The rise of the Enterococcus: beyond vancomycin resistance. Nat Rev Microbiol. 2012;10:266-278. [PMID: 22421879 DOI: 10.1038/nrmicro2761]

Structural and functional analysis reveals the catalytic mechanism and substrate binding mode of the broad-spectrum endolysin Ply2741

The emergence of antibiotic-resistant bacteria has attracted interest in the field of endolysins. Here, we analyzed the diversity of Streptococcus endolysins and identified a new endolysin, Ply2741, that exhibited broad-spectrum bactericidal activity. Our results demonstrated that Ply2741 could effectively eradicate multidrug-resistant gram-positive pathogens in vitro and in vivo. Structural analysis revealed that the bactericidal activity of Ply2741 depends on the classic "Cys-His-Asn" catalytic triad. Site-directed mutagenesis results further identified that the conserved residue Gln29, located near the catalytic triad, also contributes to the lytic activity of Ply2741. Furthermore, the key residues (R189 and W250) in the Ply2741 cell wall binding domain (CBD) responsible for binding to peptidoglycan were revealed by molecular docking and fluorescence-activated cell sorting (FACS) analysis. Ply2741 demonstrates a broad lytic spectrum, with significant bactericidal activity against Enterococcus, Staphylococcus, and Streptococcus and species. To the best of our knowledge, we found that residue Gln29 participated in the lytic activity of endolysin for the first time. Additionally, we systematically elucidate the binding mode and key residues of the Ply2741CBD. This study proposes Ply2741 as a potential antibiotic substitute and provides a structural basis for the modification and design of endolysins.

A nano-enabled adjunctive therapy to prevent vancomycin resistance evolution: Toward nano-anti-antibiotics

Vancomycin (VAN), a cationic glycopeptide antibiotic, represents a last-resort therapeutic remedy for life-threatening infections caused by multidrug resistant Gram-positive pathogens. However, biliary excretion of intravenously administered VAN in the gastrointestinal (GI) tract results in the VAN-resistant Enterococcus faecium emergence, a major cause of hospital-acquired infections. Instead of developing new antibiotics, we hypothesize that breaking the connection between intravenous antibiotic use and GI antimicrobial resistance may protect current antibiotics. Here, we develop a novel anti-VAN material via hybridizing hairy cellulose nanocrystals with a Food and Drug Administration (FDA)-approved resin to remove the excess antibiotic from the GI tract before it impacts bacteria and selects for resistance. In vitro studies show that VAN removal is regulated by electrostatic interactions via a time-dependent diffusion-controlled process that is not significantly influenced by the physiological pH, ionic strength, or the components of simulated intestinal fluid. Aligned with the in vitro findings, the oral administration of anti-VAN adjuvant effectively sequesters VAN in the murine GI tract and prevents the VAN resistance enrichment following the VAN treatment of E. faecium colonized mice. The anti-VAN adjunctive therapy may protect intravenous VAN, which is a step forward in addressing the global threat of antimicrobial resistance.

Co-carriage of diverse vancomycin-resistant Enterococcus faecium ST80-lineages by 70% of patients in an Irish hospital

Background

Vancomycin-resistant Enterococcus faecium (VREfm) are significant nosocomial pathogens. Irish VREfm comprise diverse vanA-encoding ST80-complex type (CT) lineages. Recent studies indicate that within-patient VREfm diversity could confound surveillance. This study investigated the intra-host VREfm genetic diversity among colonized Irish hospital patients.

Methods

Rectal VREfm (n = 150) from 10 patients (15 isolates each) were investigated by WGS, core-genome MLST and split k-mer (SKA)-SNP analysis. Plasmids and vanA-transposons from 39 VREfm representative of CTs identified were resolved by hybrid assembly of short-read (Illumina) and long-read (Oxford Nanopore Technologies) sequences. Plasmid relatedness was assessed based on Mash distances. Thirty vancomycin-susceptible E. faecium (VSEfm) from four VREfm-positive patients were also investigated.

Results

All isolates were clade A1 and most were ST80 (VREfm, 147/150; VSEfm, 25/30). Seventy-percent of patients (7/10) harboured either two (n = 4), three (n = 2) or four (n = 1) VREfm CTs. Individual patient isolate pairs from different CTs differed significantly (median SKA-SNPs 2933), but differences were minimal between isolate pairs of the same CT (median SKA-SNPs 0). In total, 193 plasmids were identified in 39 VREfm investigated. Near-identical plasmids (≥99.5% average nucleotide identity) were identified in divergent CTs from multiple patients. Most VREfm (28/39, 72%) harboured vanA on closely related transferable, linear plasmids. Divergent CTs within individual patients harboured either indistinguishable vanA-transposons or vanA-transposons with distinct organizational iterations. Four VSEfm from different CTs investigated harboured similar plasmids to VREfm.

Conclusion

VREfm within-host diversity is highly prevalent in Irish hospital patients, which complicates surveillance. Linear plasmids play an important role in the emergence of Irish VREfm.

The optrA, cfr(D) and vanA genes are co-located on linear plasmids in linezolid- and vancomycin-resistant enterococcal clinical isolates in Italy

OBJECTIVES

To characterize the optrA-, cfr(D)- and vanA-carrying linear plasmids detected in three MDR enterococcal clinical isolates.

METHODS

Enterococcus faecium (868), E. faecium (1001) and Enterococcus faecalis (2048), which were linezolid- and vancomycin-resistant due to the presence of optrA, cfr(D) and vanA genes, were tested for their susceptibility to several antibiotics. Characterization of the genetic elements carrying antibiotic resistance genes and ST determination were achieved using WGS data. The plasmid topology was evaluated by S1-PFGE. Resistance gene transferability was assessed by filter-mating experiments.

RESULTS

The linezolid- and vancomycin-resistant enterococci also showed resistance to tedizolid, chloramphenicol, tetracycline, erythromycin, ampicillin and levofloxacin. Both E. faecium 868 and E. faecium 1001 belonged to ST80 (included in clade A1), whereas E. faecalis 2048 was associated with ST6. WGS analysis revealed a plasmid co-localization of the optrA, cfr(D) and vanA genes. optrA was carried by Tn6674-like or Tn7695-like transposons; cfr(D) was associated with a truncated guaA gene, both flanked by IS1216 with opposite polarity; vanA was found on a Tn1546-like transposon containing IS1542 and IS1251 transposases. PFGE of S1 nuclease-treated and untreated DNAs displayed the linear topology of optrA-, cfr(D)- and vanA-harbouring plasmids. Only E. faecium 868 was able to transfer linezolid and vancomycin genes to an enterococcal recipient.

CONCLUSIONS

To the best of our knowledge this is the first report on the occurrence of a linear plasmid in E. faecalis. Linear plasmids can play a key role in the spread of oxazolidinone and glycopeptide resistance with serious consequences for public health.

In Vitro Activity of Bacteriophages Against Ocular Methicillin-resistant S. aureus Isolates Collected in the US

INTRODUCTION

Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of sight-threatening infections in the US. These strains pose a significant challenge in managing ocular infections, as they frequently exhibit resistance to first-line empirical antibiotics. To assess the potential of bacteriophages as innovative topical therapies for treatment of recalcitrant ocular infections, we evaluated the in vitro antimicrobial activity of a set of anti-S. aureus phages against a collection of ocular MRSA clinical isolates collected in the US.

METHODS

The host range of six phages (V4SA2, V1SA9, V1SA12, V1SA19, V1SA20 and V1SA22) was assessed using the spot assay on a panel of 50 multidrug-resistant (MDR) ocular MRSA isolates selected to be representative of clones circulating in the US. Subsequently, liquid culture-based host range assay was performed for the three most active phages using different multiplicity of infection (MOI of 10-2, 1 or 100 phages/bacteria).

RESULTS

In total, 90.0% of bacterial isolates were susceptible to at least one of the six phages. The spot host range assay showed that phages V1SA19, V1SA20 and V1SA22 had the broadest spectrum, being active against 86%, 84% and 82% of the isolates, respectively, including the MDR-MRSA CC5 and the community-associated CC8 lineages. A phage dose effect was observed across the liquid culture-based host range assay.

CONCLUSION

Phages V1SA19, V1SA20 and V1SA22 exhibited high antimicrobial activity against ocular MRSA. Bacteriophages represent a promising anti-infective strategy in ophthalmology that could be explored for improved topical therapy of recalcitrant MRSA infections.

Molecular characterization of histidine and tyrosine decarboxylating Enterococcus species isolated from some milk products

BACKGROUND

Fermented foods can cause adverse effects on human health because of the biogenic amines (BAs) accumulating through amino acid decarboxylation. This study investigated the presence of BAs including tyramine and histamine in 240 samples of some cheese and fermented milk samples using high-performance liquid chromatography. Another aim of this study is to isolate and identify Enterococcus spp. as the most important and frequent BA producer in the examined samples. The isolated Enterococcus spp. was investigated phenotypically for their capacity to produce amino acid decarboxylase enzyme using decarboxylase microplate assay, and genotypically through molecular detection of some genes encoding amino acid decarboxylation (tyrdc and hdc). Biogenic amines producing enterococci were then investigated for their antimicrobial resistance, biofilm production as well as their virulence determinants.

RESULTS

Tyramine and histamine could be detected in 86.7 and 87.9% of the investigated samples with 52.9% being contaminated with Enterococcus spp. Significant correlation between the incidence of Enterococci enterococci and BAs formed in the examined samples (P < 0.0001). tyrdc and hdc genes were detected in 85 and 5% of amino acid decarboxylating Enterococcus spp., respectively. A high percentage of Enterococcus isolates (57.5%) were multidrug-resistant and resistance against penicillin was widespread among isolates followed by tetracycline, vancomycin, erythromycin and linezolid. Also, 77.5% of the isolates were capable of forming biofilms and a highly significant correlation (P < 0.0001) was found between biofilm formation and multidrug resistance. The results showed that the rates of most virulence genes gelE, esp, ace, asa1, and cylA were 77.5. 47.5, 47.5, 35 and 7.5%, respectively, while the hyl gene was not detected in any isolates.

CONCLUSION

The study highlights the significant presence of BAs (TYM and HIS) in cheese and fermented milk samples, with a strong correlation between enterococci contamination and TYM production. The high prevalence of tyramine-producing Enterococcus species poses a notable public health concern especially with the high prevalence of multidrug-resistant, biofilm production and virulence in BAs producing Enterococcus spp. in dairy products, emphasizing the urgent need for improved antimicrobial stewardship among food producers and veterinarians to mitigate the risk of transferring resistant strains to humans.

Antimicrobial Resistance and Genomic Insights into Enterococcus faecalis Isolates from Broilers and Their Handlers in Punjab, India

Enterococcus faecalis, a common constituent of human and animal gut microbiota, has emerged as a significant pathogen due to its antimicrobial resistance (AMR) capabilities. This study investigates AMR profiles, virulence factors, and genetic diversity of E. faecalis isolates from broiler farms in Ludhiana, Punjab, India, to explore transmission dynamics between poultry and handlers. A total of 240 samples were collected from 20 farms, comprising 200 broiler droppings, 34 hand swabs from poultry handlers, and 6 human stool samples. Selective media and standard microbiological techniques were employed to isolate and identify E. faecalis. Whole genome sequencing (WGS) was performed on representative isolates to uncover antimicrobial resistance genes (ARGs) and virulence factors. E. faecalis was isolated from 47% of broiler droppings and 26.47% of handler hand swabs, whereas no isolates were recovered from stool samples. High resistance was observed for erythromycin (96.11%), tetracycline (78.64%), ciprofloxacin (76.69%), streptomycin (76.69%), and linezolid (65.04%), with 83.49% of isolates exhibiting multidrug resistance (MDR). Vancomycin resistance genes (vanC1-34.95% and vanC2/C3-9.70%) were also detected. WGS analysis of four isolates identified ARGs such as dfrE, efrA, vanT gene in vanG cluster, vanY gene in vanB cluster, ermB, tet45, tetM, tetA, aac(6')-Ie-aph(2″)-Ia, ant(4')-Ib, aph(3')-Ia, sul1, sul3, mphA, qnrS1, and catA8, as well as virulence factors associated with biofilm formation, adherence, capsule formation, and protease production. Sequence typing identified was ST-1866, ST-7317, and ST-403, with ST-7317 common between broiler droppings and handler swab isolates, indicating potential transmission. While these findings highlight poultry environments as reservoirs for MDR E. faecalis, the directionality of transmission (zoonotic vs. reverse zoonotic) remains unclear. This underscores the need for expanded surveillance and molecular studies to better understand transmission dynamics and mitigate risks to farm workers and public health.

Whole-genome analysis and antimicrobial resistance phenotype of Vagococcus fluvialis isolated from wild Niviventer

Vagococcus fluvialis (V. fluvialis), a Gram-positive bacterium belonging to the Enterococcaceae family, has been associated with human infections, including bacteremia and endocarditis. Its zoonotic potential raises concerns for public health, yet research on its antimicrobial resistance and pathogenicity is still limited. This study aimed to isolate and characterize V. fluvialis from wild Niviventer, analyze its genomic features (including antimicrobial resistance and virulence genes), and evaluate its antibiotic susceptibility profile to assess potential public health risks. We first isolated V. fluvialis (strain 25C42) from the rectum of wild Niviventer, confirmed through Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing. Whole-genome sequencing (WGS) was performed using second-and third-generation technologies, with subsequent quality control and assembly. Six databases including KEGG, COG, CARD and VFDB were used for genome annotation. Antibiotic susceptibility was evaluated according to Clinical and Laboratory Standards Institute (CLSI) guidelines, determining the minimum inhibitory concentrations (MIC) for 16 antibiotics. Strain 25C42 was identified as V. fluvialis, confirmed by MALDI-TOF MS and 16S rRNA sequencing. WGS revealed a genome length of 2,720,341 bp, GC content of 32.57%. Functional genomic analysis identified 2,268 genes in the COG database and 2,023 genes in KEGG, highlighting key metabolic and cellular processes. Notably, 119 virulence genes and 65 antimicrobial resistance genes were found, indicating significant resistance potential. Phylogenetic analysis demonstrated a close relationship with other Vagococcus species, particularly V. fluvialis (ANI 98.57%, DDH 88.6%). Antibiotic susceptibility tests indicated strain 25C42 was resistant to clindamycin, tetracycline, rifampicin, cefoxitin and levofloxacin. Our findings reveal that the wild rodent-derived V. fluvialis strain 25C42 harbors clinically relevant antimicrobial resistance determinants and virulence-associated genes. The high genomic integrity and extensive functional gene annotation underscore its metabolic versatility. Notably, strain 25C42 exhibits significant antimicrobial resistance, necessitating ongoing surveillance and research to understand its implications for public health and environmental monitoring, as well as strategies for effective therapeutic intervention.

Genome analysis reveals a biased distribution of virulence and antibiotic resistance genes in the genus Enterococcus and an abundance of safe species

Enterococci are lactic acid bacteria (LAB) that, as their name implies, often are found in the gastrointestinal tract of animals. Like many other gut-dwelling LAB, for example, various lactobacilli, they are frequently found in other niches as well, including plants and fermented foods from all over the world. In fermented foods, they contribute to flavor and other organoleptic properties, help extend shelf life, and some even possess probiotic properties. There are many positive attributes of enterococci; however, they have been overshadowed by the occurrence of antibiotic-resistant and virulent strains, often reported for the two species, Enterococcus faecalis and Enterococcus faecium. More than 40,000 whole-genome sequences covering 64 Enterococcus type species are currently available in the National Center for Biotechnology Information repository. Closer inspection of these sequences revealed that most represent the two gut-dwelling species E. faecalis and E. faecium. The remaining 62 species, many of which have been isolated from plants, are thus quite underrepresented. Of the latter species, we found that most carried no potential virulence and antibiotic resistance genes, an observation that is aligned with these species predominately occupying other niches. Thus, the culprits found in the Enterococcus genus mainly belong to E. faecalis, and a biased characterization has resulted in the opinion that enterococci do not belong in food. Since enterococci possess many industrially desirable traits and frequently are found in other niches besides the gut of animals, we suggest that their use as food fermentation microorganisms is reconsidered.IMPORTANCEWe have retrieved a large number of Enterococcus genome sequences from the National Center for Biotechnology Information repository and have scrutinized these for the presence of virulence and antibiotic resistance genes. Our results show that such genes are prevalently found in the two species Enterococcus faecalis and Enterococcus faecium. Most other species do not harbor any virulence and antibiotic resistance genes and display great potential for use as food fermentation microorganisms or as probiotics. The study contributes to the current debate on enterococci and goes against the mainstream perception of enterococci as potentially dangerous microorganisms that should not be associated with food and health.

Unveiling gut microbiota and metabolic functions contributed to polyvinyl chloride degradation in Spodoptera frugiperda larvae

The accumulation of synthetic plastic waste, particularly polyvinyl chloride (PVC), threatens ecosystems globally. While microbial biodegradation represents a sustainable solution, limited effective PVC-degrading microbial bioresources have been identified. Here, we investigated the gut microbiota of Spodoptera frugiperda larvae, revealing a consistent microbial profile dominated by Enterococcus in both gut contents and tissues. PVC film feeding induced significant microbiota shifts, with functional parallels to PVC powder-fed Tenebrio molitor larvae despite taxonomic divergence. Through enzyme-centric analysis, we found an Enterococcus casseliflavus strain from the gut of S. frugiperda larvae could encode a NAD-dependent oxidoreductase that directly dechlorinates additive-free PVC, representing the first case of enzymatic polymer dechlorination. This enzyme reduced PVC molecular weight (Mn: 12.02 %; Mw: 14.07 %) and notably liberated chloride ions (6.48 mg/L with NADH as a co-factor). Our findings demonstrate the PVC-degrading capacity of S. frugiperda gut microbiota and reveal its dechlorination mechanism, offering an enzymatic candidate for developing novel biocatalysts and engineered microbial strains for enhanced biodegradation. By unravelling insect-associated microbes and enzymes, this work lays a theoretical foundation for their application potentials in sustainable PVC wastes upcycling and microplastic remediation.

Zwitterionic Molecularly Imprinted Hairy Cellulose Nanocrystals Enable Selective Vancomycin Removal

Access to free, off-target, and nontherapeutic doses of antibiotics is a key driving factor in the emergence of antimicrobial resistance (AMR). Intravenously (IV) administered vancomycin (VAN) is among the last-line antibiotics for treating infections caused by multidrug-resistant Gram-positive bacteria. A fraction of the total IV dose unwantedly reaches the gastrointestinal tract, driving AMR. Selective VAN removal from the complex intestinal fluid may reduce the probability of AMR emergence; however, it remains a significant challenge due to the competitive adsorption of other species. Here, we engineer novel VAN-imprinted polymerized zwitterionic hairy cellulose nanocrystals (ViPZ-HCNC) that selectively capture VAN with a removal capacity of ∼ 235 mg g-1 at an imprinting factor of ∼ 7.5. ViPZ-HCNC provide the first nanocellulose-based material with an excellent selectivity for VAN against lysine, lysozyme, and bovine serum albumin, which efficiently remove VAN from calcium ion-containing solutions and simulated intestinal fluids. Additionally, ViPZ-HCNC are not toxic against NIH/3T3 murine fibroblast cells. We envision that ViPZ-HCNC may pave the way for developing soft materials that selectively remove off-target VAN from a broad range of media, preventing VAN resistance evolution. This research is a step forward in addressing the long-lasting AMR challenge using a biobased platform.

Global trends in antimicrobial resistance of Enterococcus faecium: a systematic review and meta-analysis of clinical isolates

Background

Multidrug-resistant bacteria are associated with a high number of deaths and pose a significant global concern. In recent decades, among these resistant bacteria, Enterococcus faecium, a hospital-acquired pathogen, has attracted more attention.

Objective

The present study aims to document the current state of resistance in E. faecium globally by considering several variables, including geographical locations, temporal trends, and sources of infection.

Methods

We searched studies in PubMed, Scopus, and Web of Science (30 November 2022). All statistical analyses were carried out using the statistical package R.

Results

Our meta-analysis of antibiotic resistance across various clinical isolates revealed substantial heterogeneity and variability. The average resistance proportions ranged from 2% for linezolid to 62.8% for erythromycin, with significant differences observed across different time periods, countries, and World Health Organization regional offices.

Conclusion

Our findings confirm the high antibacterial activity of linezolid against E. faecium isolates. Additionally, our investigation reveals a gradual increase and a concerning upward trend in resistance rates for nearly all agents in recent years. However, the significant reduction in resistance rates for certain antibiotics suggests that these drugs could potentially regain their effectiveness in the future.

Enterococci for human health: A friend or foe?

Enterococci are widely distributed in nature and exhibit good temperature and pH tolerance, making them suitable for industrial fermentation. It can produce bacteriocins, natural antibacterial substances utilized in food preservation. Some Enterococci are employed as probiotics to regulate human immunity and maintain healthy intestinal environments. However, recent scientific studies have highlighted the pathogenicity and multidrug resistance of Enterococci, classifying it as an important pathogen in clinical infections. Moreover, increasing evidence has linked Enterococcus sp., particularly Enterococcus faecalis and Enterococcus faecium, to clinical diseases, raising concerns about their safety and posing the question, how should we approach the conflicting nature of the pathogenic and beneficial effects of Enterococci? This review provides the recent advancements in Enterococci research and incorporates the perspectives of international authoritative organizations and institutions to comprehensively analyze the beneficial and harmful characteristics of Enterococci in the fields of science, clinical and industrial applications, aiming to address three important questions: whether Enterococci are beneficial or harmful to humans, their potential use in medical treatments, and the criteria to evaluate their safety. The goal is to explore the feasibility of the standardized use of Enterococci and provide guidance on the scientific selection and utilization of probiotics.

Urushiol-dextran SPIONs magnetic recyclable nanoparticles immobilizing vancomycin (V@DU@Fe) for antibacterial application

In this study, magnetic nanocarriers (DU@Fe, Davg = 281.6 nm, zeta potential -28.0 mV) were fabricated using dextran, urushiol as the shell and superparamagnetic iron oxide nanoparticles (SPIONs) as the core. Subsequently, the specific ligand Lys-D-Ala-D-Ala of vancomycin (Van) was grafted onto the surface of DU@Fe, which generated nanoparticles (Lys-D-Ala-D-Ala@DU@Fe) with an average particle size of 385.5 nm and a zeta potential of -16.8 mV via specific and robust interaction. Ultimately, the immobilization capacity of Van reached up to 294.1 mg·g-1 for efficient antibacterial properties. Moreover, the assembly process adhered to the pseudo-second-order kinetics model (R2 = 0.998-0.999) and the Langmuir adsorption isotherm model (R2 = 0.999, 30 °C). Notably, V@DU@Fe effectively adhered to the cell envelopes of both Gram-negative and Gram-positive bacteria, achieving rapid bactericidal effects within 1 h. Furthermore, it maintained over 85.0 % of its initial antibacterial efficiency against S. aureus and S. epidermidis even after six recycles. Therefore, this study provides strategies and methods for the development of urushiol-dextran intelligent SPIONs nanomedicines.

Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium

Gastrointestinal colonization by the nosocomial pathogen vancomycin-resistant Enterococcus faecium (VREfm) can lead to bloodstream infections with high mortality rates. Shifts in VREfm lineages found within healthcare settings occur, but reasons underlying these changes are not understood. Here we sequenced 710 VREfm clinical isolates collected between 2017 and 2022 from a large tertiary care centre. Genomic analyses revealed a polyclonal VREfm population, although 46% of isolates formed genetically related clusters, suggesting a high transmission rate. Comparing these data to a global collection of 15,631 publicly available VREfm genomes collected between 2002 and 2022 identified replacement of the sequence type (ST) 17 VREfm lineage by emergent ST80 and ST117 lineages at the local and global level. Comparative genomic and functional analyses revealed that emergent lineages encoded bacteriocin T8, which conferred a competitive advantage over bacteriocin T8-negative strains in vitro and upon colonization of the mouse gut. Bacteriocin T8 carriage was also strongly associated with strain emergence in the global genome collection. These data suggest that bacteriocin T8-mediated competition may have contributed to VREfm lineage replacement.

Insights into ecology, pathogenesis, and biofilm formation of Enterococcus faecalis from functional genomics

SUMMARYEnterococcus faecalis is a significant resident of the gastrointestinal tract of most animals, including humans. Although generally non-pathogenic in healthy hosts, this microbe is adept at the exploitation of compromises in host immune functions, resulting in life-threatening opportunistic infections whose treatments are complicated by a high degree of intrinsic and acquired resistance to antimicrobial chemotherapy. Historically, progress in enterococcal research was limited by a lack of experimental models that replicate natural infection pathways and the relevance of in vitro studies to the natural biology of the organism. In this review, we summarize the history of enterococcal research during the 20th and early 21st centuries and describe more recent genetic and genomic tools and screens developed to address challenges in the field. We also describe how the results of recent studies reveal the importance of previously uncharacterized enterococcal genes, and we provide examples of interesting determinants that have emerged as important contributors to enterococcal biology. These factors may also serve as targets for future vaccines and chemotherapeutic agents to combat life-threatening hospital infections.

Development of a strain-specific PCR as a diagnostic tool for surveillance, detection, and monitoring of vancomycin-resistant Enterococcus faecium during outbreak

INTRODUCTION

Vancomycin-resistant Enterococcus faecium (VREfm) poses a significant concern in healthcare settings, particularly during outbreaks. Traditional antibiotic susceptibility testing may fail to detect occult vancomycin resistance, and long culture times delay diagnosis. While whole genome sequencing (WGS) is the most accurate method for tracing infectious disease transmissions, its response times are not rapid enough to optimally support controlling of ongoing outbreaks. To address this limitation, we investigated the genomic diversity among outbreak isolates and developed outbreak-specific PCR tests for rapid VREfm carrier screening using strain-specific biomarkers identified through comparative genomics.

MATERIALS AND METHODS

Total DNA from VREfm isolates was sequenced using Oxford Nanopore and Illumina platforms. Multi locus sequence types (MLST-ST) and core genome sequence type clusters (cgMLST-CT) were determined with Ridom SeqSphere + software. Comparative analysis of whole genomes was conducted using Lasergene software (DNASTAR).

RESULTS

A large VREfm outbreak involving 111 patients caused by E. faecium ST117-CT469 was identified in the Northern Netherlands, spanning from August 2021 to September 2024. A subset of 55 E. faecium ST117-CT469 isolates were evaluated by WGS and outbreak specific PCRs. Antibiotic susceptibility testing revealed occult vancomycin resistance in the outbreak strain. Comparative genomics identified unique markers specific to E. faecium ST117-CT469. Two PCR assays were developed for rapid outbreak detection: a traditional PCR assay distinguishing outbreak from non-outbreak strains based on amplicon size and a TaqMan real-time PCR assay. Both assays demonstrated 100% reproducibility and specificity. The TaqMan assay was able to detect as little as 5 fg of bacterial DNA in the presence of human DNA, equivalent to approximately one bacterial genomic copy. Sequence analysis of WGS data for all 55 outbreak isolates showed perfect nucleotide sequence conservation in the regions where the primers and probe hybridized. Sequence comparison against NCBI GenBank entries confirmed the perfect specificity of both PCR assays for detecting the ST117-CT469 outbreak strain.

CONCLUSIONS

These PCR tests maintain the accuracy and discriminatory power of WGS for identifying the ST117-CT469 outbreak strain but are more cost-effective, faster, and easier to use compared to WGS. They enhance VREfm outbreak management by providing an efficient method for rapid screening. Application of strain-specific PCR based on WGS data is currently the most effective screening method during large, ongoing outbreaks.

Lasso peptides sviceucin and siamycin I exhibit anti-virulence activity and restore vancomycin effectiveness in vancomycin-resistant pathogens

Antibiotic resistance is a major threat to human health and new drugs are urgently needed. Ideally, these drugs should have several cellular targets in pathogens, decreasing the risk of resistance development. We show here that two natural ribosomally synthesized lasso peptides (LPs), sviceucin and siamycin I, (1) abolish bacterial virulence of pathogenic enterococci, (2) restore vancomycin clinical susceptibility of vancomycin-resistant (VR) enterococci in vitro and in a surrogate animal model, and (3) re-sensitize VR Staphylococcus aureus. Mode of action (MoA) analyses showed that they do so by inhibiting the histidine kinases (HKs) FsrC and VanS controlling these phenotypes. Strains resistant to the vancomycin/LP combination were difficult to obtain, and were still fully susceptible to the anti-virulence effect of the LPs, highlighting the advantage of multiple targets. Together with the highly sought-after MoA as HK inhibitors, such properties make these lasso peptides promising candidates for the development of next generation antibiotics.

Genome-wide analysis of Enterococcus faecalis genes that facilitate interspecies competition with Lactobacillus crispatus

Enterococci are opportunistic pathogens notorious for causing a variety of infections. While both Enterococcus faecalis and Lactobacillus crispatus are commensal residents of the vaginal tract, the molecular mechanisms that enable E. faecalis to take advantage of a vaginal biome with lower counts of lactobacilli to colonize the vaginal tract and induce aerobic vaginitis remain unknown. Here, we show that L. crispatus eradicates E. faecalis in a contact-independent manner. Using transposon sequencing to identify E. faecalis OG1RF transposon (Tn) mutants that are either under-represented or over-represented when co-cultured with L. crispatus, we found that Tn mutants with disruption in the dltABCD operon, that encodes the proteins responsible for the D-alanylation of teichoic acids, and OG1RF_11697 encoding for an uncharacterized hypothetical protein are more susceptible to killing by L. crispatus. Inversely, Tn mutants with disruption in ldh1, which encodes for L-lactate dehydrogenase, are more resistant to L. crispatus killing. Using the Galleria mellonella infection model, we show that co-injection of L. crispatus with E. faecalis OG1RF enhances larvae survival while this L. crispatus-mediated protection was lost in larvae co-infected with either L. crispatus and E. faecalisΔldh1 or Δldh1Δldh2 strains. Last, using RNA sequencing to identify E. faecalis genes that are differently expressed in the presence of L. crispatus, we found major changes in the expression of genes associated with glycerophospholipid metabolism, central metabolism, and general stress responses. The findings in this study provide insights into how E. faecalis mitigate assaults by L. crispatus.IMPORTANCEEnterococcus faecalis is an opportunistic pathogen notorious for causing a multitude of infections. As vaginal commensals, E. faecalis must interact with Lactobacillus crispatus, but how E. faecalis overcomes or mitigate assaults by L. crispatus killing remains unknown. We show that L. crispatus eradicates E. faecalis temporally in a contact-independent manner. Using high-throughput molecular approaches, we identified genetic determinants that enable E. faecalis to compete with L. crispatus. This study represents an important first step for the identification of adaptive genetic traits required for enterococci to tolerate assaults by lactobacilli.

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.

Replicative selfish genetic elements are driving rapid pathogenic adaptation of Enterococcus faecium

Understanding how healthcare-associated pathogens adapt in clinical environments can inform strategies to reduce their burden. Here, we investigate the hypothesis that insertion sequences (IS), prokaryotic transposable elements, are a dominant mediator of rapid genomic evolution in healthcare-associated pathogens. Among 28,207 publicly available pathogen genomes, we find high copy numbers of the replicative ISL3 family in healthcare-associated Enterococcus faecium, Streptococcus pneumoniae and Staphylococcus aureus. In E. faecium, the ESKAPE pathogen with the highest IS density, we find that ISL3 proliferation has increased in the last 30 years. To enable better identification of structural variants, we long read-sequenced a new, single hospital collection of 282 Enterococcal infection isolates collected over three years. In these samples, we observed extensive, ongoing structural variation of the E. faecium genome, largely mediated by active replicative ISL3 elements. To determine if ISL3 is actively replicating in clinical timescales in its natural, gut microbiome reservoir, we long read-sequenced a collection of 28 longitudinal stool samples from patients undergoing hematopoietic cell transplantation, whose gut microbiomes were dominated by E. faecium. We found up to six structural variants of a given E. faecium strain within a single stool sample. Examining longitudinal samples from one individual in further detail, we find ISL3 elements can replicate and move to specific positions with profound regulatory effects on neighboring gene expression. In particular, we identify an ISL3 element that upon insertion replaces an imperfect -35 promoter sequence at a folT gene locus with a perfect -35 sequence, which leads to substantial upregulation of expression of folT, driving highly effective folate scavenging. As a known folate auxotroph, E. faecium depends on other members of the microbiota or diet to supply folate. Enhanced folate scavenging may enable E. faecium to thrive in the setting of microbiome collapse that is common in HCT and other critically ill patients. Together, ISL3 expansion has enabled E. faecium to rapidly evolve in healthcare settings, and this likely contributes to its metabolic fitness and may strongly influence its ongoing trajectory of genomic evolution.

Exploring the intricacies of antimicrobial resistance: Understanding mechanisms, overcoming challenges, and pioneering innovative solutions

Antimicrobial resistance (AMR) poses a growing global threat. This review examines AMR from diverse angles, tracing the story of antibiotic resistance from its origins to today's crisis. It explores the rise of AMR, from its historical roots to the urgent need to counter this escalating menace. The review explores antibiotic classes, mechanisms, resistance profiles, and genetics. It details bacterial resistance mechanisms with illustrative examples. Multidrug-resistant bacteria spotlight AMR's resilience. Modern AMR control offers hope through precision medicine, stewardship, combination therapy, surveillance, and international cooperation. Converging traditional and innovative treatments presents an exciting frontier as novel compounds seek to enhance antibiotic efficacy. This review calls for global unity and proactive engagement to address AMR collectively, emphasizing the quest for innovative solutions and responsible antibiotic use. It underscores the interconnectedness of science, responsibility, and action in combatting AMR. Humanity faces a choice between antibiotic efficacy and obsolescence. The call is clear: unite, innovate, and prevail against AMR.

Temporal trends of enterococcal and vancomycin-resistant Enterococcus faecium bacteraemia in the northern Dutch-German cross-border region: A 10-y multicentre analysis (2013-2022)

OBJECTIVE

To analyse the trends in occurrence of enterococcal and vancomycin-resistant Enterococcus faecium (VREfm) bacteraemia in the northern Dutch-German cross-border region.

METHODS

A retrospective cross-sectional study was conducted using positive blood culture results from two university hospitals, the University Medical Centre Groningen (UMCG) and the Klinikum Oldenburg (KOL) between 1 January 2013 to 31 December 2022.

RESULTS

Over the 10-y period, 738 enterococcal bacteraemia episodes were observed at KOL and 1091 at UMCG, involving 685 and 999 patients, respectively. E. faecium was the predominant species in both institutions (60.3% at KOL and 60.8% at UMCG). The median age of patients with enterococcal, E. faecium, E. faecalis and VREfm bacteraemia was consistently higher at KOL than at UMCG (p=.029). In both institutions, over half of the enterococcal bacteraemia cases (53.4% at KOL, 55.8% at UMCG) were observed in intensive care units and haematology/oncology wards. From 2018 to 2022, UMCG had higher overall incidence rates of E. faecium, and E. faecalis bacteraemia, while KOL had a significantly higher incidence of VREfm (0.56 vs. 0.05 per 10,000 patient-d, p<.0001). There was a significant upward trend in VREfm bacteraemia cases (p=.01) and in the proportion of VREfm among bacteraemia caused by E. faecium (p=.027) at KOL, but such a trend was not observed at UMCG during the study period.

CONCLUSIONS

The results reveal a significant difference in VREfm bacteraemia occurrences between a German and Dutch hospital in a cross-border region, reflecting national trends yet showing regional variation.

Antibiotic Resistance Gene Expression in Veterinary Probiotics: Two Sides of the Coin

The rapid proliferation of antimicrobial resistance has emerged as one of the most pressing animal and public health challenges of our time. Probiotics, extensively employed in human and veterinary medicine, are instrumental in maintaining a balanced microbiome and mitigating its disruption during antibiotic therapy. While their numerous benefits are well documented, probiotics also present potential risks, notably the capacity to harbor antimicrobial resistance genes. This genetic reservoir could contribute to the emergence and spread of antimicrobial resistance by facilitating the horizontal transfer of resistance genes to pathogenic bacteria within the gut. This review critically examines the presence of antimicrobial resistance genes in commonly used probiotic strains, explores the underlying mechanisms of resistance, and provides a balanced analysis of the benefits and risks associated with their use. By addressing these dual aspects, this paper highlights the need for vigilant evaluation of probiotics to preserve their therapeutic potential while minimizing public health risks.

Effects of dietary metabolizable energy and crude protein levels on laying performance, egg quality and fecal microbiota of Taihe Silky Fowl during the peak laying period

OBJECTIVE

The experiment aimed to study the effect of dietary metabolizable energy (ME) and crude protein (CP) on laying performance, egg quality, serum routine biochemical and lipid metabolism indicators, the apparent digestibility of nutrients, and fecal microbiota of Taihe Silky Fowl (TSF) during the peak laying period.

METHODS

A total of 540 26-week-old TSF female fowls were randomly allocated to 9 groups with 5 replicates per group and 12 fowls per replicate. The fowls were fed with a 3×3 factorial arrangement of treatments diets (ME:10.88,11.30, or 11.72 MJ/kg; CP: 15, 16, or 17%).

RESULTS

With the increasing CP level, the egg weight (p = 0.023), egg production (p = 0.047), and egg mass (p = 0.022) enhanced, while the feed conversion rate (FCR) (p = 0.023) decreased. As the ME levels grew, the average daily feed intake (p<0.001) and FCR (p = 0.045) decreased. With enhanced ME, the triglycerides (p = 0.037), total cholesterol (p = 0.041), and high-density lipoprotein cholesterol (p = 0.028) increased, whereas the low-density serum lipoprotein cholesterol (p = 0.039) decreased. The apparent digestibility of CP increased as the ME level increased (p = 0.029) and as the CP level decreased (p = 0.027). At the same time, the apparent digestibility of gross energy increased as the ME level increased (p = 0.018). Different levels of ME or CP changed the composition of fecal microbiota, 17% CP increased the abundance of Bifidobacterium.

CONCLUSION

It is suggested that 10.88 MJ/kg dietary ME and 17% CP level are suitable for the nutritional requirements of TSF during the peak laying period.

Vancomycin-resistant Enterococcus faecium: A current perspective on resilience, adaptation, and the urgent need for novel strategies

Vancomycin-resistant Enterococcus faecium (VREfm) has become a critical opportunistic pathogen, urgently requiring new antimicrobial strategies due to its rising prevalence and significant impact on patient safety and healthcare costs. VREfm continues to evolve through mutations and the acquisition of new genes via horizontal gene transfer, contributing to resistance against several last-resort antibiotics. Although primarily hospital-associated, VREfm are also detected in the community, food chain, livestock, and environmental sources like wastewater, indicating diverse transmission pathways and the need for a One Health approach. Advances in genomics have shed light on VREfm's persistence in hospital settings, particularly its adaptation to the gastrointestinal tract of hospitalized patients, recent clonal shifts, and the dominance of specific clonal lineages. Despite extensive research, significant gaps remain in understanding the molecular mechanisms behind VREfm's unique adaptation to clinical environments. In this review, we aim to present an overview of VREfm current prevalence, mechanisms of resistance, and unveil the adaptive traits that have facilitated VREfm's rise and global success. A particular focus is given to key plasmids, namely linear plasmids, virulence factors, and bacteriocins as potential drivers in the global emergence of the ST78 clonal lineage. We also address diagnostic challenges and the limited treatment options available for VREfm, as well as emerging antibiotic alternatives aimed at restoring gut microbiota balance and curbing VREfm proliferation. A multifaceted approach combining research, clinical practices, and public health policies is crucial to mitigate the impact of this superbug and preserve antimicrobial effectiveness for future generations.

Drug susceptibility of uropathogens isolated from patients treated at the Mazovian Specialized Hospital in Radom

Urinary tract infections (UTI) are a significant problem among populations worldwide. It is mainly associated with the increasing incidence of recurrence, complications and the increasing drug resistance of uropathogens. The aim of this study was to demonstrate the prevalence of resistance among pathogens causing urinary tract infections. The material for the study was data obtained from the Mazovian Specialized Hospital (M.S.H) in Radom over a period of 2 years. Urine was collected from hospitalized patients with UTI. Statistical calculations were performed using statistical software. During the study period, 3,917 patients underwent microbiological examination of urine, and almost 15% of them were found to be infected with UTI. Based on statistical analysis of drug susceptibility of the most common uropathogens, it was shown that urinary tract infections caused by Escherichia coli or Klebsiella pneumoniae, among others, often show high resistance to fluoroquinolones and β-lactam antibiotics. Proteus mirabilis strains have been shown to be more resistant to aminoglycosides and fluoroquinolones than to beta-lactams. In the case of Pseudomonas aeruginisa, resistance to fluoroquinolones predominates. On the other hand, UTI caused by Acientobacter baumannii should be treated based on the results of drug susceptibility testing due to the increasing prevalence of multidrug-resistant strains.

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.

Multi-omic signatures of host response associated with presence, type, and outcome of enterococcal bacteremia

Despite the prevalence and severity of enterococcal bacteremia (EcB), the mechanisms underlying systemic host responses to the disease remain unclear. Here, we present an extensive study that profiles molecular differences in plasma from EcB patients using an unbiased multi-omics approach. We performed shotgun proteomics and metabolomics on 105 plasma samples, including those from EcB patients and healthy volunteers. Comparison between healthy volunteer and EcB-infected patient samples revealed significant disparities in proteins and metabolites involved in the acute phase response, inflammatory processes, and cholestasis. Several features distinguish these two groups with remarkable accuracy. Cross-referencing EcB signatures with those of Staphylococcus aureus bacteremia revealed shared reductions in cholesterol metabolism proteins and differing responses in platelet alpha granule and neutrophil-associated proteins. Characterization of Enterococcus isolates derived from patients facilitated a nuanced comparison between EcB caused by Enterococcus faecalis and Enterococcus faecium, uncovering reduced immunoglobulin abundances in E. faecium cases and features capable of distinguishing the underlying microbe. Leveraging extensive patient metadata, we now have identified features associated with mortality or survival, revealing significant multi-omic differences and pinpointing histidine-rich glycoprotein and fetuin-B as features capable of distinguishing survival status with excellent accuracy. Altogether, this study aims to culminate in the creation of objective risk stratification algorithms-a pivotal step toward enhancing patient management and care. To facilitate the exploration of this rich data source, we provide a user-friendly interface at https://gonzalezlab.shinyapps.io/EcB_multiomics/.

IMPORTANCE

Enterococcus infections have emerged as the second most common nosocomial infection, with enterococcal bacteremia (EcB) contributing to thousands of patient deaths annually. To address a lack of detailed understanding regarding the specific systemic response to EcB, we conducted a comprehensive multi-omic evaluation of the systemic host response observed in patient plasma. Our findings reveal significant features in the metabolome and proteome associated with the presence of infection, species differences, and survival outcome. We identified features capable of discriminating EcB infection from healthy states and survival from mortality with excellent accuracy, suggesting potential practical clinical utility. However, our study also established that systemic features to distinguish Enterococcus faecalis from Enterococcus faecium EcB show only a moderate degree of discriminatory accuracy, unlikely to significantly improve upon current diagnostic methods. Comparisons of differences in the plasma proteome relative to healthy samples between bacteremia caused by Enterococcus and Staphylococcus aureus suggest the presence of bacteria-specific responses alongside conserved inflammatory reactions.

Advances in Protein Structure Prediction Highlight Unexpected Commonalities Between Gram-positive and Gram-negative Conjugative T4SSs

Despite recent advances in our understanding of the structure and function of conjugative Type 4 Secretion Systems (T4SSs), there is still only very scarce data available for the ones from Gram-positive (G+) bacteria. This is a problem, as conjugative T4SSs are main drivers for the spread of antibiotic resistance genes and virulence factors. Here, we aim to increase our understanding of G+ systems, by using bioinformatic approaches to identify proteins that are conserved in all conjugative T4SS machineries and reviewing the current knowledge available for these components. We then combine this information with the most recent advances in structure prediction technologies to propose a structural model for a G+ T4SS from the model system encoded on pCF10. By doing so, we show that conjugative G+ T4SSs likely have more in common with their Gram-negative counterparts than previously expected, and we highlight the potential of predicted structural models to serve as a starting point for experimental design.

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.

Enterococci independently increase the risk for initial antibiotic treatment failure and prolonged hospitalization in adult patients with complicated urinary tract infection: a retrospective cohort study

OBJECTIVES

We aimed to investigate the impact of enterococci on initial antibiotic treatment (IAT) failure and prolonged hospitalization in complicated urinary tract infection (cUTI) cases, and to identify risk factors for enterococcal cUTI.

METHODS

Adult cUTI patients were analyzed to compare the differences between the Enterococcus and non-Enterococcus groups. Univariate and multivariate analyses were employed to identify independent risk factors.

RESULTS

This study included 419 patients, with the Enterococcus group showing significantly higher IAT failure rates and an extended average length of stay by 4.4 days compared to the non-Enterococcus group. Multivariate analysis identified enterococci, hospital-acquired UTIs (HA-UTI), indwelling catheters, and bed rest (bedridden) as independent risk factors for IAT failure. Enterococci were notably linked to prolonged hospitalization, other independent risk factors included IAT failure, prior antimicrobial use, age-adjusted Charlson comorbidity index (ACCI) ≥ 4, hypoalbuminemia, and bed rest. Urological cancer, HA-UTI, indwelling catheters, urinary retention, and urologic surgery were risk factors for enterococcal cUTI.

CONCLUSION

We provide the first evidence that enterococci independently increase the risk for IAT failure and prolonged hospitalization in adults with cUTIs, highlighting the significance of timely identification to optimize measures including antibiotic regimens. Risk factors for enterococcal cUTI have also been identified to aid clinicians in managing this condition.

The Enterococcus secretome inhibits the growth of vancomycin-resistant Enterococcus faecalis V853 with their antiproliferative properties and nanoencapsulation effects

In our study, the secretome of the clinical isolate Enterococcus faecalis HY7 displayed antibacterial activity against the vancomycin-resistant Enterococcus faecalis V853. These bacteriocin-like substances showed thermal stability at a wide range of temperatures up to 121 °C, while proteinase K treatment resulted in a total loss of their activity. PCR-based screening for bacteriocin biosynthetic genes revealed that Enterococcus faecalis HY7 harbored multiple enterocin-producing genes, including ent A, avc A, and as-48. The production kinetics demonstrated the highest levels of bacteriocins production at 16 h, whereas the activity was diminished after 32 h of microbial growth. Notably, the partially purified bacteriocins exhibited anti-proliferative activity on the colon cancer cells, Caco2, with an IC50 value of 172.8 μg/mL. Remarkably, the nanoencapsulation of our bacteriocins in liposome showed a fourfold increase in its anti-vancomycin-resistant Enterococcus activity, which is the first report of liposome encapsulation with anti-vancomycin resistant Enterococcus bacteriocin.

Complete genome sequence of an Enterococcus devriesei strain isolated from Zophobas morio larvae

OBJECTIVES

Enterococcus spp. are typically found in multiple settings and are sometimes responsible for difficult-to-treat infections. In this context, very little is known about Enterococcus devriesei (E. devriesei), a rare species first isolated from a river lamprey. Importantly, no complete genome of E. devriesei currently exists in public repositories.

METHODS

An E. devriesei strain (Ed-CK-24) was isolated from homogenized Zophobas morio (Z. morio) larvae. Initial species identification (ID) was performed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Antimicrobial susceptibility testing (AST) was performed by broth microdilution. Whole-genome sequencing (WGS) was done using both Illumina NovaSeq 6000 and Nanopore MinION to generate a complete genome assembly. WGS data were used to confirm species ID, antimicrobial resistance genes (ARGs) and plasmid replicon sequences screening. A database search for other E. devriesei genomes in National Center for Biotechnology Information (NCBI) was performed and used for 16S rRNA and core-genome phylogeny analyses.

RESULTS

WGS and bioinformatic analyses were performed, resulting in a complete genome assembly and allowing accurate taxonomic classification of Ed-CK-24 strain as E. devriesei. Alignment of 16S rRNA sequences of representative Enterococcus spp. further supported the ID of Ed-CK-24. A core-genome phylogenetic analysis revealed no clonal relationships between Ed-CK-24 and other E. devriesei derived from multiple sources. The Ed-CK-24 strain was resistant to clindamycin and quinupristin/dalfopristin. ARG screening identified the lsa(A) gene, carried on a 633,497 bp circular megaplasmid.

CONCLUSIONS

WGS of Ed-CK-24 allowed high-resolution genomic comparison and epidemiologic analysis of E. devriesei. Its isolation from Z. morio larvae, commonly used in pet food, warns for further surveillance as the human pathogenic potential of this species remains unknown.

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.

Antarmycins: Discovery, Biosynthesis, Anti-pathogenic Bacterial Activity, and Mechanism of Action from Deep-Sea-Derived Pseudonocardia antarctica

The rapid emergence of antimicrobial-resistant pathogenic microbes has accelerated the search for novel therapeutic agents. Here we report the discovery of antarmycin A (1), an antibiotic containing a symmetric 16-membered macrodiolide core with two pendant vancosamine moieties, one of which is glucosylated, from deep-sea-derived Pseudonocardia antarctica SCSIO 07407. The biosynthetic gene cluster of 1 was identified on a giant plasmid featuring transferable elements. In-depth biosynthetic investigation enabled us to (i) identify a set of seven genes associated with the product of the vancosamine moiety; (ii) discover two glycosyltransferases dedicated to the transfer of pendant sugars; and (iii) isolate rhamnose-modified antarmycin B (2) and a deglucosylated derivative antarmycin C (3) from genetically engineered mutant strains. Antibacterial assays revealed that 1 displays superior antibacterial properties with potent in vitro activities against the critical priority pathogens, multidrug-resistant Enterococcus faecium and methicillin-resistant Staphylococcus aureus, fast bacterial killing, insusceptibility to antimicrobial resistance, and high in vivo efficiency in infection models. Mechanistic investigations revealed that 1 disrupts the bacterial cell membrane through a mechanism involving interactions between the vancosamine moieties and membrane-embedded phosphatidylglycerol/phosphatidylethanolamine. The results provide insights into the biological generation of vancosamine in natural products and demonstrate the potential of 1 as an effective lead to address the growing antimicrobial resistance threats.

Integrated Microbiome and Metabolome Analysis Reveals Correlations Between Gut Microbiota Components and Metabolic Profiles in Mice With Mitoxantrone-Induced Cardiotoxicity

Purpose

Mitoxantrone (MTX) is largely restricted in clinical usage due to its significant cardiotoxicity. Multiple studies have shown that an imbalance in the gut-heart axis plays an important role in the development of cardiovascular disease (CVD). We aim to explore the possible correlations between gut microbiota (GM) compositions and cardiometabolic (CM) disorder in MTX-triggered cardiotoxicity mice.

Methods

MTX cumulative dose of 6 mg/kg was administered to healthy Kunming male mice to trigger cardiotoxicity, with 1 mg/kg twice weekly for a duration of 3 weeks. Plasma CK-MB and LDH levels were determined, and the heart tissue histopathology was assessed, followed by utilizing an integrated liquid chromatography-mass spectrometry (LC-MS)-based heart metabolomics study alongside the 16S ribosomal RNA (rRNA) sequencing method to assess MTX impact on GM and CM profiles in mice, establishing associations between GM and CM profiles through the Pearson correlation coefficient calculation.

Results

MTX caused CK-MB and LDH level elevations and cardiotoxicity in our mouse model. MTX primarily affected the processes of protein digestion and absorption, mineral absorption, membrane transport, production of aminoacyl-transfer RNA (tRNA), metabolism of nucleotides, lipids, and amino acids, as well as autophagy. Additionally, MTX increased Romboutsia, Enterococcus, and Turicibacter abundances and lowered norank_f__Muribaculaceae, Alistipes, Odoribacter, norank_f__Lachnospiraceae, norank_f__Ruminococcaceae, norank_f__Oscillospiraceae, unclassified_f__Ruminococcaceae, NK4A214_group, Colidextribacter, norank_f__norank_o__Clostridia_vadinBB60_group, Rikenella, and Anaerotruncus abundances. The correlation analyses showcased variations in the abundance of diverse flora, such as Romboutsia, Enterococcus, Turicibacter, and norank_f__Muribaculaceae, which were related to MTX-induced cardiac injury.

Conclusion

Our study supports the claim that MTX provokes cardiotoxicity by modifying CM and GM profiles. Our results offer new possibilities for controlling MTX-triggered cardiotoxicity.

Updated review of research on the role of the gut microbiota and microbiota-derived metabolites in acute pancreatitis progression and inflammation-targeted therapy

Acute pancreatitis (AP) is characterized by autodigestion of the pancreas, and some patients may rapidly progress to systemic inflammation, pancreatic necrosis, and multi-organ failure. Numerous studies have detailed the bidirectional communication networks between the pancreas and the intestinal microbiota, as well as its metabolites. Such crosstalk affects the progression of AP and recovery through intestinal barrier disruption. Furthermore, advances in experimental research and clinical studies have indicated that gut microorganisms exhibit distinct alterations in response to different levels of severity and etiologies of AP. This information has greatly expanded our knowledge of the role of the gut microflora and microbial metabolites in the pathology of disease and has reinforced the basis of therapeutic approaches that target candidate intestinal microbiota. In this review, we aim to provide an overview of the composition and diversity of the gut microbial community, to highlight the candidate bacteria and microbiota-derived metabolites responsible for AP, and to elucidate their interactions with and regulation of immune-relevant receptors in intestinal epithelial cells (IECs) in the host. Future research should focus on identifying and characterizing AP-associated bacterial strains, elucidating their distinct pathogenic mechanisms across different etiologies and stages of AP, and leveraging these insights to develop preventive and therapeutic strategies.

Polymeric Anti-Antibiotic Microparticles to Prevent Antibiotic Resistance Evolution

Vancomycin (VAN) and daptomycin (DAP) are among the last-resort antibiotics for treating multidrug-resistant Gram-positive bacterial infections. They are administered intravenously (IV); however, ≈5 - 10% of the total IV dose is released in the gastrointestinal (GI) tract via biliary excretion, driving resistance emergence in commensal Enterococcus faecium (E. faecium) populations. Here, it is reported that sevelamer (SEV), a Food and Drug Administration (FDA)-approved anion-exchange polymeric microparticle, captures anionic DAP within minutes and cationic VAN within hours, inactivating the antibacterial efficacy of DAP and VAN. In vitro SEV-mediated VAN or DAP transient removal is successfully described by a diffusion-adsorption mechanism. In vivo oral SEV treatment effectively prevented VAN resistance enrichment following the VAN treatment of E. faecium-colonized mice. This work shows, for the first time, that the adjuvant SEV therapy prevents antimicrobial resistance in nosocomial pathogens by eliminating off-target antibiotics. It is envisioned that SEV may protect DAP and VAN from resistance development, potentially addressing the long-lasting antimicrobial resistance.

Usefulness of a TDM-Guided Approach for Optimizing Teicoplanin Exposure in the Treatment of Secondary Bloodstream Infections Caused by Glycopeptide-Susceptible Enterococcus faecium

To assess the clinical usefulness of teicoplanin optimized by means of a therapeutic drug monitoring (TDM)-guided approach for treating secondary bloodstream infections (BSIs) caused by Enterococcus faecium. Hospitalized patients having in the period 1 March 2021-31 October 2024 a documented BSI caused by glycopeptide-susceptible Enterococcus faecium being treated with teicoplanin as definitive targeted therapy optimized by means of a real-time TDM-guided expert clinical pharmacological advice (ECPA) program were retrospectively included. Teicoplanin trough concentrations (Cmin) ranging from 20 to 30 mg/L were defined as the desired target of efficacy based on international guidelines. Univariate analysis was performed for assessing variables potentially associated with microbiological failure (defined as persistence at the infection site of the index Enterococcus faecium strain after more than 7 days from starting treatment as documented by follow-up blood cultures). Overall, 67 patients (median age 70 years; male 55.2%) were included. Catheter-related BSIs (50.7%) and intrabdominal/biliary tract (29.9%) infections were the main sources of Enterococcus faecium BSI. The desired target of teicoplanin Cmin was attained in 62.7% of patients at the first TDM assessment and significantly increased to 85.1% (p = 0.003) at subsequent TDM-guided ECPA instances during the overall treatment course. Microbiological eradication was obtained in 95% of cases (63/67). In the univariate analysis, failing effective source control was the only variable associated with an increased risk of microbiological failure (75.0% vs. 12.7%; p = 0.01). Targeted TDM-guided teicoplanin therapy, coupled with effective source control of the primary infection site by granting microbiological eradication in the vast majority of cases, may be considered a reasonable strategy for managing glycopeptide-susceptible Enterococcus faecium secondary BSIs.

Berberine alleviates enterotoxigenic Escherichia coli-induced intestinal mucosal barrier function damage in a piglet model by modulation of the intestinal microbiome

Introduction

Enterotoxic Escherichia coli (ETEC) is the main pathogen that causes diarrhea, especially in young children. This disease can lead to substantial morbidity and mortality and is a major global health concern. Managing ETEC infections is challenging owing to the increasing prevalence of antibiotic resistance. Berberine, categorized as a substance with similarities in "medicine and food," has been used in China for hundreds of years to treat gastrointestinal disorders and bacteria-induced diarrhea. This study investigated the preventive effect of dietary berberine on the intestinal mucosal barrier induced by ETEC and the microbial community within the intestines of weaned piglets.

Methods

Twenty-four piglets were randomly divided into four groups. Piglets were administered either a standard diet or a standard diet supplemented with berberine at concentrations of 0.05 and 0.1%. and orally administered ETEC or saline.

Results

Dietary supplementation with berberine reduced diamine oxidase, d-lactate, and endotoxin levels in piglets infected with ETEC (P < 0.05). Berberine increased jejunal villus height, villus/crypt ratio, mucosal thickness (P < 0.05), and goblet cell numbers in the villi and crypts (P < 0.05). Furthermore, berberine increased the optical density of mucin 2 and the mucin 2, P-glycoprotein, and CYP3A4 mRNA expression levels (P < 0.05). Berberine increased the expressions of zonula occludins-1 (ZO-1), zonula occludins-2 (ZO-2), Claudin-1, Occludin, and E-cadherin in the ileum (P < 0.05). Moreover, berberine increased the expression of BCL2, reduced intestinal epithelial cell apoptosis (P < 0.05) and decreased the expression of BAX and BAK in the duodenum and jejunum, as well as that of CASP3 and CASP9 in the duodenum and ileum (P < 0.05). Berberine decreased the expression of IL-1β, IL-6, IL-8, TNF-α, and IFN-γ (P < 0.05) and elevated total volatile fatty acids, acetic acid, propionic acid, valeric acid, and isovaleric acid concentrations (P < 0.05). Notably, berberine enhanced the abundance of beneficial bacteria including Enterococcus, Holdemanella, Weissella, Pediococcus, Muribaculum, Colidextribacter, Agathobacter, Roseburia, Clostridium, Fusicatenibacter, and Bifidobacterium. Simultaneously, the relative abundance of harmful and pathogenic bacteria, such as Prevotella, Paraprevotella, Corynebacterium, Catenisphaera, Streptococcus, Enterobacter, and Collinsella, decreased (P < 0.05).

Discussion

Berberine alleviated ETEC-induced intestinal mucosal barrier damage in weaned piglets models. This is associated with enhancement of the physical, chemical, and immune barrier functions of piglets by enhancing intestinal microbiota homeostasis.

A study on antimicrobial activity of lysine-like peptoids for the development of new antimicrobials

The development of new medicines with unique methods of antimicrobial action is desperately needed due to the emerging multidrug-resistant bacteria, such as methicillin-resistant Staphylococcus aureus. Therefore, antimicrobial peptoids have emerged as potential new antimicrobials. Thirteen peptoid analogues have been designed and synthesized via solid phase synthesis. These peptoids have undergone a biological analysis to determine the structure-activity relationships that define their antibacterial activity. Each peptoid is composed of nine repeating N-substituted glycine monomers (9-mer). The monomer units were synthesized with three distinct alkyl side chain lengths: four-carbon butyl monomers, six-carbon hexyl monomers, and eight-carbon octyl monomers. Out of 12 different peptoids, only one peptoid called Tosyl-Octyl-Peptoid (TOP) demonstrated significant broad-spectrum bactericidal activity. TOP kills bacteria under non-dividing and dividing conditions. The Minimum Inhibitory Concentrations values of TOP for Staphylococcus epidermidis, Escherichia coli and Klebsiella were 20 µM, whereas Methicillin-resistant Staphylococcus aureus and Methicillin-sensitive Staphylococcus aureus were 40 µM. The highest MIC values were observed for Pseudomonas aeruginosa at 80 µM. The selectivity ratio was calculated, by dividing the 10% haemolysis activity (5 mM) by the median of the MIC (50 µM) yielding a selective ratio for TOP as 100. This selective ratio is well above previously reported peptidomimetics selective ratio of around 20. TOP shows broad-spectrum bactericidal action in both dividing and non-dividing bacteria in co-culture systems and intracellular bacterial killing activity. These results add new information about the antimicrobial peptoids and aid in the future design of synthetic peptoids with increased therapeutic potential.

Genetic diversity and distinction of Enterococcus faecium and Enterococcus lactis in traditional Montenegrin brine cheeses and salamis

Introduction

Enterococcus faecium is a widespread acid-lactic bacterium found in the environment, humans, and animal microbiota, and it also plays a role in the production of traditional food. However, the worldwide emergence of multidrug-resistant E. faecium strains represents a major public health threat and is the primary reason that the genus Enterococcus is not recommended for the Qualified Presumption of Safety (QPS) list of the European Food Safety Authority (EFSA), raising concerns about its presence in food products.

Methods

In this study, 39 E. faecium and 5 E. lactis isolates were obtained from artisanal brine cheeses and dry sausages, sourced from 21 different Montenegrin producers. The isolates were collected following the ISO 15214:1998 international method and processed for whole-genome sequencing (WGS).

Results

Genome analysis based on core genome multilocus sequence type (cgMLST) revealed a high diversity among isolates. Furthermore, the isolates carried antimicrobial resistance genes; the virulence genes acm, sgrA, and ecbA; the bacteriocin genes Enterolysin A, Enterocin A, Enterocin P, Duracin Q, Enterocin B, Bacteriocin 31, Enterocin EJ97, Sactipeptides, and Enterocin SEK4; the secondary metabolite genes T3PKS, cyclic lactone autoinducer, RiPP-like, and NRPS and a maximum of eight plasmids.

Conclusion

This study highlights the need for careful monitoring of E. faecium and E. lactis strains in food to ensure they do not pose any potential risks to consumer safety.

Characteristics and Prevalence of Vancomycin-variable Enterococcus faecium bacteremia in southern Taiwan

BACKGROUND

Vancomycin-variable enterococci (VVE) are vanA-carrying Enterococcus faecium that are phenotypically susceptible to vancomycin and can only be detected using molecular methods, leading to the possibility of treatment failure and posing threats to infection control. This study aimed to determine the prevalence of VVE and its associated clinical risk factors.

METHODS

This retrospective study was conducted in two hospitals in southern Taiwan. Patients with phenotypically vancomycin-susceptible E. faecium bacteremia were enrolled between 2017 and 2021. VVEs were defined as isolates harboring the vanA gene that were phenotypically susceptible to vancomycin. Vancomycin-susceptible E. faecium (VSE) isolates were phenotypically susceptible to vancomycin and lacked vanA or vanB genes.

RESULTS

Of the 142 enrolled patients, 121 (85.2%) had VSE and 21 (14.8%) had VVE. Resistance rates to penicillin, tetracycline, and fosfomycin were higher in VVE isolates. Malignancy (adjusted odds ratio [aOR] = 4.87; 95% confidence interval [CI] 1.54-15.41, p = 0.007) and central venous catheter usage (aOR = 4.69; 95% CI 1.49-14.78, p = 0.008) were the independent risk factors associated with VVE bacteremia. Being male (aOR = 0.12, CI 0.03-0.44, p = 0.002) was less likely to be associated with VVE bacteremia. Although VVE was not associated with 30-day mortality (38.1% [VVE] vs. 35.5% [VSE], p = 0.822), one case of subsequent vancomycin-resistant enterococci infection in the VVE group with vancomycin treatment (4.8%, 1/21) was identified, which led to subsequent mortality.

CONCLUSIONS

The prevalence of VVE was high among E. faecium isolates with vancomycin-susceptible phenotypes in southern Taiwan. Although the current study revealed that VVE bacteremia was not associated with poor clinical outcome, further multicenter surveillance survey is recommended to evaluate the possible impact of VVE on public health in Taiwan.

Clonal expansion of Tn1546-like transposon-carrying vancomycin-resistant Enterococcus faecium, a nationwide study in Taiwan, 2004-2018

OBJECTIVES

The prevalence of vancomycin-resistant Enterococcus faecium (VREfm) has increased significantly in Taiwan. We investigated the molecular epidemiology of clinical VREfm isolates to increase our understanding on their spread and changes in population structure over a 14-year span.

METHODS

A total of 1113 E. faecium isolates were collected biennially from 2004 to 2018 in Taiwan. MICs were determined by broth microdilution. Whole-genome sequencing (WGS) was performed on 229 VREfm isolates to characterize their genetic environment of vancomycin resistance and wgMLST was used to investigate their clonal relationship.

RESULTS

Among the 229 isolates, ST17 and ST78 predominated, especially during the later years, and their prevalences increased from 14.6% (7/48) and 25.0% (12/48) in 2004-2010 to 47.5% (87/181) and 29.8% (54/181) in 2012-2018, respectively. Four types of vanA-carrying Tn1546 variants were detected, with type 1 and type 2 predominated. Type 1 Tn1546 contained an addition of IS1251, while type 2 resembled type 1 but had an addition of IS1678. wgMLST revealed several distinct clusters of ST17 and ST78 isolates, with type 1 Tn1546-harbouring ST17-Cluster 16 being the largest and most widespread clones throughout the study years. Type 2 Tn1546-carrying ST78 became a predominant clone (Cluster 21) after 2012. Isolates within these clusters are highly similar despite being from different hospitals, regions, and study year.

CONCLUSION

The increase of VREfm in Taiwan was attributed to horizontal transfer of vanA-carrying Tn1546 variants between different STs and spread of persistent clones. This study highlights the importance of integrating WGS into surveillance to combat antimicrobial resistance.

Deciphering the Resistome and Mobiolme of an Avian-Associated Enterococus faecalis ST249 Clone that Acquired Vancomycin Resistance Isolated from Neutropenic Patient in Tunisia

This study aimed to characterize the first vancomycin-resistant Enterococcus faecalis (VREfs) isolate from patient with neutropenic in Tunisia by whole-genome sequencing (WGS). This strain was detected from routine rectal swab from an 8-year-old child with bone marrow aplasia, residing in a rural area, on September 20, 2021. The strain was isolated after 12 days of hospitalization at the National Bone Marrow Transplant Center. Minimum Inhibitory Concentrations of vancomycin and teicoplanin were >256 and 16 mg/L, respectively. WGS revealed that the strain belonged to the ST249 clone, exclusively reported in avian (poultry and ducks) vancomycin-susceptible E. faecalis isolates in six studies from four countries, primarily Denmark. The vanA gene was carried by the Tn1546 transposon mobilized by a pTW9-like plasmid. The ardA gene, a CRISPR-Cas system neutralization factor, was detected in this strain. In summary, this is the first report of avian-associated E. faecalis ST249 in clinical samples. Initially vancomycin susceptible, the strain acquired a pTW9-like plasmid carrying the classical vanA-Tn1546 transposon. This acquisition was facilitated by the sex pheromone-response mechanisms and the ardA gene and CRISPR-Cas system neutralization.

IS6 family insertion sequences promote optrA dissemination between plasmids varying in transfer abilities

Plasmids are the primary vectors for intercellular transfer of the oxazolidinone and phenicol cross-resistance gene optrA, while insertion sequences (ISs) are mobile genetic elements that can mobilize plasmid-borne optrA intracellularly. However, little is known about how the IS-mediated intracellular mobility facilitates the dissemination of the optrA gene between plasmid categories that vary in transfer abilities, including non-mobilizable, mobilizable, and conjugative plasmids. Here, we performed a holistic genomic study of 52 optrA-carrying plasmids obtained from searches guided by the Comprehensive Antibiotic Resistance Database. Among the 132 ISs identified within 10 kbp from the optrA gene in the plasmids, IS6 family genes were the most prevalent (86/132). Homologous gene arrays containing IS6 family genes were shared between different plasmids, especially between mobilizable and conjugative plasmids. All these indicated the central role of IS6 family genes in disseminating plasmid-borne optrA. Thirty-three of the 52 plasmids were harbored by Enterococcus faecalis found mainly in humans and animals. By Nanopore sequencing and inverse PCR, the potential of the enterococcal optrA to be transmitted from a mobilizable plasmid to a conjugative plasmid mediated by IS6 family genes was further confirmed in Enterococcus faecalis strains recovered from the effluents of anaerobic digestion systems for treating chicken manure. Our findings highlight the increased intercellular transfer abilities and dissemination risk of plasmid-borne optrA gene caused by IS-mediated intracellular mobility, and underscore the importance of routinely monitoring the dynamic genetic contexts of clinically important antibiotic resistance genes to effectively control this critical public health threat. KEY POINTS: • IS6 was prevalent in optrA-plasmids varying in intercellular transfer abilities. • Enterococcal optrA-plasmids were widespread among human, animal, and the environment. • IS6 elevated the dissemination risk of enterococcal optrA-plasmids.

Albumin nanoparticles are a promising drug delivery system in dentistry

Periodontal infection is a long-lasting inflammatory condition caused by the growth and development of an abnormal and harmful community of microorganisms. This destructive illness leads to the loss of the tissues that support the teeth, degradation of the bone surrounding the teeth, and eventually tooth loss. To treat oral infections, it is necessary to use nonsurgical methods such as antibiotics. However, the indiscriminate and incorrect use of antibiotics results in drug resistance. Among these alternate therapeutic options, using nanoparticles to treat infectious dental disease was particularly significant. Consequently, researchers have worked to develop an effective and satisfactory drug delivery method for treating periodontal and dental illnesses. Albumin nanoparticles serve a considerable function as carriers in the drug delivery of chemical and biomolecular medications, such as anticancer treatments; they have several advantages, including biocompatibility and biodegradability, and they are well-tolerated with no adverse effects. Albumin nanoparticles have several benefits over other nanomaterials. Protein nanocarriers provide advantages such as biocompatibility, biodegradability, reduced immunogenicity, and lower cytotoxicity. Furthermore, this nanoparticle demonstrated significant intrinsic antibacterial properties without being loaded with antibiotic medicines. As a medication and antibacterial nanoparticle delivery method, albumin nanoparticles have substantial applications in periodontal and dental infectious disorders such as periodontal infection, apical periodontitis, and peri-implantitis. As a result, in this article, we studied the usage of albumin nanoparticles in dental disorders.

Comparative metagenomics of microbial communities and resistome in southern farming systems: implications for antimicrobial stewardship and public health

Agricultural practices significantly influence microbial diversity and the distribution of virulence and antimicrobial resistance (AMR) genes, with implications for ecosystem health and food safety. This study used metagenomic sequencing to analyze 60 samples (30 per state) including water, soil, and manure (10 each) from Alabama (a mix of cattle and poultry sources) and Tennessee (primarily from cattle). The results highlighted a rich microbial diversity, predominantly comprising Bacteria (67%) and Viruses (33%), with a total of over 1,950 microbial species identified. The dominant bacterial phyla were Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, with the viral communities primarily represented by Phixviricota and Uroviricota. Distinct state-specific microbial profiles were evident, with Alabama demonstrating a higher prevalence of viral populations and unique bacterial phyla compared to Tennessee. The influence of environmental and agricultural practices was reflected in the microbial compositions: soil samples were notably rich in Actinobacteria, water samples were dominated by Proteobacteria and Cyanobacteria, and manure samples from Alabama showed a predominance of Actinobacteria. Further analyses, including diversity assessment and enterotype clustering, revealed complex microbial structures. Tennessee showed higher microbial diversity and phylogenetic complexity across most sample types compared to Alabama, with poultry-related samples displaying distinct diversity trends. Principal Coordinate Analysis (PCoA) highlighted notable state-specific variations, particularly in manure samples. Differential abundance analysis demonstrated elevated levels of Deinococcus and Ligilactobacillus in Alabama, indicating regional effects on microbial distributions. The virulome analysis revealed a significant presence of virulence genes in samples from Alabama. The community resistome was extensive, encompassing 109 AMR genes across 18 antibiotic classes, with manure samples displaying considerable diversity. Ecological analysis of the interactions between AMR gene subtypes and microbial taxa revealed a sophisticated network, often facilitated by bacteriophages. These findings underscore the critical role of agricultural practices in shaping microbial diversity and resistance patterns, highlighting the need for targeted AMR mitigation strategies in agricultural ecosystems to protect both public health and environmental integrity.