Linezolid-resistant clinical isolates of meticillin-resistant coagulase-negative staphylococci and Enterococcus faecium from China

Staphylococcus capitis: insights into epidemiology, virulence, and antimicrobial resistance of a clinically relevant bacterial species

SUMMARYStaphylococcus capitis is divided into two subspecies, S. capitis subsp. ureolyticus (renamed urealyticus in 1992; ATCC 49326) and S. capitis subsp. capitis (ATCC 27840), and fits with the archetype of clinically relevant coagulase-negative staphylococci (CoNS). S. capitis is a commensal bacterium of the skin in humans, which must be considered an opportunistic pathogen of interest particularly as soon as it is identified in a clinically relevant specimen from an immunocompromised patient. Several studies have highlighted the potential determinants underlying S. capitis pathogenicity, resistance profiles, and virulence factors. In addition, mobile genetic element acquisitions and mutations contribute to S. capitis genome adaptation to its environment. Over the past decades, antibiotic resistance has been identified for S. capitis in almost all the families of the currently available antibiotics and is related to the emergence of multidrug-resistant clones of high clinical significance. The present review summarizes the current knowledge concerning the taxonomic position of S. capitis among staphylococci, the involvement of this species in human colonization and diseases, the virulence factors supporting its pathogenicity, and the phenotypic and genomic antimicrobial resistance profiles of this species.

Recent advances in the exploration of oxazolidinone scaffolds from compound development to antibacterial agents and other bioactivities

Bacterial infections cause a variety of life-threatening diseases, and the continuous evolution of drug-resistant bacteria poses an increasing threat to current antimicrobial regimens. Gram-positive bacteria (GPB) have a wide range of genetic capabilities that allow them to adapt to and develop resistance to practically all existing antibiotics. Oxazolidinones, a class of potent bacterial protein synthesis inhibitors with a unique mechanism of action involving inhibition of bacterial ribosomal translation, has emerged as the antibiotics of choice for the treatment of drug-resistant GPB infections. In this review, we discussed the oxazolidinone antibiotics that are currently on the market and in clinical development, as well as an updated synopsis of current advances on their analogues, with an emphasis on innovative strategies for structural optimization of linezolid, structure-activity relationship (SAR), and safety properties. We also discussed recent efforts aimed at extending the activity of oxazolidinones to gram-negative bacteria (GNB), antitumor, and coagulation factor Xa. Oxazolidinone antibiotics can accumulate in GNB by a conjugation to siderophore-mediated β-lactamase-triggered release, making them effective against GNB.

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.

Mechanisms of linezolid resistance in Staphylococcus capitis with the novel mutation C2128T in the 23S rRNA gene in China

PURPOSE

The objective of this study was to investigate the molecular characteristics and potential resistance mechanisms of linezolid-resistant (LZR) Staphylococcus capitis isolates from a tertiary hospital in China.

METHODS

S. capitis isolates were obtained from clinical patient specimens; three of the isolates came from blood cultures and one from the hydrothorax. The agar dilution and E-test methods were used to identify antibiotic resistance. The chloramphenicol-florfenicol resistance (cfr) gene carrier status of the strains was determined by PCR. Whole-genome sequencing (WGS) was used to identify point mutations and L3, L4, and L22 mutations and to study the genetic environment of the cfr gene and the relationships between strains.

RESULTS

The 4 isolates obtained in this study were all linezolid-resistant Staphylococcus strains. A similar of susceptibility profile pattern was observed in all four S. capitis strains, each of which exhibited a multidrug-resistant phenotype. A potentially novel mutation, C2128T, was identified, and the cfr genes of S. capitis strains were all positive. Additionally, the same mutations (C2128T and G2600T) were identified in all 23S rRNA sequences of the isolates, whereas mutations were lacking in the L3, L4, and L22 ribosomal proteins. The genetic environments surrounding cfr were identical in all four isolates. A schematic diagram of the phylogenetic tree showed that they were closely related to AYP1020, CR01, and TW2795, and a total of seven drug resistance genes were identified in these strains.

CONCLUSIONS

The study indicated that the resistance of the Staphylococcus capitis strains to linezolid was caused by multiple mechanisms, and a potential novel mutation, C2128T, that may have an impact on bacterial resistance was identified.

Global Expansion of Linezolid-Resistant Coagulase-Negative Staphylococci

Coagulase-negative staphylococci (CoNS) for a long time were considered avirulent constituents of the human and warm-blooded animal microbiota. However, at present, S. epidermidis, S. haemolyticus, and S. hominis are recognized as opportunistic pathogens. Although linezolid is not registered for the treatment of CoNS infections, it is widely used off-label, promoting emergence of resistance. Bioinformatic analysis based on maximum-likelihood phylogeny and Bayesian clustering of the CoNS genomes obtained in the current study and downloaded from public databases revealed the existence of international linezolid-resistant lineages, each of which probably had a common predecessor. Linezolid-resistant S. epidermidis sequence-type (ST) 2 from Russia, France, and Germany formed a compact group of closely related genomes with a median pairwise single nucleotide polymorphism (SNP) difference of fewer than 53 SNPs, and a common ancestor of this lineage appeared in 1998 (1986-2006) before introduction of linezolid in practice. Another compact group of linezolid-resistant S. epidermidis was represented by ST22 isolates from France and Russia with a median pairwise SNP difference of 40; a common ancestor of this lineage appeared in 2011 (2008-2013). Linezolid-resistant S. hominis ST2 from Russia, Germany, and Brazil also formed a group with a high-level genome identity with median 25.5 core-SNP differences; the appearance of the common progenitor dates to 2003 (1996-2012). Linezolid-resistant S. hominis isolates from Russia demonstrated associated resistance to teicoplanin. Analysis of a midpoint-rooted phylogenetic tree of the group confirmed the genetic proximity of Russian and German isolates; Brazilian isolates were phylogenetically distant. repUS5-like plasmids harboring cfr were detected in S. hominis and S. haemolyticus.

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.

The emergence of plasmid-borne cfr-mediated linezolid resistant-staphylococci in Vietnam

OBJECTIVES

Linezolid is one of the last resort antibiotics effectively used in the treatment of infections caused by multidrug-resistant Gram-positive bacteria. Recent outbreaks of Linezolid resistance have been the great concern worldwide, while many countries have not experienced it. In this work, we aimed to evaluate the existence of linezolid resistance and further clarify potential resistance mechanism(s) in staphylococcal isolates obtained from the hospital in Vietnam, a country in which linezolid resistance had not been previously detected.

METHODS

Seventy staphylococcal clinical isolates including MRSA (n=63) and methicillin-resistant coagulase-negative staphylococci (MRCNS, n=7) were collected and analyzed for linezolid resistance. Linezolid-resistant isolates were submitted for whole genome sequencing to search for the resistance determinants.

RESULTS

We identified two coagulase-negative staphylococcal isolates that were resistant to linezolid. Whole genome sequencing revealed several alterations in the 23S rRNA and L3, L17, L22, L24, L30 ribosomal proteins. Importantly, both isolates harbour the chloramphenicol/florfenicol resistance (cfr) gene on a plasmid. The plasmid was closely identical to the pLRSA417 plasmid that was originally reported in China.

CONCLUSIONS

To the best of our knowledge, this is the first report of cfr-mediated linezolid resistance in clinically isolated staphylococci in Vietnam. We suggest that adequate surveillance is necessary to monitor the dissemination of linezolid resistance among staphylococcal species and other important pathogens.

Genomic and functional characterization of fecal sample strains of Proteus cibarius carrying two floR antibiotic resistance genes and a multiresistance plasmid-encoded cfr gene

The objective of this study was to investigate the molecular characteristics and horizontal transfer of florfenicol resistance gene-related sequences in Proteus strains isolated from animals. A total of six Proteus strains isolated from three farms between 2015 and 2016 were screened by polymerase chain reaction (PCR) for known florfenicol resistance genes. Proteus cibarius G11, isolated from the fecal material of a goose, was found to harbor both cfr and floR genes. Whole genome sequencing revealed that the strain harbored two copies of the floR gene: one was located on the chromosome and the other was located on a plasmid named pG11-152. Two floR-containing fragments 4028 bp in length were identical and showed transposon-like structures. The cfr gene was found on a plasmid named pG11-51 and flanked by a pair of IS26s. Thus, mobile genetic elements played an important role in floR replication and horizontal resistance gene transfer. Therefore, increasing attention should be paid to monitoring the spread of resistance genes and resistance in real time.

High Level Aminoglycoside Resistance And Distribution Of The Resistance Genes In Enterococcus faecalis And Enterococcus faecium From Teaching Hospital In Malaysia

Background

Enterococcus faecium and Enterococcus faecalis are among the predominant species causing hospital-acquired infections. Currently, enterococcal infections are treated using combination therapy of an aminoglycoside with cell-wall active agents, which led to high level aminoglycoside resistance (HLAR) and vancomycin resistance (VRE) among enterococci. The aim of this study was to determine the prevalence of HLAR and the distribution of the resistance genes among clinical E. faecalis and E. faecium isolates in Malaysia.

Materials and methods

Seventy-five enterococci isolates recovered from different clinical sources were re-identified by subculturing on selective medium, Gram staining, biochemical profiling (API 20 Strep), and 16s rRNA sequencing. Antimicrobial susceptibility testing (AST) was performed using Kirby-Bauer disc diffusion, E-test, and broth microdilution methods. PCR amplification was used to detect the presence of aminoglycoside modifying enzyme (AME) genes [aac(6')-Ie-aph(2")-Ia, aph(2")-Ib, aph(2")-Ic, aph(2")-Id, aph(3')-IIIa]. Descriptive data analysis was used to analyze the antibiotic susceptibility profiles and the distribution of HLAR genes.

Results

The majority of the isolates recovered from the clinical samples are E. faecalis (66.7%), with the highest recovery from the pus. The prevalence of HLGR (51%) is higher when compared to HLSR (45-49%). Analysis of the resistance genes showed that bifunctional genes aac(6')-Ie-aph(2")-Ia and aph(3')-IIIa contributed to the HLAR E. faecalis and E. faecium. The other AME genes [aph(2")-Ib, aph(2")-Ic, aph(2")-Id] were not detected in this study.

Conclusion

This study provides the first prevalence data on HLAR and the distribution of the AME genes among E. faecalis and E. faecium isolates from Malaysia. These highlight the need for continued antibiotic surveillance to minimize its emergence and further dissemination.

Linezolid resistant coagulase negative staphylococci (LRCoNS) with novel mutations causing blood stream infections (BSI) in India

Background

Coagulase-negative Staphylococci (CoNS) have emerged as a major causative agent of blood-stream infections (BSI). Linezolid (LZD) is currently used for treating glycopeptide and methicillin-resistant staphylococci. It is important to understand the resistance mechanism and probable transmission of LZD resistant (LR) CoNS within the hospital.

Methods

Clinically significant LRCoNS from patients with BSI were characterized using MALDI-TOF and 16S rRNA gene sequence analysis. Antimicrobial susceptibility and MIC of vancomycin and LZD were determined. LZD resistance mechanisms using PCR for the cfr gene and mutation in the V domain of the 23S rRNA gene were studied.

Results

The MIC of LZD ranged from 8 to 32 μg/ml. LR was observed in three different CoNS species from diverse locations within the hospital. The cfr gene was identified in all the isolates. Sequence analysis of V domain region of 23S rRNA gene confirmed mutation in single copy among 12/15 isolates with novel mutations: G2614 T and C2384T. All infections were nosocomially acquired and LZD resistance was emerging in the absence of prior LZD use. Horizontal spread of resistant isolates and cfr gene among diverse species were the probable mechanisms of transmission.

Conclusion

The study highlights the novel mutations associated with LRCoNS and the importance of surveillance & transmission pathway within the hospital. It also systematically discusses the published information on LRCoNS.

Distribution of the optrA gene in Enterococcus isolates at a tertiary care hospital in China

OBJECTIVES

Linezolid-resistant Enterococcus have spread worldwide. This study investigated the prevalence of linezolid-non-susceptible Enterococcus (LNSE) and the potential mechanism and molecular epidemiology of LNSE isolates from Nanjing, China.

METHODS

Linezolid susceptibility of 2555 Enterococcus was retrospectively determined by Etest. Vancomycin and teicoplanin MICs were determined for LNSE by Etest. PCR and DNA sequencing were used to investigate the potential molecular mechanism. Clonal relatedness between LNSE isolates was analysed by MLST. WGS was also performed.

RESULTS

A total of 27 Enterococcus isolates (24 Enterococcus faecalis, 3 Enterococcus faecium) with linezolid MICs of 4-48μg/mL were identified, among which 20 E. faecalis and 3 E. faecium were positive for optrA. No mutations were found in genes encoding domain V of 23S rRNA or ribosomal proteins L3/L4; the cfr gene was not found. The 24 linezolid-non-susceptible E. faecalis were classified into eight STs (ST16, ST480, ST476, ST631, ST585, ST428, ST25 and ST689). The three linezolid-non-susceptible E. faecium were classified as ST17, ST400 and ST195. Comparison of the deduced OptrA amino acid sequences of the 23 optrA-positive isolates by PCR-based sequencing and WGS with that of the original OptrA from E. faecalis E349 revealed seven variants (KD, EDP, EDM, D, EDD, RDK and DP) in 16 isolates, with no mutations in the remaining 7 isolates. optrA was found downstream of fexA by searching the pE349 sequence based on WGS data.

CONCLUSIONS

Emergence of LNSE with optrA-mediated resistance and clonal dissemination of ST16 E. faecalis in our hospital may pose a potential public-health threat.

Dissemination of cfr-mediated linezolid resistance among Staphylococcus species isolated from a teaching hospital in Beijing, China

Objective

The aim of the present study was to report the dissemination of cfr and fexA genes mediated by linezolid resistance among Staphylococcus species.

Methods

Three methicillin-resistant staphylococci that were collected from a teaching hospital in Beijing were identified as linezolid-resistant. These three staphylococci were Staphylococcus aureus, S. haemolyticus, and S. cohnii. Mutations in domain V of 23S ribosomal RNA, ribosomal proteins, and the cfr, fexA, and optrA genes were analysed.

Results

The three isolates had no mutations of 23S ribosomal RNA, but showed mutations in the cfr and fexA genes. Mutations in the gene for ribosomal protein L3, which resulted in the amino acid exchanges Gly108Glu, Ser158Phe, and Asp159Tyr, were identified in S. cohnii X4535.

Conclusions

This is the first report of the cfr gene in clinical linezolid-resistant methicillin-resistant S. aureus isolated from Beijing. L3 mutations coupled with the cfr and fexA genes may act synergistically. Potential transmissibility of this agent, even without prior exposure to linezolid, may have serious epidemiological repercussions.

Linezolid: a promising option in the treatment of Gram-positives

Linezolid, an oxazolidinone antimicrobial agent that acts by inhibiting protein synthesis in a unique fashion, is used in the treatment of community-acquired pneumonia, skin and soft-tissue infections and other infections caused by Gram-positive bacteria including VRE and methicillin-resistant staphylococci. Currently, linezolid resistance among these pathogens remains low, commonly <1.0%, although the prevalence of antibiotic resistance is increasing in many countries. Therefore, the development of resistance by clinical isolates should prompt increased attention of clinical laboratories to routinely perform linezolid susceptibility testing for this important agent and should be taken into account when considering its therapeutic use. Considering the importance of linezolid in the treatment of infections caused by Gram-positive bacteria, this review was undertaken to optimize the clinical use of this antibiotic.

Diversity of staphylococcal cassette chromosome mec elements in nosocomial multiresistant Staphylococcus haemolyticus isolates

Staphylococcus haemolyticus is the second, most frequently isolated coagulase-negative staphyloccus (CoNS) from patients with hospital-acquired infections, and it is usually resistant to methicillin and other semisynthetic penicillins. The purpose of this study was to characterize staphylococcal cassette chromosome mec (SCCmec) elements and assess the in-vitro activity of antibiotics against 60 S. haemolyticus strains recovered from hospitalized patients. All these strains expressed methicillin resistance and carried a mecA gene. Moreover, all strains possessed a multiresistant phenotype, i.e., exhibited resistance to more than three classes of antibiotics. Eleven strains (18 %) harbored the SCCmec type V, containing ccrC and mec complex C. Three isolates harboring the ccrC gene did not contain a known mec complex. One strain positive for mec complex C was not typeable for ccr. This suggests that ccrC and mec complex C may exist autonomously. Only four strains carried mec complex B, whereas none of the S. haemolyticus harboured mec complex A. A new combination, which is mec complex B-ccrAB ship, was found in S. haemolitycus. The ccrAB ship was also identified in two strains of S. haemolitycus in which the mec gene complex was not identified. The results of the present study indicate that in S. haemolyticus the mec gene complex and the ccr genes are highly divergent. However, ccr sequence analysis does not allow the identification of a new allotype, based on a cut-off value of 85 % identity. The ccr genes in the S. haemolitycus strain showed ≥96 % sequence identity to the ccrAB2 genes.

Emerging issues in antimicrobial resistance of bacteria from food-producing animals

During the last decade, antimicrobial resistance in bacteria from food-producing animals has become a major research topic. In this review, different emerging resistance properties related to bacteria of food-producing animals are highlighted. These include: extended-spectrum β-lactamase-producing Enterobacteriaceae; carbapenemase-producing bacteria; bovine respiratory tract pathogens, such as Pasteurella multocida and Mannheimia haemolytica, which harbor the multiresistance mediating integrative and conjugative element ICEPmu1; Gram-positive and Gram-negative bacteria that carry the multiresistance gene cfr; and the occurrence of numerous novel antimicrobial resistance genes in livestock-associated methicillin-resistant Staphylococcus aureus. The emergence of the aforementioned resistance properties is mainly based on the exchange of mobile genetic elements that carry the respective resistance genes.

Insights on virulence from the complete genome of Staphylococcus capitis

Staphylococcus capitis is an opportunistic pathogen of the coagulase negative staphylococci (CoNS). Functional genomic studies of S. capitis have thus far been limited by a lack of available complete genome sequences. Here, we determined the closed S. capitis genome and methylome using Single Molecule Real Time (SMRT) sequencing. The strain, AYP1020, harbors a single circular chromosome of 2.44 Mb encoding 2304 predicted proteins, which is the smallest of all complete staphylococcal genomes sequenced to date. AYP1020 harbors two large mobile genetic elements; a plasmid designated pAYP1020 (59.6 Kb) and a prophage, ΦAYP1020 (48.5 Kb). Methylome analysis identified significant adenine methylation across the genome involving two distinct methylation motifs (1972 putative 6-methyladenine (m6A) residues identified). Putative adenine methyltransferases were also identified. Comparative analysis of AYP1020 and the closely related CoNS, S. epidermidis RP62a, revealed a host of virulence factors that likely contribute to S. capitis pathogenicity, most notably genes important for biofilm formation and a suite of phenol soluble modulins (PSMs); the expression/production of these factors were corroborated by functional assays. The complete S. capitis genome will aid future studies on the evolution and pathogenesis of the coagulase negative staphylococci.

Investigation of mechanisms and molecular epidemiology of linezolid nonsusceptible Enterococcus faecalis isolated from a teaching hospital in China

The epidemiological and molecular characteristics of eight linezolid nonsusceptible Enterococcus faecalis isolated from a teaching hospital in China (January to July 2014) were investigated. The target site modifications and cfr gene associated with linezolid resistance were not found. Results of the epidemiological investigation indicated that linezolid resistance possibly occurred on several independent occasions and was often not related to linezolid administration.

Identification and characterization of cfr-positive Staphylococcus aureus isolates from community-onset infectious patients in a county hospital in China

The cfr gene was detected in 14 meticillin-susceptible Staphylococcus aureus isolates recovered from outpatients with community-onset infections in a county hospital in China. The MIC of linezolid was 4 μg ml- 1 in eight isolates and 2 μg ml- 1 in six isolates. All isolates were susceptible to vancomycin and teicoplanin, but had elevated MICs for penicillin (0.5-128 μg ml- 1), chloramphenicol (2-32 μg ml- 1), clindamycin (0.5-128 μg ml- 1) and erythromycin (4-128 μg ml- 1). Nine isolates had mutations on domain V of 23S rRNA and/or the ribosomal L proteins that were not located close to the linezolid-binding pocket. Southern blotting experiments demonstrated that the cfr genes in all 14 isolates resided on plasmids. Sequence analysis of the 5.6 kb cfr-carrying plasmid segment revealed 99 % identity to the corresponding sequences in plasmid pSS-01 from animal staphylococci and plasmid pRM-01 from human staphylococci. Five isolates belonged to sequence type (ST)188 and three to ST965; the two ST types were previously reported in isolates of animal origin in some areas of China. These results indicate that the cfr-carrying plasmids in this study are likely of animal origin. The present study shows that cfr-harbouring S. aureus isolates have emerged in some areas of China and that cfr-carrying isolates may be transmitted between animals and humans.

Dissemination of the same cfr-carrying plasmid among methicillin-resistant Staphylococcus aureus and coagulase-negative staphylococcal isolates in China

Six cfr-harboring methicillin-resistant Staphylococcus aureus (MRSA) isolates, which belonged to the same clone of sequence type 5 (ST5)-staphylococcal cassette chromosome mec element II (SCCmec II)-spa t311, were investigated in this study. Complete sequencing of a cfr-carrying plasmid, pLRSA417, revealed an 8,487-bp fragment containing a Tn4001-like transposon, cfr, orf1, and ISEnfa4. This segment, first identified in an animal plasmid, pSS-01, was observed in several plasmids from clinical coagulase-negative staphylococci in China, suggesting that the cfr gene, which might originate from livestock, was located in the same mobile element and disseminated among different clinical staphylococcal species.

Clonal dissemination of linezolid-resistant Staphylococcus capitis with G2603T mutation in domain V of the 23S rRNA and the cfr gene at a tertiary care hospital in China

Background

The present study aims to investigate the potential mechanism of linezolid-resistant Staphylococcus capitis (LRSC) isolates collected from our hospital.

Methods

The susceptibilities of 5 Staphylococcus capitis isolates displaying resistance towards linezolid were determined by E-test. Polymerase chain reactions (PCRs) and DNA sequencing were used to investigate the potential molecular mechanism. Clonal relatedness between these strains was analyzed by pulsed-field gel electrophoresis (PFGE).

Results

The MICs of linezolid on these 5 isolates were >256 μg/mL. The G2603T mutation was observed in the domain V of the 23S rRNA with cfr gene being also widely detected among these 5 strains. PFGE analysis displayed close genetic relatedness between these linezolid-resistant isolates.

Conclusions

The emergence of LRSC isolates carrying G2603T mutation in the domain V of the 23S rRNA and harboring cfr gene in our hospital may pose a potential challenge to the public health.

Mechanisms of linezolid resistance in staphylococci and enterococci isolated from two teaching hospitals in Shanghai, China

BACKGROUND

Linezolid is one of the most effective treatments against Gram-positive pathogens. However, linezolid-resistant/intermediate strains have recently emerged in worldwide. The purpose of this study was to analyse the prevalence and resistance mechanisms of linezolid-resistant/intermediate staphylococci and enterococci in Shanghai, China.

RESULTS

Thirty-two linezolid-resistant/intermediate strains, including 14 Staphylococcus capitis, three Staphylococcus aureus, 14 Enterococcus faecalis and one Enterococcus faecium clinical isolates, were collected in this study which displayed linezolid MICs of 8 to 512 μg/ml, 8-32 μg/ml, 4-8 μg/ml and 4 μg/ml, respectively. All linezolid-resistant S. capitis isolates had a novel C2131T mutation and a G2603T mutation in the 23S rRNA region, and some had a C316T (Arg106Cys) substitution in protein L4 and/or harboured cfr. Linezolid-resistant S. aureus isolates carried a C389G (Ala130Gly) substitution in protein L3, and/or harboured cfr. The cfr gene was flanked by two copies of the IS256-like element, with a downstream orf1 gene. Linezolid-resistant/intermediate enterococci lacked major resistance mechanisms. The semi-quantitative biofilm assay showed that 14 linezolid-resistant E. faecalis isolates produced a larger biofilm than linezolid-susceptible E. faecalis strains. Transmission electron microscopy showed the cell walls of linezolid-resistant/intermediate strains were thicker than linezolid-susceptible strains.

CONCLUSION

Our data indicated that major resistance mechanisms, such as mutations in 23S rRNA and ribosomal proteins L3 and L4, along with cfr acquisition, played an important role in linezolid resistance. Secondary resistance mechanisms, such as biofilm formation and cell wall thickness, should also be taken into account.

Factors influencing linezolid-nonsusceptible coagulase-negative staphylococci dissemination among patients in the intensive care unit: a retrospective cohort study

BACKGROUND

The aim of the present study was to identify risk factors for linezolid-nonsusceptible coagulase-negative staphylococci (CNS) dissemination in the intensive care unit.

METHODS

Among the 246 patients included, 33 revealed a linezolid-nonsusceptible CNS-positive culture specimen, 68 were positive for linezolid-susceptible CNS and 145 served as controls. Isolates were characterized by phenotypic and genotypic methods to species level, susceptibility to antistaphylococcal agents and clones.

RESULTS

Among the 33 linezolid-nonsusceptible CNS patients, 29 revealed Staphylococcus epidermidis and 4 Staphylococcus capitis. All S. epidermidis strains belonged to the ST22 clone (by multilocus sequence typing), 26 carried both C2534T and T2504A and 3 strains were C2543T mutations. S. capitis strains were stratified as a common pulsed-field gel electrophoresis type and carried the G2576T mutation. Risk factors for linezolid-nonsusceptible CNS isolation were linezolid administration and mean number of linezolid-nonsusceptible CNS-positive patients in nearby beds per day.

CONCLUSIONS

These results reinforce the aspect of rational antibiotic usage, but also highlight the need for strict infection control measures to prevent the dissemination of linezolid-nonsusceptible CNS.

Investigation of mechanism and molecular epidemiology of linezolid-resistant Enterococcus faecalis in China

Enterococcus is a major cause of important nosocomial infections. Linezolid, the first member of an entirely new class of antibiotics (oxazolidinones), is effective against serious infections caused by Enterococcus. However, resistance to linezolid has been discovered throughout the world rapidly. From 2011 to 2013, nine linezolid-resistant E. faecalis isolates were collected and the possible mechanisms of linezolid resistance, including mutations in domain V of 23S rRNA genes and in ribosomal proteins L3 and L4, and the multiresistance gene cfr, were investigated. Furthermore, an epidemiological survey of the nine linezolid-resistant E. faecalis isolates was performed by pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and DiversiLab. The three methods were compared to evaluate their merits and demerits, respectively. We failed to find the resistance mechanisms that have been revealed in recent years by PCR and sequencing analysis in the linezolid-resistant E. faecalis. Epidemiological investigation suggested that a small-scale outbreak of linezolid-resistant E. faecalis emerged in neurosurgery ICU from March to May of 2013. DiversiLab was a reliable typing tool and a suitable alternative to PFGE because it was as discriminatory as PFGE and better than MLST.

Linezolid update: stable in vitro activity following more than a decade of clinical use and summary of associated resistance mechanisms

Linezolid, approved for clinical use since 2000, has become an important addition to the anti-Gram-positive infection armamentarium. This oxazolidinone drug has in vitro and in vivo activity against essentially all Gram-positive organisms, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). The in vitro activity of linezolid was well documented prior to its clinical application, and several ongoing surveillance studies demonstrated consistent and potent results during the subsequent years of clinical use. Emergence of resistance has been limited and associated with invasive procedures, deep organ involvement, presence of foreign material and mainly prolonged therapy. Non-susceptible organisms usually demonstrate alterations in the 23S rRNA target, which remain the main resistance mechanism observed in enterococci; although a few reports have described the detection of cfr-mediated resistance in Enterococcus faecalis. S. aureus isolates non-susceptible to linezolid remain rare in large surveillance studies. Most isolates harbour 23S rRNA mutations; however, cfr-carrying MRSA isolates have been observed in the United States and elsewhere. It is still uncertain whether the occurrences of such isolates are becoming more prevalent. Coagulase-negative isolates (CoNS) resistant to linezolid were uncommon following clinical approval. Surveillance data have indicated that CoNS isolates, mainly Staphylococcus epidermidis, currently account for the majority of Gram-positive organisms displaying elevated MIC results to linezolid. In addition, these isolates frequently demonstrate complex and numerous resistance mechanisms, such as alterations in the ribosomal proteins L3 and/or L4 and/or presence of cfr and/or modifications in 23S rRNA. The knowledge acquired during the past decades on this initially used oxazolidinone has been utilized for developing new candidate agents, such as tedizolid and radezolid, and as linezolid patents soon begin to expire, generic brands will certainly become available. These events will likely establish a new chapter for this successful class of antimicrobial agents.

Molecular characterization of Rifr mutations in Enterococcus faecalis and Enterococcus faecium

Mutation rate is an important factor affecting the appearance and spread of acquired antibiotic resistance. The frequencies and types of enterococci mutations were determined in this study. The MICs of rifampicin in enterococci and their rifampicin-resistant mutants were determined by the Clinical and Laboratory Standards Institute (CLSI) agar dilution method. The Enterococcus faecalis isolates A15 and 18165 showed no significant differences in mutation frequencies or mutation rates. In Enterococcus faecium, the mutation frequency and mutation rate were both 6·4-fold lower than in E. faecalis. The spectrum of mutations characterized in E. faecium B42 differed significantly from that of E. faecalis. The types and rate of mutations indicated that E. faecalis had a higher potential to develop linezolid resistance. Rifampicin resistance was associated with mutations in the rpoB gene. Rifampicin MICs for the E. faecalis mutant were 2048 mg/l, but rifampicin MICs for E. faecium mutants ranged from 64 to 1024 mg/l.

Distinction between the Cfr methyltransferase conferring antibiotic resistance and the housekeeping RlmN methyltransferase

The cfr gene encodes the Cfr methyltransferase that primarily methylates C-8 in A2503 of 23S rRNA in the peptidyl transferase region of bacterial ribosomes. The methylation provides resistance to six classes of antibiotics of clinical and veterinary importance. The rlmN gene encodes the RlmN methyltransferase that methylates C-2 in A2503 in 23S rRNA and A37 in tRNA, but RlmN does not significantly influence antibiotic resistance. The enzymes are homologous and use the same mechanism involving radical S-adenosyl methionine to methylate RNA via an intermediate involving a methylated cysteine in the enzyme and a transient cross-linking to the RNA, but they differ in which carbon atom in the adenine they methylate. Comparative sequence analysis identifies differentially conserved residues that indicate functional sequence divergence between the two classes of Cfr- and RlmN-like sequences. The differentiation between the two classes is supported by previous and new experimental evidence from antibiotic resistance, primer extensions, and mass spectrometry. Finally, evolutionary aspects of the distribution of Cfr- and RlmN-like enzymes are discussed.

Cfr-mediated linezolid-resistance among methicillin-resistant coagulase-negative staphylococci from infections of humans

Four methicillin-resistant coagulase-negative staphylococci (MRCoNS), one Staphylococcus haemolyticus and three Staphylococcus cohnii, from infections of humans collected via the Ministry of Health National Antimicrobial Resistance Surveillance Net (Mohnarin) program in China were identified as linezolid-resistant. These four isolates were negative for the 23S rRNA mutations, but positive for the gene cfr. Mutations in the gene for the ribosomal protein L3, which resulted in the amino acid exchanges Gly152Asp and Tyr158Phe, were identified in S. haemolyticus 09D279 and S. cohnii NDM113, respectively. In each isolate, the cfr gene was located on a plasmid of ca. 35.4 kb, as shown by S1 nuclease pulsed-field gel electrophoresis and Southern blotting experiments. This plasmid was indistinguishable from the previously described plasmid pSS-02 by its size, restriction pattern, and a sequenced 14-kb cfr-carrying segment. Plasmid pSS-02 was originally identified in staphylococci isolated from pigs. This is the first time that a cfr-carrying plasmid has been detected in MRCoNS obtained from intensive care patients in China. Based on the similarities to the cfr-carrying plasmid pSS-02 from porcine coagulase-negative staphylococci, a transmission of this cfr-carrying plasmid between staphylococci from pigs and humans appears to be likely.