Five-Year Summary of In Vitro Activity and Resistance Mechanisms of Linezolid against Clinically Important Gram-Positive Cocci in the United States from the LEADER Surveillance Program (2011 to 2015)

Resistance to linezolid in Staphylococcus aureus by mutation, modification, and acquisition of genes

Linezolid binds to the 50S subunit of the bacterial ribosome, inhibiting bacterial protein synthesis by preventing the formation of the initiation complex. Oxazolidinone antimicrobial drugs represent the last line of defense in treating Staphylococcus aureus infections; thus, resistance to linezolid in S. aureus warrants high priority. This article examines the major mechanisms of resistance to linezolid in S. aureus, which include: mutations in the domain V of 23S rRNA (primarily G2576); chromosomal mutations in the rplC, rplD, and rplV genes (encoding the ribosomal uL3, uL4, and uL22 proteins, respectively); the exogenous acquisition of the methylase encoded by the chloramphenicol-florfenicol resistance (cfr) gene; the endogenous methylation or demethylation of 23S rRNA; the acquisition of optrA and poxtA resistance genes; and the existence of the LmrS multidrug efflux pump. In conclusion, these mechanisms mediate resistance through mutations or modifications to the bacterial target, thereby reducing the affinity of linezolid for the peptidyl transferase center (PTC) binding site or by preventing the binding of linezolid to the PTC through a ribosomal protective effect. The existence of additional, unexplained resistance mechanisms requires further investigation and verification.

Epidemiology and genetic diversity of linezolid-resistant Enterococcus clinical isolates in Belgium from 2013 to 2021

OBJECTIVES

Linezolid-resistant opportunistic human pathogens Enterococcus faecalis and Enterococcus faecium are emerging health threats as limited therapeutic options remain. The aim of this study was to investigate the epidemiology, resistance mechanisms, and genetic diversity of linezolid-resistant enterococci (LRE) isolated between 2013 and 2021 and received at the Belgian National Reference Centre (NRC) for Enterococci.

METHODS

Linezolid susceptibility testing was performed upon request on 2458 submitted enterococci strains. Whole-genome sequencing was performed on all LRE strains.

RESULTS

Seventy-eight LRE human isolates, of which 63 (81%) E. faecalis and 15 (19%) E. faecium strains, were submitted to the Belgian NRC for Enterococci. Of the linezolid-resistant E. faecalis strains, 97% harboured the optrA gene (56% wild-type pE349) and 3% the poxtA gene. Of the linezolid-resistant E. faecium strains, 54% harboured the G2576T point mutation in the V domain of the 23S rRNA genes, 23% the poxtA, and 23% the optrA gene. Furthermore, two E. faecium strains were identified with a combination of two resistance mechanisms ([i] optrA and poxtA, and [ii] cfr(B) and G2576T point mutation, respectively). Vancomycin resistance was observed in 15% (n = 12) of the LRE. ST480 (n = 42/63 typed strains, 67%) was the most frequently detected sequence type (ST) in linezolid-resistant E. faecalis strains, while ST203 (n = 5/15 typed strains, 33%) was the most frequently detected ST in linezolid-resistant E. faecium strains.

CONCLUSIONS

E. faecalis isolates harbouring optrA were the predominant LRE in Belgium, with ST480 as the most prominent multilocus sequence typing. Linezolid resistance in E. faecium could be attributed to either chromosomal mutations or transferable resistance determinants.

Emergence of linezolid-resistant Enterococcus faecium in a tertiary hospital in Copenhagen

Linezolid is used as first-line treatment of infections caused by vancomycin-resistant Enterococcus faecium. However, resistance to linezolid is increasingly detected. The aim of the present study was to elucidate the causes and mechanisms for the increase in linezolid-resistant E. faecium at Copenhagen University Hospital - Rigshospitalet. We therefore combined patient information on linezolid treatment with whole-genome sequencing data for vancomycin- or linezolid-resistant E. faecium isolates that had been systematically collected since 2014 (n=458). Whole-genome sequencing was performed for multilocus sequence typing (MLST), identification of linezolid resistance-conferring genes/mutations and determination of phylogenetically closely related strains. The collection of E. faecium isolates belonged to prevalent vancomycin-resistant MLST types. Among these, we identified clusters of closely related linezolid-resistant strains compatible with nosocomial transmission. We also identified linezolid-resistant enterococcus isolates not genetically closely related to other isolates compatible with de novo generation of linezolid resistance. Patients with the latter isolates were significantly more frequently exposed to linezolid treatment than patients with related linezolid-resistant enterococcus isolates. We also identified six patients who initially carried a vancomycin-resistant, linezolid-sensitive enterococcus, but from whom vancomycin-resistant, linezolid-resistant enterococci (LVRE) closely related to their initial isolate were recovered after linezolid treatment. Our data illustrate that linezolid resistance may develop in the individual patient subsequent to linezolid exposure and can be transmitted between patients in a hospital setting.

Clinical, Bacteriological, and Genetic Characterization of Bone and Joint Infections Involving Linezolid-Resistant Staphylococcus epidermidis: a Retrospective Multicenter Study in French Reference Centers

The choice of the best probabilistic postoperative antibiotics in bone and joint infections (BJIs) is still challenging. Since the implementation of protocolized postoperative linezolid in six French referral centers, linezolid-resistant multidrug-resistant Staphylococcus epidermidis (LR-MDRSE) strains were isolated in patients with BJI. We aimed here to describe clinical, microbiological, and molecular patterns associated with these strains. All patients with at least one intraoperative specimen positive for LR-MDRSE between 2015 and 2020 were included in this retrospective multicenter study. Clinical presentation, management, and outcome were described. LR-MDRSE strains were investigated by MIC determination for linezolid and other anti-MRSA antibiotics, characterization of genetic determinants of resistance, and phylogenetic analysis. Forty-six patients (colonization n = 10, infection n = 36) were included in five centers, 45 had prior exposure to linezolid, 33 had foreign devices. Clinical success was achieved for 26/36 patients. Incidence of LR-MDRSE increased over the study period. One hundred percent of the strains were resistant to oxazolidinones, gentamicin, clindamycin, ofloxacin, rifampicin, ceftaroline, and ceftobiprole, and susceptible to cyclins, daptomycin, and dalbavancin. Susceptibility to delafloxacin was bimodal. Molecular analysis was performed for 44 strains, and the main mutation conferring linezolid resistance was the 23S rRNA G2576T mutation. All strains belonged to the sequence type ST2 or its clonal complex, and phylogenetic analysis showed emergence of five populations corresponding geographically to the centers. We showed the emergence of new clonal populations of highly linezolid-resistant S. epidermidis in BJIs. Identifying patients at risk for LR-MDRSE acquisition and proposing alternatives to systematic postoperative linezolid use are essential. IMPORTANCE The manuscript describes the emergence of clonal linezolid-resistant strains of Staphylococcus epidermidis (LR-MDRSE) isolated from patients presenting with bone and joint infections. Incidence of LR-MDRSE increased over the study period. All strains were highly resistant to oxazolidinones, gentamicin, clindamycin, ofloxacin, rifampicin, ceftaroline, and ceftobiprole, but were susceptible to cyclins, daptomycin, and dalbavancin. Susceptibility to delafloxacin was bimodal. The main mutation conferring linezolid resistance was the 23S rRNA G2576T mutation. All strains belonged to the sequence type ST2 or its clonal complex, and phylogenetic analysis showed emergence of five populations corresponding geographically to the centers. LR-MDRSE bone and joint infections seem to be accompanied by an overall poor prognosis related to comorbidities and therapeutic issues. Identifying patients at risk for LR-MDRSE acquisition and proposing alternatives to systematic postoperative linezolid use become essential, with a preference for parenteral drugs such as lipopeptids or lipoglycopeptids.

Enterococcal Phages: Food and Health Applications

Enterococcus is a diverse genus of Gram-positive bacteria belonging to the lactic acid bacteria (LAB) group. It is found in many environments, including the human gut and fermented foods. This microbial genus is at a crossroad between its beneficial effects and the concerns regarding its safety. It plays an important role in the production of fermented foods, and some strains have even been proposed as probiotics. However, they have been identified as responsible for the accumulation of toxic compounds-biogenic amines-in foods, and over the last 20 years, they have emerged as important hospital-acquired pathogens through the acquisition of antimicrobial resistance (AMR). In food, there is a need for targeted measures to prevent their growth without disturbing other LAB members that participate in the fermentation process. Furthermore, the increase in AMR has resulted in the need for the development of new therapeutic options to treat AMR enterococcal infections. Bacteriophages have re-emerged in recent years as a precision tool for the control of bacterial populations, including the treatment of AMR microorganism infections, being a promising weapon as new antimicrobials. In this review, we focus on the problems caused by Enterococcus faecium and Enterococcus faecalis in food and health and on the recent advances in the discovery and applications of enterococcus-infecting bacteriophages against these bacteria, with special attention paid to applications against AMR enterococci.

Linezolid resistance: detection of the cfr(B) gene in French clinical MRSA strains

OBJECTIVES

To describe two linezolid-resistant MRSA strains carrying the cfr(B) gene detected in the French National Reference Centre for staphylococci.

METHODS

Two linezolid-resistant MRSA strains isolated from cystic fibrosis patients in two different French hospitals in 2017 and 2019 were examined to explore the mechanisms of linezolid resistance. Antimicrobial susceptibility was tested using broth microdilution and gradient strips. The genetic determinants of linezolid resistance were assessed by a multiplex PCR targeting cfr/cfr(B), optrA and poxtA genes, by amplification and sequencing of individual 23S rRNA genes and by WGS using both Illumina and Nanopore technologies.

RESULTS

The two MRSA strains were resistant to linezolid but susceptible to tedizolid, and PCR-positive for cfr/cfr(B). The WGS analysis indicated that they belonged to two different STs (ST8-MRSA-IV and ST5382-MRSA-IV) and that they both harboured the cfr(B) gene on the same 9.7 kb Tn6218-like chromosomal transposon, a finding only previously reported in Enterococcus sp. and Clostridioides difficile.

CONCLUSIONS

To the best of our knowledge, this is the first description of the presence of cfr(B) in staphylococci, more specifically in linezolid-resistant MRSA strains. This finding illustrates the risk of horizontal intergenus transfer of oxazolidinone resistance genes in Staphylococcus aureus and highlights the need to monitor such emergence in this species.

An 11-year linezolid-resistant Staphylococcus capitis clone dissemination with a similar cfr-carrying plasmid in China

Linezolid resistance has represented a global concern with its wide dissemination among nosocomial pathogens in recent years. One hundred and two linezolid-resistant Staphylococcus capitis (LRSC) were constantly isolated from 2011 to 2021, which demonstrated single clonal dissemination in a Chinese tertiary hospital. A structurally similar cfr-carrying plasmid was identified among 90 isolates. A chromosomal cfr was located beside a Tn4001-like transposon and ISEnfa4 in one strain (LR95). The loss of cfr-carrying plasmid was observed in 11 isolates and the in vitro passage experiments. Conjugation experiments demonstrated the horizontal transferability of the cfr-carrying plasmid into Staphylococcus aureus RN4220. Both cfr-positive LRSC and S. aureus showed no significant differences in growth rates, while only the former displayed competition defect, suggesting this plasmid imposed a certain fitness cost on LRSC. Hence, ongoing measurements are supposed to be adopted to control the spread of these antimicrobial-resistant bacteria.

Activity of Tedizolid and Comparator Agents Against Gram-positive Isolates Causing Skin and Skin Structure Infections in Pediatric Patients in United States Hospitals (2015-2019)

BACKGROUND

Tedizolid was approved by the United States Food and Drug Administration to treat acute bacterial skin and skin structure infections in adults in 2014, and in 2020, United States Food and Drug Administration expanded the approval of tedizolid to treat pediatric patients 12 years of age and older. This study assessed the activity of tedizolid and comparator agents against clinical surveillance isolates collected from pediatric patients with skin and skin structure infection in the United States.

METHODS

A total of 2747 gram-positive organisms (1 per patient) were collected in 2015 to 2019 from pediatric (≤17 years old) patients with skin and skin structure infections. The isolates were collected from 33 US medical centers and susceptibility tested against tedizolid and comparators by reference broth microdilution methods. Susceptibility results for main pathogens were stratified by patient age: ≤1 years old (851 isolates), 2 to 5 years old (623), 6 to 12 years old (754) and 13 to 17 years old (519).

RESULTS

Staphylococcus aureus (n = 2163) was the main pathogen recovered from all age groups, followed by β-hemolytic streptococci (n = 460). Tedizolid inhibited all S. aureus , including methicillin-resistant S. aureus (MRSA) isolates (41.0%), regardless of the age group. MRSA rates varied by age group; MRSA was highest among ≤1 years old (45.0%) and lowest in the 13 to 17 years old (32.7%) groups. Linezolid, daptomycin and vancomycin also displayed susceptibility rates of 100% against S. aureus isolates. Clindamycin (81.3%-98.5%), tetracycline (91.6%-97.1%) and trimethoprim-sulfamethoxazole (97.0%-100%) susceptibility rates varied among age groups and methicillin resistance profiles. Overall, tedizolid, linezolid, daptomycin and vancomycin inhibited all gram-positive pathogens in this collection.

CONCLUSIONS

Tedizolid was very active against a large collection of gram-positive pathogens causing skin and skin structure infection in pediatric patients, including MRSA isolates.

Linezolid-resistance Staphylococcus aureus – Prevalence, Emerging Resistance Mechanisms, Challenges and Perspectives

Staphylococcus aureus, an opportunistic pathogen, can root several infections viz skin and tissue infections, bacteraemia, food poisoning, pneumonia, and many other clinical conditions with some variations of virulence factors. In treatment of infections, caused by this Gram-positive pathogen, several antibiotics are being used importantly Methicillin and Vancomycin. This pathogen has high capability of antibiotic resistance development and had evolved new strains such as Methicillin-resistant Staphylococcus aureus (MRSA), and Vancomycin-resistant Staphylococcus aureus (VRSA). Meta-analysis in Ethiopia showed that pooled prevalence of MRSA in environment, food, animal, and human was 54%, 77%, 15%, and 38% respectively (2022). Risk of MRSA isolates from burn ICU was 55 % higher (2018). In Bangladesh, 37.1% isolates from frozen meat chicken (2021) were identified as MRSA. This problem is being dealt with a novel drug called Linezolid which has been proved effective against both MRSA and VRSA. Exacerbating the situation, this pathogen has shown resistance against this unprecedented drug by means of a number of drug resistance mechanisms. Its prevalence has been reporting since the adoption of the drug, but with a minute ratio at one time/place to the very high percentage at another time/place. This inconsistent prevalence must not be ignored, and its surveillance should be augmented as antibiotic treatment is critical for fighting against microbial infections. This review highlights the worldwide reports in which Staphylococcus aureus of either wildtype or Methicillin or Vancomycin resistance that have shown resistance to Linezolid drug for the past 2 decades. At the same time where incidences of Linezolid Resistant Staphylococcus aureus (LRSA) indications are reporting, there is a call for comprehensive strategies to overcome this challenge of antibiotic resistance.

Sentinel Surveillance Reveals Emerging Daptomycin-Resistant ST736 Enterococcus faecium and Multiple Mechanisms of Linezolid Resistance in Enterococci in the United States

Enterococcus faecalis and faecium with resistance to daptomycin and/or linezolid are emerging globally. We present the genomic characterization of daptomycin- and linezolid-resistant E. faecalis and E. faecium surveillance isolates from the United States, 2013-2016. Daptomycin resistance was low among E. faecalis (2/364, 0.5%) and E. faecium (17/344, 5%). The majority (71%, 12/17) of daptomycin-resistant E. faecium isolates belonged to the emerging ST736 clone and contained mutations in liaFSR and cls previously associated with resistance. However, 1/2 E. faecalis and 3/17 E. faecium did not contain these mutations previously associated with daptomycin resistance. Linezolid resistance was rare among E. faecalis (1/364, 0.3%) and E. faecium (2/344, 0.6%). These two E. faecium isolates, one of which was also resistant to daptomycin and vancomycin, contained the 23S rRNA nucleotide mutation (G2576T) associated with linezolid resistance. Long-read sequencing revealed the linezolid-resistant E. faecalis isolate contained chromosomal- and plasmid-encoded copies of optrA. The chromosomal optrA was located on the recently described Tn6674 multiresistance transposon. The second copy of optrA was encoded on an ∼65 kb mosaic plasmid, with component regions sharing high sequence identity to optrA-encoding multiresistance plasmids of animal origin. The optrA-encoding plasmid contained open reading frames predicted to encode proteins associated with a pheromone-responsive plasmid transfer system, and filter mating experiments confirmed the plasmid was conjugative. Continued surveillance of enterococci is necessary to assess the prevalence and trends of daptomycin and linezolid resistance in the United States, characterize resistance mechanisms and how they transfer, and monitor for emerging sequence types associated with resistance.

Dose Optimization of Combined Linezolid and Fosfomycin against Enterococcus by Using an In Vitro Pharmacokinetic/Pharmacodynamic Model

The rapid spread of antibiotic resistance among Enterococcus has prompted considerable interest in determining the dosage regimen of linezolid combined with fosfomycin. A checkerboard assay was employed to evaluate whether linezolid combined with fosfomycin had a synergistic effect on Enterococcus isolates from the hospital, including three drug-resistant strains (MIC of linezolid [MIC_LZD], ≥8 mg/L; MIC of fosfomycin [MIC_FOF], ≥256 mg/L). The in vitro static time-kill assay, dynamic pharmacokinetic (PK)/pharmacodynamic (PD) model, and semimechanistic PK/PD model were used to explore and predict effective combined dosage regimens. The checkerboard assay and in vitro static time-kill assay demonstrated that linezolid combined with fosfomycin has a synergistic effect on drug-resistant and sensitive Enterococcus. In the in vitro PK/PD model, the dosage regimen of linezolid (8 mg/L or 12 mg/L, steady-state concentration) combined with fosfomycin (6 g or 8 g) via a 0.5-h infusion every 8 h effectively suppressed bacterial growth at 24 h with a 3 log₁₀ CFU/mL decrease compared with the initial inocula against two resistant and one sensitive Enterococcus isolates. The semimechanistic PK/PD model predicted that linezolid (more than 16 mg/L) combined with fosfomycin (6 g or 10 g) via a 0.5-h infusion every 8 h was required to achieve a 4 log₁₀ CFU/mL decrease at 24 h against Enterococcus isolates (MIC_LZD ≥ 8 mg/L and MIC_FOF ≥ 256 mg/L). According to the prediction of the semimechanical PK/PD model, the effect of the combination was driven by linezolid, with fosfomycin enhancing the effect. Our study is the first to explore the synergistic effects of these two drugs from a qualitative and quantitative perspective and provides a simulation tool for future studies.

IMPORTANCE In this study, we found that linezolid combined with fosfomycin could kill Enterococcus in vitro and that the administered dose was significantly lower after the combination treatment, which could reduce adverse effects and the development of drug resistance. The potential mechanism of the two-drug combination against Enterococcus was revealed from a quantitative perspective, which is an important step toward dose optimization in simulated humans. We hope that our research will help build a better relationship between clinicians and patients as we work together to address the challenges of antibiotic resistance in the 21st century.

Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria

Seven mobile oxazolidinone resistance genes, including cfr, cfr(B), cfr(C), cfr(D), cfr(E), optrA, and poxtA, have been identified to date. The cfr genes code for 23S rRNA methylases, which confer a multiresistance phenotype that includes resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A compounds. The optrA and poxtA genes code for ABC-F proteins that protect the bacterial ribosomes from the inhibitory effects of oxazolidinones. The optrA gene confers resistance to oxazolidinones and phenicols, while the poxtA gene confers elevated MICs or resistance to oxazolidinones, phenicols, and tetracycline. These oxazolidinone resistance genes are most frequently found on plasmids, but they are also located on transposons, integrative and conjugative elements (ICEs), genomic islands, and prophages. In these mobile genetic elements (MGEs), insertion sequences (IS) most often flanked the cfr, optrA, and poxtA genes and were able to generate translocatable units (TUs) that comprise the oxazolidinone resistance genes and occasionally also other genes. MGEs and TUs play an important role in the dissemination of oxazolidinone resistance genes across strain, species, and genus boundaries. Most frequently, these MGEs also harbor genes that mediate resistance not only to antimicrobial agents of other classes, but also to metals and biocides. Direct selection pressure by the use of antimicrobial agents to which the oxazolidinone resistance genes confer resistance, but also indirect selection pressure by the use of antimicrobial agents, metals, or biocides (the respective resistance genes against which are colocated on cfr-, optrA-, or poxtA-carrying MGEs) may play a role in the coselection and persistence of oxazolidinone resistance genes.

Genomic and Phenotypic Analysis of Linezolid-Resistant Staphylococcus epidermidis in a Tertiary Hospital in Innsbruck, Austria

Whole genome sequencing is a useful tool to monitor the spread of resistance mechanisms in bacteria. In this retrospective study, we investigated genetic resistance mechanisms, sequence types (ST) and respective phenotypes of linezolid-resistant Staphylococcus epidermidis (LRSE, n = 129) recovered from a cohort of patients receiving or not receiving linezolid within a tertiary hospital in Innsbruck, Austria. Hereby, the point mutation G2603U in the 23S rRNA (n = 91) was the major resistance mechanism followed by the presence of plasmid-derived cfr (n = 30). The majority of LRSE isolates were ST2 strains, followed by ST5. LRSE isolates expressed a high resistance level to linezolid with a minimal inhibitory concentration of ≥256 mg/L (n = 83) in most isolates, particularly in strains carrying the cfr gene (p < 0.001). Linezolid usage was the most prominent (but not the only) trigger for the development of linezolid resistance. However, administration of linezolid was not associated with a specific resistance mechanism. Restriction of linezolid usage and the monitoring of plasmid-derived cfr in LRSE are potential key steps to reduce linezolid resistance and its transmission to more pathogenic Gram-positive bacteria.

Antimicrobial susceptibility of bacteremic vancomycin-resistant Enterococcus faecium to eravacycline, omadacycline, lipoglycopeptides, and other comparator antibiotics: Results from the 2019-2020 Nationwide Surveillance of Multicenter Antimicrobial Resistance in Taiwan (SMART)

Multicenter surveillance of antimicrobial susceptibility was performed for 235 vancomycin-resistant Enterococcus faecium (VREfm) isolates from 18 Taiwanese hospitals. The minimum inhibitory concentrations (MICs) of eravacycline, omadacycline, lipoglycopeptides, and other comparator antibiotics were determined using the broth microdilution method. Nearly all isolates of VREfm were not susceptible to teicoplanin, dalbavancin, and telavancin, with susceptibility rates of 0.5%, 1.7% and 0.5%, respectively. Tigecycline and eravacycline were active against 93.2% and 89.7% of the VREfm isolates, respectively. Moreover, the susceptibility rates of quinupristin/dalfopristin, tedizolid, and linezolid were 59.1%, 84.2%, and 77.4%, respectively. Additionally, 94% of the VREfm isolates were classified as susceptible to daptomycin, and the MICs of omadacycline required to inhibit VREfm growth by 50% and 90% were 0.12 and 0.5 mg/L, respectively. Susceptibility rates of VREfm isolates to synthetic tetracyclines and daptomycin were slightly lower and to oxazolidinone-class antibiotics were much lower in Taiwan than those in other parts of the world. Continuous monitoring of VREfm resistance to novel antibiotics, including synthetic tetracyclines, oxazolidinone-class antibiotics, and daptomycin, is needed in Taiwan.

In-Host Emergence of Linezolid Resistance in a Complex Pattern of Toxic Shock Syndrome Toxin-1-Positive Methicillin-Resistant Staphylococcus aureus Colonization in Siblings with Cystic Fibrosis

Methicillin-resistant Staphylococcus aureus (MRSA) can cause chronic lung infections in patients with Cystic Fibrosis (CF). One option for managing them is the use of linezolid. We hereby report the in-host emergence of linezolid resistance (LR) in MRSA in CF siblings via a population analysis. A collection of 171 MRSA strains from 68 samples were characterized by determining their linezolid Minimal Inhibitory Concentrations (MICs), analyzing the locus of staphylococcal protein A (spa) and whole genome sequencing. Courses of linezolid were retraced. Strains belonged to three spa types (t002, t045, t127) and two sequence types (ST1, ST5). Emergence of LR occurred under treatment, one year apart in both siblings, in the CC5-MRSA-I Geraldine clone harboring the toxic shock syndrome toxin-1-encoding gene. Resistance was related to a G2576T substitution present in a variable number of 23S rRNA gene copies. Susceptible and resistant strains were co-isolated within samples. Single Nucleotide Polymorphism-based analysis revealed complex colonizations by highly diversified, clonally related populations. LR remains rare in MRSA and there are very few longitudinal analyses documenting its emergence. Analyzing a large MRSA collection revealed new aspects of LR emergence: it emerges in specific subclonal lineages resulting from adaptive diversification of MRSA in the CF lung and this heterogeneity of intra-sample resistance may contribute to compromising antibiotic management.

Linezolid Resistance in Enterococcus faecalis Associated With Urinary Tract Infections of Patients in a Tertiary Hospitals in China: Resistance Mechanisms, Virulence, and Risk Factors

Background:Enterococcus faecalis has been commonly considered as one of the major pathogens of the urinary tract infection (UTI) in human host worldwide, whereas the molecular characteristics of E. faecalis clinical isolates from the patients with UTI in China remains seldomly reported. This study aimed to investigate the resistance mechanism, molecular characteristics and risk factors of E. faecalis clinical isolates from patients with UTI in China.

Methods: A total of 115 non-duplicated E. faecalis clinical isolates from patients with UTI were retrospectively collected in a tertiary hospital in China and their clinical data was further analyzed. The linezolid and tedizolid susceptibility were determined by agar dilution. The resistance genes, including erm(A), erm(B), erm(C), tet(M), optrA, cfr, cfr(B), poxtA, and MLST-based housekeeping genes were investigated by PCR.

Results: In 115 non-duplicated E. faecalis clinical isolates from the patients with UTI in this hospital setting, the frequency of linezolid or tedizolid-resistant/intermediate isolates were 22.61 and 13.04%, respectively, and the frequency of linezolid-resistant/intermediate E. faecalis clinical isolates carrying with erm(A) were 86%. Among the five linezolid-resistant E. faecalis strains found in this study, three optrA-positive isolates and the other two linezolid-resistant strains were G2576U genetic mutations in the V domain of the 23S rRNA genes. The ST clonality analysis indicated that 31.42% (11/35) of ST16 E. faecalis UTI isolates were not susceptible to linezolid. Moreover, the univariable analysis indicated that the high risk factors of linezolid-resistant/intermediate E. faecalis infections involved the indwelling catheter, trachea cannula catheter and the carriage of erm(A) or optrA. Furthermore, the indwelling catheter and trachea cannula catheter were demonstrated as the independent predictors of linezolid-resistant/intermediate E. faecalis strains in patients with UTI by multivariable analysis.

Conclusion: Linezolid-resistant/intermediate E. faecalis associated with urinary tract infections of patients in this hospital setting from China might be explained by the high carriage frequency of optrA genes and moreover, indwelling catheter and trachea cannula should be considered as the independent predictors of linezolid-resistant/intermediate E. faecalis infections. The transmission mechanism of linezolid-resistant/intermediate E. faecalis in this hospital setting should be further studied.

Trends in Antibiotic Resistance Among Ocular Microorganisms in the United States From 2009 to 2018

Question

What are the antibiotic resistance profiles and trends among common ocular pathogens across the United States?

Findings

In this cross-sectional study of more than 6000 ocular isolates of Staphylococcus aureus, coagulase-negative staphylococci, Streptococcus pneumoniae, Pseudomonas aeruginosa, and Haemophilus influenzae collected between 2009 and 2018, methicillin resistance and multidrug resistance were prevalent among staphylococci. Antibiotic resistance profiles were mostly unchanged during 10 years.

Meaning

These in vitro antibiotic resistance data may assist clinicians in selecting appropriate antibiotics for treatment of ocular infections.

Importance

Antibiotic resistance in ocular infections can affect treatment outcomes. Surveillance data on evolving antibacterial susceptibility patterns inform the treatment of such infections.

Objective

To assess overall antibiotic resistance profiles and trends among bacterial isolates from ocular sources collected during 10 years.

Design, Setting, and Participants

This cross-sectional study of longitudinal data from the ongoing, nationwide, prospective, laboratory-based surveillance study, the Antibiotic Resistance Monitoring in Ocular Microorganisms (ARMOR) study, included clinically relevant isolates of Staphylococcus aureus, coagulase-negative staphylococci (CoNS), Streptococcus pneumoniae, Pseudomonas aeruginosa, and Haemophilus influenzae cultured from patients with ocular infections at US centers from January 1, 2009, to December 31, 2018.

Main Outcomes and Measures

Minimum inhibitory concentrations were determined for various combinations of antibiotics and species. Odds ratios (ORs) were determined for concurrent antibiotic resistance; analysis of variance and χ² tests were used to evaluate resistance rates by patient age and geographic region; Cochran-Armitage tests identified changing antibiotic susceptibility trends over time.

Results

A total of 6091 isolates (2189 S aureus, 1765 CoNS, 590 S pneumoniae, 767 P aeruginosa, and 780 H influenzae) from 6091 patients were submitted by 88 sites. Overall, 765 S aureus (34.9%) and 871 CoNS (49.3%) isolates were methicillin resistant and more likely to be concurrently resistant to macrolides (azithromycin: S aureus: OR, 18.34 [95% CI, 13.64-24.67]; CoNS: OR, 4.59 [95% CI, 3.72-5.66]), fluoroquinolones (ciprofloxacin: S aureus: OR, 22.61 [95% CI, 17.96-28.47]; CoNS: OR, 9.73 [95% CI, 7.63-12.40]), and aminoglycosides (tobramycin: S aureus: OR, 18.29 [95% CI, 13.21-25.32]; CoNS: OR, 6.28 [95% CI, 4.61-8.56]) compared with methicillin-susceptible isolates (P < .001 for all). Multidrug resistance was observed among methicillin-resistant S aureus (577 [75.4%]) and CoNS (642 [73.7%]) isolates. Antibiotic resistance among S pneumoniae isolates was highest for azithromycin (214 [36.3%]), whereas P aeruginosa and H influenzae isolates showed low resistance overall. Differences in antibiotic resistance were found among isolates by patient age (S aureus: F = 28.07, P < .001; CoNS: F = 11.46, P < .001) and geographic region (S aureus: F = 8.03, P < .001; CoNS: F = 4.79, P = .003; S pneumoniae: F = 8.14, P < .001; P aeruginosa: F = 4.32, P = .005). Small changes in antibiotic resistance were noted over time (≤2.5% per year), with decreases in resistance to oxacillin/methicillin (oxacillin: −2.16%; 95% CI, −3.91% to −0.41%; P < .001) and other antibiotics among S aureus isolates, a decrease in ciprofloxacin resistance among CoNS (−1.38%; 95% CI, −2.24% to −0.52%; P < .001), and an increase in tobramycin resistance among CoNS (0.71%; 95% CI, –0.29% to 1.71%; P = .03). Besifloxacin retained consistently low minimum inhibitory concentrations.

Conclusions and Relevance

Antibiotic resistance may be prevalent among staphylococcal isolates, particularly among older patients. In this study, a few small differences in antibiotic resistance were observed by geographic region or longitudinally.

Linezolid-resistant MRSA-CC398 carrying the cfr gene, and MRSA-CC9 isolates from pigs with signs of infection in Spain

AIMS

To perform the molecular characterization of 23 Staphylococcus aureus isolates from pigs with signs of infections recovered in Spanish farms during 2018-2019.

METHODS AND RESULTS

The antimicrobial resistance pattern and virulence profile were determined. The molecular typing was performed by different molecular techniques. The transferability of the cfr gene was assessed by conjugation and its genetic environment was determined by PCR mapping. In all, 21 isolates were methicillin-resistant S. aureus (MRSA) carrying the mecA gene (SCCmecV or non-typeable SCCmec), whereas the remaining two were methicillin-susceptible (MSSA). All but one MRSA isolates (n = 20) belonged to the CC398, being the spa t011 the most prevalent (n = 11). The remaining MRSA and the two MSSA isolates were ascribed to ST9/CC9. The S. aureus isolates exhibited resistance to (number of resistant isolates): β-lactamics (21), erythromycin and/or clindamycin (20), aminoglycosides (7), tetracycline (22), fluoroquinolones (14), chloramphenicol (5) and linezolid (1). The S. aureus isolates did not carry any of the virulence genes studied. One MRSA belonging to the CC398 showed linezolid resistance mediated by the cfr gene. The cfr gene was co-located with fexA in the Tn558 variant previously reported in the S. aureus plasmid pSCFS7.

CONCLUSIONS

Two major livestock-associated genetic lineages were detected among pigs with signs of infection in Spain. The presence of the cfr gene among LA-MRSA-CC398 is of great concern not only for veterinary medicine, but also for humans in close contact.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work describes the molecular characterization of S. aureus isolates recovered from pigs with signs of infection and we report, as far as we know, the first description of MRSA-CC9 from pigs in Spain. Moreover, the detection of a MRSA-CC398 isolate carrying the multiresistance cfr gene highlights the need for continuous surveillance and awareness of LA-MRSA.

Emergence of optrA-Mediated Linezolid-Nonsusceptible Enterococcus faecalis in a Tertiary Care Hospital

This study investigated resistance mechanisms and epidemiology of emerging linezolid-nonsusceptible Enterococcus faecalis (LNSEF) in a tertiary care hospital. LNSEF isolated from clinical samples were collected from November 2017 to June 2019. The isolates were investigated for linezolid resistance and the associated molecular mechanisms, including mutations of 23S rRNA domain V and acquisition of the cfr or optrA resistance gene. We used pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing for the molecular typing of the isolates. Among 4,318 E. faecalis isolates, 10 (0.23%) were linezolid-nonsusceptible. All LNSEF isolates were optrA-positive and cfr-negative. Of these isolates, five were sequence type (ST) 476, two ST585, one ST16, one ST16-like, and one ST480. Six LNSEF isolates obtained in the first year clustered to three types in the PFGE analysis: two ST476 isolates of type A, two ST585 isolates of type B, and two ST16 or ST16-like isolates of type C. Seven cases were of community-onset and three were hospital acquired, but total of eight were healthcare-associated including five community-onset. None of the patients had a history of linezolid treatment, and in one patient, we detected linezolid-susceptible E. faecalis one month before LNSEF detection. In conclusion, heterogenous clones of optrA-positive LNSEF emerged in the hospital mainly via community-onset.

Coexistence of the Oxazolidinone Resistance-Associated Genes cfr and optrA in Enterococcus faecalis From a Healthy Piglet in Brazil

Oxazolidinones are one of the most important antimicrobials potentially active against glycopeptide- and β-lactam-resistant Gram-positive pathogens. Linezolid—the first oxazolidinone to be approved for clinical use in 2000 by the US Food and Drug Administration—and the newer molecule in the class, tedizolid, inhibit protein synthesis by suppressing the formation of the 70S ribosomal complex in bacteria. Over the past two decades, transferable oxazolidinone resistance genes, in particular cfr and optrA, have been identified in Firmicutes isolated from healthcare-related infections, livestock, and the environment. Our goals in this study were to investigate the genetic contexts and the transferability of the cfr and optrA genes and examine genomic features, such as antimicrobial resistance genes, plasmid incompatibility types, and CRISPR-Cas defenses of a linezolid-resistant Enterococcus faecalis isolated in feces from a healthy pig during an antimicrobial surveillance program for animal production in Brazil. The cfr gene was found to be integrated into a transposon-like structure of 7,759 nt flanked by IS1216E and capable of excising and circularizing, distinguishing it from known genetic contexts for cfr in Enterococcus spp., while optrA was inserted into an Inc18 broad host-range plasmid of >58 kb. Conjugal transfer of cfr and optrA was shown by filter mating. The coexistence of cfr and optrA in an E. faecalis isolated from a healthy nursery pig highlights the need for monitoring the use of antibiotics in the Brazilian swine production system for controlling spread and proliferation of antibiotic resistance.

[National surveillance of clinical isolates of Enterococcus faecalis resistant to linezolid carrying the optrA gene in Colombia, 2014-2019]

OBJECTIVE

To describe the epidemiological, phenotypical and genetic characteristics of clinical isolates carrying the optrA gene identified in antimicrobial resistance surveillance by the laboratory of the National Institute of Health of Colombia.

METHODS

Between October 2014 and February 2019, 25 isolates of Enterococcus spp. resistant to linezolid were received. Antimicrobial identification and sensitivity were determined using Vitek 2 and the minimum inhibitory concentration (MIC) to linezolid was established with E-test. The optrA gene was detected by PCR, and the genetic diversity of optrA-positive isolates was tested with Diversilab®. Six isolates were selected to perform whole genome sequencing.

RESULTS

The optrA gene was confirmed in 23/25 isolates of E. faecalis from seven departments in Colombia. The isolates presented a MIC to linezolid between 8 and >256µg/mL. Typing by Diversilab® showed a wide genetic variability. All the isolates analyzed by whole genome sequencing showed the resistance genes fexA, ermB, lsaA, tet(M), tet(L) and dfrG in addition to optrA and were negative for other mechanisms of resistance to linezolid. Three type sequences and three optrA variants were identified: ST16 (optrA-2), ST476 (optrA-5) and ST618 (optrA-6). The genetic environment of the optrA-2 (ST16) isolates presented the impB, fex, optrA segment, associated with plasmid, while in two isolates (optrA-6 and optrA-5) the transferable chromosomal element Tn6674-like was found.

CONCLUSION

OptrA-positive clinical isolates present a high genetic diversity, with different optrA clones and variants related to two types of structures and different mobile genetic elements.

From Etest to Vitek 2: Impact of Enterococcal Linezolid Susceptibility Testing Methodology on Time to Active Therapy

Different linezolid antimicrobial susceptibility testing (AST) methodologies yield various results. In 2018, we transitioned our linezolid AST methodology from the Etest to Vitek 2. We sought to evaluate the impact of this change on antibiotic use among 181 inpatients with vancomycin-resistant enterococcal (VRE) infections. The transition from Etest to Vitek 2 resulted in an increase in linezolid susceptibility (38% versus 96%; P < 0.001) and a reduction in time to active antibiotic therapy (3 versus 2.6 days; P = 0.007).

Synergy of Linezolid with Several Antimicrobial Agents against Linezolid-Methicillin-Resistant Staphylococcal Strains

Linezolid is a synthetic oxazolydinone active against multi-resistant Gram-positive cocci that inhibits proteins synthesis by interacting with the 50S ribosomal subunit. Although linezolid-resistant strains are infrequent, several outbreaks have been recently described, associated with prolonged treatment with the antibiotic. As an alternative to monotherapy, the combination of different antibiotics is a commonly used option to prevent the selection of resistant strains. In this work, we evaluated combinations of linezolid with classic and new aminoglycosides (amikacin, gentamicin and plazomicin), carbapenems (doripenem, imipenem and meropenem) and fosfomycin on several linezolid- and methicillin-resistant strains of Staphylococcus aureus and S. epidermidis, isolated in a hospital intensive care unit in Madrid, Spain. Using checkerboard and time-kill assays, interesting synergistic effects were encountered for the combination of linezolid with imipenem in all the staphylococcal strains, and for linezolid-doripenem in S.epidermidis isolates. The combination of plazomicin seemed to also have a good synergistic or partially synergistic activity against most of the isolates. None of the combinations assayed showed an antagonistic effect.

In vitro activity of radezolid against Enterococcus faecium and compared with linezolid

This study aims to explore the antimicrobial activity and resistance mechanism of radezolid against Enterococcus faecium, and to compare it with linezolid. A total of 232 E. faecium isolates were collected, and the minimal inhibitory concentrations of radezolid and linezolid were determined. The radezolid- or linezolid-nonsusceptible isolates were selected by passage in vitro under antibiotic pressure. Oxazolidinone-resistant chromosomal genes and plasmid-borne genes cfr, optrA, and poxtA were detected by PCR and sequenced. Radezolid MIC₉₀ was 4 times lower than linezolid in the 232 E. faecium isolates, including the linezolid-nonsusceptible isolates. This study found that 6.5% (15/232) of the E. faecium isolates carried the plasmid-borne genes cfr and 9.5% (22/232) carried the optrA gene, but only one of these isolates had a linezolid MIC ≥ 4 mg l^-1. Among the 13 isolates with linezolid MIC ≥ 4 mg l^-1 or radezolid MIC ≥ 1 mg l^-1, genetic mutations in the V domain of 23S rRNA were only found in four isolates. The MICs of linezolid or radezolid against three E. faecium isolates increased to 4-16 times of the initial MICs after 140 days of daily passage in drug-containing medium. The radezolid MICs remained 8-16 times lower than linezolid in those linezolid-induced resistant isolates. Conversely, the radezolid MICs increased while the linezolid MICs remained unchanged in the most of the radezolid-induced resistant isolates. Radezolid exhibits excellent antimicrobial activity against E. faecium, and has minimal cross resistance with linezolid.

Effect of the Lysin Exebacase on Cardiac Vegetation Progression in a Rabbit Model of Methicillin-Resistant Staphylococcus aureus Endocarditis as Determined by Echocardiography

Methicillin-resistant Staphylococcus aureus (MRSA) poses significant therapeutic challenges related to its frequency in clinical infections, innate virulence properties, and propensity for multiantibiotic resistance. MRSA is among the most common causes of endovascular infections, including infective endocarditis (IE). Our objective was to employ transthoracic echocardiography (TTE) to evaluate the effect of exebacase, a novel direct lytic agent, in experimental aortic valve MRSA IE. TTE was utilized to evaluate the in vivo effect of exebacase on MRSA-infected vegetation progression when combined with daptomycin (versus daptomycin alone). Primary intravegetation outcomes were maximum size, weights at sacrifice, and MRSA counts at infection baseline versus after 4 days of daptomycin treatment (alone or in addition to exebacase administered once on treatment day 1). A single dose of exebacase in addition to daptomycin cleared significantly more intravegetation MRSA than daptomycin alone. This was associated with a statistical trend toward reduced maximum vegetation size in the exebacase plus daptomycin versus the daptomycin alone therapy groups (P = 0.07). Also, mean vegetation weights in the exebacase-treated group were significantly lower than those of the daptomycin alone group (P < 0.0001). Maximum vegetation size by TTE correlated with vegetation weight (P = 0.005). In addition, intravegetation MRSA counts in the combination group were significantly lower than those of untreated controls (P < 0.0001) and the daptomycin alone group (P < 0.0001). This study suggests that exebacase has a salutary impact on MRSA-infected vegetation progression when combined with daptomycin, especially in terms of vegetation MRSA burden, size, and weight. Moreover, TTE appears to be an efficient noninvasive tool to assess therapeutic efficacies in experimental MRSA IE.

The global prevalence of Daptomycin, Tigecycline, Quinupristin/Dalfopristin, and Linezolid-resistant Staphylococcus aureus and coagulase-negative staphylococci strains: a systematic review and meta-analysis

Objective

Methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative Staphylococcus (MRCoNS) are among the main causes of nosocomial infections, which have caused major problems in recent years due to continuously increasing spread of various antibiotic resistance features. Apparently, vancomycin is still an effective antibiotic for treatment of infections caused by these bacteria but in recent years, additional resistance phenotypes have led to the accelerated introduction of newer agents such as linezolid, tigecycline, daptomycin, and quinupristin/dalfopristin (Q/D). Due to limited data availability on the global rate of resistance to these antibiotics, in the present study, the resistance rates of S. aureus, Methicillin-resistant S. aureus (MRSA), and CoNS to these antibiotics were collected.

Method

Several databases including web of science, EMBASE, and Medline (via PubMed), were searched (September 2018) to identify those studies that address MRSA, and CONS resistance to linezolid, tigecycline, daptomycin, and Q/D around the world.

Result

Most studies that reported resistant staphylococci were from the United States, Canada, and the European continent, while African and Asian countries reported the least resistance to these antibiotics. Our results showed that linezolid had the best inhibitory effect on S. aureus. Although resistances to this antibiotic have been reported from different countries, however, due to the high volume of the samples and the low number of resistance, in terms of statistical analyzes, the resistance to this antibiotic is zero. Moreover, linezolid, daptomycin and tigecycline effectively (99.9%) inhibit MRSA. Studies have shown that CoNS with 0.3% show the lowest resistance to linezolid and daptomycin, while analyzes introduced tigecycline with 1.6% resistance as the least effective antibiotic for these bacteria. Finally, MRSA and CoNS had a greater resistance to Q/D with 0.7 and 0.6%, respectively and due to its significant side effects and drug-drug interactions; it appears that its use is subject to limitations.

Conclusion

The present study shows that resistance to new agents is low in staphylococci and these antibiotics can still be used for treatment of staphylococcal infections in the world.

Assessment of Tedizolid In Vitro Activity and Resistance Mechanisms against a Collection of Enterococcus spp. Causing Invasive Infections, Including Isolates Requiring an Optimized Dosing Strategy for Daptomycin from U.S. and European Medical Centers, 2016 to 2018

High-level aminoglycoside resistance was noted in 30.0% of Enterococcus faecalis and 25.2% of Enterococcus faecium isolates. Only 3.3% and 2.1% of E. faecalis isolates had elevated daptomycin MIC (≥2 mg/liter) and vancomycin resistance, respectively. In contrast, 37.4% to 40.3% of E. faecium isolates exhibited these phenotypes. Tedizolid inhibited 98.9% to 100.0% of enterococci causing serious invasive infections, including resistant subsets. Oxazolidinone resistance was mainly driven by G2576T; however, optrA and poxtA genes were also detected, including poxtA in the United States and Turkey.

The treatment of resistant staphylococcal infections

Staphylococcus aureus of the many staphylococcal species is the most common cause of both skin and soft tissue infection and severe staphylococcal infections including Staphylococcus aureus bacteremia (SAB). Many antibiotics are active against the staphylococci, yet over the last 40 years antibiotic resistance, particularly resistance to beta-lactam antibiotics, has plagued antimicrobial therapy. The term “methicillin resistance” is a historic term and now refers to the ability of staphylococci, in particular methicillin-resistant Staphylococcus aureus (MRSA), to resist the action of beta-lactam antibiotics. This resistance is encoded by the mecA gene carried in a complex genetic cassette, SCC mec. Vancomycin and old antibiotics remain the keystone of treatment for resistant staphylococci. Other newer agents, and some older agents, show good activity against resistant staphylococci which are the focus of this review: trimethoprim-sulfamethoxazole, ceftaroline, daptomycin, fosfomycin, linezolid, dalbavancin, televancin, and omadacycline. Other agents with novel mechanisms of action are under development, for use as single anti-staphylococcal agents or for combination use to augment the action of the primary anti-staphylococcal agent. Vancomycin therapy carries specific risks, particularly renal dysfunction, but despite its foibles, vancomycin remains the standard of care for the treatment of resistant staphylococcal infections. Some clinicians implement an early switch from vancomycin at the earliest signs of renal dysfunction. The near horizon holds promise also of augmentation of both cellular and humoral responses to staphylococcal infection. Pending newer clinical trials that show clear superiority of one anti-staphylococcal agent over another or over vancomycin, it will remain to expert clinical judgment in determining antibiotic choice and duration of anti-staphylococcal therapy.

Spread of clonal linezolid-resistant Staphylococcus epidermidis in an intensive care unit associated with linezolid exposure

The aim of the study was to determine factors associated with spread of linezolid (LNZ)-resistant Staphylococcus epidermidis isolates in a surgical intensive care unit (ICU). A case-control study was conducted in one French adult surgical ICU. From January 2012 to December 2016, patients with at least a single positive LNZ-resistant S. epidermidis blood culture were matched to control with LNZ-susceptible S. epidermidis blood culture in a 1:4 manner. Cases were compared to controls regarding baseline clinical characteristics and LNZ exposure before positive blood culture. Bacterial isolates were genotyped by using pulsed-field gel electrophoresis (PFGE) and MLST. We identified 13 LNZ-resistant S. epidermidis isolates, 1 in 2012, 3 in 2014, 6 in 2015, and 3 in 2016. LNZ use increased steadily from 8 DDDs/100 patient days in 2010 to 19 in 2013 and further decrease by more of 50% in 2015 and 2016. The only independent risk factors associated to LNZ-resistant S. epidermidis isolation were length of stay in ICU before infection (OR 1.45; 95% CI 1.07-1.98), prior exposure to LNZ (OR 109; 95% CI 3.9-3034), and Charlson comorbidities score (OR 3.19; 95% CI 1.11-9.14). PFGE typing showed that all LNZ-resistant isolates were clonal belonging to ST2 and that LNZ-susceptible isolates were highly diverse. We report herein that previous exposure to LNZ substantially increased the risk of occurrence of LNZ resistance in S. epidermidis even in the case of clonal spread of LNZ-resistant isolates. These findings highlight the need for reducing the use of LNZ to preserve its efficacy in the future.

Linezolid and Its Immunomodulatory Effect: In Vitro and In Vivo Evidence

Recent studies have explored the effects of some antibacterial agents on various aspects of the immune response to infection in addition to their bactericidal effects. As a synthetic oxazolidinone class of antibacterial agent, linezolid (LZD) exhibits activity against a broad range of Gram-positive bacteria. In the present review, we summarized the effects of LZD on the immune response and new approaches that can exploit such interactions for the treatment of bacterial infections. In vitro and pre-clinical evidence demonstrate that LZD suppresses the phagocytic ability, cytokine synthesis, and secretion of immune cells as well as the expressions of immune-related genes at the mRNA level under the stimulation of endotoxin or pathogens. Immunomodulatory effects of LZD can not only reduce the inflammatory damage induced by exaggerated or prolonged release of pro-inflammatory cytokines during infections but can also be applied to alleviate the symptoms of non-infectious inflammatory conditions. Further research is necessary to explore the molecular mechanisms involved and confirm these findings in clinical practice.

The emergence of Staphylococcus epidermidis simultaneously nonsusceptible to linezolid and teicoplanin in China

Two linezolid-resistant and teicoplanin-intermediate Staphylococcus epidermidis strains were isolated from blood cultures in China. The 2 S. epidermidis strains were methicillin-resistant and showed multidrug-resistance patterns; in addition, population analysis profiling/area under the curve (PAP/AUC) result showed heterogeneous resistant to vancomycin. Comparing to teicoplanin susceptible strains, the 2 isolates showed reduced autolytic activity. Pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) indicated that the 2 S. epidermidis isolates belonged to the same clone. Furthermore, the cfr gene, a G2576T mutation, and a novel C2146T mutation were detected in the 2 isolates. This was the first report of S. epidermidis simultaneously nonsusceptible to linezolid and teicoplanin in China.

Linezolid use in German acute care hospitals: results from two consecutive national point prevalence surveys

Background

Linezolid belongs to a reserve group of antibiotics. In recent years, reports on linezolid resistance in gram-positive cocci have become more frequent. Overuse of linezolid is a relevant factor for resistance development. The objective of this study was to describe current prescription practices of linezolid in German hospitals and identify targets for antimicrobial stewardship interventions.

Methods

We analyzed all linezolid prescriptions from the datasets of the consecutive national point prevalence surveys performed in German hospitals in 2011 and 2016. In both surveys, data on healthcare-associated infections and antimicrobial use were collected following the methodology of the European Centre for Disease Prevention and Control.

Results

Overall, the percentage of linezolid among all documented antimicrobials increased significantly from 2011 to 2016 (p < 0.01). In 2011, 0.3% (119 of 41,539) patients received linezolid, in 2016 this proportion was significantly higher (0.4%; 255 of 64,412 patients; p < 0.01). In 2016, intensive care units (ICUs) were the wards most frequently prescribing linezolid. The largest proportion of patients receiving linezolid were non-ICU patients. Roughly 38% of linezolid prescriptions were for treatment of skin/soft tissue and respiratory tract infections. In 2016, linezolid was administered parenterally in 70% (n = 179) of cases. Multivariable analysis showed that the ward specialty ICU posed an independent risk factor, while Northern and Southwestern regions in Germany were independent protective factors for a high rate of linezolid prescriptions.

Conclusions

In conclusion, we detected potentials for improving linezolid prescription practices in German hospitals. Given the emergence of linezolid resistance, optimization of linezolid use must be a target of future antimicrobial stewardship activities.

ZAAPS programme results for 2016: an activity and spectrum analysis of linezolid using clinical isolates from medical centres in 42 countries

Objectives

To report the linezolid activity, resistance mechanisms and epidemiological typing of selected isolates observed during the 2016 Zyvox® Annual Appraisal of Potency and Spectrum (ZAAPS) programme.

Methods

A total of 8325 organisms were consecutively collected from 76 centres in 42 countries (excluding the USA). Broth microdilution susceptibility testing was performed and isolates displaying linezolid MICs of ≥4 mg/L were molecularly characterized.

Results

Linezolid inhibited 99.8% of all Gram-positive pathogens at the respective susceptible breakpoints and showed a modal MIC of 1 mg/L, except for CoNS, for which the modal MIC result was 0.5 mg/L. Among isolates displaying linezolid MICs of ≥4 mg/L, one Staphylococcus aureus (linezolid MIC of 4 mg/L) harboured cfr and belonged to ST72, while four CoNS (MICs of 16-32 mg/L; ST2) showed drug target alterations. Two Enterococcus faecium (ST117) from a single site in Rome were linezolid non-susceptible (MICs of 8 mg/L) and had G2576T mutations. Eight linezolid-non-susceptible Enterococcus faecalis (MICs of 4 mg/L; 4 sites in 4 countries; ST256, ST480, ST766 and ST775) carried optrA and isolates carrying optrA from the same medical centre were genetically related. One Streptococcus gallolyticus (MIC of 4 mg/L) and one Streptococcus mitis (MIC of 16 mg/L) carried optrA and G2576T mutations, respectively.

Conclusions

These results document the continued long-term in vitro potency of linezolid. Alterations in the 23S rRNA and/or L3/L4 proteins remain the main oxazolidinone resistance mechanisms in E. faecium and CoNS, whereas optrA emerged as the sole mechanism in E. faecalis. Surveillance and infection control will be important strategies to detect optrA and prevent it from disseminating.

Probabilistic chemotherapy in knee and hip replacement infection: the place of linezolid

Prosthetic joint infection (PJI) can occur with a wide range of microorganisms and clinical features. After replacement surgery of prosthetic joint, prescription of probabilistic broad-spectrum antimicrobial therapy is usual, while awaiting microbial culture results. The aim of our study was to describe the antibiotic susceptibility of microorganisms isolated from hip and knee PJI. The data were collected to determine the best alternative to the usual combination of piperacillin-tazobactam (TZP) or cefotaxime (CTX) and vancomycin (VAN). Based on a French prospective, multicenter study, we analyzed microbiological susceptibility to antibiotics of 183 strains isolated from patients with confirmed hip or knee PJI. In vitro susceptibility was evaluated: TZP+VAN, TZP+linezolid (LZD), CTX+VAN, and CTX+LZD. We also analyzed resistance to different antibiotics commonly used as oral alternatives. Among the 183 patients with PJI, 62 (34%) had a total knee prosthesis, and 121 (66%) a hip prosthesis. The main identified bacteria were Staphylococcus aureus (32.2% of isolates), coagulase-negative staphylococci (27.3%), Enterobacteriaceae (14.2%), and Streptococcus (13.7%). Infections were polymicrobial for 28 (15.3%) patients. All combinations were highly effective: CTX+VAN, CTX+LZD, TZP+VAN, and TZP+LZD (93.4%, 94%, 98.4%, and 98.9% of all cases respectively). Use of LZD instead of VAN in combination with a broad-spectrum beta-lactam covers almost all of the bacteria isolated in PJI. This association should be considered in probabilistic chemotherapy, as it is particularly easy to use (oral administration and no vancomycin monitoring).

Tedizolid in vitro activity against Gram-positive clinical isolates causing bone and joint infections in hospitals in the USA and Europe (2014–17)

Background

Despite the advances in current healthcare, bone and joint infections (BJIs) are a major clinical challenge that frequently involve prolonged systemic antibiotic use. Healthcare providers consider tedizolid an attractive candidate for therapy in adults and children with BJI.

Objectives

We tested tedizolid against a US and European collection of Gram-positive BJI isolates (n = 797) consecutively collected from 2014 to 2017.

Methods

Organisms were tested by broth microdilution susceptibility methods following current CLSI guidelines and interpreted by both CLSI and EUCAST breakpoint criteria.

Results

Staphylococcus aureus (59.3%; 58.6% in the USA and 60.4% in Europe) was the most common pathogen with a 29.6% MRSA rate and tedizolid MIC50/90 of 0.12/0.25 mg/L (100% susceptible). CoNS (15.0% of BJI in adults and <5% in children) had tedizolid MIC50/90 values of 0.12/0.12 mg/L (99.1% susceptible). Tedizolid exhibited MIC50/90 values of 0.12/0.25 mg/L for all streptococci and enterococci. Overall, high susceptibility rates (>95%) for vancomycin, daptomycin and linezolid were observed and, based on MIC90 values, tedizolid (MIC90 0.12–0.25 mg/L) was 4- to 8-fold more potent than linezolid (MIC90 0.5–2  mg/L) against this collection of Gram-positive pathogens causing BJI.

Conclusions

This study showed that tedizolid had potent in vitro activity against contemporary Gram-positive cocci causing BJI in adults and children in US and European hospitals.

Low Prevalence of Gram-Positive Isolates Showing Elevated Lefamulin MIC Results during the SENTRY Surveillance Program for 2015-2016 and Characterization of Resistance Mechanisms

This study investigated the molecular mechanisms possibly associated with non-wild-type MICs for lefamulin among staphylococci and streptococci included in the lefamulin surveillance program from 2015 to 2016. A total of 2,919 Staphylococcus aureus, 276 coagulase-negative staphylococci (CoNS), 3,923 Streptococcus pneumoniae, 389 β-hemolytic, and 178 viridans group streptococci isolates were included in the surveillance studies. Eleven (0.3% of all S. aureus) S. aureus isolates with lefamulin MICs above the staphylococcal epidemiological cutoff (ECOFF) value (>0.25 μg/ml) were selected for this study. Eight (72.7%) S. aureus (lefamulin MIC, 0.5 to 4 μg/ml) isolates carried vga(A or E), one isolate (MIC, 32 μg/ml) carried lsa(E), one isolate (MIC, 16 μg/ml) had an alteration in L4, and one strain (MIC, 0.5 μg/ml) did not carry any of the investigated resistance mechanisms. A total of 14 (5.1% of all CoNS) CoNS isolates had lefamulin MICs (0.5 to >32 μg/ml) above the ECOFF. Similar to S. aureus, 8 (57.1%) CoNS (lefamulin MIC, 1 to 8 μg/ml) isolates carried vga(A or B), while 2 isolates (MIC, 4 to 32 μg/ml) carried cfr High genetic diversity was observed among staphylococci, although 3 S. aureus isolates belonged to sequence type 398 (ST398). Among the 3 Streptococcus agalactiae and 3 viridans group streptococci (0.1% of all streptococci surveyed) isolates selected for additional characterization, all but 1 isolate carried lsa(E). This study documents a low occurrence of surveillance isolates exhibiting a non-wild-type MIC for lefamulin, and among these isolates, vga and lsa(E) prevailed in staphylococci and streptococci, respectively.

A selective culture medium for screening linezolid-resistant gram-positive bacteria

The SuperLinezolid medium was developed for screening resistance to linezolid (LZD) in Gram-positive bacteria (Staphylococcus spp., Enterococcus spp.). It was evaluated using LZD-susceptible (n = 20) and LZD-resistant (n = 17) Gram-positive isolates. The sensitivity was found to be 82% at 24 h (3 out of 17 isolates being missed), and reached 100% at 48 h. At 48 h, a single LZD-susceptible isolate grew (specificity 95%). By testing stools spiked with LZD-resistant Gram-positive strains, an excellent performance of the medium was observed, with a lowest detection limit ranging from 10¹ to 10² CFU/ml. Overall, this medium is accurate for detection of LZD-resistant Gram-positive isolates after 24 h of culture.

In vitro activities of daptomycin combined with fosfomycin or rifampin on planktonic and adherent linezolid-resistant isolates of Enterococcus faecalis

PURPOSE

This study aimed to explore daptomycin combined with fosfomycin or rifampin against the planktonic and adherent linezolid-resistant isolates of Enterococcus faecalis.

METHODOLOGY

Four linezolid-resistant and four linezolid-sensitive isolates of E. faecalis which formed biofilms were collected for this study. Biofilm biomasses were detected by crystal violet staining and the adherent cells in the mature biofilms were quantified by c.f.u. determination.

RESULTS

Daptomycin alone, or combined with fosfomycin or rifampin (4×MIC) demonstrated bactericidal activities on the planktonic cells, and daptomycin combined with fosfomycin killed more planktonic cells (at least 1-log10 c.f.u. ml^-1) than daptomycin or fosfomycin alone. Daptomycin alone (16×MIC) showed anti-biofilm activities against the mature biofilms and bactericidal activities on the adherent cells, while daptomycin combined with fosfomycin (16×MIC) demonstrated significantly more anti-biofilm activities than daptomycin or fosfomycin alone and effectively killed the adherent cells in the mature biofilms. The high concentration of daptomycin (512 mg l^-1 ) combined with fosfomycin indicated more bactericidal activities on the adherent cells and more anti-biofilm activities against the mature biofilms than daptomycin 64 mg l^-1 (16×MIC) combined with fosfomycin. The addition of rifampin increased the anti-biofilm and bactericidal activities of daptomycin against the mature biofilms and the adherent cells of two isolates, however, which was not observed in other isolates.

CONCLUSIONS

Daptomycin combined with fosfomycin demonstrated better effect on the planktonic and adherent linezolid-resistant isolates of E. faecalis than daptomycin or fosfomycin alone. The role of rifampin in the treatment of E. faecalis isolates is discrepant and needs more studies.

Antimicrobial Resistance Surveillance and New Drug Development

Surveillance represents an important informational tool for planning actions to monitor emerging antimicrobial resistance. Antimicrobial resistance surveillance (ARS) programs may have many different designs and can be grouped in 2 major categories based on their main objectives: (1) public health ARS programs and (2) industry-sponsored/product-oriented ARS programs. In general, public health ARS programs predominantly focus on health care and infection control, whereas industry ARS programs focus on an investigational or recently approved molecule(s). We reviewed the main characteristics of industry ARS programs and how these programs contribute to new drug development. Industry ARS programs are generally performed to comply with requirements from regulatory agencies responsible for commercial approval of antimicrobial agents, such as the US Food and Drug Administration, European Medicines Agency, and others. In contrast to public health ARS programs, which typically collect health care and diverse clinical data, industry ARS programs frequently collect the pathogens and perform the testing in a central laboratory setting. Global ARS programs with centralized testing play an important role in new antibacterial and antifungal drug development by providing information on the emergence and dissemination of resistant organisms, clones, and resistance determinants. Organisms collected by large ARS programs are extremely valuable to evaluate the potential of new agents and to calibrate susceptibility tests once a drug is approved for clinical use. These programs also can provide early evaluations of spectrum of activity and postmarketing trends required by regulatory agencies, and the programs may help drug companies to select appropriate dosing regimens and the appropriate geographic regions in which to perform clinical trials. Furthermore, these surveillance programs provide useful information on the potency and spectrum of new antimicrobial agents against indications and organisms in which clinicians have little or no experience. In summary, large ARS programs, such as the SENTRY Antimicrobial Surveillance Program, contribute key data for new drug development.

Temporal and Geographic Variation in Antimicrobial Susceptibility and Resistance Patterns of Enterococci: Results From the SENTRY Antimicrobial Surveillance Program, 1997-2016

Background

The SENTRY Antimicrobial Surveillance Program was established in 1997 and presently encompasses more than 750 000 bacterial isolates from over 400 medical centers worldwide. Among these pathogens, enterococci represents a prominent cause of bloodstream (BSIs), intra-abdominal (IAIs), skin and skin structure, and urinary tract infections (UTIs). In the present study, we reviewed geographic and temporal trends in Enterococcus species and resistant phenotypes identified throughout the SENTRY Program.

Methods

From 1997 to 2016, a total of 49 491 clinically significant enterococci isolates (15 species) were submitted from 298 medical centers representing the Asia-Pacific (APAC), European, Latin American (LATAM), and North American (NA) regions. Bacteria were identified by standard algorithms and matrix-assisted laser desorption ionization–time of flight mass spectrometry. Susceptibility (S) testing was performed by reference broth microdilution methods and interpreted using Clinical and Laboratory Standards Institute/US Food and Drug Administration and European Committee on Antimicrobial Susceptibility Testing criteria.

Results

The most common Enterococcus species in all 4 regions were Enterococcus faecalis (64.7%) and E. faecium (EFM; 29.0%). Enterococci accounted for 10.7% of BSIs in NA and was most prominent as a cause of IAIs (24.0%) in APAC and of UTIs (19.8%) in LATAM. A steady decrease in the susceptibility to ampicillin and vancomycin was observed in all regions over the 20-year interval. Vancomycin-resistant enterococci (VRE) accounted for more than 8% of enterococcal isolates in all regions and was most common in NA (21.6%). Among the 7615 VRE isolates detected, 89.1% were the VanA phenotype (91.0% EFM) and 10.9% were VanB. Several newer antimicrobial agents demonstrated promising activity against VRE, including daptomycin (99.6–100.0% S), linezolid (98.0%–99.6% S), oritavancin (92.2%–98.3% S), tedizolid (99.5%–100.0% S), and tigecycline (99.4%–100.0% S).

Conclusions

Enterococci remained a prominent gram-positive pathogen in the SENTRY Program from 1997 through 2016. The overall frequency of VRE was 15.4% and increased over time in all monitored regions. Newly released agents with novel mechanisms of action show promising activity against VRE.

Antibiotic resistance among ocular pathogens: current trends from the ARMOR surveillance study (2009-2016)

BACKGROUND

The Antibiotic Resistance Monitoring in Ocular micRoorganisms study is an ongoing surveillance study that tracks antibiotic resistance among bacterial isolates from ocular infections across the United States. We report antibiotic resistance rates and trends from 2009 through 2016.

MATERIALS AND METHODS

Staphylococcus aureus, coagulase-negative staphylococci (CoNS), Streptococcus pneumoniae, Pseudomonas aeruginosa, and Haemophilus influenzae from various ocular infections were obtained from participating United States centers. Isolates were sent to a central laboratory for determination of antibiotic resistance profiles. Minimum inhibitory concentrations were determined by broth microdilution according to the Clinical and Laboratory Standards Institute for drugs from more than ten antibiotic classes, and isolates were classified as susceptible or resistant based on systemic breakpoints, wherever available. Resistance rates were also evaluated based on decade of patient life and longitudinally over the 8-year time period.

RESULTS

A total of 1,695 S. aureus, 1,475 CoNS, 474 S. pneumoniae, 586 H. influenzae, and 599 P. aeruginosa were collected from 87 sites. Resistance was high among staphylococci and pneumococci, with methicillin resistance detected in 621 (36.6%) S. aureus and 717 (48.6%) CoNS isolates. Multidrug resistance (≥3 drug classes) was observed among staphylococci, particularly in methicillin-resistant (MR) isolates (MR S. aureus [MRSA]: 76.2%; MR CoNS [MRCoNS]: 73.5%). Differences in methicillin resistance among staphylococci were observed based on patient age, with higher rates observed in older patients (P<0.0001). For certain organism-antibiotic combinations, there were significant changes in resistance over time, including a decrease in methicillin resistance among S. aureus (but not CoNS); no notable trends were observed for S. pneumoniae.

CONCLUSION

Antibiotic resistance was prevalent among gram-positive organisms, and MR staphylococcal isolates were more likely to be multidrug resistant. Although a small decrease in methicillin resistance was observed among S. aureus over time, the continued high prevalence of in vitro methicillin resistance should be considered when treating patients with ocular infections.

Omadacycline Enters the Ring: A New Antimicrobial Contender

Omadacycline is a novel aminomethylcycline approved for the treatment of community‐acquired bacterial pneumonia and acute bacterial skin and skin structure infections. This article reviews existing data pertaining to the biochemistry, mechanism of action, pharmacokinetics/pharmacodynamics, in vitro activity, and current progress with omadacycline in clinical trials. Omadacycline inhibits protein synthesis by binding to the 30S subunit of the bacterial ribosome at the tetracycline‐binding site with an affinity similar to glycylcyclines. It is able to bypass older tetracycline resistance mechanisms and demonstrates activity against bacterial strains that are tetracycline resistant. In addition, omadacycline displays broad‐spectrum activity against gram‐positive organisms (including methicillin‐resistant Staphylococcus aureus and vancomycin‐resistant enterococci), gram‐negative organisms, atypical organisms, and anaerobes. It has been evaluated against infections in adults both intravenously and orally. Dosage adjustments are not required for patients with renal impairment. Omadacycline displays a comparable efficacy and safety profile to standard‐of‐care agents, with the most common side effects observed being gastrointestinal. Currently available data for omadacycline suggest that this is a promising agent added to our antimicrobial armamentarium.

Complete Genome Sequence and Characterization of Linezolid-Resistant Enterococcus faecalis Clinical Isolate KUB3006 Carrying a cfr(B)-Transposon on Its Chromosome and optrA-Plasmid

Linezolid (LZD) has become one of the most important antimicrobial agents for infections caused by gram-positive bacteria, including those caused by Enterococcus species. LZD-resistant (LR) genetic features include mutations in 23S rRNA/ribosomal proteins, a plasmid-borne 23S rRNA methyltransferase gene cfr, and ribosomal protection genes (optrA and poxtA). Recently, a cfr gene variant, cfr(B), was identified in a Tn6218-like transposon (Tn) in a Clostridioides difficile isolate. Here, we isolated an LR Enterococcus faecalis clinical isolate, KUB3006, from a urine specimen of a patient with urinary tract infection during hospitalization in 2017. Comparative and whole-genome analyses were performed to characterize the genetic features and overall antimicrobial resistance genes in E. faecalis isolate KUB3006. Complete genome sequencing of KUB3006 revealed that it carried cfr(B) on a chromosomal Tn6218-like element. Surprisingly, this Tn6218-like element was almost (99%) identical to that of C. difficile Ox3196, which was isolated from a human in the UK in 2012, and to that of Enterococcus faecium 5_Efcm_HA-NL, which was isolated from a human in the Netherlands in 2012. An additional oxazolidinone and phenicol resistance gene, optrA, was also identified on a plasmid. KUB3006 is sequence type (ST) 729, suggesting that it is a minor ST that has not been reported previously and is unlikely to be a high-risk E. faecalis lineage. In summary, LR E. faecalis KUB3006 possesses a notable Tn6218-like-borne cfr(B) and a plasmid-borne optrA. This finding raises further concerns regarding the potential declining effectiveness of LZD treatment in the future.

Linezolid resistance genes and genetic elements enhancing their dissemination in enterococci and streptococci

Linezolid is considered a last resort drug in treatment of severe infections caused by Gram-positive pathogens, resistant to other antibiotics, such as vancomycin-resistant enterococci (VRE), methicillin-resistant staphylococci and multidrug resistant pneumococci. Although the vast majority of Gram-positive pathogenic bacteria remain susceptible to linezolid, resistant isolates of enterococci, staphylococci and streptococci have been reported worldwide. In these bacteria, apart from mutations, affecting mostly the 23S rRNA genes, acquisition of such genes as cfr, cfr(B), optrA and poxtA, often associated with mobile genetic elements (MGE), plays an important role for resistance. The purpose of this paper is to provide an overview on diversity and epidemiology of MGE carrying linezolid-resistance genes among clinically-relevant Gram-positive pathogens such as enterococci and streptococci.

Characterization of a Multiresistance Plasmid Carrying the optrA and cfr Resistance Genes From an Enterococcus faecium Clinical Isolate

Enterococcus faecium E35048, a bloodstream isolate from Italy, was the first strain where the oxazolidinone resistance gene optrA was detected outside China. The strain was also positive for the oxazolidinone resistance gene cfr. WGS analysis revealed that the two genes were linked (23.1 kb apart), being co-carried by a 41,816-bp plasmid that was named pE35048-oc. This plasmid also carried the macrolide resistance gene erm(B) and a backbone related to that of the well-known Enterococcus faecalis plasmid pRE25 (identity 96%, coverage 65%). The optrA gene context was original, optrA being part of a composite transposon, named Tn6628, which was integrated into the gene encoding for the ζ toxin protein (orf19 of pRE25). The cfr gene was flanked by two ISEnfa5 insertion sequences and the element was inserted into an lnu(E) gene. Both optrA and cfr contexts were excisable. pE35048-oc could not be transferred to enterococcal recipients by conjugation or transformation. A plasmid-cured derivative of E. faecium E35048 was obtained following growth at 42°C, and the complete loss of pE35048-oc was confirmed by WGS. pE35048-oc exhibited some similarity but also notable differences from pEF12-0805, a recently described enterococcal plasmid from human E. faecium also co-carrying optrA and cfr; conversely it was completely unrelated to other optrA- and cfr-carrying plasmids from Staphylococcus sciuri. The optrA-cfr linkage is a matter of concern since it could herald the possibility of a co-spread of the two genes, both involved in resistance to last resort agents such as the oxazolidinones.