Low prevalence of Cfr-mediated linezolid resistance among methicillin-resistant Staphylococcus aureus in a Spanish hospital: case report on linezolid resistance acquired during linezolid therapy

Prevalence of mecA- and mecC-Associated Methicillin-Resistant Staphylococcus aureus in Clinical Specimens, Punjab, Pakistan

Methicillin-resistant Staphylococcus aureus (MRSA) is a clinically prevalent bacterium and is resistant to many drugs. Genetic factors such as mec genes are considered to be responsible for this resistance. Recently, Staphylococcal Cassette Chromosome mec (SCCmec) element mutations produced mecC, a new genetic variant that encodes a transpeptidase enzyme (63% similarity with mecA-encoded PBP2a). This cross-sectional study was conducted to establish the prevalence of the mecA and mecC genes among phenotypically identified MRSA and their effectiveness against different antibiotics in clinical specimens. The prevalence of Staphylococcus aureus was 10.2% (n = 102) in the total number of clinical specimens collected (n = 1000). However, the prevalence of MRSA was 6.3% (n = 63) of the total samples collected, while it was 61.8% among total Staphylococcus aureus isolates. mec genes were confirmed in 96.8% (n = 61) isolates of MRSA, while 3.2% (n = 2) were found to be negative for mec genes. The combination of mecA and mecC was detected in 57.1% (n = 36) of the MRSA isolates. The prevalence of lone mecA was 31.8% (n = 20) and that of lone mecC was 7.9% (n = 5) among all the MRSA samples. Penicillin and amoxicillin/clavulanic acid were the most resistant antibiotics followed by norfloxacin (91.2%), levofloxacin (87.1%), ciprofloxacin (83.9%), azithromycin (78.6%), erythromycin (77.4%), moxifloxacin (69.8%), and sulfamethoxazole/trimethoprim (54.9%). On the other hand, vancomycin and teicoplanin (98.4%) were more effective drugs against MRSA followed by linezolid (96.7%), clindamycin (84.6%), chloramphenicol (83.7%), fusidic acid (70.6%), gentamicin (67.7%), and tetracycline (56.8%). In conclusion, a significant prevalence of mecA and mecC has been found among MRSA isolated from clinical specimens, which is likely responsible for antibiotic resistance in MRSA in our clinical settings. However, vancomycin, teicoplanin, and linezolid were found the top three most effective drugs against MRSA in our clinical settings. Thus, MRSA endemics in local areas require routine molecular and epidemiological investigation.

A.7van den BijllaardtW.8van MansfeldR.9van DijkK.10ZwartB.11DiederenB. M. W.12Dorigo-ZetsmaJ. W.13NotermansD. W.14Ott CerteA.15AngW.16da SilvaJ.17VlekA. L. M.18BuitingA. G. M.19BodeL.20PaltansingS.21van GriethuysenA. J.22den ReijerM.23van TrijpM. J. C. A.24WongM.25MullerA. E.26van der LindenM. P. M.27van RijnM.28DebastS. B.29WaarK.30KolwijckE.31AlnaiemiN.32SchulinT.33DinantS.34van MensS. P.35MellesD. C.36StuartJ. W. T. Cohen37GrutekeP.38OverdevestI. T. M. A.39van DamA.40MaatI.41MarahaB.42SinnigeJ. C.43MattssonE. E.44van MeerM.45StamA.46de JongE.47VainioS. J.48HeikensE.49SteingroverR.50TroelstraA.51BathoornE.52TrienekensT. A. M.53van DamD. W.54de BrauwerE. I. G. B.55BerkhoutH.56. cfr and fexA genes in methicillin-resistant Staphylococcus aureus from humans and livestock in the Netherlands

Background

Although the Netherlands is a country with a low endemic level of methicillin-resistant Staphylococcus aureus (MRSA), a national MRSA surveillance has been in place since 1989. In 2003 livestock emerged as a major reservoir of MRSA and currently livestock-associated MRSA (clonal complex CC398) make up 25% of all surveillance isolates. To assess possible transfer of resistant strains or resistance genes, MRSA obtained from humans and animals were characterized in detail.

Methods

The sequenced genomes of 6327 MRSA surveillance isolates from humans and from 332 CC398 isolates from livestock-related samples were analyzed and resistance genes were identified. Several isolates were subjected to long-read sequencing to reconstruct chromosomes and plasmids.

Results

Here we show the presence of the multi-resistance gene cfr in seven CC398 isolates obtained from humans and in one CC398 isolate from a pig-farm dust sample. Cfr induces resistance against five antibiotic classes, which is true for all but two isolates. The isolates are genetically unrelated, and in seven of the isolates cfr are located on distinct plasmids. The fexA gene is found in 3.9% surveillance isolates and in 7.5% of the samples from livestock. There is considerable sequence variation of fexA and geographic origin of the fexA alleles.

Conclusions

The rare cfr and fexA resistance genes are found in MRSA from humans and animals in the Netherlands, but there is no evidence for spread of resistant strains or resistance plasmids. The proportion of cfr-positive MRSA is low, but its presence is worrying and should be closely monitored.

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.

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.

Low Proportion of Linezolid and Daptomycin Resistance Among Bloodborne Vancomycin-Resistant Enterococcus faecium and Methicillin-Resistant Staphylococcus aureus Infections in Europe

Vancomycin-resistant Enterococcus faecium (VREF) and methicillin-resistant Staphylococcus aureus (MRSA) are associated with significant health burden. We investigated linezolid and daptomycin resistance among VREF and MRSA in the EU/EEA between 2014 and 2018. Descriptive statistics and multivariable logistic regression were used to analyze 6,949 VREF and 35,131 MRSA blood isolates from patients with bloodstream infection. The population-weighted mean proportion of linezolid resistance in VREF and MRSA between 2014 and 2018 was 1.6% (95% CI 1.33–2.03%) and 0.28% (95% CI 0.32–0.38%), respectively. Daptomycin resistance in MRSA isolates was similarly low [1.1% (95% CI 0.75–1.6%)]. On the European level, there was no temporal change of daptomycin and linezolid resistance in MRSA and VREF. Multivariable regression analyses showed that there was a higher likelihood of linezolid and daptomycin resistance in MRSA (aOR: 2.74, p < 0.001; aOR: 2.25, p < 0.001) and linezolid in VREF (aOR: 1.99, p < 0.001) compared to their sensitive isolates. The low proportion of linezolid and daptomycin resistance in VREF and MRSA suggests that these last-resort antibiotics remain effective and will continue to play an important role in the clinical management of these infections in Europe. However, regional and national efforts to contain antimicrobial resistance should continue to monitor the trend through strengthened surveillance that includes genomic surveillance for early warning and action.

Pleuromutilins: Potent Drugs for Resistant Bugs-Mode of Action and Resistance

Pleuromutilins are antibiotics that selectively inhibit bacterial translation and are semisynthetic derivatives of the naturally occurring tricyclic diterpenoid pleuromutilin, which received its name from the pleuromutilin-producing fungus Pleurotus mutilus Tiamulin and valnemulin are two established derivatives in veterinary medicine for oral and intramuscular administration. As these early pleuromutilin drugs were developed at a time when companies focused on major antibacterial classes, such as the β-lactams, and resistance was not regarded as an issue, interest in antibiotic research including pleuromutilins was limited. Over the last decade or so, there has been a resurgence in interest to develop this class for human use. This has resulted in a topical derivative, retapamulin, and additional derivatives in clinical development. The most advanced compound is lefamulin, which is in late-stage development for the intravenous and oral treatment of community-acquired bacterial pneumonia and acute bacterial skin infections. Overall, pleuromutilins and, in particular, lefamulin are characterized by potent activity against Gram-positive and fastidious Gram-negative pathogens as well as against mycoplasmas and intracellular organisms, such as Chlamydia spp. and Legionella pneumophila Pleuromutilins are unaffected by resistance to other major antibiotic classes, such as macrolides, fluoroquinolones, tetracyclines, β-lactam antibiotics, and others. Furthermore, pleuromutilins display very low spontaneous mutation frequencies and slow, stepwise resistance development at sub-MIC in vitro. The potential for resistance development in clinic is predicted to be slow as confirmed by extremely low resistance rates to this class despite the use of pleuromutilins in veterinary medicine for >30 years. Although rare, resistant strains have been identified in human- and livestock-associated environments and as with any antibiotic class, require close monitoring as well as prudent use in veterinary medicine. This review focuses on the structural characteristics, mode of action, antibacterial activity, and resistance development of this potent and novel antibacterial class for systemic use in humans.

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.

First Report of cfr-Carrying Plasmids in the Pandemic Sequence Type 22 Methicillin-Resistant Staphylococcus aureus Staphylococcal Cassette Chromosome mec Type IV Clone

Linezolid is often the drug of last resort for serious methicillin-resistant Staphylococcus aureus (MRSA) infections. Linezolid resistance is mediated by mutations in 23S rRNA and genes for ribosomal proteins; cfr, encoding phenicol, lincosamide, oxazolidinone, pleuromutilin, and streptogramin A (PhLOPS_A) resistance; its homologue cfr(B); or optrA, conferring oxazolidinone and phenicol resistance. Linezolid resistance is rare in S. aureus, and cfr is even rarer. This study investigated the clonality and linezolid resistance mechanisms of two MRSA isolates from patients in separate Irish hospitals. Isolates were subjected to cfr PCR, PhLOPS_A susceptibility testing, 23S rRNA PCR and sequencing, DNA microarray profiling, spa typing, pulsed-field gel electrophoresis (PFGE), plasmid curing, and conjugative transfer. Whole-genome sequencing was used for single-nucleotide variant (SNV) analysis, multilocus sequence typing, L protein mutation identification, cfr plasmid sequence analysis, and optrA and cfr(B) detection. Isolates M12/0145 and M13/0401 exhibited linezolid MICs of 64 and 16 mg/liter, respectively, and harbored identical 23S rRNA and L22 mutations, but M12/0145 exhibited the mutation in 2/6 23S rRNA alleles, compared to 1/5 in M13/0401. Both isolates were sequence type 22 MRSA staphylococcal cassette chromosome mec type IV (ST22-MRSA-IV)/spa type t032 isolates, harbored cfr, exhibited the PhLOPS_A phenotype, and lacked optrA and cfr(B). They differed by five PFGE bands and 603 SNVs. Isolate M12/0145 harbored cfr and fexA on a 41-kb conjugative pSCFS3-type plasmid, whereas M13/0401 harbored cfr and lsa(B) on a novel 27-kb plasmid. This is the first report of cfr in the pandemic ST22-MRSA-IV clone. Different cfr plasmids and mutations associated with linezolid resistance in genotypically distinct ST22-MRSA-IV isolates highlight that prudent management of linezolid use is essential.

Complete nucleotide sequence of cfr-carrying IncX4 plasmid pSD11 from Escherichia coli

We report the complete nucleotide sequence of a plasmid carrying the multiresistance gene cfr. This plasmid was isolated from an Escherichia coli strain of swine origin in 2011. This 37,672-bp plasmid, pSD11, had an IncX4 backbone similar to those of the IncX4 plasmids obtained from the United States and Australia, in which the cfr gene was flanked by two copies of IS26 and a truncated Tn1331 was inserted.

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.