title: Deletions in a ribosomal protein-coding gene are associated with tigecycline resistance in Enterococcus faecium.
abstract: Enterococcus faecium is an emerging nosocomial pathogen associated with antibiotic therapy in the hospital environment. Whole-genome sequences were determined for three pairs of related, consecutively collected E. faecium clinical isolates to determine putative mechanisms of resistance to tigecycline. The first isolates (1S, 2S and 3S) in each of the three pairs were sensitive to tigecycline [minimum inhibitory concentration (MIC) of 0.125 mg/L]. Following tigecycline therapy, the second isolate in each pair demonstrated increased resistance to tigecycline. Two isolates (1R and 2R) were resistant (MIC of 8 mg/L) and one isolate (3I) demonstrated reduced susceptibility (MIC of 0.5 mg/L). Mutations distinguishing each pair of sensitive and resistant isolates were determined through alignment to a reference genome and variant detection. In addition, a de novo assembly of each isolate genome was constructed to confirm mutations. A total of 16 mutations in eleven coding sequences were determined. Mutations in the rpsJ gene, which encodes a structural protein forming part of the 30S ribosomal subunit, were detected in each of the pairs. Mutations were in regions proximal to the predicted tigecycline-binding site. Predicted amino acid substitutions were detected in 1R and 3I. The resistant strains were additionally associated with deletions of 15 nucleotides (2R) and 3 nucleotides (1R). This study confirms that amino acid substitutions in rpsJ contribute towards reduced susceptibility to tigecycline and suggests that deletions may be required for tigecycline resistance in E. faecium.
authors.affiliation: Clinical Microbiology Department, Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre (NIHR SRMRC), Queen Elizabeth Hospital, Birmingham, UK.
authors.forename: Marc
authors.initials: M
authors.lastname: Niebel
authors.affiliation: National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre (NIHR SRMRC), Queen Elizabeth Hospital, Birmingham, UK; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
authors.forename: Joshua
authors.initials: J
authors.lastname: Quick
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Ana Maria Guzman
authors.initials: AM
authors.lastname: Prieto
authors.affiliation: Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Reference Microbiology Services, Public Health England, Colindale, London, UK.
authors.forename: Robert L R
authors.initials: RL
authors.lastname: Hill
authors.affiliation: Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Reference Microbiology Services, Public Health England, Colindale, London, UK.
authors.forename: Rachel
authors.initials: R
authors.lastname: Pike
authors.affiliation: Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
authors.forename: Damon
authors.initials: D
authors.lastname: Huber
authors.affiliation: Clinical Microbiology Department, Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.
authors.forename: Miruna
authors.initials: M
authors.lastname: David
authors.affiliation: Department of Life Sciences, University of Roehampton, London, UK.
authors.forename: Michael
authors.initials: M
authors.lastname: Hornsey
authors.affiliation: Blizard Institute, Queen Mary University London, London, UK.
authors.forename: David
authors.initials: D
authors.lastname: Wareham
authors.affiliation: Clinical Microbiology Department, Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre (NIHR SRMRC), Queen Elizabeth Hospital, Birmingham, UK.
authors.forename: Beryl
authors.initials: B
authors.lastname: Oppenheim
authors.affiliation: Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Reference Microbiology Services, Public Health England, Colindale, London, UK.
authors.forename: Neil
authors.initials: N
authors.lastname: Woodford
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Willem
authors.initials: W
authors.lastname: van Schaik
authors.affiliation: Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK. Electronic address: n.j.loman@bham.ac.uk.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Loman
mesh_terms: D019943:Amino Acid Substitution; D000900:Anti-Bacterial Agents / Q000494:pharmacology* / Q000627:therapeutic use; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D024881:Drug Resistance, Bacterial; D016984:Enterococcus faecium / Q000187:drug effects* / Q000235:genetics*; D016680:Genome, Bacterial; D016908:Gram-Positive Bacterial Infections / Q000188:drug therapy / Q000382:microbiology; D008826:Microbial Sensitivity Tests; D008911:Minocycline / Q000031:analogs & derivatives* / Q000494:pharmacology / Q000627:therapeutic use; D008969:Molecular Sequence Data; D012269:Ribosomal Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion; D000078304:Tigecycline
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D012269:Ribosomal Proteins; D000078304:Tigecycline; D008911:Minocycline
keywords: Enterococcus; Resistance; Tigecycline; Whole-genome sequencing