Next Article in Journal
Effects of Maresin 1 (MaR1) on Colonic Inflammation and Gut Dysbiosis in Diet-Induced Obese Mice
Next Article in Special Issue
Association of Virulence and Antibiotic Resistance in Salmonella—Statistical and Computational Insights into a Selected Set of Clinical Isolates
Previous Article in Journal
Feature of Adhesins Produced by Human Clinical Isolates of Mycobacterium intracellulare, Mycobacterium intracellulare subsp. chimaera and Closely Related Species
Previous Article in Special Issue
An Endolysin LysSE24 by Bacteriophage LPSE1 Confers Specific Bactericidal Activity against Multidrug-Resistant Salmonella Strains
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Microorganisms
Volume 8
Issue 8
10.3390/microorganisms8081155
microorganisms-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Mechanisms of Linezolid Resistance Among Enterococci of Clinical Origin in Spain—Detection of optrA- and cfr(D)-Carrying E. faecalis

by
Laura Ruiz-Ripa
1,
Andrea T. Feßler
2,
Dennis Hanke
2,
Inga Eichhorn
2,
José Manuel Azcona-Gutiérrez
3,
Mar Olga Pérez-Moreno
4,
Cristina Seral
5,
Carmen Aspiroz
6,
Carla Andrea Alonso
3,
Luis Torres
7,
Juan-Ignacio Alós
8,
Stefan Schwarz
2 and
Carmen Torres
1,*
1
Área de Bioquímica y Biología Molecular, Universidad de La Rioja, 26006 Logroño, Spain
2
Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
3
Servicio Microbiología, Hospital San Pedro, 26006 Logroño, Spain
4
Servicio Microbiología, Hospital Verge de la Cinta, 43500 Tortosa, Spain
5
Servicio Microbiología, Hospital Universitario Lozano Blesa, 50009 Zaragoza, Spain
6
Servicio Microbiología, Hospital Royo-Villanova, 50015 Zaragoza, Spain
7
Servicio Microbiología, Hospital San Jorge, 22004 Huesca, Spain
8
Servicio Microbiología, Hospital Universitario de Getafe, 28905 Getafe, Spain
*
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(8), 1155; https://doi.org/10.3390/microorganisms8081155
Submission received: 8 July 2020 / Revised: 24 July 2020 / Accepted: 28 July 2020 / Published: 30 July 2020
(This article belongs to the Special Issue Control and Detection of Multiple Antibiotic Resistant Pathogens)
Browse Figures
Versions Notes

Abstract

:
The mechanisms of linezolid resistance among 13 E. faecalis and 6 E. faecium isolates, recovered from six Spanish hospitals during 2017–2018, were investigated. The presence of acquired linezolid resistance genes and mutations in 23S rDNA and in genes encoding for ribosomal proteins was analyzed by PCR and amplicon sequencing. Moreover, the susceptibility to 18 antimicrobial agents was investigated, and the respective molecular background was elucidated by PCR-amplicon sequencing and whole genome sequencing. The transferability of the linezolid resistance genes was evaluated by filter-mating experiments. The optrA gene was detected in all 13 E. faecalis isolates; and one optrA-positive isolate also carried the recently described cfr(D) gene. Moreover, one E. faecalis isolate displayed the nucleotide mutation G2576T in the 23S rDNA. This mutation was also present in all six E. faecium isolates. All linezolid-resistant enterococci showed a multiresistance phenotype and harbored several antimicrobial resistance genes, as well as many virulence determinants. The fexA gene was located upstream of the optrA gene in 12 of the E. faecalis isolates. Moreover, an erm(A)-like gene was located downstream of optrA in two isolates recovered from the same hospital. The optrA gene was transferable in all but one E. faecalis isolates, in all cases along with the fexA gene. The cfr(D) gene was not transferable. The presence of optrA and mutations in the 23S rDNA are the main mechanisms of linezolid resistance among E. faecalis and E. faecium, respectively. We report the first description of the cfr(D) gene in E. faecalis. The presence of the optrA and cfr(D) genes in Spanish hospitals is a public health concern.

Graphical Abstract

1. Introduction

On the one hand, enterococci, especially the species Enterococcus faecalis (Efs) and Enterococcus faecium (Efm) can be harmless colonizers of the human intestinal tract, but on the other hand, they are also one of the most important bacterial genera related to hospital-associated infections worldwide. Enterococci possess intrinsic resistance to different antimicrobial agents commonly used to treat infections caused by Gram-positive pathogens, such as cephalosporins and aminoglycosides (low-level resistance). They also have a great capacity to acquire mobile genetic elements carrying antimicrobial resistance genes, which limits the therapeutic options [1].
Linezolid was the first oxazolidinone approved for clinical use in human medicine and is considered as a last resort antimicrobial agent. It is an important treatment option for serious infections (such as nosocomial and community-acquired pneumonia, and complicated skin and soft tissue infections) caused by multiresistant Gram-positive bacteria, including vancomycin-resistant enterococci [2,3,4].
The most common mechanism of oxazolidinone resistance among clinical isolates is attributable to point mutations in the central loop of domain V of the 23S rDNA, which, in some cases, has been related to long-term treatment with linezolid. The most common nucleotide exchange described is G2576T (E. coli numbering) although other mutations have been reported (e.g., C2534T, T2500A, and G2447T) [1,5]. Moreover, different amino acid exchanges, deletions, and insertions in the ribosomal proteins L3 (rplC), L4 (rplD), and L22 (rplV)—although of lesser significance—have also been associated with decreased susceptibility to linezolid [1,3].
To date, up to five acquired linezolid resistance genes have been described among Enterococcus spp.: cfr, cfr(B), cfr(D), optrA, and poxtA. The multiresistance gene cfr, which encodes an rRNA methyltransferase [6], was first described in the plasmid pSCFS1 from Staphylococcus sciuri [7] and was thereafter reported in various Gram-positive and Gram-negative bacteria of diverse origin [8]. Besides resistance towards oxazolidinones, it also confers resistance to phenicols, lincosamides, pleuromutilins, and streptogramin A antimicrobials (PhLOPSA phenotype). In addition, variants of the cfr gene [cfr(B), cfr(D)] have been described in clinical enterococcal isolates [9,10,11]. However, the contribution of cfr-like genes to reduce the susceptibility to linezolid in enterococci is still under debate [11,12]. The optrA gene encodes an ATP-binding cassette F (ABC-F) protein [13] that confers resistance to oxazolidinones and phenicols. It was originally described among animal and human Efs and Efm isolates from China [14]. More recently, the new gene poxtA—which confers decreased susceptibility to oxazolidinones, phenicols, and tetracycline—was initially reported in a clinical methicillin-resistant Staphylococcus aureus strain. Like optrA, this gene encodes a protein of the antibiotic resistance (ARE) ABC-F family but shows only 32% amino acid identity with OptrA [15]. The poxtA gene has also been detected in Efs and Efm and is usually located in a composite transposon [15,16].
Although linezolid resistance remains uncommon (>99% of Gram-positive pathogens are still susceptible) [17], different antimicrobial surveillance studies/programs demonstrated that the number of linezolid-resistant Enterococcus (LRE) has increased during recent years [17,18,19,20]. Thus, this study aimed at determining the mechanisms of linezolid resistance and studying the molecular characteristics of LRE recovered from Spanish hospitals.

2. Materials and Methods

2.1. Bacterial Collection

A total of 13 Efs (Table 1) and six Efm isolates (Table 2) identified by matrix assisted laser desorption ionization-time of flight (MALDI-TOF) (Bruker Daltonics, Bremen, Germany) and classified as intermediate or resistant to linezolid [21], were recovered during 2017–2018 in six hospitals located in five different regions of Spain. The hospitals that took part in this study are the following: Hospital San Pedro (Logroño), Hospital Royo-Villanova (Zaragoza), Hospital Lozano Blesa (Zaragoza), Hospital Verge de la Cinta (Tortosa), Hospital San Jorge (Huesca), and Hospital Universitario de Getafe (Getafe) (Supplementary Figure S1).

2.2. Antimicrobial Resistance Phenotype

The susceptibility to penicillin, ampicillin, erythromycin, clindamycin, gentamicin, streptomycin, tetracycline, ciprofloxacin, levofloxacin, linezolid, vancomycin, teicoplanin, daptomycin, and sulfamethoxazole-trimethoprim was studied using the MicroScan® system (Beckmann Coulter, Nyon, Switzerland). The MICs to chloramphenicol, florfenicol, kanamycin, and rifampicin were determined by broth macrodilution using Staphylococcus aureus ATCC® 29213 and E. faecalis ATCC® 29212 (Manassas, VA, USA) as quality controls, and to linezolid and tedizolid by E-test® (bioMérieux, Durham, NC, USA). The antimicrobial susceptibility testing was performed, depending on the hospital, according to CLSI [21] or EUCAST [22] standards. The CLSI criteria [21] were used in the case of linezolid for all enterococcal isolates.

2.3. Mechanisms of Linezolid Resistance

All LRE were checked for the presence of the linezolid resistance genes cfr, cfr(B), cfr(D), optrA, and poxtA by PCR and confirmed by amplicon sequencing (Supplementary Table S1). Mutations in the domain V of the 23S rDNA were studied by PCR (Supplementary Table S1) and amplicon sequencing, and by digestion of the amplicon with the NheI restriction enzyme [23]. Mutations leading to amino acid changes in the ribosomal proteins L3, L4, and L22 were determined in all isolates by PCR and amplicon sequencing (Supplementary Table S1). The obtained sequences were compared with those of the linezolid-susceptible wild type strains E. faecium DO (GenBank accession number CP003583) and E. faecalis ATCC® 29212 (GenBank accession number CP008816) using the EMBOSS Needle pairwise alignment from the EBI website.

2.4. Molecular Characterization

LREfs isolates were subjected to whole genome sequencing (WGS). After a pretreatment of the enterococci with an enzyme solution (20 mg/mL lysozyme, 20 mM TRIS-HCl, pH = 8, 2 mM EDTA, 1.2% Triton) for 30 min at 37 °C, 20 µL of proteinase K and 1 µL of RNAse (2 µg/µL) were added, the samples were mixed and incubated for 2 min at room temperature. Then, the DNA extraction was carried out using the QIAamp® DNA Mini Kit (QIAGEN, Hilden, Germany) following the manufacturer’s instructions. The libraries for WGS were prepared using the Nextera XT library preparation kit (Illumina Inc., San Diego, CA, USA) according to the manufacturer’s instructions. The sequencing (2 × 300 bp paired-end sequencing in 40-fold multiplexes) was performed on the Illumina MiSeq (Illumina Inc., San Diego, CA, USA) platform. Sequences were de novo assembled using MIRA (Biomatters, Auckland, New Zealand), and annotated using RAST [24]. The nucleotide sequences were analyzed using Geneious (Biomatters, Auckland, New Zealand), and with the online tools ResFinder 3.2 [25], VirulenceFinder 2.0 [26], and MLST 2.0 [27] of the Center for Genomic Epidemiology (http://www.genomicepidemiology.org/), and ISfinder [28]. The nucleotide sequence alignments were performed using Geneious alignment with default settings and the amino acid alignments using the BLOSUM62 cost matrix. The primers used to determine the linkage of optrA-fexA are listed in the Supplementary Table S1.
LREfm isolates were characterized by PCR and subsequent amplicon sequencing, when applicable. On the basis of the antimicrobial resistance phenotype, the presence of the antimicrobial resistance genes erm(A), erm(B), erm(C), msr(C), lnu(B), lsa(A), lsa(B), lsa(E), aac(6′)-Ii, aac(6′)-Ie-aph(2″)-Ia, aph(3″), ant(6)-Ia, str, tet(K), tet(L), tet(M), tet(O), fexA, fexB, catpC194, catpC221, catpC223, catA, dfrA, dfrD, dfrG, and dfrK was tested by PCR (Supplementary Table S1). PCR and amplicon sequencing were used to detect mutations that led to amino acid changes in the GyrA and ParC proteins of fluoroquinolone-resistant isolates and in the penicillin binding protein 5 (PBP5) of those isolates that were classified as resistant or intermediate to β-lactam antibiotics (Supplementary Table S1). The obtained sequences were compared with those of the reference strain E. faecium DO. The isolates were subjected to Multilocus Sequence Typing (MLST) following standard methodology (Supplementary Table S1). The presence of the virulence genes coding for enterococcal surface protein (esp), hyaluronidase (hyl), gelatinase (gelE), adhesin to collagen (ace) from Efs, and aggregation substances (agg) were checked by PCR (Supplementary Table S1).

2.5. Clonal Relatedness

CSI Phylogeny 1.4 [29] with default parameters, was used to map the genomes of the 13 LREfs isolates against the E. faecalis ATCC® 29212 to infer a phylogeny-based analysis on the concatenated alignment of the high quality single nucleotide polymorphisms (SNPs). A maximum likelihood tree was constructed using FastTree 2.1.7 [29] (Lawrence Berkeley National Lab, CA, USA).
The clonal relatedness of Efm isolates was determined by pulsed-field gel electrophoresis (PFGE) of total DNA restricted with the enzyme SmaI, as previously described [30]. For classification of Efm as different clones, the criteria of Tenover et al. [31] were followed.

2.6. Conjugation Assays

Conjugation experiments were performed with all Efs isolates as donors to evaluate the transferability of the linezolid resistance genes by the filter-mating method [32]. E. faecalis JH2-2, which belongs to the sequence type ST8, was used as recipient strain and the selection of transconjugants was performed on BHI agar plates containing 10 mg/L florfenicol, 100 mg/L rifampicin, and 25 mg/L fusidic acid. Transconjugants were confirmed by MLST (Supplementary Table S1). The MICs of the transconjugants for different antimicrobial agents were determined by broth macrodilution using S. aureus ATCC® 29213 and E. faecalis ATCC® 29212 as quality controls, and by E-test® [21]. The respective antimicrobial resistance genotype was investigated by PCR (Supplementary Table S1).

3. Results

3.1. Mechanisms of Oxazolidinone Resistance

The characteristics of the 13 LREfs isolates are shown in Table 1. The sources of LREfs varied but eight out of 13 isolates (62%) originated from urine samples. LREfs displayed linezolid MICs between 4–16 mg/L and all of them showed tedizolid resistance (MICs 1 mg/L). The optrA gene was identified in all Efs isolates (n = 13), and the X528 isolate also harbored the cfr(D) gene. Moreover, the nucleotide point mutation G2576T within domain V of the 23S rDNA gene was detected in one optrA-positive isolate. In addition, the X523 and X524 optrA-carrying isolates showed mutations that account for the amino acid change V109A or A114V in the ribosomal protein L4, respectively (not associated to linezolid resistance). The amino acid alignment of the deduced OptrA sequences determined in this study with the wild-type OptrA protein originally described in E. faecalis E349 (GenBank accession number KP399637), revealed the presence of different variants: wild-type (n = 10), Y176D and T481P (n = 2), as well as T572P (n = 1) (Table 1). The Cfr(D) of Efs X528 showed 100% amino acid identity to that of E. faecium 15-307-1 (GenBank accession number MG707078). Neither cfr, cfr(B), nor poxtA genes were detected among the LREfs.
The six LREfm isolates were recovered from surgical wounds (n = 2), blood (n = 2), urine (n = 1), and an abscess (n = 1) (Table 2). The MICs to linezolid ranged from 4 to 32 mg/L. In the LREfm isolates, the mutation G2576T in 23S rDNA was detected in all isolates (Table 2). Moreover, the C9902 and C10269 isolates showed the amino acid change A35T in the ribosomal protein L22 (not associated to linezolid resistance). The transferable linezolid resistance genes optrA, poxtA, cfr, cfr(B), and cfr(D) were not detected among the LREfm isolates.

3.2. Molecular Characterization and Clonal Relatedness

The 13 LREfs isolates belonged to the sequence types ST480 (n = 4), ST585 (n = 3), ST6 (n = 1), ST16 (n = 1), ST21 (n = 1), and ST35 (n = 1) and to the novel sequence type ST896 (n = 2) (Table 1). The Figure S2 shows the phylogenetic relatedness of the 13 Efs isolates based on the SNPs analysis. The minimum and maximum SNPs difference detected were 11 and 16567, respectively. The isolates C9737 and X526, that belonged to the novel ST896 and were recovered from the same hospital, were those that showed the minimum SNPs difference and were grouped in one phylogenetic cluster very distantly from the rest. The isolates belonging to the ST480 and ST585 were grouped in two phylogenetic clusters in accordance with their STs (Figure S2).
In the case of the LREfm, four out of six isolates were assigned to ST117, and the others to ST17 or ST262 (Table 2). The PFGE fragment patterns revealed that all six isolates belonged to different clones (A to F) (Figure S3).

3.3. Resistance to Non-Oxazolidinone Agents

All LRE showed a multidrug resistance phenotype (resistant to three or more classes of antimicrobial agents), but were susceptible to vancomycin, teicoplanin and daptomycin, among others (Table 1 and Table 2). All LREfm showed penicillin and ampicillin resistance and exhibited several amino acid changes in the deduced sequence of the PBP5 (Table 2). All LRE displayed resistance to macrolides and lincosamides with the detection of different combinations of the resistance genes erm(A), erm(B), msr(C), lnu(B), lsa(A), and lsa(E). High-level resistance to at least one aminoglycoside was detected in 12 LREfs and in all LREfm, mediated by the resistance genes aac(6′)-aph(2″), aac(6′)-Ii, aph(3′)-III, ant(6)-Ia, and/or str. Tetracycline resistance was found in all LREfs isolates and in one LREfm isolate mediated by tet(L), tet(M), and/or tet(O) genes. The analysis of the WGS and the PCR-amplicon sequencing results revealed the presence of amino acid changes in the GyrA (S83Y or S83I) and/or ParC (S80I) proteins in fluoroquinolone-resistant isolates (11 LREfs and all LREfm). All LREfs isolates showed resistance to florfenicol (MICs 32–64 mg/L) and chloramphenicol (MICs 32–128 mg/L) and harbored the fexA gene, but were negative for the fexB gene. The catA and catpC221 genes were also detected among LREfs. All LREfm, in contrast, showed susceptibility to chloramphenicol and florfenicol. Eight LREfs and all LREfm isolates harbored the trimethoprim resistance gene dfrG and these isolates were also classified as resistant to sulfamethoxazole-trimethoprim (Table 1 and Table 2).

3.4. Virulence Profile

In total, 22 different virulence genes were detected among the LRE isolates, including those implicated in biofilm formation, bacterial adherence, and production of cytolysins, among others (Table 1 and Table 2). Ten of these virulence genes (ace, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, and tpx) were detected in all LREfs. The gene for the Enterococcus surface protein, esp, was present in one LREfs and four LREfm isolates. One LREfm isolate did not contain any of the virulence genes studied (Table 1 and Table 2).

3.5. Genetic Environment of the optrA and cfr(D) Genes

The nucleotide sequence alignment of the genetic environment of the linezolid resistance gene optrA in the 13 LREfs isolates is shown in Figure 1. The genetic context showed different degrees of nucleotide sequence identity with one another although in some isolates the optrA flanking sequences could only be partially identified due to the contig length. The region upstream of the optrA gene showed high sequence similarity in the isolates C9901 (GenBank accession number MN848142), X527, X528, C9952 (GenBank accession number MN731744), C8946, C9736, and C9884 although they were recovered from different hospitals. In the isolates C9901, X527, X528, and C9952, the tnp gene encoding an ISL3 family transposase and the impB gene which is involved in DNA repair, were detected upstream of the optrA gene. In the case of isolate X526 (GenBank accession number MN731743), one site-specific recombinase gene was identified. The fexA gene, which confers resistance to fluorinated and non-fluorinated phenicols, was detected upstream of the optrA gene in 12 isolates, although in the isolates X523 and C9737 it could not be totally revealed because of incomplete sequencing with the primers used. Moreover, an erm(A)-like gene was located downstream of the optrA gene in two isolates recovered from the same hospital. This erm(A)-like gene showed 100% nucleotide identity to that detected in the optrA gene cluster of plasmid p10-2-2 of E. faecalis strain 10-2-2 (GenBank accession number KT862775) [33]. We did not identify any rep gene or insertion sequence elements (ISs) in the genetic context of the optrA gene in the 13 LREfs investigated.
Regarding the cfr(D) gene, we could identify the presence of a guaA gene encoding a glutamine-hydrolyzing guanosine monophosphate synthase in the downstream region. Upstream of the cfr(D) gene, due to the short sequence length, we could only detect three reading frames for proteins with unknown function. The 4545 bp of the genetic environment of the cfr(D) gene revealed 100% nucleotide identity to that of plasmid 4 of E. faecium E8014 (GenBank accession number LR135354).

3.6. Transferability of the optrA and cfr(D) Genes

The optrA gene was successfully transferred by conjugation to E. faecalis JH2-2 in 12 out of the 13 isolates. The single isolate for which the optrA gene was not transferred was the isolate C8946. The optrA gene was transferred in all cases together with the fexA gene (Table 3). All transconjugants (TC) exhibited resistance to chloramphenicol (MICs 32–64 mg/L), florfenicol (MICs 32–64 mg/L), tedizolid (MICs 1 mg/L), and were classified as intermediate or resistant to linezolid (MICs 4–8 mg/L). Moreover, the transconjugants TC-C9951 and TC-C9952 showed resistance to erythromycin (MICs 128–256 mg/L) and clindamycin (MICs >256 mg/L) and harbored the erm(A)-like gene. In addition, TC-9951 was resistant to tetracycline and carried the resistance genes tet(L) and tet(O) (MIC 128 mg/L) (Table 3). The cfr(D) gene was not transferable.

4. Discussion

Since linezolid is a last resort antimicrobial agent in the treatment of serious infections caused by Gram-positive pathogens, linezolid resistance represents a great public health concern. Hence, it is very important to determine the mechanisms of this resistance in clinical isolates. The first description of LRE in Spain occurred in 2003, shortly after the introduction of this antimicrobial agent for clinical use in humans in 2001 in this country [34]. Since then, the occurrence of linezolid resistance among enterococci has increased considerably over recent years in Spain and worldwide [3,4,14,17,18,19,20,35,36]. Spreading linezolid resistance is not only a problem in the clinical setting but it has also become a concern in the livestock environment caused by the presence of transferable linezolid resistance genes [1,4,14,33]. Traditionally, mutations in domain V of 23S rDNA have been considered as the main mechanism involved in linezolid resistance among clinical isolates [1,3,4,5]. However, this study and other previous findings have demonstrated changes in the mechanisms of linezolid resistance in the clinical setting [14,18,19,20,36,37,38,39,40,41,42].
In this work, linezolid resistance was detected in the species E. faecalis and E. faecium. This could be expected since they are the most common enterococcal species related to hospital-associated infections [1,4,5]. However, in the clinical setting, previous studies reported the presence of linezolid resistance in other enterococcal species such as E. thailandicus, E. gallinarum, and E. avium [31,34]. The optrA and cfr(D) genes were the only linezolid resistance genes detected in our study, although the cfr, cfr(B), and poxtA genes have been previously detected in Efs and/or Efm of clinical origin [10,16,41]. In Spain, a recent study conducted among clinical LRE of different hospitals revealed a high prevalence of the optrA gene among LREfs isolates and the presence of two poxtA-carrying isolates, while cfr-like genes were absent [37].
The optrA gene is widely spread among enterococci in different countries, but especially present in China [14,18,19,38,39,40,41,42]. In the case of Spain, more than the 80% of LREfs isolates recovered from Spanish hospitals during 2015–2018 carried the optrA gene [37]. Generally, the optrA gene confers relatively low MICs to linezolid (4–16 mg/L) [14,17,18,19,35,36,38,39,40,41,42], which is in agreement with our results. So far, numerous variants of the optrA gene have been described in Efs and Efm from humans, animals, and food items and some of these variants seemed to be associated with higher or lower linezolid MICs [43,44]. In this study, the amino acid changes Y176D and T481P in OptrA, DP (aspartic acid-proline) variant, were detected in two Efs isolates. This variant has already been described in clinical isolates from China [18,38,43,44]. However, one isolate showed a novel amino acid change in OptrA at position T572P.
In this study, we report, to the best of our knowledge, the first description of the cfr(D) gene in the species E. faecalis. The Cfr(D) shares 64% amino acid identity to Cfr, but there is controversy about its contribution to linezolid resistance, as it confers a PhLOPSA resistance phenotype when expressed in Escherichia coli but not in Efs or Efm [11]. The cfr(D) gene has only been detected in clinical Efm isolates from France and Australia, and, as the isolate of this study, they co-harbored the optrA gene [11,45].
The G2576T mutation in the 23S rDNA is the main mechanism implicated in linezolid resistance of Efm isolates investigated in this study, which is in accordance with previous findings [3,19,35,37]. A low rate of amino acid changes in the ribosomal proteins has been observed among LRE in this study, which is consistent with previous studies which observed that these are more commonly found among clinical coagulase-negative staphylococci than in S. aureus or enterococci [3]. As far as we know, the amino acid changes detected in the ribosomal proteins L4 (V109A and A114V) and L22 (A35T) in this study have not been reported in LRE. Different amino acid changes in these ribosomal proteins have been previously described in linezolid-susceptible strains [3,42], so it is questionable whether the mutations detected in this study are associated with decreased susceptibility to linezolid; for this reason, these amino acid changes have not been included in Table 1 and Table 2.
In this study, LREfs isolates belonged to seven different STs, but the predominance (eight out of 13 isolates) of isolates typed as ST480, ST585, or ST16 is in accordance with prior studies among clinical optrA-positive LREfs in Spain [37] and worldwide [14,20,40]. However, we did not detect the ST116, which is also frequently found among optrA-positive Efs of different origins [14,40]. Regarding Efm, all isolates were assigned to the hospital-associated subclade A1, which is the most important genogroup among Efm related to clinical infections and responsible for hospital outbreaks worldwide [46]. Efm isolates belonging to this subclade recovered from both humans and livestock have been previously reported as carrying the optrA gene [14,37].
The multiresistance phenotypes and genotypes observed are commonly seen among LRE [35,40]. Fortunately, all isolates in our study were susceptible to daptomycin and vancomycin, which would be considered as alternative antimicrobial options. The resistance rates to macrolides and lincosamides (100%), as well as fluoroquinolones (89%), detected in this study were very high, which is in accordance with previous studies among clinical LRE [35,40]. As reported by other authors for clinical LRE [30,36], the examined isolates harbored various virulence genes of great importance for the pathogenesis of enterococci. Many of these virulence determinants, such as the collagen binding protein Ace and the pilus protein EbpA, are shared by all isolates and seem to be generally widespread among LREfs of clinical origin [36,40]. The esp gene is one of the most important enterococcal virulence genes, which contributes to the colonization and persistence of enterococcal infections and is frequently detected among isolates recovered from human infections. Moreover, four out of six LREfm isolates carried the virulence gene esp, which is known to be located on a putative pathogenicity island that is present in the majority of Efm isolates belonging to the subclade A1 [46].
The optrA gene was confirmed to have a great capacity to disseminate among different Gram-positive bacteria [14]. It is often located on conjugative plasmids that commonly carry other antimicrobial resistance genes and is frequently found in combination with the fexA gene [14,33,37,44]. Likewise, when optrA is located in the chromosomal DNA, the fexA gene is often identified in its genetic environment [20,23,37,44]. In 12 out of 13 LREfs isolates of our study, the fexA gene was located upstream of optrA. The remaining Efs isolate also carried the fexA gene but the sequenced genetic environment of optrA did not cover the possible presence or absence of fexA. When located on plasmids, the insertion sequence IS1216E was frequently identified upstream and/or downstream of the optrA gene [33,36,37,44], however, we did not detect this IS1216E element. Moreover, we also did not detect the putative transcriptional regulator araC commonly located just upstream the optrA gene [33,43,44] when located in the chromosomal DNA. The impB and tnp genes, both detected in four LREfs isolates, are commonly found as part of the optrA gene cluster of different plasmids, such as in E. faecalis strain XY17 plasmid pXY17 (GenBank accession number KT862780) [33]. The antimicrobial susceptibility of the transconjugants is in accordance with the resistance genotype detected. The transferability of the optrA gene together with other antimicrobial resistance genes in 12 LREfs isolates suggests its possible plasmid location; however, additional experiments would be required to confirm this point. Besides optrA, the erm(A)-like gene was detected in the transconjugants TC-9951 and TC-9952, which was expected, since it was located downstream of optrA in both isolates. The tet(L) and tet(O) genes were transferred together with optrA, fexA, and the erm(A)-like gene in the case of TC-C9951. These tetracycline resistance genes were detected on the same contig, which was identical—as well as the contigs containing optrA, fexA, and erm(A) genes—to the respective parts of Enterococcaceae strain E508 plasmid pE508 (GenBank accession number MK425645). This observation suggests that these five resistance genes could be located on the same plasmid.
Although the co-transferability of the optrA and cfr(D) genes by conjugation has been previously described in the species E. faecium [11], in this work the cfr(D) gene was not transferable.

5. Conclusions

In conclusion, we have shown that the main mechanism involved in linezolid resistance among clinical LREfs is conferred by the optrA gene, whereas in LREfm the presence of mutations in the domain V of the 23S rDNA is the major cause for linezolid resistance. Moreover, we report the first detection of the cfr(D) gene in Efs. Some of the most important virulence factors of Enterococcus spp. were detected among LRE, which, if coupled with the multidrug resistance phenotype, is a public health concern.

Supplementary Materials

The following are available online at https://www.mdpi.com/2076-2607/8/8/1155/s1. Table S1: Primer pairs used for the molecular typing, and the detection of antimicrobial resistance and virulence genes. Figure S1: Location of the six Spanish hospitals that took part in this study. Figure S2: Phylogenetic relatedness of the 13 E. faecalis isolates based on single nucleotide polymorphism (SNP) analysis performed using CSI Phylogeny. Figure S3: Pulsed field gel electrophoresis (PFGE) of whole-cell DNA of E. faecium isolates after digestion with the enzyme SmaI.

Author Contributions

C.T. and S.S. designed the study, performed its supervision, and obtained the funding; L.R.-R., A.T.F., D.H., and I.E. performed the experiments and analyzed the data. J.M.A.-G., M.O.P.-M., C.S., C.A., C.A.A., L.T., and J.-I.A. isolated the clinical strains. All authors drafted the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This work was partially supported by project SAF2016-76571-R from the Agencia Estatal de Investigación (AEI) of Spain and the Fondo Europeo de Desarrollo Regional (FEDER) of EU and the Federal Ministry of Education and Research (BMBF) under project number 01KI1727D as part of the Research Network Zoonotic Infectious Diseases. Laura Ruiz-Ripa has a pre-doctoral fellowship from the Universidad de La Rioja.

Acknowledgments

Part of this work was presented at the 28th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Madrid, April 2018.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Torres, C.; Alonso, C.A.; Ruiz-Ripa, L.; León-Sampedro, R.; Del Campo, R.; Coque, T.M. Antimicrobial resistance in Enterococcus spp. of animal origin. Microbiol. Spectr. 2018, 6, 185–227. [Google Scholar] [CrossRef]
  2. Batts, D.H. Linezolid—A new option for treating gram-positive infections. Oncology 2000, 14, 23–29. [Google Scholar] [PubMed]
  3. Mendes, R.E.; Deshpande, L.M.; Jones, R.N. Linezolid update: Stable in vitro activity following more than a decade of clinical use and summary of associated resistance mechanisms. Drug Resist. Updat. 2014, 17, 1–12. [Google Scholar] [CrossRef] [PubMed]
  4. Bi, R.; Qin, T.; Fan, W.; Ma, P.; Gu, B. The emerging problem of linezolid-resistant enterococci. J. Glob. Antimicrob. Resist. 2018, 13, 11–19. [Google Scholar] [CrossRef]
  5. Miller, W.R.; Munita, J.M.; Arias, C.A. Mechanisms of antibiotic resistance in enterococci. Expert Rev. Anti Infect. Ther. 2014, 12, 1221–1236. [Google Scholar] [CrossRef]
  6. Kehrenberg, C.; Schwarz, S.; Jacobsen, L.; Hansen, L.H.; Vester, B. A new mechanism for chloramphenicol, florfenicol and clindamycin resistance: Methylation of 23S ribosomal RNA at A2503. Mol. Microbiol. 2005, 57, 1064–1073. [Google Scholar] [CrossRef]
  7. Schwarz, S.; Werckenthin, C.; Kehrenberg, C. Identification of a plasmid-borne chloramphenicol-florfenicol resistance gene in Staphylococcus sciuri. Antimicrob. Agents Chemother. 2000, 44, 2530–2533. [Google Scholar] [CrossRef] [Green Version]
  8. Shen, J.; Wang, Y.; Schwarz, S. Presence and dissemination of the multiresistance gene cfr in Gram-positive and Gram-negative bacteria. J. Antimicrob. Chemother. 2013, 68, 1697–1706. [Google Scholar] [CrossRef]
  9. Deshpande, L.M.; Ashcraft, D.S.; Kahn, H.P.; Pankey, G.; Jones, R.N.; Farrell, D.J.; Mendes, R.E. Detection of a new cfr-like gene, cfr (B), in Enterococcus faecium isolates recovered from human specimens in the United States as part of the SENTRY Antimicrobial Surveillance Program. Antimicrob. Agents Chemother. 2015, 59, 6256–6261. [Google Scholar] [CrossRef] [Green Version]
  10. Kuroda, M.; Sekizuka, T.; Matsui, H.; Suzuki, K.; Seki, H.; Saito, M.; Hanaki, H. Complete genome sequence and characterization of linezolid-resistant Enterococcus faecalis clinical isolate KUB3006 carrying a cfr (B)-transposon on its chromosome and optrA-plasmid. Front. Microbiol. 2018, 9, 2576. [Google Scholar] [CrossRef] [Green Version]
  11. Guerin, F.; Sassi, M.; Dejoies, L.; Zouari, A.; Schutz, S.; Potrel, S.; Auzou, M.; Collet, A.; Lecointe, D.; Auger, G.; et al. Molecular and functional analysis of the novel cfr (D) linezolid resistance gene identified in Enterococcus faecium. J. Antimicrob. Chemother. 2020, 75, 1699–1703. [Google Scholar] [CrossRef] [PubMed]
  12. Bender, J.K.; Fleige, C.; Klare, I.; Fiedler, S.; Mischnik, A.; Mutters, N.T.; Dingle, K.E.; Werner, G. Detection of a cfr(B) variant in German Enterococcus faecium clinical isolates and the impact on linezolid resistance in Enterococcus spp. PLoS ONE 2016, 11, e0167042. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  13. Sharkey, L.K.; Edwards, T.A.; O’Neill, A.J. ABC-F proteins mediate antibiotic resistance through ribosomal protection. mBio 2016, 7, e01975. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  14. Wang, Y.; Lv, Y.; Cai, J.; Schwarz, S.; Cui, L.; Hun, Z.; Zhang, R.; Li, J.; Zhao, Q.; He, T.; et al. A novel gene, optrA, that confers transferable resistance to oxazolidinones and phenicols and its presence in Enterococcus faecalis and Enterococcus faecium of human and animal origin. J. Antimicrob. Chemother. 2015, 70, 2182–2190. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  15. Antonelli, A.; D’Andrea, M.M.; Brenciani, A.; Galeotti, C.L.; Morroni, G.; Pollini, S.; Varaldo, P.E.; Rossolini, G.M. Characterization of poxtA, a novel phenicol-oxazolidinone-tetracycline resistance gene from an MRSA of clinical origin. J. Antimicrob. Chemother. 2018, 73, 1763–1769. [Google Scholar] [CrossRef] [Green Version]
  16. Papagiannitsis, C.C.; Tsilipounidaki, K.; Malli, E.; Petinaki, E. Detection in Greece of a clinical Enterococcus faecium isolate carrying the novel oxazolidinone resistance gene poxtA. J. Antimicrob. Chemother. 2019, 74, 2461–2462. [Google Scholar] [CrossRef]
  17. Mendes, R.E.; Deshpande, L.; Streit, J.M.; Sader, H.S.; Castanheira, M.; Hogan, P.A.; Flamm, R.K. ZAAPS programme results for 2016: An activity and spectrum analysis of linezolid using clinical isolates from medical centres in 42 countries. J. Antimicrob. Chemother. 2018, 73, 1880–1887. [Google Scholar] [CrossRef] [Green Version]
  18. Cui, L.; Wang, Y.; Lv, Y.; Wang, S.; Song, Y.; Li, Y.; Liu, J.; Xue, F.; Yang, W.; Zhang, J. Nationwide surveillance of novel oxazolidinone resistance gene optrA in Enterococcus isolates in China from 2004 to 2014. Antimicrob. Agents Chemother. 2016, 60, 7490–7493. [Google Scholar] [CrossRef] [Green Version]
  19. Deshpande, L.M.; Castanheira, M.; Flamm, R.K.; Mendes, R.E. Evolving oxazolidinone resistance mechanisms in a worldwide collection of enterococcal clinical isolates: Results from the SENTRY Antimicrobial Surveillance Program. J. Antimicrob. Chemother. 2018, 73, 2314–2322. [Google Scholar] [CrossRef] [Green Version]
  20. Sassi, M.; Guérin, F.; Zouari, A.; Beyrouthy, R.; Auzou, M.; Fines-Guyon, M.; Potrel, S.; Dejoies, L.; Collet, A.; Boukthir, S.; et al. Emergence of optrA-mediated linezolid resistance in enterococci from France, 2006–2016. J. Antimicrob. Chemother. 2019, 74, 1469–1472. [Google Scholar] [CrossRef]
  21. CLSI. Performance Standards for Antimicrobial Susceptibility Testing, CLSI Supplement M100, 28th ed.; Clinical and Laboratory Standards Institute: Wayne, PA, USA, 2018. [Google Scholar]
  22. EUCAST. Breakpoint Tables for Interpretation of MICs and Zone Diameters. Version, 8th ed.; The European Committee on Antimicrobial Susceptibility Testing: Växjö, Sweden, 2018. [Google Scholar]
  23. Hong, T.; Li, X.; Wang, J.; Sloan, C.; Cicogna, C. Sequential linezolid-resistant Staphylococcus epidermidis isolates with G2576T mutation. J. Clin. Microbiol. 2007, 45, 3277–3280. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  24. Aziz, R.K.; Bartels, D.; Best, A.A.; DeJongh, M.; Disz, T.; Edwards, R.A.; Formsma, K.; Gerdes, S.; Glass, E.M.; Kubal, M.; et al. The RAST Server: Rapid annotations using subsystems technology. BMC Genom. 2008, 9, 75. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  25. Zankari, E.; Hasman, H.; Cosentino, S.; Vestergaard, M.; Rasmussen, S.; Lund, O.; Aarestrup, F.M.; Larsen, M.V. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 2012, 67, 2640–2644. [Google Scholar] [CrossRef] [PubMed]
  26. Joensen, K.G.; Scheutz, F.; Lund, O.; Hasman, H.; Kaas, R.S.; Nielsen, E.M.; Aarestrup, F.M. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J. Clin. Micobiol. 2014, 52, 1501–1510. [Google Scholar] [CrossRef] [Green Version]
  27. Larsen, M.V.; Cosentino, S.; Rasmussen, S.; Friis, C.; Hasman, H.; Marvig, R.L.; Jelsbak, L.; Sicheritz-Pontén, T.; Ussery, D.W.; Aarestrup, F.M.; et al. Multilocus sequence typing of total genome sequenced bacteria. J. Clin. Micobiol. 2012, 50, 1355–1361. [Google Scholar] [CrossRef] [Green Version]
  28. Siguier, P.; Perochon, J.; Lestrade, L.; Mahillon, J.; Chandler, M. ISfinder: The Reference Centre for Bacterial Insertion Sequences. Nucleic Acids Res. 2006, 34, D32–D36. [Google Scholar] [CrossRef] [Green Version]
  29. Kaas, R.S.; Leekitcharoenphon, P.; Aarestrup, F.M.; Lund, O. Solving the problem of comparing whole bacterial genomes across different sequencing platforms. PLoS ONE 2014, 9, e104984. [Google Scholar] [CrossRef] [Green Version]
  30. López, M.; Alvarez-Martínez, M.J.; Marco, F.; Torres, C. Glycopeptide-resistant Enterococcus faecium. Analysis of the resistance genotype, virulence and genetic Lines. Enferm. Infecc. Microbiol Clin. 2013, 31, 10–14. [Google Scholar] [CrossRef]
  31. Tenover, F.C.; Arbet, R.D.; Goering, R.V.; Mickelsen, P.A.; Murray, B.E.; Persing, D.H.; Swaminathan, B. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: Criteria for bacterial strain typing. J. Clin. Microbiol. 1995, 33, 2233–2239. [Google Scholar] [CrossRef] [Green Version]
  32. Dunny, G.M.; Craig, R.A.; Carron, R.L.; Clewell, D.B. Plasmid transfer in Streptococcus faecalis: Production of multiple sex pheromones by recipients. Plasmid 1979, 2, 454–465. [Google Scholar] [CrossRef] [Green Version]
  33. He, T.; Shen, Y.; Schwarz, S.; Cai, J.; Lv, Y.; Li, J.; Feßler, A.T.; Zhang, R.; Wu, C.; Shen, J.; et al. Genetic environment of the transferable oxazolidinone/phenicol resistance gene optrA in Enterococcus faecalis isolates of human and animal origin. J. Antimicrob. Chemother. 2016, 71, 1466–1473. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  34. Sánchez-Gómez, J.C.; Fraile-Malmierca, F.; Valverdé-Romero, E.D.; Sánchez, M.; García-Rodríguez, J.A.; García-Sánchez, J.E. Linezolid-resistant Enterococcus faecalis: First report in Spain. J. Chemother. 2006, 18, 440–442. [Google Scholar] [CrossRef]
  35. Gawryszewska, I.; Żabicka, D.; Hryniewicz, W.; Sadowy, E. Linezolid-resistant enterococci in Polish hospitals: Species, clonality and determinants of linezolid resistance. Eur. J. Clin. Microbiol. Infect. Dis. 2017, 36, 1279–1286. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  36. Cámara, J.; Camoez, M.; Tubau, F.; Pujol, M.; Ayats, J.; Ardanuy, C.; Domínguez, M.Á. Detection of the novel optrA gene among linezolid-resistant enterococci in Barcelona, Spain. Microb. Drug Resist. 2019, 25, 87–93. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  37. Moure, Z.; Lara, N.; Marín, M.; Sola-Campoy, P.J.; Bautista, V.; Gómez-Bertomeu, F.; Gómez-Dominguez, C.; Pérez-Vázquez, M.; Aracil, B.; Campos, J.; et al. Interregional spread in Spain of linezolid-resistant Enterococcus spp. isolates carrying the optrA and poxtA genes. Int. J. Antimicrob. Agents 2020, 21, 105977. [Google Scholar] [CrossRef]
  38. Cai, J.; Wang, Y.; Schwarz, S.; Lv, H.; Li, Y.; Liao, K.; Yu, S.; Zhao, K.; Gu, D.; Wang, X.; et al. Enterococcal isolates carrying the novel oxazolidinone resistance gene optrA from hospitals in Zhejiang, Guangdong, and Henan, China, 2010–2014. Clin. Microbiol. Infect. 2015, 21, 1095.e1–1095.e4. [Google Scholar] [CrossRef] [Green Version]
  39. Lee, S.M.; Huh, H.J.; Song, D.J.; Shim, H.J.; Park, K.S.; Kang, C.I.; Ki, C.S.; Lee, N.Y. Resistance mechanisms of linezolid-nonsusceptible enterococci in Korea: Low rate of 23S rRNA mutations in Enterococcus faecium. J. Med. Microbiol. 2017, 66, 1730–1735. [Google Scholar] [CrossRef]
  40. Chen, M.; Pan, H.; Lou, Y.; Wu, Z.; Zhang, J.; Huang, Y.; Yu, W.; Qiu, Y. Epidemiological characteristics and genetic structure of linezolid-resistant Enterococcus faecalis. Infect. Drug Resist. 2018, 11, 2397–2409. [Google Scholar] [CrossRef] [Green Version]
  41. Zhang, Y.; Dong, G.; Li, J.; Chen, L.; Liu, H.; Bi, W.; Lu, H.; Zhou, T. A high incidence and coexistence of multiresistance genes cfr and optrA among linezolid-resistant enterococci isolated from a teaching hospital in Wenzhou, China. Eur. J. Clin. Microbiol. Infect. Dis. 2018, 37, 1441–1448. [Google Scholar] [CrossRef]
  42. Hua, R.; Xia, Y.; Wu, W.; Yang, M.; Yan, J. Molecular epidemiology and mechanisms of 43 low-level linezolid-resistant Enterococcus faecalis strains in Chongqing, China. Ann. Lab. Med. 2019, 39, 36–42. [Google Scholar] [CrossRef] [Green Version]
  43. Cai, J.; Schwarz, S.; Chi, D.; Wang, Z.; Zhang, R.; Wang, Y. Faecal carriage of optrA-positive enterococci in asymptomatic healthy humans in Hangzhou, China. Clin. Microbiol. Infect. 2019, 25, 630.e1–630.e6. [Google Scholar] [CrossRef] [PubMed]
  44. Wu, Y.; Fan, R.; Wang, Y.; Lei, L.; Feßler, A.T.; Wang, Z.; Wu, C.; Schwarz, S.; Wang, Y. Analysis of combined resistance to oxazolidinones and phenicols among bacteria from dogs fed with raw meat/vegetables and the respective food items. Sci. Rep. 2019, 9, 1–10. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  45. Pang, S.; Boan, P.; Lee, T.; Gangatharan, S.; Tan, S.J.; Daley, D.; Lee, Y.T.; Coombs, G.W. Linezolid-resistant ST872 Enteroccocus faecium harbouring optrA and cfr (D) oxazolidinone resistance genes. Int. J. Antimicrob. Agents 2020, 55, 105831. [Google Scholar] [CrossRef]
  46. Lee, T.; Pang, S.; Abraham, S.; Coombs, G.W. Antimicrobial-resistant CC17 Enterococcus faecium: The past, the present and the future. J. Glob. Antimicrob. Resist. 2019, 16, 36–47. [Google Scholar] [CrossRef] [PubMed] [Green Version]
Microorganisms 08 01155 g001 550
Figure 1. BLAST comparison of the genetic environment of the optrA gene in the 13 clinical LREfs isolates. Coding sequences (CDS) are colored according to their function: red, antimicrobial resistance; blue, recombination and transposition; orange, known function; grey, unknown function. The percentage of identity and scale bar legends are shown on the right.
Figure 1. BLAST comparison of the genetic environment of the optrA gene in the 13 clinical LREfs isolates. Coding sequences (CDS) are colored according to their function: red, antimicrobial resistance; blue, recombination and transposition; orange, known function; grey, unknown function. The percentage of identity and scale bar legends are shown on the right.
Microorganisms 08 01155 g001
Table
Table 1. Characterization of 13 clinical linezolid-resistant E. faecalis isolates investigated in this study.
Table 1. Characterization of 13 clinical linezolid-resistant E. faecalis isolates investigated in this study.
IsolateHospital 1YearType of SampleMLST/CCLinezolid MIC (mg/L)Mechanisms of Linezolid Resistance 2Antimicrobial Resistance Phenotype 3Antimicrobial Resistance GenotypeVirulence Genes
C9884HSJ2017UrineST585/CC416optrAERY-CLI-GEN-KAN-STR-TET-CHL-FFC-LZD-TDZ-SXT-CIP 4-LEVerm(B), lnu(B), lsa(A), lsa(E), aac(6′)-Ie-aph(2″)-Ia, aph(3″)-III, ant(6)-Ia, str, tet(M), tet(L), optrA, fexA, dfrGgelE, ace, agg, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, ebpC, fsrB, tpx
C8946HUG2017Leg wound exudateST48016optrAERY-CLI-GEN-KAN-STR-TET-CHL-FFC-LZD-TDZ-SXT-CIP 4,5-LEVerm(B), lnu(B), lsa(A), lsa(E), aac(6′)-Ie-aph(2″)-Ia, aph(3″)-III, ant(6)-Ia, tet(M), tet(L), optrA, fexA, dfrGhylA, ace, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, ebpB, tpx
C9901HUG2017UrineST21/CC2116optrAERY-CLI-KAN-STR-TET-CHL-FFC-LZD-TDZerm(B), lnu(B), lsa(A), lsa(E), aph(3″)-III, ant(6)-Ia, tet(M), tet(L), optrA, fexAgelE, hylA, hylB, ace, agg, cylL, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, ebpC, fsrB, tpx
C9951HSP2017UrineST168optrA (Y176D, T481P); 23S rDNA (G2576T)ERY-CLI-GEN-KAN-STR-TET-CHL-FFC-LZD-TDZ-SXTerm(A)-like, erm(B), lnu(B), lsa(A), lsa(E), aac(6′)-Ie-aph(2″)-Ia, aph(3″)-III, ant(6)-Ia, tet(M), tet(L), tet(O), optrA, fexA, dfrGace, agg, cylA, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, ebpC, tpx
C9952HSP2017UrineST358optrA (Y176D, T481P)ERY-CLI-GEN-KAN-STR-TET
CHL-FFC-LZD-TDZ-CIP 4,6-LEV		erm(A)-like, erm(B), lnu(B), lsa(A), lsa(E), aac(6′)-Ie-aph(2″)-Ia, aph(3″)-III, ant(6)-Ia, tet(M), tet(L), optrA, fexAgelE, hylB, ace, cylA, cylL, cylM, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, ebpB, fsrB, tpx
C9736HVC2017UrineST585/CC416optrAERY-CLI-GEN-KAN-STR-TET-CHL-FFC-LZD-TDZ-SXT-CIP 4-LEVerm(B), lnu(B), lsa(A), lsa(E), aac(6′)-Ie-aph(2″)-Ia, aph(3″)-III, ant(6)-Ia, str, tet(M), tet(L), optrA, fexA, dfrGgelE, ace, agg, cylL, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, ebpC, fsrB, tpx
C9737HVC2017UrineST89616optrAERY-CLI-KAN-STR-TET-CHL-FFC-LZD-TDZ-CIP 4,5-LEVerm(B), lnu(B), lsa(A), lsa(E), aph(3″)-III, ant(6)-Ia, tet(M), optrA, fexA, catpC221esp, gelE, hylA, hylB, ace, agg, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, ebpB, tpx
X523HVC2018Otic exudateST4808optrA (T572P)ERY-CLI-TET-CHL-FFC-LZD-TDZ-SXT-CIP 4,5-LEVlsa(A), lsa(E), tet(M), tet(L), optrA, fexA, dfrGhylA, ace, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, ebpB, tpx
X524HVC2018UrineST4808optrAERY-CLI-GEN-KAN-STR-TET-CHL-FFC-LZD-TDZ-SXT-CIP 4,5-LEVerm(B), lsa(A), lsa(E), aac(6′)-Ie-aph(2″)-Ia, aph(3″)-III, ant(6)-Ia, tet(M), tet(L), optrA, fexA, dfrGhylA, ace, agg, cylL, cylM, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, ebpB, tpx
X525HVC2018UlcerST585/CC48optrAERY-CLI-GEN-KAN-STR-TET-CHL-FFC-LZD-TDZ-SXT-CIP 4-LEVerm(B), lnu(B), lsa(A), lsa(E), aac(6′)-Ie-aph(2″)-Ia, aph(3″)-III, ant(6)-Ia, str, tet(M), tet(L), optrA, fexA, catA, dfrGgelE, ace, agg, cylL, efaAfs, elrA, srtA, cob, cad, camE, ebpA, ebpC, fsrB, tpx
X526HVC2018UrineST8964optrAERY-CLI-KAN-STR-TET-CHL-FFC-LZD-TDZ-CIP 4,5-LEVerm(B), lnu(B), lsa(A), lsa(E), aph(3″)-III, ant(6)-Ia, tet(M), optrA, fexA, catpC221gelE, hylA, hylB, ace, cylA, cylL, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, ebpB, fsrB, tpx
X527HVC2018UlcerST6/CC216optrAERY-CLI-GEN-KAN-STR-TET-CHL-FFC-LZD-TDZ-CIP 4,5-LEVerm(B), lsa(A), aac(6′)-aph(2″), aph(3″)-III, ant(6)-Ia, tet(M), optrA, fexAgelE, hylA, hylB, ace, agg, efaAfs, elrA, srtA, cob, cad, camE, ebpA, ebpB, ebpC, fsrB, tpx
X528HVC2018AbscessST48016optrA; cfr(D)ERY-CLI-KAN-STR-TET-CHL-FFC-LZD-TDZ-SXT-CIP 4,5-LEVerm(B), lsa(A), aph(3′’)-III, ant(6)-Ia, tet(M), tet(L), cfr(D), optrA, fexA, dfrGhylA, ace, agg, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, ebpB, tpx
1 HSJ, Hospital San Jorge; HUG, Hospital Universitario de Getafe; HSP, Hospital San Pedro; HVC, Hospital Verge de la Cinta; 2 In brackets the mutations or amino acid changes detected;3 ERY, erythromycin; CLI, clindamycin; GEN, gentamicin; KAN, kanamycin; STR, streptomycin; TET, tetracycline; CIP, ciprofloxacin; LEV, levofloxacin; CHL, chloramphenicol; FFC, florfenicol; LZD, linezolid; TDZ, tedizolid; SXT, sulfamethoxazole-trimethoprim-; 4 Amino acid change S80I in the ParC protein; 5 Amino acid change S83Y in the GyrA protein; 6 Amino acid change S83I in the GyrA protein.
Table
Table 2. Characterization of the six clinical linezolid-resistant E. faecium isolates investigated in this study.
Table 2. Characterization of the six clinical linezolid-resistant E. faecium isolates investigated in this study.
IsolateHospital 1YearType of SamplePFGE PatternMLSTLZD MIC (mg/L)Mechanisms of LZD Resistance 2Antimicrobial Resistance Phenotype 3Antimicrobial Resistance Genotype 4Virulence Genes
C9902HLB2017AbscessAST17823S rDNA (G2576T)PEN 5-AMP-ERY-CLI-KAN-STR-CIP 8-LEV-LZD-SXTerm(B), msrC, aac(6′)-Ii, aph(3″)-III, ant(6)-Ia, dfrGesp, hyl
C9903HLB2017Surgical woundBST2621623S rDNA (G2576T)PEN 5-AMP-ERY-CLI-GEN-KAN-STR-TET-CIP 8-LEV-LZD-SXTmsr(C), lsa(E), aac(6′)-Ie-aph(2″)-Ia, aac(6′)-Ii, ant(6)-Ia, tet(M), tet(L), dfrG
C10262HLB2017BloodCST1173223S rDNA (G2576T)PEN 6-AMP-ERY-CLI-KAN-STR-CIP 8-LEV-LZD-SXTerm(B), msr(C), aac(6′)-Ii, aph(3″)-III, ant(6)-Ia, dfrGesp, hyl
C9950HSP2017BloodDST117423S rDNA (G2576T)PEN 7-AMP-ERY-CLI-KAN-STR-CIP 8-LEV-LZD-SXTerm(B), msr(C), aac(6′)-Ii, aph(3″)-III, ant(6)-Ia, dfrGesp, hyl
C9953HSP2017UrineEST1171623S rDNA (G2576T)PEN I,5-AMP-ERY-CLI-KAN-STR-CIP 8-LEV-LZD-SXTerm(B), msr(C), aac(6′)-Ii, aph(3″)-III, ant(6)-Ia, dfrGhyl
C10269HRV2017Surgical woundFST1171623S rDNA (G2576T)PEN 6-AMP-ERY-CLI-KAN-STR-CIP 8-LEV-LZD-SXTerm(B), msr(C), aac(6′)-Ii, aph(3″)-III, ant(6)-Ia, dfrGesp, hyl
1 HLB, Hospital Lozano Blesa; HSP, Hospital San Pedro; HRV, Hospital Royo Villanova;2 In brackets the mutations detected; 3 PEN, penicillin; AMP, ampicillin; ERY, erythromycin; CLI, clindamycin; GEN, gentamicin; KAN, kanamycin; STR, streptomycin; TET, tetracycline; CIP, ciprofloxacin; LEV, levofloxacin; LZD, linezolid; SXT, trimethoprim-sulfamethoxazole. I, intermediate; 4 The msrC and aac(6′)-Ii resistance genes are intrinsic to E. faecium; 5 Amino acid changes detected in the penicillin binding protein 5 (PBP5): G66E, A68T, E85D, E100Q, K144Q, T172A, L177I, D204G, A216S, T324A, V462A, insertion 466S, M485A, N496K, A499T, E525D, N546T, A558T, G582S, E629V, K632Q, P642L, D644N, and P667S; 6 Amino acid changes detected in the PBP5: G66E, A68T, E85D, E100Q, K144Q, T172A, L177I, D204G, A216S, T324A, insertion 466S, M485A, N496K, F497I, A499T, E525D, N546T, A558T, G582S, E629V, K632Q, P642L, D644N, and P667S; 7 Amino acid changes detected in the PBP5: G66E, E85D, E100Q, K144Q, T172A, L177I, D204G, A216S, T324A, V462A, insertion 466S, M485A, N496K, A499T, E525D, N546T, A558T, G582S, E629V, K632Q, P642L, D644N, and P667S; 8 Amino acid change S80I and S83Y in the ParC and the GyrA proteins, respectively.
Table
Table 3. Minimum inhibitory concentrations (MICs) of the recipient E. faecalis JH2-2, the E. faecalis donor strains, and the respective transconjugants.
Table 3. Minimum inhibitory concentrations (MICs) of the recipient E. faecalis JH2-2, the E. faecalis donor strains, and the respective transconjugants.
StrainGenotypeMIC (mg/L) 1
ERYCLITETCHLFFCLZDTDZ
E. faecalisJH2-2 (recipient)-120.1254421
E. faecalisC9884erm(B), lnu(B), lsa(A), lsa(E), aac(6′)-aph(2″), aph(3″)-III, ant(6)-Ia, str, tet(M), tet(L), optrA, fexA, dfrG>2562561286464161
E. faecalisTC-C9884optrA, fexA120.125326481
E. faecalisC9901erm(B), lnu(B), lsa(A), lsa(E), aph(3″)-III, ant(6)-Ia, tet(M), tet(L), optrA, fexA>256>256>2563264161
E. faecalisTC-C9901optrA, fexA120.125326441
E. faecalisC9951erm(A)-like, erm(B), lnu(B), lsa(A), lsa(E), aac(6′)-aph(2″), aph(3″)-III, ant(6)-Ia, tet(M), tet(L), tet(O), optrA, fexA, dfrG>256>256128646481
E. faecalisTC-C9951erm(A)-like, tet(L), tet(O), optrA, fexA256>256128646441
E. faecalisC9952erm(A)-like, erm(B), lnu(B), lsa(A), lsa(E), aac(6′)-aph(2″), aph(3″)-III, ant(6)-Ia, tet(M), tet(L), optrA, fexA256>256>256326481
E. faecalisTC-C9952erm(A)-like, optrA, fexA128>2560.125326441
E. faecalisC9736erm(B), lnu(B), lsa(A), lsa(E), aac(6′)-aph(2″), aph(3″)-III, ant(6)-Ia, str, tet(M), tet(L), optrA, fexA, dfrG>25612825612832161
E. faecalisTC-C9736optrA, fexA120.125643281
E. faecalisC9737erm(B), lnu(B), lsa(A), lsa(E), aph(3″)-III, ant(6)-Ia, tet(M), optrA, fexA, catpC221>2561281283264161
E. faecalisTC-C9737optrA, fexA120.125323281
E. faecalisX523lsa(A), lsa(E), tet(M), tet(L), optrA, fexA, dfrG128>256128326481
E. faecalisTC-X523optrA, fexA120.125326481
E. faecalisX524erm(B), lsa(A), lsa(E), aac(6′)-aph(2″), aph(3″)-III, ant(6)-Ia, tet(M), tet(L), optrA, fexA, dfrG256256256326481
E. faecalisTC-X524optrA, fexA120.125326481
E. faecalisX525erm(B), lnu(B), lsa(A), lsa(E), aac(6′)-aph(2″), aph(3″)-III, ant(6)-Ia, str, tet(M), tet(L), optrA, fexA, catA, dfrG>256128128646481
E. faecalisTC-X525optrA, fexA120.125323281
E. faecalisX526erm(B), lnu(B), lsa(A), lsa(E), aph(3″)-III, ant(6)-Ia, tet(M), optrA, fexA, catpC221>256128128326441
E. faecalisTC-X526optrA, fexA120.125326441
E. faecalisX527erm(B), lsa(A), aac(6′)-aph(2″), aph(3″)-III, ant(6)-Ia, tet(M), optrA, fexA>2562561283264161
E. faecalisTC-X527optrA, fexA120.125326481
E. faecalisX528erm(B), lsa(A), aph(3″)-III, ant(6)-Ia, tet(M), tet(L), cfr(D), optrA, fexA, dfrG>256>256>2563264161
E. faecalisTC-X528optrA, fexA120.125326481
1 ERY, erythromycin; CLI, clindamycin; TET, tetracycline; CHL, chloramphenicol; FFC, florfenicol; LZD, linezolid; TDZ, tedizolid; the genotypes of the transconjugants are displayed in bold.

Share and Cite

MDPI and ACS Style

Ruiz-Ripa, L.; Feßler, A.T.; Hanke, D.; Eichhorn, I.; Azcona-Gutiérrez, J.M.; Pérez-Moreno, M.O.; Seral, C.; Aspiroz, C.; Alonso, C.A.; Torres, L.; et al. Mechanisms of Linezolid Resistance Among Enterococci of Clinical Origin in Spain—Detection of optrA- and cfr(D)-Carrying E. faecalis. Microorganisms 2020, 8, 1155. https://doi.org/10.3390/microorganisms8081155

AMA Style

Ruiz-Ripa L, Feßler AT, Hanke D, Eichhorn I, Azcona-Gutiérrez JM, Pérez-Moreno MO, Seral C, Aspiroz C, Alonso CA, Torres L, et al. Mechanisms of Linezolid Resistance Among Enterococci of Clinical Origin in Spain—Detection of optrA- and cfr(D)-Carrying E. faecalis. Microorganisms. 2020; 8(8):1155. https://doi.org/10.3390/microorganisms8081155

Chicago/Turabian Style

Ruiz-Ripa, Laura, Andrea T. Feßler, Dennis Hanke, Inga Eichhorn, José Manuel Azcona-Gutiérrez, Mar Olga Pérez-Moreno, Cristina Seral, Carmen Aspiroz, Carla Andrea Alonso, Luis Torres, and et al. 2020. "Mechanisms of Linezolid Resistance Among Enterococci of Clinical Origin in Spain—Detection of optrA- and cfr(D)-Carrying E. faecalis" Microorganisms 8, no. 8: 1155. https://doi.org/10.3390/microorganisms8081155

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop