Emergence of resistance in response to antibiotic treatment is a serious complication during infection, yet, our understanding of the underlying mechanisms remains incomplete. Since 2014, we collected 5,558 bacteremic isolates from 2,674 patients at Mount Sinai Hospital and identified 341 instances of acquired resistance. In one case, a patient with an Enterococcus faecium bloodstream infection (BSI) was treated with vancomycin, daptomycin and linezolid. Vancomycin resistance (VRE) developed first, followed by linezolid (Fig. 1). Linezolid is approved by the U.S. FDA to treat VRE-BSI, and few cases of resistance have been reported. Daptomycin and quinupristin-dalfopristin are also currently used first-line agents against VRE. Whole-genome sequencing was performed to identify the genomic changes responsible for the emerging resistance.
Vitek 2 antibiotic susceptibility profiles for all isolates were confirmed by E-tests. Complete genomes were assembled for 6 isolates using PacBio long-read sequencing data (>100x coverage), and Illumina short-read data was used to correct remaining single-nucleotide indel and base calling errors. Antibiotic resistance genes were annotated using Prokka and CARD, and NUCmer and Mauve were used to identify single nucleotide variants and structural changes associated with observed resistance changes.
Our comparative whole-genome analysis identified multiple novel genomic changes during treatment that affected genes associated with daptomycin and vancomycin resistance, as well as genes associated with quinupristin-dalfopristin resistance, although the patient was not treated with the latter drug. Linezolid resistance could not be attributed to any known resistance gene or variant by CARD, suggesting involvement of a novel mechanism.
Whole-genome analysis of clinical isolates resolved a complex case of acquired resistance to multiple antibiotics, and provides a unique platform to identify and characterize mechanisms of emerging resistance in response to treatment.
Figure 1. Vitek results and treatment for VRE-BSI patient. Antibiotic treatments are highlighted and Vitek 2 profiles are shown as lines.
R. Sebra, None
A. Kasarskis, None
C. Hamula, None
H. Van Bakel, None