Vancomycin-resistant enterococcal infections: epidemiology, clinical manifestations, and optimal management

The Evolving Landscape of Infective Endocarditis: Difficult-to-Treat Resistance Bacteria and Novel Diagnostics at the Foreground

Infective endocarditis (IE) is a relatively rare but potentially life-threatening disease characterized by substantial mortality and long-term sequelae among the survivors. In recent decades, a dramatic change in the profile of patients diagnosed with IE has been observed primarily in developed countries, most likely due to an aging population and a recent increase in invasive medical procedures. Nowadays, the typical IE patient is usually older, with complex comorbidities, and a history significant for cardiac disease, including degenerative heart valve disease, prosthetic valves, or cardiovascular implantable electronic devices (CIEDs). Moreover, as patient risk factors change, predisposing them to more healthcare-associated IE, the microbiology of IE is also shifting; there are growing concerns regarding the rise in the incidence of IE caused by difficult-to-treat resistance (DTR) bacteria in at-risk patients with frequent healthcare contact. The present review aims to explore the evolving landscape of IE and summarize the current knowledge on novel diagnostics to ensure timely diagnosis and outline optimal therapy for DTR bacterial IE.

Receipt of Fluoroquinolone Prophylaxis is not Associated With Development of Vancomycin-Resistant Enterococcus Colonization During Pediatric Hematopoietic Cell Transplantation

Fluoroquinolones are used to prevent bloodstream infections in pediatric hematopoietic cell transplant (HCT) recipients. We performed a retrospective cohort study in 799 pediatric HCT patients to evaluate the association between fluoroquinolone prophylaxis and VRE colonization. Propensity score analyses were performed. Fluoroquinolone prophylaxis was not associated with VRE colonization.

Vancomycin-resistant Enterococcus (VRE) isolates from dogs and cats in veterinary hospitals in Brazil

BACKGROUND

In veterinary medicine, particularly concerning dogs and cats, there is limited data regarding vancomycin-resistant Enterococcus (VRE). However, multidrug-resistant Enterococcus is frequently identified, raising concerns about the potential for spreading these resistant microorganisms to humans due to their zoonotic nature. This study aimed to identify VRE colonizing animals admitted to a veterinary hospital and to determine the presence of the major resistance genes responsible for vancomycin resistance.

RESULTS

Enterococcus was found to carry the vanA gene in 52.54% of cases, the vanB gene in 23.73%, the vanC gene in 20.34%, and the vanE gene in 3.39%. The antimicrobials with the lowest resistance were chloramphenicol (5.08%) and ampicillin (6.78%). In contrast, the highest resistance was observed with enrofloxacin (79.66%), rifampicin (67.80%), and ciprofloxacin (61.02%). Seven Enterococcus isolates showed resistance to vancomycin as well as high-level aminoglycoside resistance (HLAR).

CONCLUSION

A total of 46 animals were found to be colonized by VRE, of which 16 were healthy. The vanA gene was the most commonly isolated (52.54%), followed by vanB (23.73%), vanC (20.34%), and vanE (3.39%). This represents the first report of the vanE gene being identified in a dog in Brazil. Among the 59 Enterococcus isolates, 84.75% (n = 50) were found to be multidrug resistant. The colonization of VRE and Enterococcus HLAR in dogs and cats poses a public health concern, as it increases the risk of environmental dissemination and has implications for One Health.

Distribution and Antibiotic Resistance Analysis of 13,048 Clinically Common Isolates

Objective

This study investigated the distribution and antibiotic resistance profiles of common bacteria isolated from clinical specimens at a hospital's microbiology laboratory between 2020 and 2022.

Methods

A retrospective analysis was conducted on microbial culture results from clinical specimens collected over three years, including sample types, departmental distribution, pathogen species, and resistance profiles.

Results

A total of 13,048 unique pathogenic strains were isolated, predominantly from respiratory and urine specimens. Secretion specimens exhibited the highest positive detection rate (73.6%), while blood specimens showed a lower rate (9.7%). The five most frequently isolated pathogens were: Klebsiella pneumoniae (K. pneumoniae) (19.6%), Pseudomonas aeruginosa (P. aeruginosa) (14.7%), Escherichia coli (E. coli) (9.2%), Acinetobacter baumannii (A. baumannii) (8.0%), and Candida albicans (C. albicans) (7.0%). Gram-negative bacteria constituted 53.7% of all isolates (7009/13,048). A total of 7590 multidrug-resistant organisms (MDRO) were identified, corresponding to a detection rate of 21.3% (7590/35,613). The detection rates of carbapenem-resistant Enterobacteriaceae (CRE) increased annually: 7.2% (2020), 8.6% (2021), and 14.4% (2022).

Conclusion

The annual detection rate of CRE increased during the study period, while the rate of methicillin-resistant Staphylococcus aureus (MRSA) declined. Timely and effective interventions targeting pathogenic bacteria are essential for controlling and mitigating nosocomial infection risks.

In vitro resensitization of multidrug-resistant clinical isolates of Enterococcus faecium and E. faecalis through phage-antibiotic synergy

Bacteriophages are an increasingly attractive option for the treatment of antibiotic-resistant infections, but their efficacy is difficult to discern due to the confounding effects of antibiotics. Phages are generally delivered in conjunction with antibiotics, and thus, when patients improve, it is unclear whether the phages, antibiotics, or both are responsible. This question is particularly relevant for enterococcus infections, as limited data suggest phages might restore antibiotic efficacy against resistant strains. Enterococci can develop high-level resistance to vancomycin, a primary treatment. We assessed clinical and laboratory isolates of Enterococcus faecium and Enterococcus faecalis to determine whether we could observe synergistic interactions between phages and antibiotics. We identified synergy between multiple phages and antibiotics including linezolid, ampicillin, and vancomycin. Notably, antibiotic susceptibility did not predict synergistic interactions with phages. Vancomycin-resistant isolates (n = 6) were eradicated by the vancomycin-phage combination as effectively as vancomycin-susceptible isolates (n = 2). Transcriptome analysis revealed significant gene expression changes under antibiotic-phage conditions, especially for linezolid and vancomycin, with upregulated genes involved in nucleotide and protein biosynthesis and downregulated stress response and prophage-related genes. While our results do not conclusively determine the mechanism of the observed synergistic interactions between antibiotics and phages, they do confirm and build upon previous research that observed these synergistic interactions. Our work highlights how using phages can restore the effectiveness of vancomycin against resistant isolates. This finding provides a promising, although unexpected, strategy for moving forward with phage treatments for vancomycin-resistant Enterococcus infections.

Changing dynamics of bloodstream infections due to methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium in Germany, 2017-2023: a continued burden of disease approach

BACKGROUND

Antimicrobial resistance is a global threat to public health, with methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VREfm) being major contributors. Despite their clinical impact, comprehensive assessments of changes of the burden of bloodstream infections in terms of Disability-Adjusted Life Years (DALYs) and attributable deaths over time are lacking, particularly in Germany.

METHODS

We used data from the Antimicrobial Resistance Surveillance system, which covered about 30% of German hospitals. Bloodstream infections were defined by a VREfm or MRSA-positive blood culture. We estimated incidences as a first step to further use these rates to calculate DALYs and attributable deaths using the Burden of Communicable Disease in Europe toolkit. The analysis included stratification by age, sex and region.

RESULTS

From 2017 to 2023, 6262 MRSA and 5442 VREfm blood culture-positive isolates were identified. The incidence of MRSA bloodstream infections decreased from 4.0 to 2.1 per 100,000 population, with estimated DALYs decreasing from 14.6 to 8.6 per 100,000 and attributable deaths from 591 to 316. Conversely, VREfm-BSI incidence doubled from 1.7 to a peak of 3.0 (2021) before declining back to 1.7 per 100,000 in 2023, with estimated DALYs increasing from 8.9 to 16.5 and then decreasing to 8.5 per 100,000 and attributable deaths increasing from 317 to 327. Men and people over 60 years had the highest burden, with noticeable regional differences.

CONCLUSION

MRSA and VREfm bloodstream infections followed different trends in the past and now present a comparable burden in Germany. Both pathogens pose a significant threat, particularly to hospitalised older aged men. Our findings highlight the need for targeted prevention and continued surveillance of MRSA and VREfm to reduce infections and their impact.

Strongyloides stercoralis combined with concurrent multiple pathogens infections in an immunosuppressed patient: a case report

Background

Strongyloides stercoralis is an opportunistic pathogenic parasite. Most individuals with normal immune function may not exhibit significant symptoms, and the signs are atypical, which can easily lead to missed diagnoses and delayed treatment. People with underlying diseases and weakened immunity are prone to develop severe conditions after infection with Strongyloides stercoralis.

Case presentation

We report an immunocompromised patient in whom the pathogen was initially not detectable using traditional parasitic detection techniques. However, Strongyloides stercoralis was identified in both the alveolar lavage fluid and blood through metagenomic next-generation sequencing. Subsequently, Strongyloides stercoralis was detected in the alveolar lavage fluid after multiple rounds of testing using traditional microscopic examination techniques. Based on the mNGS results and other examination findings, the patient was diagnosed with Strongyloides stercoralis in combination with concurrent multiple pathogens infections. After the combined drug therapy of Meropenem, Vancomycin, and Albendazole, the patient's condition was gradually brought under control.

Conclusion

This case demonstrates the advantage of integrating traditional detection methods with metagenomics next-generation sequencing technology in the etiological diagnosis of immunocompromised individuals. It is conducive to clarifying the etiological diagnosis of patients and thereby facilitating the timely initiation of corresponding treatments.

Linking spatial drug heterogeneity to microbial growth dynamics in theory and experiment

Diffusion and migration play pivotal roles in microbial communities - shaping, for example, colonization in new environments and the maintenance of spatial structures of biodiversity. While previous research has extensively studied free diffusion, such as range expansion, there remains a gap in understanding the effects of biologically or physically deleterious confined environments. In this study, we examine the interplay between migration and spatial drug heterogeneity within an experimental meta-community of E. faecalis, a Gram-positive opportunistic pathogen. When the community is confined to spatially-extended habitats ('islands') bordered by deleterious conditions, we find that the population level response depends on the trade-off between the growth rate within the island and the rate of transfer into regions with harsher conditions, a phenomenon we explore by modulating antibiotic concentration within the island. In heterogeneous islands, composed of spatially patterned patches that support varying levels of growth, the population's fate depends critically on the specific spatial arrangement of these patches - the same spatially averaged growth rate leads to diverging responses. These results are qualitatively captured by simple simulations, and analytical expressions which we derive using first-order perturbation approximations to reaction-diffusion models with explicit spatial dependence. Among all possible spatial arrangements, our theoretical and experimental findings reveal that the arrangement with the highest growth rates at the center most effectively mitigates population decline, while the arrangement with the lowest growth rates at the center is the least effective. Extending this approach to more complex experimental communities with varied spatial structures, such as a ring-structured community, further validates the impact of spatial drug arrangement. Our findings suggest new approaches to interpreting diverging clinical outcomes when applying identical drug doses and inform the possible optimization of spatially-explicit dosing strategies.

Management of Recurrent Vancomycin-resistant Enterococcus faecium Bacteremia With Oritavancin: A Case Report

BACKGROUND/AIM

Vancomycin-resistant Enterococcus causes significant morbidity, mortality, and excess healthcare costs when compared to vancomycin-susceptible isolates. Patients with hematological malignancies, especially those who undergo hematopoietic stem cell transplantation, are at a particularly high risk for infections with vancomycin-resistant Enterococcus, with mortality ranging from 40-100%. Linezolid and daptomycin are the two most commonly used antibiotics for treatment of vancomycin-resistant enterococcal infections, however, there has been recent emergence of resistance to these drugs as well.

CASE REPORT

We report the case of a 48-year-old male with hematological malignancy and graft failure post hematopoietic stem cell transplantation complicated by dialysis-dependent acute kidney injury and recurrent neutropenic fevers due to vancomycin-resistant Enterococcus faecium (VREf) bacteremia. Despite central line changes, and strict aseptic precautions, the bacteremia returned, showing resistance to daptomycin and linezolid after the second recurrence. As a final effort, using limited clinical data and in vitro studies, we utilized oritavancin off-label as salvage therapy for refractory VREf bacteremia, with subsequent clearance of blood cultures.

CONCLUSION

This is a rare case of successful off-label use of oritavancin for recurrent multidrug-resistant VREf bacteremia in a patient with hematological malignancy after undergoing hematopoietic stem cell transplantation. It is important to increase awareness of the potential use of this novel antibiotic with increasing resistance of VREf to first-line agents.

Enterococcus faecium: evolution, adaptation, pathogenesis and emerging therapeutics

The opportunistic pathogen Enterococcus faecium colonizes humans and a wide range of animals, endures numerous stresses, resists antibiotic treatment and stubbornly persists in clinical environments. The widespread application of antibiotics in hospitals and agriculture has contributed to the emergence of vancomycin-resistant E. faecium, which causes many hospital-acquired infections. In this Review, we explore recent discoveries about the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of E. faecium and vancomycin-resistant E. faecium. These studies provide critical insights necessary for developing novel preventive and therapeutic approaches against vancomycin-resistant E. faecium and also reveal the intricate interrelationships between the environment, the microorganism and the host, providing knowledge that is broadly relevant to how antibiotic-resistant pathogens emerge and endure.

Development and application of a rapid visual detection technique for VanA gene in vancomycin-resistant Enterococcus faecium

The objective of this study was to establish a rapid visual diagnosis method for vancomycin-resistant Enterococcus faecium (VREFm) based on multienzyme isothermal rapid amplification (MIRA) combined with lateral flow strips (LFSs). The MIRA primers and probes were specifically designed to maintain the sequence of the VanA gene of VREFm. We optimized the reaction time and temperature and thoroughly assessed the specificity and sensitivity of the MIRA-LFS system. We also compared the MIRA-LFS method with the polymerase chain reaction (PCR) assay and the disc diffusion method. We then evaluated the MIRA-LFS assay for consistency testing and clinical application. The MIRA-LFS technique completed the amplification process within 30 min, and the results were observed on LFS. The method demonstrated high sensitivity, with a minimum detection limit of 1.066 CFU/µL for VREFm and exhibited specificity without cross-reactivity with other pathogenic bacteria. When applied to the detection of clinical samples, the method exhibited consistency with the PCR and agar dilution methods. The combined use of MIRA and LFS in this study facilitates simplifying the workflow for detecting VREFm, which is of great significance for rapidly detecting the enterococcal infections and preventing and controlling the nosocomial infections.

IMPORTANCE

One of the key approaches to treating and controlling vancomycin-resistant Enterococcus faecium (VREFm) is an accurate and rapid diagnosis. To achieve this goal, a simple and rapid method must be constructed for immediate detection in the field. Multienzyme isothermal rapid amplification (MIRA) is an isothermal rapid amplification method that allows amplification reactions to be completed under room temperature conditions. When combined with lateral flow strips (LFSs), MIRA-LFS enables the rapid detection of pathogenic microorganisms. However, the MIRA method often produces false signals. These false signals are eliminated by using base mismatches introduced in primers and probes. The MIRA-LFS system was constructed with high specificity and sensitivity for the detection of VREfm, without the limitation of sophisticated instruments. This enables the prompt formulation of diagnostic and therapeutic decisions.

Drug Repurposing: Research Progress of Niclosamide and Its Derivatives on Antibacterial Activity

The development of antibiotic resistance complicates the treatment of infectious diseases and is a global public health threat. However, drug repurposing can address this resistance issue and reduce research and development costs. Niclosamide is a salicylanilide compound approved by the Food and Drug Administration (FDA), and it has been used clinically for treating parasitic infections for many years. Recent studies have shown that niclosamide can inhibit bacterial and fungus activity by affecting the quorum sensing system, biofilm formation, cell membrane potential, and other mechanisms. Here, we discuss recent advances in the antimicrobial applications of niclosamide and its derivatives to provide new perspectives in treating infectious diseases.

Review of Antimicrobial Properties of Titanium Dioxide Nanoparticles

There is a growing interest in the utilization of metal oxide nanoparticles as antimicrobial agents. This review will focus on titanium dioxide nanoparticles (TiO2 NPs), which have been demonstrated to exhibit high antimicrobial activity against bacteria and fungi, chemical stability, low toxicity to eukaryotic cells, and therefore high biocompatibility. Despite the extensive research conducted in this field, there is currently no consensus on how to enhance the antimicrobial efficacy of TiO2 NPs. The aim of this review is to evaluate the influence of various factors, including particle size, shape, composition, and synthesis parameters, as well as microbial type, on the antibacterial activity of TiO2 NPs against bacteria and fungi. Furthermore, the review offers a comprehensive overview of the methodologies employed in the synthesis and characterization of TiO2 NPs. The antimicrobial activity of TiO2 exhibits a weak dependence on the microorganism species. A tendency towards increased antibacterial activity is observed with decreasing TiO2 NP size. The dependence on the shape and composition is more pronounced. The most pronounced antimicrobial potential is exhibited by amorphous NPs and NPs doped with inorganic compounds. This review may be of interest to specialists in biology, medicine, chemistry, and other related fields.

6-Methoxyldihydrochelerythrine Chloride Inhibiting Intra and Extracellular Drug-Resistant Bacteria

Vancomycin-resistant enterococcus (VRE) is a major nosocomial pathogen that exhibits enhanced infectivity due to its robust virulence and biofilm-forming capabilities. In this study, 6-methoxyldihydrochelerythrine chloride (6-MDC) inhibited the growth of exponential-phase VRE and restored VRE's sensitivity to vancomycin. 6-MDC predominantly suppressed the de novo biosynthetic pathway of pyrimidine and purine in VRE by the RNA-Seq analysis, resulting in obstructed DNA synthesis, which subsequently weakened bacterial virulence and impeded intracellular survival. Furthermore, 6-MDC inhibited biofilm formation, eradicated established biofilms, reduced virulence, and enhanced the host immune response to prevent intracellular survival and replication of VRE. Finally, 6-MDC reduced the VRE load in peritoneal fluid and cells significantly in a murine peritoneal infection model. This paper provides insight into the potential antimicrobial target of benzophenanthridine alkaloids for the first time.

The Probiotic Enterococcus Lactis SF68 as a Potential Food Fermentation Microorganism for Safe Food Production

Due to the reports describing virulent and multidrug resistant enterococci, their use has become a topic of controversy despite most of them being safe and commonly used in traditionally fermented foods worldwide. We have characterized Enterococcus lactis SF68, a probiotic strain approved by the European Food Safety Authority (EFSA) for use in food and feed, and find that it has a remarkable potential in food fermentations. Genome analysis revealed the potential of SF68 to metabolize a multitude of carbohydrates, including lactose and sucrose, which was substantiated experimentally. Bacteriocin biosynthesis clusters were identified and SF68 was found to display a strong inhibitory effect against Listeria monocytogenes. Fermentation-wise, E. lactis SF68 was remarkably like Lactococcus lactis and displayed a clear mixed-acid shift on slowly fermented sugars. SF68 could produce the butter aroma compounds, acetoin and diacetyl, the production of which was enhanced under aerated conditions in a strain deficient in lactate dehydrogenase activity. Overall, E. lactis SF68 was found to be versatile, with a broad carbohydrate utilization capacity, a capacity for producing bacteriocins, and an ability to grow at elevated temperatures. This is key to eliminating pathogenic and spoilage microorganisms that are frequently associated with fermented foods.

The VanS sensor histidine kinase from type-B VRE recognizes vancomycin directly

V ancomycin- r esistant e nterococci (VRE) are among the most common causes of nosocomial infections and have been prioritized as targets for new therapeutic development. Many genetically distinct types of VRE have been identified; however, they all share a common suite of resistance genes that function together to confer resistance to vancomycin. Expression of the resistance phenotype is controlled by the VanRS two-component system. This system senses the presence of the antibiotic, and responds by initiating transcription of resistance genes. VanS is a transmembrane sensor histidine kinase, and plays a fundamental role in antibiotic resistance by detecting vancomycin or its effects; it then transduces this signal to the VanR transcription factor, thereby alerting the organism to the presence of the antibiotic. Despite the critical role played by VanS, fundamental questions remain about its function, and in particular about how it senses vancomycin. Here, we focus on a purified VanRS system from one of the most clinically prevalent forms of VRE, type B. We show that in a native-like membrane environment, the autokinase activity of type-B VanS is strongly stimulated by vancomycin. We additionally demonstrate that this effect is mediated by a direct physical interaction between the antibiotic and the type-B VanS protein, and localize the interacting region to the protein's periplasmic domain. This represents the first time that a direct sensing mechanism has been confirmed for any VanS protein.

Significance Statement

When v ancomycin- r esistant e nterococci (VRE) sense the presence of vancomycin, they remodel their cell walls to block antibiotic binding. This resistance phenotype is controlled by the VanS protein, a histidine kinase that senses the antibiotic or its effects and signals for transcription of resistance genes. However, the mechanism by which VanS detects the antibiotic has remained unclear, with no consensus emerging as to whether the protein interacts directly with vancomycin, or instead detects some downstream consequence of vancomycin's action. Here, we show that for one of the most clinically relevant types of VRE, type B, VanS is activated by direct binding of the antibiotic. Such mechanistic insights will likely prove useful in circumventing vancomycin resistance.

Antibiotic Resistance in Enterococci and Enterobacteriaceae from Laboratory-Reared Fresh Mealworm Larvae (Tenebrio molitor L.) and Their Frass

The occurrence of antibiotic-resistant bacteria in foodstuff involves a human health risk. Edible insects are a precious resource; however, their consumption raises food safety issues. In this study, the occurrence of antibiotic resistant bacteria in laboratory-reared fresh mealworm larvae (Tenebrio molitor L.) and frass was assessed. Antibiotics were not used during the rearing. Enterobacteriaceae and enterococci were isolated from 17 larvae and eight frass samples. In total, 62 and 69 isolates presumed to belong to Enterobacteriaceae and Enterococcus spp., respectively, were obtained and tested for antibiotic susceptibility via disk diffusion. Based on the results, isolates were grouped, and representative resistant isolates were identified at species level through 16S rRNA gene sequencing. For enterococci resistance, percentages higher than 15% were observed for vancomycin and quinupristin-dalfopristin, whereas Enterobacteriaceae resistance higher than 25% was found against cefoxitin, ampicillin, and amoxicillin-clavulanic acid. Based on the species identification, the observed resistances seemed to be intrinsic both for enterococci and Enterobacteriaceae, except for some β-lactams resistance in Shigella boydii (cefoxitin and aztreonam). These could be due to transferable genetic elements. This study suggests the need for further investigations to clarify the role of edible insects in the spreading of antibiotic resistance determinants through the food chain.

Genomic sequencing surveillance of patients colonized with vancomycin-resistant Enterococcus (VRE) improves detection of hospital-associated transmission

Background

Vancomycin-resistant enterococcal (VRE) infections pose significant challenges in healthcare. Transmission dynamics of VRE are complex, often involving patient colonization and subsequent transmission through various healthcare-associated vectors. We utilized a whole genome sequencing (WGS) surveillance program at our institution to better understand the contribution of clinical and colonizing isolates to VRE transmission.

Methods

We performed whole genome sequencing on 352 VRE clinical isolates collected over 34 months and 891 rectal screening isolates collected over a 9-month nested period, and used single nucleotide polymorphisms to assess relatedness. We then performed a geo-temporal transmission analysis considering both clinical and rectal screening isolates compared with clinical isolates alone, and calculated 30-day outcomes of patients.

Results

VRE rectal carriage constituted 87.3% of VRE acquisition, with an average monthly acquisition rate of 7.6 per 1000 patient days. We identified 185 genetically related clusters containing 2-42 isolates and encompassing 69.6% of all isolates in the dataset. The inclusion of rectal swab isolates increased the detection of clinical isolate clusters (from 53% to 67%, P<0.01). Geo-temporal analysis identified hotspot locations of VRE transmission. Patients with clinical VRE isolates that were closely related to previously sampled rectal swab isolates experienced 30-day ICU admission (17.5%), hospital readmission (9.2%), and death (13.3%).

Conclusions

Our findings describe the high burden of VRE transmission at our hospital and shed light on the importance of using WGS surveillance of both clinical and rectal screening isolates to better understand the transmission of this pathogen. This study highlights the potential utility of incorporating WGS surveillance of VRE into routine hospital practice for improving infection prevention and patient safety.

Lusutrombopag as a Repurposing Drug in Combination with Aminoglycosides against Vancomycin-Resistant Enterococcus

Due to the widespread abuse of antibiotics, drug resistance in Enterococcus has been increasing. However, the speed of antibiotic discovery cannot keep pace with the acquisition of bacterial resistance. Thus, drug repurposing is a proposed strategy to solve the crises. Lusutrombopag (LP) has been approved as a thrombopoietin receptor agonist by the Food and Drug Administration. This study demonstrated that LP exhibited significant antimicrobial activities against vancomycin-resistant Enterococcus in vitro with rare resistance occurrence. Further, LP combined with tobramycin exhibited synergistic antimicrobial effects in vitro and in vivo against Enterococcus. No in vitro or in vivo detectable toxicity was observed when using LP. Mechanism studies indicated that the disrupted proton motive force may account for LP's antimicrobial activity. In summary, these results demonstrate that LP has the previously undocumented potential to serve as an antibacterial agent against refractory infections caused by Enterococcus.

Comparison of the incidence of nausea and vomiting between linezolid and vancomycin using claims database: a retrospective cohort study

BACKGROUND

Nausea and vomiting during linezolid therapy have been reported as part of safety analyses in clinical trials. We have previously examined the incidence of vomiting during linezolid therapy (18.1%). A previous study conducted at a single hospital showed low external validity. It is necessary to verify whether these results can be reproduced using generalizable data sources.

AIM

To evaluate the incidence of nausea and vomiting during linezolid therapy compared with vancomycin using a Japanese claims database.

METHOD

Patients administered linezolid or vancomycin were selected from the database between January 2005 and June 2017. The primary endpoint was the comparison of nausea and vomiting between the linezolid and vancomycin groups. We conducted propensity score matching (PSM) to adjust for patient characteristics. To assess risk factors for nausea and vomiting, logistic regression was conducted as the secondary endpoint. We defined nausea and vomiting as the first prescription of antiemetics during linezolid or vancomycin therapy as a surrogate endpoint.

RESULTS

In total, 1215 patients were enrolled. After PSM, the number of patients in the linezolid and vancomycin groups was 241. Nausea and vomiting were observed in 11.2% and 5.0% of patients in the linezolid and vancomycin groups, respectively (p < 0.05). Linezolid administration was extracted as a risk factor for nausea and vomiting (odds ratio, 2.09; 95% confidence interval, 1.02-4.30).

CONCLUSION

This study clarified the relationship between linezolid and nausea and vomiting using a Japanese claims database. Further studies are required to elucidate the unknown mechanisms of linezolid-induced nausea and vomiting.

Promiscuous, persistent and problematic: insights into current enterococcal genomics to guide therapeutic strategy

Vancomycin-resistant enterococci (VRE) are major opportunistic pathogens and the causative agents of serious diseases, such as urinary tract infections and endocarditis. VRE strains mainly include species of Enterococcus faecium and E. faecalis which can colonise the gastrointestinal tract (GIT) of patients and, following growth and persistence in the gut, can transfer to blood resulting in systemic dissemination in the body. Advancements in genomics have revealed that hospital-associated VRE strains are characterised by increased numbers of mobile genetic elements, higher numbers of antibiotic resistance genes and often lack active CRISPR-Cas systems. Additionally, comparative genomics have increased our understanding of dissemination routes among patients and healthcare workers. Since the efficiency of currently available antibiotics is rapidly declining, new measures to control infection and dissemination of these persistent pathogens are urgently needed. These approaches include combinatory administration of antibiotics, strengthening colonisation resistance of the gut microbiota to reduce VRE proliferation through commensals or probiotic bacteria, or switching to non-antibiotic bacterial killers, such as bacteriophages or bacteriocins. In this review, we discuss the current knowledge of the genomics of VRE isolates and state-of-the-art therapeutic advances against VRE infections.

Molecular Genomic Analyses of Enterococcus cecorum from Sepsis Outbreaks in Broilers

Extensive genomic analyses of Enterococcus cecorum isolates from sepsis outbreaks in broilers suggest a polyphyletic origin, likely arising from core genome mutations rather than gene acquisition. This species is a normal intestinal flora of avian species with particular isolates associated with osteomyelitis. More recently, this species has been associated with sepsis outbreaks affecting broilers during the first 3 weeks post-hatch. Understanding the genetic and management basis of this new phenotype is critical for developing strategies to mitigate this emerging problem. Phylogenomic analyses of 227 genomes suggest that sepsis isolates are polyphyletic and closely related to both commensal and osteomyelitis isolate genomes. Pangenome analyses detect no gene acquisitions that distinguish all the sepsis isolates. Core genome single nucleotide polymorphism analyses have identified a number of mutations, affecting the protein-coding sequences, that are enriched in sepsis isolates. The analysis of the protein substitutions supports the mutational origins of sepsis isolates.

Antibiotic Resistance to Molecules Commonly Prescribed for the Treatment of Antibiotic-Resistant Gram-Positive Pathogens: What Is Relevant for the Clinician?

Antibiotic resistance in Gram-positive pathogens is a relevant concern, particularly in the hospital setting. Several antibiotics are now available to treat these drug-resistant pathogens, such as daptomycin, dalbavancin, linezolid, tedizolid, ceftaroline, ceftobiprole, and fosfomycin. However, antibiotic resistance can also affect these newer molecules. Overall, this is not a frequent phenomenon, but it is a growing concern in some settings and can compromise the effectiveness of these molecules, leaving few therapeutic options. We reviewed the available evidence about the epidemiology of antibiotic resistance to these antibiotics and the main molecular mechanisms of resistance, particularly methicillin-resistant Sthaphylococcus aureus, methicillin-resistant coagulase-negative staphylococci, vancomycin-resistant Enterococcus faecium, and penicillin-resistant Streptococcus pneumoniae. We discussed the interpretation of susceptibility tests when minimum inhibitory concentrations are not available. We focused on the risk of the emergence of resistance during treatment, particularly for daptomycin and fosfomycin, and we discussed the strategies that can be implemented to reduce this phenomenon, which can lead to clinical failure despite appropriate antibiotic treatment. The judicious use of antibiotics, epidemiological surveillance, and infection control measures is essential to preserving the efficacy of these drugs.

Novel drug candidates against antibiotic-resistant microorganisms: A review

Antibiotic resistance is fast spreading globally, leading to treatment failures and adverse clinical outcomes. This review focuses on the resistance mechanisms of the top five threatening pathogens identified by the World Health Organization's global priority pathogens list: carbapenem-resistant Acinetobacter baumannii, carbapenem-resistant Pseudomonas aeruginosa, carbapenem-resistant, extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, vancomycin-resistant Enterococcus faecium and methicillin, vancomycin-resistant Staphylococcus aureus. Several novel drug candidates have shown promising results from in vitro and in vivo studies, as well as clinical trials. The novel drugs against carbapenem-resistant bacteria include LCB10-0200, apramycin, and eravacycline, while for Enterobacteriaceae, the drug candidates are LysSAP-26, DDS-04, SPR-206, nitroxoline, cefiderocol, and plazomicin. TNP-209, KBP-7072, and CRS3123 are agents against E. faecium, while Debio 1450, gepotidacin, delafloxacin, and dalbavancin are drugs against antibiotic-resistant S. aureus. In addition to these identified drug candidates, continued in vitro and in vivo studies are required to investigate small molecules with potential antibacterial effects screened by computational receptor docking. As drug discovery progresses, preclinical and clinical studies should also be extensively conducted on the currently available therapeutic agents to unravel their potential antibacterial effect and spectrum of activity, as well as safety and efficacy profiles.

Enterococcus species: insights into antimicrobial resistance and whole-genome features of isolates recovered from livestock and raw meat in Ghana

Introduction

Enterococcus spp. have gradually evolved from commensals to causing life-threatening hospital-acquired infections globally due to their inherent antimicrobial resistance ability and virulence potential. Enterococcus spp. recovered from livestock and raw meat samples were characterized using antimicrobial susceptibility testing and whole-genome sequencing.

Materials and methods

Isolates were confirmed using the MALDI-ToF mass spectrometer, and antimicrobial susceptibility was determined using the Kirby-Bauer disk diffusion method. Whole genome sequencing was performed on isolates resistant to two or more antibiotics. Bioinformatics analysis was performed to determine sequence types, resistance and virulence gene content and evolutionary relationships between isolates from meat and livestock samples, and other enterococci genomes curated by PATRIC. eBURST analysis was used to assign genomes to clonal complexes.

Results

Enterococcus spp. were predominantly E. faecalis (96/236; 41%) and E. faecium (89/236; 38%). Overall, isolates showed resistance to erythromycin (78/236; 33%), tetracycline (71/236; 30%), ciprofloxacin (20/236; 8%), chloramphenicol (12/236; 5%), linezolid (7/236; 3%), ampicillin (4/236; 2%) and vancomycin (1/236, 0.4%). Resistance to two or more antimicrobial agents was detected among 17% (n = 40) Enterococcus spp. Resistance genes for streptogramins [lsa(A), lsa(E), msr(C)], aminoglycosides [aac(6')-Ii, aph(3')-III, ant(6)-Ia, aac(6')-aph(2″), str], amphenicol [cat], macrolides [erm(B), erm(T), msr(C)], tetracyclines [tet(M), tet(L), tet(S)] and lincosamides [lsa(A), lsa(E), lnu(B)] were detected among the isolates. Genes for biofilm formation, adhesins, sex pheromones, cytolysins, hyaluronidase, oxidative stress resistance, quorum-sensing and anti-phagocytic activity were also identified. Potential plasmids with replicon sequences (rep1, rep2, repUS43, repUS47, rep9a, rep9b) and other mobile genetic elements (Tn917, cn_5536_ISEnfa1, Tn6009, ISEnfa1, ISEfa10) were detected. Clinically relevant E. faecium ST32 and ST416 clones were identified in meat samples.

Conclusion

The occurrence of antimicrobial-resistant Enterococcus spp. in livestock and raw meat samples, carrying multiple resistance and virulence genes, including known clones associated with hospital-acquired infections, underscores the critical need for employing robust tools like whole genome sequencing. Such tools provide detailed data essential for ongoing surveillance efforts aimed at addressing the challenge of antimicrobial resistance with a focus on one health.

Gene and domain shuffling in lytic cassettes of Enterococcus spp. bacteriophages

The genomes of Enterococcus faecalis and Enterococcus faecium bacteriophages were analysed for gene shuffling in the lytic cassettes of bacteriophages infecting. It was found that enterococcal bacteriophages could be classified into well-defined groups based on the size of their genomes and each size group had its own conserved gene composition of lytic cassettes. Enterococcal bacteriophages use a relatively broad spectrum of holins and endolysins with variable cell-wall binding (CWB) and catalytic domains, and most of them utilise a lytic cassette with more than two genes. Enterococcal bacteriophages most commonly use endolysins with amidase catalytic domains and the CWB domain SH3_5. Some bacteriophages possess in their lytic cassette a holin-like gene with the XhlA domain protein, characteristic of hemolysin. Regardless of the shuffling of genes encoding holins and endolysins in lytic modules, a novel example of CWB domain shuffling within enterococcal endolysins was identified.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03775-w.

Epidemiology of vancomycin-resistant enterococci in the United Arab Emirates: a retrospective analysis of 12 years of national AMR surveillance data

INTRODUCTION

Enterococci are usually low pathogenic, but can cause invasive disease under certain circumstances, including urinary tract infections, bacteremia, endocarditis, and meningitis, and are associated with peritonitis and intra-abdominal abscesses. Increasing resistance of enterococci to glycopeptides and fluoroquinolones, and high-level resistance to aminoglycosides is a concern. National antimicrobial resistance (AMR) surveillance data for enterococci from the Middle East and North Africa (MENA) and the Gulf region is scarce.

METHODS

A retrospective 12-year analysis of N = 37,909 non-duplicate diagnostic Enterococcus spp. isolates from the United Arab Emirates (UAE) was conducted. Data was generated by routine patient care during 2010-2021, collected by trained personnel and reported by participating surveillance sites to the UAE National AMR Surveillance program. Data analysis was conducted with WHONET.

RESULTS

Enterococcus faecalis was the most commonly reported species (81.5%), followed by Enterococcus faecium (8.5%), and other enterococci species (4.8%). Phenotypically vancomycin-resistant enterococci (VRE) were found in 1.8% of Enterococcus spp. isolates. Prevalence of VRE (%VRE) was highest for E. faecium (8.1%), followed by E. faecalis (0.9%). A significant level of resistance to glycopeptides (%VRE) for these two species has been observed in the majority of observed years [E. faecalis (0-2.2%), 2010: 0%, 2021: 0.6%] and E. faecium (0-14.2%, 2010: 0%, 2021: 5.8%). Resistance to fluoroquinolones was between 17 and 29% (E. faecalis) and was higher for E. faecium (between 42 and 83%). VRE were associated with higher patient mortality (RR: 2.97), admission to intensive care units (RR: 2.25), and increased length of stay (six excess inpatient days per VRE case), as compared to vancomycin-susceptible Enterococcus spp.

DISCUSSION

Published data on Enterococcus infections, in particular VRE-infections, in the UAE and MENA region is scarce. Our data demonstrates that VRE-enterococci are relatively rare in the UAE, however showing an increasing resistance trend for several clinically important antibiotic classes, causing a concern for the treatment of serious infections caused by enterococci. This study also demonstrates that VRE were associated with higher mortality, increased intensive care unit admission rates, and longer hospitalization, thus poorer clinical outcome and higher associated costs in the UAE. We recommend the expansion of current surveillance techniques (e.g., local VRE screening), stricter infection prevention and control strategies, and better stewardship interventions. Further studies on the molecular epidemiology of enterococci are needed.

Vancomycin resistant enterococcus risk factors for hospital colonization in hematological patients: a matched case-control study

BACKGROUND

Vancomycin-resistant enterococcus (VRE) was the fastest growing pathogen in Europe in 2022 (+ 21%) but its clinical relevance is still unclear. We aim to identify risk factors for acquired VRE rectal colonization in hematological patients and evaluate the clinical impact of VRE colonization on subsequent infection, and 30- and 90-day overall mortality rates, compared to a matched control group.

METHODS

A retrospective, single center, case-control matched study (ratio 1:1) was conducted in a hematological department from January 2017 to December 2020. Case patients with nosocomial isolation of VRE from rectal swab screening (≥ 48 h) were matched to controls by age, sex, ethnicity, and hematologic disease. Univariate and multivariate logistic regression compared risk factors for colonization.

RESULTS

A total of 83 cases were matched with 83 controls. Risk factors for VRE colonization were febrile neutropenia, bone marrow transplant, central venous catheter, bedsores, reduced mobility, altered bowel habits, cachexia, previous hospitalization and antibiotic treatments before and during hospitalization. VRE bacteraemia and Clostridioides difficile infection (CDI) occurred more frequently among cases without any impact on 30 and 90-days overall mortality. Vancomycin administration and altered bowel habits were the only independent risk factors for VRE colonization at multivariate analysis (OR: 3.53 and 3.1; respectively).

CONCLUSIONS

Antimicrobial stewardship strategies to reduce inappropriate Gram-positive coverage in hematological patients is urgently required, as independent risk factors for VRE nosocomial colonization identified in this study include any use of vancomycin and altered bowel habits. VRE colonization and infection did not influence 30- and 90-day mortality. There was a strong correlation between CDI and VRE, which deserves further investigation to target new therapeutic approaches.

Successful Outpatient Treatment of Severe Diabetic-Foot Myositis and Osteomyelitis Caused by Extensively Drug-Resistant Enterococcus faecalis with Teicoplanin plus Rifampicin: A Case Report

BACKGROUND Foot ulcers are high-morbidity and debilitating complications of diabetes mellitus, and carry significantly increased rates of associated major amputations. They contribute to significantly worse quality of life. Osteomyelitis is a frequent complication of diabetic foot ulcers, since bacteria can contiguously spread from soft tissues to the bone, involving the cortex first and then the bone marrow. Unfortunately, clinically unsuspected osteomyelitis is frequent in persisting diabetic foot ulcers. It is associated with limb amputations and increased mortality. CASE REPORT We describe a 76-year-old man with long-standing insulin-treated type 2 diabetes, who experienced extensively drug-resistant Enterococcus faecalis diabetic foot myositis and osteomyelitis associated with sepsis. He was successfully treated with surgical debridement combined with the administration of teicoplanin plus rifampicin in the outpatient setting, completing, in total, a twelve-week course of antibiotic therapy. CONCLUSIONS Clinically unsuspected osteomyelitis in patients with persisting diabetic foot ulcers has been associated with infections from highly resistant bacteria. Early and accurate diagnosis of diabetic foot osteomyelitis, as well as proper therapeutic approach (antimicrobial and surgical), is of great importance to reduce the risk of minor and major amputations, septic shock leading to multiple organ failure, and overall mortality.

A Case of Central Venous Catheter-Related Bacteremia Caused by Enterococcus gallinarum

A chicken farmer with cirrhosis and renal failure presented with an unusual case of catheter-related bacteremia. Testing with the VITEK® 2 Compact system, MALDI-TOF mass spectrometry, and 16S rDNA sequencing identified the pathogen as E. gallinarum. This case demonstrates the importance of maintaining a high level of contextual awareness in patients exposed to avian species to make an informed diagnosis and provide prompt treatment.

A Study on Glycopeptide-Resistant Genotypes among Clinical Isolates of Enterococcus with Van B Phenotype

Background

Enterococci, although remarked as harmless commensals of the intestinal tract of humans and animals, have become a significant source of infection in hospitalized patients worldwide.The present study aimed to isolate and identify enterococci from clinical samples and to determine the genotypic characteristics of vancomycin-resistant enterococcus isolates.

Materials and Methods

A total of 774 isolates of enterococci from clinical samples were identified to the species level, and their anti-microbial susceptibility pattern was determined by Kirby Bauer Disk Diffusion method and Vitek 2 automated system. Screening for vancomycin resistance was performed by using brain heart infusion agar containing 6 micrograms/ml of vancomycin. The minimum inhibitory concentration (MIC) of vancomycin was determined by the agar dilution method and Epsilometer test (E test). Genotyping was carried out for resistant isolates by multiplex polymerase chain reaction.

Results

Thirty (3.88%) isolates were resistant to vancomycin by agar screen method. Five isolates showed intermediate resistance with anMIC of 8-16 micrograms/ml for vancomycin by agar dilution. By the E test, two isolates displayed an MIC of ≥32 micrograms/ml for vancomycin and one isolate showed an MICof ≥32 micrograms/ml for teicoplanin.Van A was the common genotype isolated. The present study reports isolates of Enterococcus faecalis with a susceptible MIC for glycopeptide and the presence of the Van A gene.

Conclusion

Heterogeneous resistance among clinical isolates of Enterococcus faecalis was observed in our study. The predominant phenotype and genotype detected among clinical isolates were Van A.

Phylogeny, Virulence, and Antimicrobial Resistance Gene Profiles of Enterococcus faecium Isolated from Australian Feedlot Cattle and Their Significance to Public and Environmental Health

The extent of similarity between E. faecium strains found in healthy feedlot beef cattle and those causing extraintestinal infections in humans is not yet fully understood. This study used whole-genome sequencing to analyse the antimicrobial resistance profile of E. faecium isolated from beef cattle (n = 59) at a single feedlot and compared them to previously reported Australian isolates obtained from pig (n = 60) and meat chicken caecal samples (n = 8), as well as human sepsis cases (n = 302). The E. faecium isolated from beef cattle and other food animal sources neither carried vanA/vanB responsible for vancomycin nor possessed gyrA/parC and liaR/liaS gene mutations associated with high-level fluoroquinolone and daptomycin resistance, respectively. A small proportion (7.6%) of human isolates clustered with beef cattle and pig isolates, including a few isolates belonging to the same sequence types ST22 (one beef cattle, one pig, and two human isolates), ST32 (eight beef cattle and one human isolate), and ST327 (two beef cattle and one human isolate), suggesting common origins. This provides further evidence that these clonal lineages may have broader host range but are unrelated to the typical hospital-adapted human strains belonging to clonal complex 17, significant proportions of which contain vanA/vanB and liaR/liaS. Additionally, none of the human isolates belonging to these STs contained resistance genes to WHO critically important antimicrobials. The results confirm that most E. faecium isolated from beef cattle in this study do not pose a significant risk for resistance to critically important antimicrobials and are not associated with current human septic infections.

Clinical application value of metagenomic second-generation sequencing technology in hematologic diseases with and without transplantation

Introduction

Hematological patients are at risk of infections. It is unknown whether the pathogenic microbial spectrum differs between HSCT and non-HSCT patients, and whether metagenomic next-generation sequencing (mNGS) of peripheral blood can be used as a substitute test specimen such as alveolar lavage.

Methods

A retrospective study was conducted to evaluate the clinical application value of mNGS in hematological patients with and without HSCT.

Results

Viruses were prevalent pathogens in both non-HSCT (44%) and HSCT (45%) patients, chiefly human cytomegalovirus and Epstein-Barr virus. In non-HSCT patients, Gram-negative bacilli accounted for 33% (predominantly Klebsiella pneumonia), and Gram-positive cocci accounted for 7% (predominantly Enterococcus faecium) of pathogens. However, in HSCT patients, Gram-negative bacilli accounted for 13% (predominantly Stenotrophomonas maltophilia), and Gram-positive cocci accounted for 24% (predominantly Streptococcus pneumonia) of pathogens. Mucor was the most common fungu s in two groups. The positive rate of pathogens by mNGS was 85.82%, higher than conventional detection (20.47%, P < 0.05). Mixed infection accounted for 67.00%, among which the mixed infection of bacteria and virus (25.99%) was the most common. 78 cases had pulmonary infection, the positive rate of traditional laboratory tests was 42.31% (33/78), and of mNGS in peripheral blood was 73.08% (57/78), showing a statistical difference (P = 0.000). The non-HSCT patients had a higher frequency of Klebsiella pneumonia (OR=0.777, 95% CI, 0.697-0.866, P = 0.01) and Torque teno virus (OR=0.883, 95% CI, 0.820-0.950, P = 0.031) infections than HSCT patients, while the rates of Streptococcus pneumonia (OR=12.828, 95% CI, 1.378-119.367, P = 0.016), Candida pseudosmooth (OR=1.100, 95% CI, 0.987-1.225, P = 0.016), human betaherpesvirus 6B (OR=6.345, 95% CI, 1.105-36.437, P = 0.039) and human polyomavirus 1 (OR=1.100, 95% CI, 0.987-1.225, P = 0.016) infections were lower. Leishmania could be detected by mNGS.

Conclusion

mNGS of peripheral blood can be used as a substitute test method for hematological patients with pulmonary infection, the detection rate of mixed infections by mNGS was high, and mNGS has high clinical recognition rate and sensitivity in pathogen detection, and provides a basis for guiding the anti-infective treatment in hematological diseases with symptoms such as fever.

Vancomycin-Resistant Enterococcus Endocarditis Complicated by Splenic Infarction and Embolic Stroke

Infective endocarditis (IE) is a serious condition associated with high morbidity and mortality rates. The risk factors for IE include underlying heart disease, intravenous drug use, cardiac surgery, and interventional procedures. Enterococci are a common cause of IE, and vancomycin-resistant enterococci (VRE) infections are becoming increasingly prevalent. In this report, we present the case of an 88-year-old female patient with multiple cardiac comorbidities who developed VRE endocarditis with splenic infarction and embolic stroke. The patient was successfully treated with a combination of antibiotics and anticoagulation therapy. This report highlights the importance of recognizing the potential complications of VRE endocarditis and the need for appropriate management to prevent adverse outcomes. To the best of our knowledge, only one other case of VRE endocarditis with multiple systemic complications has been documented so far.

Structural and functional features of a broad-spectrum prophage-encoded enzybiotic from Enterococcus faecium

Multidrug-resistant (MDR) bacteria have become a growing threat to public health. The gram-positive Enterococcus faecium is classified by WHO as a high-priority pathogen among the global priority list of antibiotic-resistant bacteria. Peptidoglycan-degrading enzymes (PDEs), also known as enzybiotics, are useful bactericidal agents in the fight against resistant bacteria. In this work, a genome-based screening approach of the genome of E. faecium allowed the identification of a putative PDE gene with predictive amidase activity (EfAmi1; EC 3.5.1.28) in a prophage-integrated sequence. EfAmi1 is composed by two domains: a N-terminal Zn²⁺-dependent N-acetylmuramoyl-L-alanine amidase-2 (NALAA-2) domain and a C-terminal domain with unknown structure and function. The full-length gene of EfAmi1 was cloned and expressed as a 6xHis-tagged protein in E. coli. EfAmi1 was produced as a soluble protein, purified, and its lytic and antimicrobial activities were investigated using turbidity reduction and Kirby-Bauer disk-diffusion assays against clinically isolated bacterial pathogens. The crystal structure of the N-terminal amidase-2 domain was determined using X-ray crystallography at 1.97 Å resolution. It adopts a globular fold with several α-helices surrounding a central five-stranded β-sheet. Sequence comparison revealed a cluster of conserved amino acids that defines a putative binding site for a buried zinc ion. The results of the present study suggest that EfAmi1 displays high lytic and antimicrobial activity and may represent a promising new antimicrobial in the post-antibiotic era.

Prevalence of Vancomycin-resistant enterococci (VRE) in Egypt (2010-2022): a systematic review and meta-analysis

BACKGROUND

Vancomycin-resistant Enterococci (VRE) represent a critical medical and public health concerns due to their association with serious nosocomial infections and a high risk of mortality. We aimed to reveal the pooled prevalence of VRE and antimicrobial resistance profiles among enterococci clinical isolates in Egypt.

METHODS

A PubMed, Scopus, Google Scholar, and Web of Science literature search was carried out in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline. Only published studies documenting the prevalence of VRE between 2010 and 2022 were included. Using the random effects model and the 95% confidence intervals, the pooled estimate of VRE was calculated by MedCalc Version 20.113. Cochran's Q and I² tests were used to evaluate the degree of heterogeneity, and publication bias was examined by visually examining the funnel plot and its associated tests (Begg's and Egger's tests).

RESULTS

The pooled prevalence of VRE among enterococci clinical isolates in Egypt was estimated to be 26% (95% CI 16.9 to 36.3). E. faecalis had a greater pooled prevalence than E. faecium, with 61.22% (95% CI 53.65 to 68.53) and 32.47% (95% CI 27 to 38.2), respectively. The VanA gene is more frequent than the VanB gene among VRE, with a pooled prevalence of 63.3% (95% CI 52.1 to 73.7) and 17.95% (95% CI 7.8 to 31), respectively. The pooled resistance rate of linezolid was substantially lower than that of ampicillin and high-level gentamicin (HLG) 5.54% (95% CI 2.33 to 10%), 65.7% (95% CI 50.8 to 79.2%), and 61.1% (95% CI 47.4 to 73.9), respectively.

CONCLUSION

The prevalence of VRE is alarmingly high in Egypt. It is imperative that antimicrobial stewardship activities and infection control programs are strictly adhered to and implemented to prevent further escalation of the problem.

The Assessment of Antimicrobial Resistance in Gram-Negative and Gram-Positive Infective Endocarditis: A Multicentric Retrospective Analysis

Background and Objectives: Multidrug-resistant microorganisms have made treating bacterial infections challenging. Resistance to antibiotics is expected to overcome efforts to produce new, effective antibacterial medication that is lifesaving in many situations. Infective endocarditis (IE) is a life-threatening infection that affects 5–15 per 100,000 patients annually and requires rapid antibiotic therapy to prevent morbidity and mortality. Materials and Methods: The present research assessed IE cases over five years, from a multicentric database, with the main objective of determining the degree of antibiotic resistance in these patients, stratified by Gram-positive and Gram-negative bacteria. Results: Bad oral hygiene was present in 58.6% of patients from the Gram-negative group (vs. 38.7% in the Gram-positive group). Non-valvular heart disease was identified in approximately 40% of all patients, and valvopathies in approximately 20%. It was observed that 37.9% of Gram-negative IE bacteria were resistant to three or more antibiotics, whereas 20.7% were susceptible. Among Gram-positive infections, S. aureus was the most commonly involved pathogen, with a multidrug-resistant pattern in 11.2% of patients, while Acinetobacter baumannii had the highest resistance pattern of all Gram-negative pathogens, with 27.4% of all samples resistant to three or more antibiotics. Patients with Gram-negative IE were 4.2 times more likely to die. The mortality risk was 4 times higher when bacteria resistant to two or more antibiotics was involved and 5.7 times higher with resistance patterns to three or more antibiotics than the reference group with no antibiotic resistance. Peripheral catheters were the most common cause of multi-resistant IE, followed by heart surgery, dental procedures, and ENT interventions. Conclusions: Even though Gram-positive infections were the most frequent (83.0% of all cases), Gram-negative IE infections are substantially more deadly than Gram-positive IE infections. However, it was also observed that patients with Gram-negative infections were more likely to have underlying comorbidities, be institutionalized, and be underweight. Although the Gram-negative infections were more severe, their resistance patterns were similar to Gram-positive bacteria. As resistance patterns increase, more efforts should be made to prevent a healthcare catastrophe. At the same time, careful prophylaxis should be considered in patients at risk, including those with central catheters, undergoing dental procedures, and with poor oral hygiene.

A Review of Detection Methods for Vancomycin-Resistant Enterococci (VRE) Genes: From Conventional Approaches to Potentially Electrochemical DNA Biosensors

Vancomycin-resistant Enterococci (VRE) genes are bacteria strains generated from Gram-positive bacteria and resistant to one of the glycopeptides antibiotics, commonly, vancomycin. VRE genes have been identified worldwide and exhibit considerable phenotypic and genotypic variations. There are six identified phenotypes of vancomycin-resistant genes: VanA, VanB, VanC, VanD, VanE, and VanG. The VanA and VanB strains are often found in the clinical laboratory because they are very resistant to vancomycin. VanA bacteria can pose significant issues for hospitalized patients due to their ability to spread to other Gram-positive infections, which changes their genetic material to increase their resistance to the antibiotics used during treatment. This review summarizes the established methods for detecting VRE strains utilizing traditional, immunoassay, and molecular approaches and then focuses on potential electrochemical DNA biosensors to be developed. However, from the literature search, no information was reported on developing electrochemical biosensors for detecting VRE genes; only the electrochemical detection of vancomycin-susceptible bacteria was reported. Thus, strategies to create robust, selective, and miniaturized electrochemical DNA biosensor platforms to detect VRE genes are also discussed.

Multidrug-Resistant Enterococcal Infection in Surgical Patients, What Surgeons Need to Know

Enterococci are organisms that can be found in the normal intestinal and skin microbiota and show remarkable ability to acquire antibiotic resistance. This is an enormous challenge for surgeons when faced with surgical site infections caused by multidrug-resistant (MDR) Enterococci. Due to an increase in the prevalence of MDR Enterococcus within the last few decades, there has been a major decrease in therapeutic options, because the majority of E. faecium isolates are now resistant to ampicillin and vancomycin and exhibit high-level resistance to aminoglycosides, traditionally three of the most useful anti-enterococcal antibiotics. There is limited data regarding the magnitude and pattern of multidrug resistance among the enterococcal genus causing surgical site infections in hospitalized patients. The scope of the review is to summarize the most recent findings in the emergence of postoperative MDR Enterococci and discuss recent mechanisms of resistance and the best treatment options available.

Development of a workflow for the detection of vancomycin-resistant Enterococcus faecium and Enterococcus faecalis from rectal swabs using the spectra VRE medium

BACKGROUND

Spectra™ VRE agar (Remel, Lenexa, KS) is a chromogenic agar that is FDA approved for screening patients for VRE colonization. The package insert recommends confirming isolates with identification and susceptibility testing, but confirming every culture delays time to result. Given the agar's historic high specificity for E. faecium isolates, we theorized the agar could be utilized as a stand-alone screening to minimize reagents and time.

AIM

Our laboratory sought to develop a workflow to optimize the use of the medium.

METHODS

We plated 3,815 rectal swabs to the Spectra VRE agar and compared results to traditional identification and susceptibility testing.

RESULTS

Dark blue or purple colonies on the agar demonstrated a sensitivity of 98% and specificity of 85% for detection of VRE faecium, but light blue colonies were significantly less specific for E. faecalis.

CONCLUSIONS

We streamlined our workflow to accept dark blue or purple colonies as VRE faecium and plan to perform additional testing only on light blue colonies. Interestingly, higher quantity of growth increased the accuracy of the agar. In the future, growth quantity may be used to further streamline the workflow once more data is obtained.

Activity of vancomycin combined with linezolid against clinical vancomycin-resistant Enterococcus strains

INTRODUCTION

Because multi-drug-resistant Gram-positive bacteria have been isolated frequently worldwide and are difficult to treat, alternative treatment choices are required. Combination antibiotherapies have a distinct advantage over monotherapies in terms of their broad spectrum and synergistic effect. In the present study, it was aimed to investigate the in vitro activity of vancomycin combined with linezolid against clinical vancomycin-resistant enterococci (VRE) strains with high-level aminoglycoside resistance.

MATERIAL AND METHODS

A total of 30 randomly selected clinical VRE strains were studied. Susceptibility to agents tested was investigated using broth microdilution assay. The inoculum of strain was adjusted to approximately 5 × 10⁵ CFU/ml in the wells. The results were interpreted in accordance with Clinical and Laboratory Standards Institute guidelines. In vitro activities of antibiotics in combination were assessed using the broth microcheckerboard technique. The fractional inhibitory concentration indexes (FICIs) were interpreted as follows: synergism, FICI ≤ 0.5; additive/indifference, FICI ≤ 0.5 - ≤ 4; antagonism, FICI > 4.

RESULTS

All strains were resistant to vancomycin and susceptible to linezolid. The MIC_50,90 and MIC_range values of antimicrobials were 512, 512, and 512-1024 μg/ml for vancomycin; 2, 2, and 2-4 μg/ml for linezolid. The rate of synergy was found to be 46.6% (14/30) for linezolid combined with vancomycin. No antagonism was observed.

CONCLUSIONS

The results of the study suggest that this combination may contribute to the treatment of VRE infections for their synergistic effect and because no antagonism was observed.

A new approach to overcoming antibiotic-resistant bacteria: Traditional Chinese medicine therapy based on the gut microbiota

With the irrational use of antibiotics and the increasing abuse of oral antibiotics, the drug resistance of gastrointestinal pathogens has become a prominent problem in clinical practice. Gut microbiota plays an important role in maintaining human health, and the change of microbiota also affects the activity of pathogenic bacteria. Interfering with antibiotic resistant bacteria by affecting gut microbiota has also become an important regulatory signal. In clinical application, due to the unique advantages of traditional Chinese medicine in sterilization and drug resistance, it is possible for traditional Chinese medicine to improve the gut microbial microenvironment. This review discusses the strategies of traditional Chinese medicine for the treatment of drug-resistant bacterial infections by changing the gut microenvironment, unlocking the interaction between microbiota and drug resistance of pathogenic bacteria.

A Retrospective Analysis of Culture-Confirmed Enterococci Bloodstream Infections in South Africa, 2016-2020: A Cross-Sectional Study

(1) Background: The emergence of multidrug resistance enterococci is a major public health concern. This study aimed to determine the prevalence and antimicrobial resistance of enterococci isolated from blood cultures over a five-year period (2016−2020) at public hospitals in South Africa. (2): Methods: A retrospective analysis of clinical enterococci isolated from bloodstream infection samples at the South African public hospitals was conducted. The ESKAPE dataset from January 2016 to December 2020 was obtained from the central data warehouse (CDW) at the National Health Laboratory Service (NHLS). (3): Results: Following de-duplication, a total of 130,352/306,592 organisms isolated from blood cultures were identified as ESKAPE pathogens. In this study, K. pneumoniae (25%; 33,082/130,352), was the most frequently isolated pathogen from blood cultures, followed by S. aureus (23%; 29,922/130,352) and enterococci (16%; 21,339/130,352). Of the enterococci cases, about 43% (9132/21,339) of cases were from the infants aged (<1-year old) and 32% (6745/21,339) from the adult patients. No changes observed in vancomycin, teicoplanin, and linezolid susceptibility; however, E. faecium and E. faecalis blood culture isolates remained highly susceptible (>97%) to these antibiotics. (4): Conclusions: The current study revealed a significant increase of E. faecalis and E. faecium blood culture isolates as compared to the previous national ESKAPE data. Low vancomycin resistance was observed. Continuous monitoring of antimicrobial resistant Enterococcus species is warranted in South Africa.

Vancomycin Resistance in Enterococcus and Staphylococcus aureus

Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus are both common commensals and major opportunistic human pathogens. In recent decades, these bacteria have acquired broad resistance to several major classes of antibiotics, including commonly employed glycopeptides. Exemplified by resistance to vancomycin, glycopeptide resistance is mediated through intrinsic gene mutations, and/or transferrable van resistance gene cassette-carrying mobile genetic elements. Here, this review will discuss the epidemiology of vancomycin-resistant Enterococcus and S. aureus in healthcare, community, and agricultural settings, explore vancomycin resistance in the context of van and non-van mediated resistance development and provide insights into alternative therapeutic approaches aimed at treating drug-resistant Enterococcus and S. aureus infections.

Agarose Gel Electrophoresis-Based RAPD-PCR-An Optimization of the Conditions to Rapidly Detect Similarity of the Alert Pathogens for the Purpose of Epidemiological Studies

Agarose gel electrophoresis is a well-known tool to detect DNA fragments amplified in polymerase chain reaction (PCR). Its usefulness has also been confirmed for epidemiological studies based on restriction fragments length polymorphism (RFLP), usually performed using pulsed-field gel electrophoresis (PFGE). Little is known on the effectiveness for alert-pathogen epidemiological studies of another less time-consuming and costly technique called randomly amplified polymorphic DNA-PCR (RAPD-PCR). Meanwhile, its usefulness is believed to be comparable to RFLP-PFGE. Therefore, the aim of the study was to establish and optimize the conditions of agarose gel electrophoresis following RAPD-PCR for 19 Enterococcus faecium strains derived from epidemic outbreaks at intensive care units. An application of different PCR primers, primer combinations, and, in particular, agarose gel concentrations and electrophoresis conditions revealed the usefulness of this relatively fast and inexpensive method based on RAPD-PCR for epidemiological studies without a compulsion to use the specialized equipment necessary for RFLP-PFGE.

Antibacterial and Antibiofilm Activity of Juglone Derivatives against Enterococcus faecalis: An In Silico and In Vitro Approach

Enterococcus faecalis is a Gram-positive bacterium that is normally found in the gastrointestinal tract of humans and animals. E. faecalis is an opportunistic pathogen that causes a number of invasive and noninvasive infections. The emergence of multidrug resistance and biofilm formation by the bacterium have rendered the treatment of E. faecalis infections very difficult. Due its high rate of resistance and biofilm formation, there are very few options of treatment. Therefore, the current study was designed to evaluate the antibacterial and biofilm activities of juglone derivatives such as 2-methoxy-6-acetyl-7-methyljuglone and 2-ethoxy-6-acetyl-7-methyljuglone against multidrug-resistant (MDR) and biofilm-producing strains of E. faecalis. Agar well diffusion and broth microdilution methods were used to determine the antibacterial activities. Biofilm attachment and preformed biofilm inhibition were determined using crystal violet staining assay. Both juglone derivatives displayed promising antibacterial and antibiofilm activities against E. faecalis. Among these compounds, 2-ethoxy-6-acetyl-7-methyljuglone possessed better inhibitory activity with minimum inhibitory concentration (MIC) of $9.7\pm 3\mu \text{M}$ as compared to 2-methoxy-6-acetyl-7-methyljuglone (MIC, $19.5\pm 2\mu \text{M}$ ). Additionally, 2-ethoxy-6-acetyl-7-methyljuglone also showed stronger antibiofilm activity than 2-methoxy-6-acetyl-7-methyljuglone. Furthermore, both the ligand molecules were docked into the binding site of the enterococcal surface protein, and the results revealed that both the molecules are actively binding in the target site. Based on these findings, juglone derivatives may be considered useful for the treatment of E. faecalis infections; however, further studies are required to elucidate the mechanism of action.

Comparative genomics and pangenomics of vancomycin-resistant and susceptible Enterococcus faecium from Irish hospitals

Introduction. Enterococcus faecium has emerged as an important nosocomial pathogen, which is increasingly difficult to treat due to the genetic acquisition of vancomycin resistance. Ireland has a recalcitrant vancomycin-resistant bloodstream infection rate compared to other developed countries.

Hypothesis/Gap statement. Vancomycin resistance rates persist amongst E. faecium isolates from Irish hospitals. The evolutionary genomics governing these trends have not been fully elucidated.

Methodology. A set of 28 vancomycin-resistant isolates was sequenced to construct a dataset alongside 61 other publicly available Irish genomes. This dataset was extensively analysed using in silico methodologies (comparative genomics, pangenomics, phylogenetics, genotypics and comparative functional analyses) to uncover distinct evolutionary, coevolutionary and clinically relevant population trends.

Results. These results suggest that a stable (in terms of genome size, GC% and number of genes), yet genetically diverse population (in terms of gene content) of E. faecium persists in Ireland with acquired resistance arising via plasmid acquisition (vanA) or, to a lesser extent, chromosomal recombination (vanB). Population analysis revealed five clusters with one cluster partitioned into four clades which transcend isolation dates. Pangenomic and recombination analyses revealed an open (whole genome and chromosomal specific) pangenome illustrating a rampant evolutionary pattern. Comparative resistomics and virulomics uncovered distinct chromosomal and mobilomal propensity for multidrug resistance, widespread chromosomal point-mutation-mediated resistance and chromosomally harboured arsenals of virulence factors. Interestingly, a potential difference in biofilm formation strategies was highlighted by coevolutionary analysis, suggesting differential biofilm genotypes between vanA and vanB isolates.

Conclusions. These results highlight the evolutionary history of Irish E. faecium isolates and may provide insight into underlying infection dynamics in a clinical setting. Due to the apparent ease of vancomycin resistance acquisition over time, susceptible E. faecium should be concurrently reduced in Irish hospitals to mitigate potential resistant infections.

In Vitro and In Vivo Studies of Oritavancin and Fosfomycin Synergism against Vancomycin-Resistant Enterococcus faecium

Therapeutic options for infections caused by vancomycin-resistant enterococci are currently suboptimal. Combination regimens where fosfomycin is used alongside existing treatments are emerging given the proven synergistic potential and PK/PD properties. In the studies presented here, we tested five vanA and five vanB clinical isolates of Enterococcus faecium using a combination of oritavancin + fosfomycin both in vitro (checkerboard, time killing) and in vivo (Galleria mellonella). The combination of oritavancin and fosfomycin increased drug susceptibility, showing a synergistic effect in 80% of isolates and an additive effect in the remaining isolates. The combination restored fosfomycin susceptibility in 85% of fosfomycin-resistant isolates. Time killing on four selected isolates demonstrated that the combination of oritavancin and fosfomycin provided a CFU/mL reduction > 2 log10 compared with the most effective drug alone and prevented the bacterial regrowth seen after 8−24 h at sub-inhibitory drug concentrations. In addition, the combination was also tested in a biofilm assay with two isolates, and a strong synergistic effect was observed in one isolate and an additive effect in the other. Finally, we demonstrated in vivo (Galleria mellonella) a higher survival rate of the larvae treated with the combination therapy compared to monotherapy (fosfomycin or oritavancin alone). Our study provides preclinical evidence to support trials combining oritavancin and fosfomycin for VRE BSI in humans, even when biofilm is involved.

Antimicrobial Resistance, Virulence Profiles, and Public Health Significance of Enterococcus faecalis Isolated from Clinical Mastitis of Cattle in Bangladesh

This study was designed to identify Enterococcus faecalis from clinical mastitis of cattle and determine their antimicrobial resistance and virulence determinants to evaluate their potential public health significance. A total of 105 composite milk samples (80 from cattle with clinical mastitis and 25 from apparently healthy cattle) were analyzed. E. faecalis were isolated by culturing on enterococcal selective media and identified by PCR and sequencing. Antimicrobial resistance phenotype was elucidated by the disc diffusion method, and MIC was determined by broth microdilution method according to CLSI guidelines. Detection of antimicrobial resistance and virulence genes was done by PCR. E. faecalis were isolated from 11.25% (9/80) of the clinical mastitis and 4% (1/25) of the apparently healthy cattle milk samples. The disc diffusion test revealed 40% isolates as resistant to tetracycline and azithromycin, respectively. Among them, 20% (2/10) of isolates showed resistance to both tetracycline and azithromycin. Tetracycline-resistant isolates showed MIC ranging from ≥64 to >128 μg/ml and carried tetracycline-resistant genes tetK, tetL, and tetM in 25%, 25%, and 50% of the resistant isolates, respectively. On the other hand, all the isolates were sensitive to amoxicillin, ampicillin, bacitracin, chloramphenicol, gentamicin, penicillin, and vancomycin. In addition, the isolates carried at least one of the nine virulence genes screened with pil having the highest frequency, followed by fsrB, fsrC, ace, sprE, gelE, and agg genes. Positive correlations were evident between ace, fsrC, gelE, and sprE genes that are associated with the attachment and biofilm formation in E. faecalis. E. faecalis isolated in this study carried antibiotic resistance and virulence determinants which explain their competence to be potential human pathogens.

Antimicrobial Susceptibility Testing for Enterococci

Enterococci are major, recalcitrant nosocomial pathogens with a wide repertoire of intrinsic and acquired resistance determinants and the potential of developing resistance to all clinically available antimicrobials. As such, multidrug-resistant enterococci are considered a serious public health threat. Due to limited treatment options and rapid emergence of resistance to all novel agents, the clinical microbiology laboratory plays a critical role in deploying accurate, reproducible, and feasible antimicrobial susceptibility testing methods to guide appropriate treatment of patients with deep-seated enterococcal infections. In this review, we provide an overview of the advantages and disadvantages of existing manual and automated methods that test susceptibility of Enterococcus faecium and Enterococcus faecalis to β-lactams, aminoglycosides, vancomycin, lipoglycopeptides, oxazolidinones, novel tetracycline-derivatives, and daptomycin. We also identify unique problems and gaps with the performance and clinical utility of antimicrobial susceptibility testing for enterococci, provide recommendations for clinical laboratories to circumvent select problems, and address potential future innovations that can bridge major gaps in susceptibility testing.