Enterococci are a group of bacteria that are commonly found in human gut and other environmental niches. While they are generally considered to be harmless, certain strains have developed resistance to multiple antibiotics, posing a significant threat to public health (1, 2). Among these strains are Enterococcus (E.) faecium and E. faecalis, which have been recognized as important nosocomial pathogens and frequently involved in serious infections in hospitalized patients, particularly in immunocompromised individuals. One of the most concerning antibiotic resistance traits in Enterococci is their resistance to vancomycin, which is often considered the last line of defense against severe infections caused by Gram-positive bacteria (3, 4).
Vancomycin resistance in E. faecium and E. faecalis presents a significant challenge in clinical settings, requiring a comprehensive understanding of the mechanisms involved to effectively combat this threat (5). Enterococci are commensal organisms in human gastrointestinal tract, but they have also emerged as leading causes of healthcare-associated infections, particularly due to their ability to acquire resistance to multiple antibiotics, including vancomycin. The acquisition and dissemination of vancomycin resistance genes among enterococcal populations have contributed to the reduced efficacy of this critical antibiotic, posing a serious public health concern (6, 7). Understanding the molecular mechanisms underpinning vancomycin resistance in these species is essential for guiding therapeutic strategies and combating the spread of resistance (8).
Molecular studies have revealed that vancomycin resistance in E. faecium and E. faecalis is often mediated by acquisition of genetic elements such as vancomycin resistance genes, including vanA, vanB, and vanC clusters. These genes encode proteins that modify peptidoglycan cell wall structure, thereby reducing the binding affinity of vancomycin and conferring resistance to the antibiotic (9, 10). The emergence of these resistant strains limits the therapeutic options available for treating enterococcal infections, particularly those caused by multidrug-resistant (MDR) organisms. In addition, the spread of these resistant strains can lead to outbreaks in healthcare settings, further complicating infection control efforts (11, 12).
The study of gene expression in VRE is increasingly necessary due to the rising prevalence of antibiotic-resistant infections, which pose significant challenges to healthcare systems worldwide. The emergence of healthcare-associated infections, including those caused by VRE, emphasizes the importance of understanding the molecular mechanisms behind this resistance, particularly through the expression of specific genes such as vanA and vanB. The unique epidemiology of VRE, influenced by factors such as overuse and misuse of antibiotics, inadequate infection control practices, and variability in healthcare infrastructure, highlights the necessity for localized research. By characterizing gene expression patterns in VRE isolates, researchers can better understand resistance mechanisms, facilitating the design of targeted interventions and antimicrobial stewardship programs that reflect local realities.
Additionally, VRE poses a significant threat to vulnerable populations, such as immunocompromised and patients in intensive care units, which are prevalent due to various health issues. Conducting gene expression studies specifically focused on VRE can contribute to enhancing infection control measures, ultimately reducing the incidence and spread of these MDR organisms within healthcare settings.
Understanding the molecular mechanisms behind vancomycin resistance in E. faecium and E. faecalis is essential for developing effective treatment strategies. This research is guided by the hypothesis that specific genetic and biochemical factors contribute to vancomycin resistance in these bacterial strains. The key questions addressed in this study include: What are the underlying genetic determinants of vancomycin resistance in E. faecium and E. faecalis? How does the expression of vanA gene influence this resistance?
The primary aim of this study was to synthesize current knowledge regarding molecular mechanisms of vancomycin resistance in these two species, with a particular emphasis on the role of vanA gene and its expression patterns. Through extensive examination of existing research, this study aimed to clarify the genetic and biochemical basis of resistance, ultimately contributing to improved treatment strategies for infections caused by these resistant bacteria.
Materials and Methods
Gene | Oligonucleotide sequence (5’ to 3’) |
PCR product (bp) |
Reference | |
ddl E. faecalis | F | ATCAAGTACAGTTAGTCTTTATTAG | 941 | (37) |
R | ACGATTCAAAGCTAACTGAATCAGT | |||
ddl E. faecium | F | TTGAGGCAGACCAGATTGACG | 657 | (37) |
R | TATGACAGCGACTCCGATTCC | |||
vanA | F | CATGACGTATCGGTAAAATC | 885 | (38) |
R | ACCGGGCAGRGTATTGAC | |||
vanB | F | CATGATGTGTCGGTAAAATC | 885 | (38) |
R | ACCGGGCAGRGTATTGAC | |||
vanC1 | F | GATGGCWGTATCCAAGGA | 467 | (38) |
R | GTGATCGTGGCGCTG | |||
vanC2.3 | F | GATGGCWGTATCCAAGGA | 429 | (38) |
R | ATCGAAAAAGCCGTCTAC |
Ethical Considerations
Genotype/Antibiotic | P-value |
vanA/Vancomycin | 0.008 |
Antibiotic treatment | Mean of 2DD for control | Mean of 2DD for treated VRE isolates | Mean of 2DD for untreated VRE isolates | Relative quantification |
E. faecalis | 0.93 | 44.84 | 5.11 | 8.6 |
E. faecium | 0.93 | 13.28 | 5.11 | 2.6 |
In this study, we identified a total of 120 isolates, with 82 (68.3%) being E. faecalis and 38 (31.6%) being E. faecium. The majority of E. faecalis isolates were obtained from urine samples (56, 68.2%), followed by tracheal samples (17, 20.7%) and wound specimens (2, 2.4%), while the majority of E. faecium isolates were also isolated from urine samples (20, 52.2%), followed by tracheal samples (6, 15.7%) and blood samples (7, 18.4%). PCR analysis confirmed the phenotypic specification of these isolates by targeting D-alanine-D-alanine ligases specific for E. faecalis and E. faecium.
The isolation rates of E. faecalis and E. faecium in this study were similar to some other researches. For instance, a study by Boccella et al (17) identified 82.2% E. faecalis and 17.8% E. faecium isolates from 16 clinical samples. But another study by Sattari-Maraji et al (18) reported isolation rates of 68.8% E. faecalis and 31.2% E. faecium isolates. Notably, the prevalence of E. faecalis is consistently high across studies, with our results aligning closely with those of Sumangala et al (19), who reported an even higher percentage of E. faecalis at 88.1%. This suggests a general trend that E. faecalis is more frequently isolated from clinical contexts than E. faecium. Conversely, the study by Nasiri and Hanifian (20) reported lower percentages of E. faecalis (36.77%) and E. faecium (27.88%), indicating variability that could stem from differences in sample size, population characteristics, or geographical factors affecting microbial prevalence. Additionally, Georges et al (16) involved a smaller group of patients (n = 44) with the mean age of 37 years, which may influence the isolation rates due to demographic factors. The Ismail Hakki EKİN et al (21) highlighted the importance of specimen types, reporting isolates from both urine and stool, whereas the current study was performed on different specimen types. Such differences underscore the impact of local healthcare settings and practices on the observed prevalence of these organisms. Overall, while the predominance of E. faecalis appears to be a common theme, significant variations in the isolation rates and contexts in which data were collected, point to the necessity for the context-specific assessments in clinical microbiology.
The use of PCR analysis to confirm phenotypic specification is a common technique in microbiology research, as it provides a more accurate identification of bacterial species based on genetic markers rather than phenotypic characteristics alone, which can be influenced by environmental factors or antibiotic resistance mechanisms (22, 23). The use of D-alanine-D-alanine ligases as targets for PCR analysis is particularly useful for distinguishing between E. faecalis and E. faecium, as these enzymes are specific to each species and can provide a reliable identification method (24, 25).
The study revealed significant differences in antibiotic resistance between E. faecium and E. faecalis isolates. E. faecium showed higher resistance rates: ampicillin (89.5%), penicillin (84.2% ± 33%), erythromycin (73.7%), gentamicin (68.4%), and ciprofloxacin (63.1%). In contrast, E. faecalis exhibited much lower resistance rates: ampicillin (5.8%), penicillin (7.2%), erythromycin (41.7%), gentamicin (53.6%), and ciprofloxacin (39.5%). These findings indicate that E. faecium isolates are more resistant to these antibiotics than E. faecalis isolates.
Comparing the results of VRE in E. faecalis and E. faecium from various studies brings up a notable contrast in prevalence and resistance patterns. According to the review by Moghimbeigi et al (26) in 2018, E. faecalis was found to be more prevalent in clinical infections, representing 69% compared to 28% for E. faecium; however, the resistance to vancomycin was significantly higher among E. faecium strains (33%) than in E. faecalis strains (3%). This indicates that while E. faecalis is more commonly isolated in clinical settings, E. faecium poses a greater challenge concerning antibiotic resistance.
Similarly, Adeyemi et al (27) in 2021, reported that among 208 Enterococci strains, 85 (40.9%) were identified as VRE, with E. faecium accounting for 71.8% of these isolates. This trend reinforces the notion that E. faecium is increasingly associated with vancomycin resistance. Our findings also revealed phenotypic resistance to vancomycin in 24 E. faecalis isolates and 13 E. faecium isolates, underscoring the rising challenge of VRE in clinical contexts. There could be several reasons for the differences in vancomycin resistance rates and prevalence between our results and those of other studies. First, geographic variation is a significant factor; differences in local antibiotic usage, infection control practices, and healthcare settings can all influence the resistance patterns of Enterococci. For example, regions with higher antibiotic consumption may see increased levels of resistance. Second, sample size and composition can affect the generalizability of findings; our study sample size may differ from those of other studies, potentially leading to variations in detected resistance rates. Third, methodological differences in isolation and identification techniques, as well as in the criteria used for classifying resistance, can yield different outcomes. If different methods for phenotypic characterization of resistance are employed, this could account for discrepancies in results. Additionally, the presence of underlying health conditions in the patient populations being studied might differ, influencing the likelihood of encountering resistant strains. Lastly, temporal factors, like changes in resistance patterns over time due to evolving bacterial genetics or changes in the local epidemiology of infections, can also result in differing outcomes, highlighting the dynamic nature of antimicrobial resistance (18). The presence of the vanA gene in these isolates further highlights the importance of monitoring antimicrobial resistance patterns and implementing strategies to prevent the spread of resistant bacteria in clinical settings (17, 28, 29).
The study also found that among 24 resistant E. faecalis isolates and 13 resistant E. faecium isolates, phenotypic resistance to vancomycin was observed in both species; however, there was a statistical correlation between vancomycin resistance and the presence of vanA gene (P<0.05). Specifically, 75% of resistant E. faecalis isolates and 69.2% of resistant E. faecium isolates contained vanA gene; all susceptible E. faecalis and E. faecium isolates lacked vanA, vanB, and vanC genes, suggesting that these genes are associated with vancomycin resistance in both species studied herein.
Our findings regarding the correlation between vancomycin resistance and the presence of vanA gene in E. faecalis and E. faecium isolates were consistent with previous research. For instance, Resende et al (30) in their study found that all VRE isolates carry vanA gene (P<0.05).
Notable differences exist in prevalence of vanA gene among vancomycin-resistant Enterococci isolates across various studies that may originate from several factors. In the study by Mirzaei et al (31) in 2013, a relatively low prevalence of vancomycin resistance was observed, with only 13.6% of Enterococci isolates demonstrating resistance. Of these, E. faecalis and E. faecium accounted for 7.7% and 6.0%, respectively reflecting a moderate level of vanA gene detection. In contrast, Moosavian et al (32) in 2018, found a significantly higher vancomycin resistance rate of 43.4% among their Enterococcus isolates, with vanA gene detected in 91.5% of the resistant strains, which indicates a stronger association between vancomycin resistance and the presence of vanA gene in their isolates compared to our findings.
Our results showed that 54.1% of resistant E. faecalis and 69.2% of resistant E. faecium isolates contained vanA gene, suggesting a robust genetic basis for the resistance but still lower than what was reported by Moosavian et al (32).
Several factors may explain these discrepancies. Firstly, geographic variability and epidemiological factors play a crucial role; the studies may have been conducted in different regions with varying levels of antibiotic use, infection control practices, and patient demographics, leading to different resistance patterns. Secondly, study design and methodologies such as sample size, diagnostic criteria, and methods for identifying resistance genes can significantly impact the results. For instance, our study may have included a more selective patient population, or the methods for isolating and identifying VRE may differ, affecting detection rates of vanA gene. Furthermore, the potential influence of underlying health conditions or hospital-associated risk factors (e.g., use of central venous catheters, previous antibiotic exposure, etc.) could vary, leading to differences in infection types and severity, which might impact the prevalence of resistant strains. Lastly, temporal changes in resistance patterns due to evolving bacterial genetics or fluctuations in clonal spread could contribute to the observed differences, highlighting the need for continuous surveillance to understand the dynamics of antimicrobial resistance in enterococci (9).
The high prevalence of VanA gene among resistant isolates in both species highlights the importance of monitoring antimicrobial resistance patterns and implementing strategies to prevent the spread of resistant bacteria carrying these genes in clinical settings (30, 33, 34). The presence of these genes in both E. faecalis and E. faecium isolates also underscores the need for further research to understand the mechanisms by which these genes contribute to vancomycin resistance and to develop new antimicrobial therapies that can overcome this resistance (9).
The study also measured the expression of vanA gene among vancomycin-treated and untreated VRE isolates using real-time RT-PCR, and found that the mean RQ values for vanA expression in the treated group were significantly higher than those of untreated group, indicating higher levels of gene expression among treated isolates compared to untreated isolates. This finding suggests that the expression of VanA gene may contribute to vancomycin resistance in these bacterial species (15, 35).
The expression of vanA gene among vancomycin-treated VRE isolates was consistent with those reported in other studies. For instance, the expression of vanA gene was significantly correlated with vancomycin resistance in Aerococcus viridans (36).
The results of this study suggest that the expression of vanA gene, which is responsible for vancomycin resistance in Enterococci, is influenced by antibiotic therapy. Specifically, we observed a significant increase in the expression of vanA gene in VRE isolates treated with vancomycin compared to untreated VRE isolates. This finding is concerning as it suggests the use of vancomycin may actually promote the expansion of vancomycin-resistant Enterococci (VRE) through the up-regulation of vanA gene.
The study identified a high prevalence of vancomycin-resistant Enterococcus (VRE) isolates, with a majority showing resistance to vancomycin due to the presence of vanA gene. The resistance rates to various antibiotics were higher in E. faecium isolates compared to E. faecalis isolates. Moreover, the study demonstrated that the expression of vanA gene was significantly higher in VRE isolates treated with vancomycin. Overall, the research provides an in-depth exploration of the genetic changes and environmental factors influencing the emergence and spread of VRE, along with discussing potential treatment strategies to address this concerning pathogen and protect public health from antibiotic-resistant microorganisms.
We would like to thank Dr. A.D. for his advices and technical support.
Ethical Considerations
All procedures performed in this study was approved by the Ethics Committee of Islamic Azad University, Iran (Registration No.: IR.IAU.TNB.REC.1403.161).
Authors’ Contributions
G.Z.: study design, implementation, and funding. A.A.S, M.R.F. and, F.H.: scientific support. All authors contributed to the article and approved the submitted version.
The authors declared that there was no financial support for this work.
Conflicts of Interest
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