Molecular basis for the emergence of a new hospital endemic tigecycline-resistant Enterococcus faecalis ST103 lineage

Abstract

Enterococcus faecalis are a major cause of nosocomial infection worldwide, and the spread of vancomycin resistant strains (VRE) limits treatment options. Tigecycline-resistant VRE began to be isolated from inpatients at a Brazilian hospital within months following the addition of tigecycline to the hospital formulary. This was found to be the result of a spread of an ST103 E. faecalis clone. Our objective was to identify the basis for tigecycline resistance in this lineage. The genomes of two closely related tigecycline-susceptible (MIC = 0.06 mg/L), and three representative tigecycline-resistant (MIC = 1 mg/L) ST103 isolates were sequenced and compared. Further, efforts were undertaken to recapitulate the emergence of resistant strains in vitro. The specific mutations identified in clinical isolates in several cases were within the same genes identified in laboratory-evolved strains. The contribution of various polymorphisms to the resistance phenotype was assessed by trans-complementation of the wild type or mutant alleles, by testing for differences in mRNA abundance, and/or by examining the phenotype of transposon insertion mutants. Among tigecycline-resistant clinical isolates, five genes contained non-synonymous mutations, including two genes known to be related to enterococcal tigecycline resistance (tetM and rpsJ). Finally, within the in vitro-selected resistant variants, mutation in the gene for a MarR-family response regulator was associated with tigecycline resistance. This study shows that E. faecalis mutates to attain tigecycline resistance through the complex interplay of multiple mechanisms, along multiple evolutionary trajectories.

Targeted IS-element sequencing uncovers transposition dynamics during selective pressure in enterococci

“…1B). IS256 occurs within a variety of ST clades and is most abundant in in ST6, ST103, ST778, and ST388 genomes, all of which are associated with hospital-adapted, opportunistic pathogenic lineages (Table S1A) 39, 40, 41, 42 . We compared the abundances of different virulence factors between genomes with and without IS256 (Fig.…”

Mechanism of Eravacycline Resistance in Clinical Enterococcus faecalis Isolates From China

“…Of particular interest, a modification (R53Q-54-57ATHK) that occurred in Tigeresistant E. faecalis strain selected in vitro resulted in a 4-fold increase in Tige resistance (Beabout et al, 2015). Most recently, Dabul et al (2019) reported that a deletion of amino acids at position 56-59 (HKYK) was present at three Tige-resistant clinical E. faecalis isolates. Furthermore, our previous study also proposed that two amino acid substitutions H56Y and K57R appeared in E. faecalis OG1RF derivative isolates resistant to Omadacycline, another Tet class of antimicrobial drugs (Lin et al, 2019).…”

In vitro activity of eravacycline and mechanisms of resistance in enterococci

“…In enterococci, the most frequent genes implicated in tetracycline resistance are tet(L), tet(M), tet(O) and tet(S) while ribosomal protection is the most common acquired mechanism of resistance [4,5]. Interestingly, TGC is not or only poorly affected by these classical tetracycline resistance determinants and the mechanism of TGC decreased susceptibility in enterococci is associated with alterations of the S10 protein of the ribosomal 30S subunit encoded by the rpsJ gene or the overexpression of tet(M) and tet(L) genes [6][7][8][9]. Even though enterococcal clinical isolates resistant to TGC have been mainly reported sporadically, some hospital outbreaks due to TGC-resistant epidemic clones have been described in Brazil [8] and Germany [9], highlighting their potential risk of spread.…”