Clonal emergence of invasive multidrug-resistant staphylococcus epidermidis deconvoluted via a combination of whole-genome sequencing and microbiome analyses

Xiqi Li, Cesar A. Arias, Samuel L. Aitken, Jessica Galloway Peña, Diana Panesso, Michael Chang, Lorena Diaz, Rafael Rios, Yazan Numan, Sammi Ghaoui, Sruti Debroy, Micah M. Bhatti, Dawn E. Simmons, Isaam Raad, Ray Hachem, Stephanie A. Folan, Pranoti Sahasarabhojane, Awdhesh Kalia, Samuel A. Shelburne

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

Background Pathobionts, bacteria that are typically human commensals but can cause disease, contribute significantly to antimicrobial resistance. Staphylococcus epidermidis is a prototypical pathobiont as it is a ubiquitous human commensal but also a leading cause of healthcare-associated bacteremia. We sought to determine the etiology of a recent increase in invasive S. epidermidis isolates resistant to linezolid. Methods Whole-genome sequencing (WGS) was performed on 176 S. epidermidis bloodstream isolates collected at the MD Anderson Cancer Center in Houston, Texas, between 2013 and 2016. Molecular relationships were assessed via complementary phylogenomic approaches. Abundance of the linezolid resistance determinant cfr was determined in stool samples via reverse-transcription quantitative polymerase chain reaction. Results Thirty-nine of the 176 strains were linezolid resistant (22%). Thirty-one of the 39 linezolid-resistant S. epidermidis infections were caused by a particular clone resistant to multiple antimicrobials that spread among leukemia patients and carried cfr on a 49-kb plasmid (herein called pMB151a). The 6 kb of pMB151a surrounding the cfr gene was nearly 100% identical to a cfr-containing plasmid isolated from livestock-associated staphylococci in China. Analysis of serial stool samples from leukemia patients revealed progressive staphylococcal domination of the intestinal microflora and an increase in cfr abundance following linezolid use. Conclusions The combination of linezolid use plus transmission of a multidrug-resistant clone drove expansion of invasive, linezolid-resistant S. epidermidis. Our results lend support to the notion that a combination of antibiotic stewardship plus infection control measures may help to control the spread of a multidrug-resistant pathobiont.

Original languageEnglish (US)
Pages (from-to)398-406
Number of pages9
JournalClinical Infectious Diseases
Volume67
Issue number3
DOIs
StatePublished - Jul 18 2018

Keywords

  • Staphylococcus epidermidis
  • cfr
  • linezolid resistance
  • microbiome
  • whole-genome sequencing

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases

Fingerprint

Dive into the research topics of 'Clonal emergence of invasive multidrug-resistant staphylococcus epidermidis deconvoluted via a combination of whole-genome sequencing and microbiome analyses'. Together they form a unique fingerprint.

Cite this