title: Virulence and resistance pattern of a novel sequence type of linezolid-resistant Enterococcus faecium identified by whole-genome sequencing.
abstract: Empirical use of linezolid has been advocated in neutropenic febrile patients colonised by vancomycin-resistant enterococci (VRE) because of the risk of bloodstream infection (BSI). This study aimed to genetically describe a vancomycin-resistant Enterococcus faecium (VREfm) BSI isolate resistant to linezolid (VRLRE) in a patient previously colonised by VREfm and to determine the incidence of colonisation and infection by VREfm in a bone marrow transplant unit over a 10-year period. Data for VREfm colonisation and infection were evaluated. PCR for the vanA and vanB genes, pulsed-field gel electrophoresis (PFGE) and microdilution antimicrobial susceptibility testing (vancomycin, teicoplanin, linezolid and aminoglycosides) were performed. Three isolates, including the VRLRE, were selected for whole-genome sequencing by Ion Torrent™, with E. faecium CP006620-Aus0085 used as a reference. Eighty-seven VREfm were analysed; all were linezolid-susceptible and harboured vanA, except for one blood isolate from a febrile neutropenic patient colonised by VREfm who received linezolid for 12 days and developed a BSI by VRLRE (linezolid MIC≥8μg/mL). Linezolid resistance was associated with a G2576T mutation in the 23SrRNA gene. PFGE analysis demonstrated that the 87 isolates belonged to four major clusters; however, the VRLRE presented only 50% similarity. Three sequence types (STs) were identified: ST412 (the predominant clone, which was more virulent compared with the other isolates); ST478 (linezolid-susceptible VREfm); and a novel ST named ST987 (VRLRE). SNP analysis showed a higher similarity between linezolid-susceptible VREfm and the predominant clone compared with VRLRE. VRLRE presented a G2576T mutation and belonged to a novel ST (ST987).
authors.affiliation: Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Gladys Villas Boas
authors.initials: GVB
authors.lastname: do Prado
authors.affiliation: Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Ana Paula
authors.initials: AP
authors.lastname: Marchi
authors.affiliation: Faculdade de Medicina Veterinária e Zootecnia da Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Luisa Zanolli
authors.initials: LZ
authors.lastname: Moreno
authors.affiliation: Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Camila
authors.initials: C
authors.lastname: Rizek
authors.affiliation: Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Ulisses
authors.initials: U
authors.lastname: Amigo
authors.affiliation: Faculdade de Medicina Veterinária e Zootecnia da Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Andrea Micke
authors.initials: AM
authors.lastname: Moreno
authors.affiliation: Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Flavia
authors.initials: F
authors.lastname: Rossi
authors.affiliation: Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Thais
authors.initials: T
authors.lastname: Guimaraes
authors.affiliation: Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Anna Sara
authors.initials: AS
authors.lastname: Levin
authors.affiliation: Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Universidade de São Paulo, São Paulo, Brazil. Electronic address: costasilviaf@ig.com.br.
authors.forename: Silvia F
authors.initials: SF
authors.lastname: Costa
mesh_terms: D000900:Anti-Bacterial Agents; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D016984:Enterococcus faecium / Q000187:drug effects / Q000235:genetics*; D016908:Gram-Positive Bacterial Infections; D006801:Humans; D000069349:Linezolid; D008826:Microbial Sensitivity Tests; D009154:Mutation; D012338:RNA, Ribosomal, 23S / Q000235:genetics*; D020713:Vancomycin Resistance; D014774:Virulence
chemical_list: D000900:Anti-Bacterial Agents; D012338:RNA, Ribosomal, 23S; D000069349:Linezolid
keywords: HSCT; Linezolid resistance; MLST; Novel ST; VRE