolate. - The report notes potential clinical and epidemiologic concern because ICE-associated mobilizable resistance determinants can disseminate across strains and species; however, details about transferability, prevalence, and clinical outcomes were not reported in the source. - The authors highlight the significance of surveillance and genomic characterization to detect mobile elements carrying resistance genes, while many experimental details and broader epidemiologic data were not provided in the abstract.
## Clinical Analysis & Structured Key Points
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Online ahead of print. # A novel integrative and conjugative element in _Streptococcus pyogenes_ carries a _cfr_ -like gene associated with linezolid resistance in other species [Daniel B Amusin](https://pubmed.ncbi.nlm.nih.gov/?term=Amusin+DB&cauthor_id=42627159)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-1 "Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.")[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-2 "Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA."), [Lacy M Simons](https://pubmed.ncbi.nlm.nih.gov/?term=Simons+LM&cauthor_id=42627159)[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-2 "Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA."), [Dulce S Garcia](https://pubmed.ncbi.nlm.nih.gov/?term=Garcia+DS&cauthor_id=42627159)[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-2 "Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA."), [Alan R Hauser](https://pubmed.ncbi.nlm.nih.gov/?term=Hauser+AR&cauthor_id=42627159)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-1 "Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.")[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-2 "Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA."), [Emma Office](https://pubmed.ncbi.nlm.nih.gov/?term=Office+E&cauthor_id=42627159)[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-2 "Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA."), [Preeti Jaggi](https://pubmed.ncbi.nlm.nih.gov/?term=Jaggi+P&cauthor_id=42627159)[ 3 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-3 "Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA."), [David B Williams](https://pubmed.ncbi.nlm.nih.gov/?term=Williams+DB&cauthor_id=42627159)[ 4 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-4 "Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA."), [Larry K Kociolek](https://pubmed.ncbi.nlm.nih.gov/?term=Kociolek+LK&cauthor_id=42627159)[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-5 "Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.")[ 6 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-6 "Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA."), [Ami B Patel](https://pubmed.ncbi.nlm.nih.gov/?term=Patel+AB&cauthor_id=42627159)[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-5 "Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.")[ 6 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-6 "Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA."), [Stanford T Shulman](https://pubmed.ncbi.nlm.nih.gov/?term=Shulman+ST&cauthor_id=42627159)[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-5 "Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.")[ 6 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-6 "Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA."), [Judith A Guzman-Cottrill](https://pubmed.ncbi.nlm.nih.gov/?term=Guzman-Cottrill+JA&cauthor_id=42627159)[ 7 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-7 "Department of Pediatrics, Division of Infectious Diseases, Oregon Health & Science University Doernbecher Children's Hospital, Portland, Oregon, USA."), [Robert R Tanz](https://pubmed.ncbi.nlm.nih.gov/?term=Tanz+RR&cauthor_id=42627159)[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-5 "Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.")[ 8 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-8 "Division of Advanced General Pediatrics & Primary Care, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA."), [Egon A Ozer](https://pubmed.ncbi.nlm.nih.gov/?term=Ozer+EA&cauthor_id=42627159)[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#full-view-affiliation-2 "Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.") Affiliations Expand ### Affiliations * 1 Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA. * 2 Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA. * 3 Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA. * 4 Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA. * 5 Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA. * 6 Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA. * 7 Department of Pediatrics, Division of Infectious Diseases, Oregon Health & Science University Doernbecher Children's Hospital, Portland, Oregon, USA. * 8 Division of Advanced General Pediatrics & Primary Care, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA. * PMID: **42627159** * DOI: [ 10.1128/msphere.00277-26 ](https://doi.org/10.1128/msphere.00277-26) Item in Clipboard # A novel integrative and conjugative element in _Streptococcus pyogenes_ carries a _cfr_ -like gene associated with linezolid resistance in other species Daniel B Amusin et al. mSphere. 2026. Show details Display options Display options Format Abstract PubMed PMID mSphere Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22mSphere%22%5Bjour%5D&sort=date&sort_order=desc) * [ Search in NLM Catalog ](https://www.ncbi.nlm.nih.gov/nlmcatalog?term=%22mSphere%22%5BTitle+Abbreviation%5D) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42627159/) . 2026 Aug 21:e0027726. doi: 10.1128/msphere.00277-26. Online ahead of print. ### Authors [Daniel B Amusin](https://pubmed.ncbi.nlm.nih.gov/?term=Amusin+DB&cauthor_id=42627159)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-1 "Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.")[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-2 "Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA."), [Lacy M Simons](https://pubmed.ncbi.nlm.nih.gov/?term=Simons+LM&cauthor_id=42627159)[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-2 "Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA."), [Dulce S Garcia](https://pubmed.ncbi.nlm.nih.gov/?term=Garcia+DS&cauthor_id=42627159)[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-2 "Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA."), [Alan R Hauser](https://pubmed.ncbi.nlm.nih.gov/?term=Hauser+AR&cauthor_id=42627159)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-1 "Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.")[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-2 "Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA."), [Emma Office](https://pubmed.ncbi.nlm.nih.gov/?term=Office+E&cauthor_id=42627159)[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-2 "Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA."), [Preeti Jaggi](https://pubmed.ncbi.nlm.nih.gov/?term=Jaggi+P&cauthor_id=42627159)[ 3 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-3 "Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA."), [David B Williams](https://pubmed.ncbi.nlm.nih.gov/?term=Williams+DB&cauthor_id=42627159)[ 4 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-4 "Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA."), [Larry K Kociolek](https://pubmed.ncbi.nlm.nih.gov/?term=Kociolek+LK&cauthor_id=42627159)[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-5 "Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.")[ 6 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-6 "Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA."), [Ami B Patel](https://pubmed.ncbi.nlm.nih.gov/?term=Patel+AB&cauthor_id=42627159)[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-5 "Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.")[ 6 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-6 "Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA."), [Stanford T Shulman](https://pubmed.ncbi.nlm.nih.gov/?term=Shulman+ST&cauthor_id=42627159)[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-5 "Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.")[ 6 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-6 "Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA."), [Judith A Guzman-Cottrill](https://pubmed.ncbi.nlm.nih.gov/?term=Guzman-Cottrill+JA&cauthor_id=42627159)[ 7 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-7 "Department of Pediatrics, Division of Infectious Diseases, Oregon Health & Science University Doernbecher Children's Hospital, Portland, Oregon, USA."), [Robert R Tanz](https://pubmed.ncbi.nlm.nih.gov/?term=Tanz+RR&cauthor_id=42627159)[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-5 "Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.")[ 8 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-8 "Division of Advanced General Pediatrics & Primary Care, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA."), [Egon A Ozer](https://pubmed.ncbi.nlm.nih.gov/?term=Ozer+EA&cauthor_id=42627159)[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42627159/#short-view-affiliation-2 "Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.") ### Affiliations * 1 Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA. * 2 Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA. * 3 Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA. * 4 Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA. * 5 Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA. * 6 Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA. * 7 Department of Pediatrics, Division of Infectious Diseases, Oregon Health & Science University Doernbecher Children's Hospital, Portland, Oregon, USA. * 8 Division of Advanced General Pediatrics & Primary Care, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA. * PMID: **42627159** * DOI: [ 10.1128/msphere.00277-26 ](https://doi.org/10.1128/msphere.00277-26) Item in Clipboard Cite Display options Display options Format Abstract PubMed PMID ## Abstract Treatment of severe invasive _Streptococcus pyogenes_ infections has historically relied on β-lactam antibiotics with adjunctive clindamycin. Rising rates of lincosamide resistance have led to adoption of linezolid as an alternative adjunctive therapy. This report describes a clinical _S. pyogenes_ isolate carrying a multi-drug resistance gene, _cfr_(C), known to confer the phenicol, lincosamide, oxazolidinone, pleuromutilin, and streptogramin A (PhLOPSA) resistance phenotype in other bacterial species. Strain GAS-390756 is a pharyngeal isolate collected from a child with pharyngitis in the United States. Whole-genome sequence analysis demonstrated that the isolate belonged to _emm_ type 89 and carried an integrative and conjugative element with _erm_(B) and _cfr_(C) cargo genes (ICE _Spy_ 390756). Antimicrobial susceptibility testing demonstrated the isolate was resistant to erythromycin and clindamycin but susceptible to linezolid, consistent with the activity of _erm_(B) but not _cfr_(C). Comparative analysis of _cfr_(C)'s genomic context suggested that the promoter sequence may have been lost during ICE _Spy_ 390756's acquisition of the gene. While GAS-390756
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