Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms

Natural transformation of antibiotic resistance genes and the enhanced adaptability in bacterial biofilm under antibiotic and heavy metal stresses

Bacterial biofilms are hotspots for the natural transformation of antibiotic resistance genes (ARGs). Antibiotics and heavy metals at the sub-minimal inhibitory concentrations (sub-MICs) are ubiquitous in water environments, but their impact on the ARG dissemination via natural transformation in biofilms and the biofilm development remains poorly understood. This study found that the individual stressors including tetracycline, sulfamethoxazole, and Zn at the sub-MIC levels, significantly enhanced ARG transformation. Notably, Zn exhibited the most obvious effect, increasing transformation frequencies by up to 4.62-fold in B. subtilis and 6.42-fold in A. baylyi biofilms. Their combined stressors increased the higher ARG transformation compared to the individual. These stressors significantly elevated ARG transformation by stimulating reactive oxygen species generation, increasing membrane permeability, and enhancing polysaccharide production. Meanwhile, the bacterial adaptability in biofilm to stressors was achieved via ARG transformation, and the biofilm growth was increased by 25.4 % in B. subtilis and 49.6 % in A. baylyi, respectively, compared to biofilms without natural transformation. Except for ARG uptake via transformation, the enhanced bacterial adaptability in biofilms to stressors can also be attributed to the expression of the plasmid-borne SOS response-related genes. These findings broaden the understanding of the influence of sub-MIC stressors in ARG dissemination in biofilm.

Isolation of Pseudonocardia strains associated with the shallow water hydrothermal vent crab Xenograpsus testudinatus from a metal-rich environment: Biochemical characterization and enzymatic characterization, molecular identification, antibacterial, antibiofilm and antioxidant activity

A shallow hydrothermal vent at Kueishantao Island, Taiwan provides a challenging environment and has been less explored for its microbial communities, especially the actinomycetes and their antibacterial and antioxidant activity. Nine actinomycete strains were isolated from the endemic hydrothermal vent crab Xenograpsus testudinatus and were identified as belonging to the rare actinomycete genus Pseudonocardia sp. Physiochemical results showed that the optimum growth conditions of these nine isolates were at pH 7, 35 °C, and 0.5-2% NaCl. Biochemical characterization showed differences between the strains. These isolates were further characterized at genetic barcoding (16s rRNA sequencing) and phenotypic levels and identified at the species/strain level as Pseudonocardia alni SCSW01, Pseudonocardia yuanmonensis SCSW02, Pseudonocardia sp. strains SCSW03, SCSW04, SCSW05, SCSW06, BCSW29, ECSW09, and ECSW018. The morphology of the strains was analyzed using an environmental scanning electron microscope (ESEM). The nine isolates showed potential antibacterial activity against gram-positive and gram-negative pathogenic strains. The confocal laser scanning microscopy (CLSM) images show live and dead cells and biofilm/antibiofilm activity of the actinomycete supernatant and crude extracts against pathogenic bacterial strains. The crude extracts of SCSW02, SCSW06, BCSW29, ECSW09, and ECSW018 showed antibiofilm activity against P. aeruginosa, E. coli, and S. aureus. The antioxidant activity such as DPPH and H2O2 scavenging assay results showed that the nine actinomycetes crude extracts hold more substantial radical scavenging properties than supernatants. Our results marked the first report of Pseudonocardia genera from the vent crab Xenograpsus testudinatus of the HV region at Kueishantao island, Taiwan.

Evolutionary relationships and genetic diversity in the BlaTEM gene among selected gram-negative bacteria

This study investigates the genetic diversity and evolutionary relationships of the blaTEM gene, a major determinant of beta-lactam antibiotic resistance. We analyzed nucleotide sequences of 32 β-lactamase-producing strains from Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Proteus mirabilis, and Acinetobacter baumannii obtained from public databases. Sequence analysis revealed 32 distinct sequences with 298 segregating sites and 303 mutations, indicating substantial genetic variability. A high level of haplotype diversity was observed, with 24 distinct haplotypes, reflecting evolutionary pressures and horizontal gene transfer. Phylogenetic analysis showed clear clades, suggesting the evolutionary relationships among blaTEM variants and interspecies gene transfer. The resistance profiles correlated with the genetic findings, particularly mutations. This analysis draws attention to the ongoing adaptive evolution of antibiotic resistance mechanisms, as well as the need for continued monitoring and novel therapeutic strategies. Further research with larger sample sizes and functional validation is needed to fully understand the implications of these variants in antibiotic resistance.

Blocking horizontal transfer of antibiotic resistance genes: an effective strategy in combating antibiotic resistance

Antimicrobial resistance (AMR) poses a significant public health threat, with emerging and novel forms of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) potentially crossing international borders and challenging the global health systems. The rate of development of antibiotic resistance surpasses the development of new antibiotics. Consequently, there is a growing threat of bacteria acquiring resistance even to newer antibiotics further complicating the treatment of bacterial infections. Horizontal gene transfer (HGT) is the key mechanism for the spread of antibiotic resistance in bacteria through the processes of conjugation, transformation, and transduction. Several compounds, other than antibiotics, have also been shown to promote HGT of ARGs. Given the crucial role of HGT in the dissemination of ARGs, inhibition of HGT is a key strategy to mitigate AMR. Therefore, this review explores the contribution of HGT in bacterial evolution, identifies specific hotspots andhighlights the role of HGT inhibitors in impeding the spread of ARGs. By specifically focusing on the HGT mechanism and its inhibition, these inhibitors offer a highly promising approach to combating AMR.

Synergistic effect of horizontal transfer of antibiotic resistance genes between bacteria exposed to microplastics and per/polyfluoroalkyl substances: An explanation from theoretical methods

Microplastics (MPs) and per/polyfluoroalkyl substances (PFASs), as emerging pollutants widely present in aquatic environments, pose a significant threat to human health through the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Molecular dynamics simulations and machine learning can accurately capture the complex interactions between molecules. This study utilized them to identify the HGT risk between bacteria under MPs and PFASs stress. This study found that MPs and PFASs significantly increase the HGT risk between bacteria, up to 1.57 and 1.59 times, respectively. Notably, long-chain PFASs and perfluoroalkyl carboxylic acids increased the HGT risk by 1.38 and 1.40 times, respectively. Additionally, MPs primarily increase the HGT risk by enhancing hydrogen bonding interaction between key proteins in the HGT pathway and "active codons". The electronegativity and polarizability of PFASs critically influence the HGT risk, acting inversely and directly proportional, respectively. The HGT risk between bacteria under the combined stress from PP-MPs and PFASs exhibits a significant synergistic effect (synergistic effect value of 27.6), which markedly increases the HGT risk. Further analysis revealed that a smaller minimum distance and sharper RDF curve peaks between key proteins and "active codons" indicate higher HGT risk. This indicates that stronger interactions lead to higher HGT risk. This study identifies the characteristics of HGT risks between bacteria in aquatic environments under the individual and combined stresses from MPs and PFASs at the molecular level. It provides a theoretical basis for mitigating ARG transfer and comprehensively assessing the health risks posed by these emerging pollutants.

A roadmap to understanding and anticipating microbial gene transfer in soil communities

SUMMARYEngineered microbes are being programmed using synthetic DNA for applications in soil to overcome global challenges related to climate change, energy, food security, and pollution. However, we cannot yet predict gene transfer processes in soil to assess the frequency of unintentional transfer of engineered DNA to environmental microbes when applying synthetic biology technologies at scale. This challenge exists because of the complex and heterogeneous characteristics of soils, which contribute to the fitness and transport of cells and the exchange of genetic material within communities. Here, we describe knowledge gaps about gene transfer across soil microbiomes. We propose strategies to improve our understanding of gene transfer across soil communities, highlight the need to benchmark the performance of biocontainment measures in situ, and discuss responsibly engaging community stakeholders. We highlight opportunities to address knowledge gaps, such as creating a set of soil standards for studying gene transfer across diverse soil types and measuring gene transfer host range across microbiomes using emerging technologies. By comparing gene transfer rates, host range, and persistence of engineered microbes across different soils, we posit that community-scale, environment-specific models can be built that anticipate biotechnology risks. Such studies will enable the design of safer biotechnologies that allow us to realize the benefits of synthetic biology and mitigate risks associated with the release of such technologies.

Inhibitory effects of reumycin produced by Streptomyces sp. TPMA0082 on virulence factors of Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic human pathogen that causes a wide range of infections. The increasing multidrug-resistance of P. aeruginosa poses a critical challenge for medical care. P. aeruginosa employs virulence factors and biofilms to establish infections in humans and protect itself from environmental stress or antibiotics. These factors are regulated by a quorum sensing mechanism involving multiple regulatory systems that act interdependently through signaling molecules. Therefore, interference with quorum sensing systems can suppress the pathogenicity of P. aeruginosa. In this study, quorum sensing inhibitors were explored from secondary metabolites derived from 111 strains of actinomycetes by targeting the las system, which is thought to be upstream of the quorum sensing cascade in P. aeruginosa. As a result, reumycin was isolated from the culture broth of Streptomyces sp. TPMA0082. Reumycin, a molecule containing a pyrimidotriazine ring, inhibited the binding of the autoinducer to the LasR receptor in the las system, thereby suppressing the production of P. aeruginosa virulence factors, including pyocyanin, rhamnolipids, elastase, motility, and biofilms, without affecting bacterial growth. Toxoflavin, a reumycin derivative with a methyl group at the N1 position, exhibited strong antibacterial activity. Fervenulin, a reumycin derivative with a methyl group at the N8 position, had a negative impact on the logarithmic growth phase of the bacteria and exhibited lower inhibitory activity against virulence factor production compared to reumycin. These findings suggest that the position and number of methyl groups attached to the pyrimidotriazine structure significantly influence its biological activity, exerting distinct effects on quorum sensing inhibition and antibacterial activity.

Deciphering antibiotic resistance, quorum sensing, and biofilm forming genes of Micrococcus luteus from hemodialysis tunneled cuffed catheter tips of renal failure patients

Catheter-related bloodstream infections create a significant challenge in healthcare system, often complicated by antibiotic resistance and biofilm formation of multi-drug resistance and virulent bacterial pathogens. This study focused on biofilm-forming efficiency, and underlying genetic mechanisms in Micrococcus luteus HL_Chru_C3, isolated from a hemodialysis catheter tip. The isolate exhibited resistance to multiple antibiotic classes, including beta-lactams and glycopeptides. Biofilm assays revealed that M. luteus HL_Chru_C3 formed optimum biofilms at high concentration of carbohydrates (500 mM), and pH 5 but there was no significant role of mineral salts. Whole-genome sequencing and bioinformatic analysis using CARD, KAAS, and KEGG databases identified genes associated with antibiotic resistance (ftsI, pbp1a/2, vanY, alr, ddl, murF, mraY, and murG), quorum sensing (genes from the opp family, sec, cylA, ccfA, phnA, phnB, phzC, rpfB, clp, and toxE), and biofilm formation (phnA, phnB, cyaB, vfr, vps, glgC, wecB, wecC, and cysE). The predicted mechanisms of action for these genes, based on homology to other organisms, suggest complex interactions contributing to the observed phenotypes. This study provides an insight into the genetic basis of antibiotic resistance and biofilm formation in M. luteus HL_Chru_C3 isolated from a hemodialysis catheter, highlighting the need for effective infection control strategies to combat CRBSIs.

Microbial diversity and interactions: Synergistic effects and potential applications of Pseudomonas and Bacillus consortia

Microbial diversity and interactions in the rhizosphere play a crucial role in plant health and ecosystem functioning. Among the myriads of rhizosphere microbes, Pseudomonas and Bacillus are prominent players known for their multifaceted functionalities and beneficial effects on plant growth. The molecular mechanism of interspecies interactions between natural isolates of Bacillus and Pseudomonas in medium conditions is well understood, but the interaction between the two in vivo remains unclear. This paper focuses on the possible synergies between Pseudomonas and Bacillus associated in practical applications (such as recruiting beneficial microbes, cross-feeding and niche complementarity), and looks forward to the application prospects of the consortium in agriculture, human health and bioremediation. Through in-depth understanding of the interactions between Pseudomonas and Bacillus as well as their application prospects in various fields, this study is expected to provide a new theoretical basis and practical guidance for promoting the research and application of rhizosphere microbes.

Whole genome analysis and biocontrol potential of endophytic Bacillus cereus EMS1 against Fusarium wilt in banana

Endophytic bacteria are essential for promoting plant growth and increasing plant resilience to various environmental stresses. Although it is well-documented that several endophytic Bacillus species exhibit plant growth-promoting properties, this is the first report on the genome study of Bacillus cereus EMS1, isolated from Musa acuminata G9 in India. This study analyzed the genomics, plant growth traits, and fusarium wilt mitigation potential of Bacillus cereus EMS1. This analysis identified specific genomic features, including potential mechanisms contributing to plant growth promotion, which were also submitted to NCBI (Bioproject ID: PRJNA784269). The in vivo study showed that EMS1 mitigated the impact of Fusarium oxysporum f. sp. cubense on banana plants. Although it did not affect the number of leaves, other parameters influenced by pathogen infection and EMS1 treatment showed notable differences, including fresh weight (Fusarium oxysporum only: 15 g; EMS1 + Fusarium oxysporum: 21 g), dry weight (Fusarium oxysporum only: 1 g; EMS1 + Fusarium oxysporum: 4.7 g), and root length (Fusarium oxysporum only: 6.5 cm; EMS1 + Fusarium oxysporum: 9 cm). Additionally, genomic analysis revealed that the EMS1 genome contains distinctive genes linked to plant growth and antimicrobial activity. Overall, the findings highlight the potential of endophytic Bacillus cereus EMS1 in promoting plant growth and enhancing banana plant resistance against Fusarium oxysporum.

The Impact of Silver Nanoparticles' Size on Biofilm Eradication

INTRODUCTION

Efficient intracanal disinfection is required for a successful regenerative endodontic treatment. Thus, this study aimed to identify the silver nanoparticles' (NPs) size (AgNPs) with the highest antibiofilm efficacy when mixed with calcium hydroxide [Ca(OH)2] to eradicate an in vitro endodontic biofilm.

METHODS

The various sizes of AgNPs and mixtures were characterized by scanning electron microscopy, transmission electron microscopy, and ultraviolet-visible spectroscopy. A total of 168 dentin root segments were prepared, sterilized, and inoculated for 3 weeks with Actinomyces naeslundii and Fusobacterium nucleatum. Samples were randomly allocated to 4 experimental groups (n = 28/group): 2 nm AgNPs + 35% Ca(OH)2, 5 nm AgNPs + 35% Ca(OH)2, 10 nm AgNPs + 35% Ca(OH)2, and 35% Ca(OH)2 alone. Samples exposed to saline and triple antibiotic paste (TAP) acted as negative and positive control groups, respectively. After 1 and 2 weeks, samples were stained with LIVE/DEAD BacLight dye and examined under a confocal laser scanning microscope to determine the proportion of dead bacteria.

RESULTS

The characterization procedure revealed a spherical NP's structure with minor aggregations. Except for Ca(OH)2 group, all groups had significantly higher antibiofilm efficacy at 2 weeks. Both the 10 nm mixture (99.5%) and TAP (99.2%) exhibited the highest antibiofilm efficacy at 2 weeks and were not significantly different from one another (P > .05). No significant difference was noted between the 2 and 5 nm mixtures at 1 week (81% and 84%) and 2 weeks (89% and 91%).

CONCLUSION

The 10 nm AgNPs (0.02%) + 35% Ca(OH)2 mixture exhibited the highest antibiofilm efficacy at 2 weeks compared to all other mixtures at both observation periods. Interestingly, the 10 nm mixture performed similarly to TAP at 2 weeks. Excluding Ca(OH)2 group, longer application significantly improved the antibiofilm efficacy of all tested medicaments.

CLINICAL RELEVANCE

The 10 nm AgNPs + 35% Ca(OH)2 mixture revealed promising results as an intracanal medicament in the regenerative endodontic treatment protocol.

Biofilm-mediated bioremediation of xenobiotics and heavy metals: a comprehensive review of microbial ecology, molecular mechanisms, and emerging biotechnological applications

Environmental pollution, driven by rapid industrialization and urbanization, has emerged as a critical global challenge in the twenty-first century. This comprehensive review explores the potential of bacterial biofilms in bioremediation, focusing on their ability to degrade and transform a wide array of pollutants, including heavy metals, persistent organic pollutants (POPs), oil spills, pesticides, and emerging contaminants, such as pharmaceuticals and microplastics. The unique structural and functional characteristics of biofilms, including their extracellular polymeric substance (EPS) matrix, enhanced genetic exchange, and metabolic cooperation, contribute to their superior pollutant degradation capabilities compared to planktonic bacteria. Recent advancements in biofilm-mediated bioremediation include the application of genetically engineered microorganisms, nanoparticle-biofilm interactions, and innovative biofilm reactor designs. The CRISPR-Cas9 system has shown promise in enhancing the degradative capabilities of biofilm-forming bacteria while integrating nanoparticles with bacterial biofilms demonstrates significant improvements in pollutant degradation efficiency. As global pollution rises, biofilm-based bioremediation emerges as a cost-effective and environmentally friendly approach to address diverse contaminants. This review signifies the need for further research to optimize these techniques and harness their full potential in addressing pressing environmental challenges.

Risk factors and prediction model for carbapenem-resistant organism infection in sepsis patients

BACKGROUND

It aimed to identify the key risk factors associated with carbapenem-resistant organism (CRO) infections in septic patients, and subsequently develop a nomogram and assess its predictive accuracy.

METHODS

The study population comprised adult critically ill patients with sepsis, drawn from the MIMIC-IV 2.0 data set. The data were split into a training set and a validation set at a 7:3 ratio. Independent predictors were identified using both univariate and multivariate logistic regression models, followed by the construction of a nomogram. The predictive performance of the model was evaluated using the C-index, receiver operating characteristic (ROC) curve, area under the curve (AUC), calibration curve, and decision curve.

RESULTS

We enrolled 8814 patients, with 529 (6%) CRO-infected and 8285 (94%) non-CRO-infected. Using risk factors such as age, gender, laboratory values (WBC_max, Creatinine_max, BUN_max, Hemoglobin_min, Sodium_max), and medical conditions (COPD, hypoimmunity, diabetes), along with medications (meropenem, ceftriaxone), we developed a predictive model for CRO infection in septic patients. The model demonstrated good performance, with AUC values of 0.747 for the training set and 0.725 for the validation set. The calibration curve indicates that predicted outcomes align well with observed outcomes. The clinical decision curve results indicate that the nomogram prediction model has a high net benefit, which is clinically beneficial.

CONCLUSIONS

The nomogram we have developed for predicting the risk of CRO infection in sepsis patients is reasonably accurate and reliable.

CLINICAL TRIAL NUMBER

Not applicable.

Trans-cinnamaldehyde nanoemulsion reduces Salmonella Enteritidis biofilm on steel and plastic surfaces and downregulates expression of biofilm associated genes

Salmonella Enteritidis is a major poultry-associated foodborne pathogen that can form sanitizer-tolerant biofilms on various surfaces. The biofilm-forming capability of S. Enteritidis facilitates its survival on farm and food processing equipment. Conventional sanitization methods are not completely effective in killing S. Enteritidis biofilms. This study investigated the efficacy of a Generally Recognized as Safe phytochemical Trans-cinnamaldehyde (TC), and in its nanoemulsion form (TCNE), for inhibiting S. Enteritidis biofilm formation and inactivating mature biofilms developed on polystyrene and stainless-steel surfaces. Moreover, the effect of TC on Salmonella genes critical for biofilm formation was studied. TCNE was prepared using a high energy sonication method with Tween 80. For biofilm inhibition assay, S. Enteritidis was allowed to form biofilms either in the presence or absence of sub-inhibitory concentration (SIC; 0.01 %) of TCNE at 25°C and the biofilm formed was quantified at 24-h intervals for 48 h. For the inactivation assay, S. Enteritidis biofilms developed at 25°C for 48 h were exposed to TCNE (0.5, 1 %) for 1, 5, and 15 min, and surviving S. Enteritidis in the biofilm were enumerated. SIC of TCNE inhibited S. Enteritidis biofilm by 45 % on polystyrene and 75 % on steel surface after 48 h at 25°C compared to control (P < 0.05). All TCNE treatments rapidly inactivated S. Enteritidis mature biofilm on polystyrene and steel surfaces (P < 0.05). The lower concentration of TCNE (0.5 %) reduced S. Enteritidis counts by 1.5 log CFU/ml as early as 1 min of exposure on both polystyrene and stainless-steel surfaces. After 15 min of exposure, TCNE at concentration of 0.5 or 1 % reduced S. Enteritidis count significantly by 4.5 log CFU or 6 log CFU/ml on polystyrene or stainless-steel surfaces. TC downregulated the expression of S. Enteritidis genes (hilA, hilC, flhD, csgA, csgD, sdiA) responsible for biofilm formation (P < 0.05). Results suggest that TCNE has potential as a natural disinfectant for controlling S. Enteritidis biofilms on common farm and food processing surfaces, such as plastic and steel.

Biofilms as potential reservoirs of antimicrobial resistance in vulnerable settings

Antimicrobial resistance is a major global health threat, characterized by the ability of microorganisms to withstand the effects of antimicrobial agents. Biofilms, as unique microbial communities, significantly contribute to this threat. They provide a protective environment for pathogens, facilitate horizontal gene transfer, and create an ideal setting for the persistence and evolution of resistant bacteria. This issue can be particularly important in low-income settings and vulnerable communities, such as formal and informal refugee and migrant camps. These settings usually have limited access to healthcare resources and appropriate treatments, contributing to the selective pressure that promotes the survival and proliferation of resistant bacteria. Thus, biofilms formed in wastewater in these areas can play a critical role in spreading antimicrobial resistance or acting as hidden reservoirs for future outbreaks. While emerging efforts focus on detecting antibiotic resistance genes and planktonic bacteria in wastewater, biofilms may be a source of under-appreciated antimicrobial resistance, creating a significant gap in our understanding of resistance dynamics in wastewater systems. Incorporating biofilm surveillance into wastewater monitoring strategies in vulnerable settings can help develop a more comprehensive understanding of resistance transmission and more effective intervention measures in these settings.

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.

Genetic diversity of dissolved free extracellular DNA compared to intracellular DNA in wastewater treatment plants

Dissolved free extracellular DNA (free-exDNA) coexists with intracellular DNA (inDNA) in aquatic environments. Free-exDNA can be taken up by bacteria through transformation, and wastewater treatment plants (WWTPs) are positioned as potential hot spots for genetic contamination. However, studies comparing the composition of free-exDNA and inDNA is limited. This study employed colloidal adsorption and foam concentration method to recover free-exDNA from different WWTP stages and compared its diversity with inDNA via metagenomic analysis. Free-exDNA concentrations were observed to increase after chlorination. Genetic analysis revealed a higher abundance of specific genes following chlorination, suggesting that free-exDNA in effluent originated from bacterial death in secondary treated water. This result indicates that free-exDNA, which increases due to chlorination, is subsequently released into the catchment. Additionally, several high-risk antibiotic-resistance genes (ARGs) were detected that colocalized with mobile genetic elements. These ARGs were expected to have a high potential for gene transfer via transformation, and the risk was highlighted. Overall, these findings deepen our understanding of horizontal gene transfer risks in WWTPs.

Insights into biofilm-mediated mechanisms driving last-resort antibiotic resistance in clinical ESKAPE pathogens

The rise of antibiotic-resistant bacteria poses a grave threat to global health, with the ESKAPE pathogens, which comprise Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. being among the most notorious. The World Health Organization has reserved a group of last-resort antibiotics for treating multidrug-resistant bacterial infections, including those caused by ESKAPE pathogens. This situation calls for a comprehensive understanding of the resistance mechanisms as it threatens public health and hinder progress toward the Sustainable Development Goal (SDG) 3: Good Health and Well-being. The present article reviews resistance mechanisms, focusing on emerging resistance mutations in multidrug-resistant ESKAPE pathogens, particularly against last-resort antibiotics, and describes the role of biofilm formation in multidrug-resistant ESKAPE pathogens. It discusses the latest therapeutic advances, including the use of antimicrobial peptides and CRISPR-Cas systems, and the modulation of quorum sensing and iron homeostasis, which offer promising strategies for countering resistance. The integration of CRISPR-based tools and biofilm-targeted approaches provides a potential framework for managing ESKAPE infections. By highlighting the spread of current resistance mutations and biofilm-targeted approaches, the review aims to contribute significantly to advancing our understanding and strategies in combatting this pressing global health challenge.

Metagenomics as a Transformative Tool for Antibiotic Resistance Surveillance: Highlighting the Impact of Mobile Genetic Elements with a Focus on the Complex Role of Phages

Extensive use of antibiotics in human healthcare as well as in agricultural and environmental settings has led to the emergence and spread of antibiotic-resistant bacteria, rendering many infections increasingly difficult to treat. Coupled with the limited development of new antibiotics, the rise of antimicrobial resistance (AMR) has caused a major health crisis worldwide, which calls for immediate action. Strengthening AMR surveillance systems is, therefore, crucial to global and national efforts in combating this escalating threat. This review explores the potential of metagenomics, a sequenced-based approach to analyze entire microbial communities without the need for cultivation, as a transformative and rapid tool for improving AMR surveillance strategies as compared to traditional cultivation-based methods. We emphasize the importance of monitoring mobile genetic elements (MGEs), such as integrons, transposons, plasmids, and bacteriophages (phages), in relation to their critical role in facilitating the dissemination of genetic resistance determinants via horizontal gene transfer (HGT) across diverse environments and clinical settings. In this context, the strengths and limitations of current bioinformatic tools designed to detect AMR-associated MGEs in metagenomic datasets, including the emerging potential of predictive machine learning models, are evaluated. Moreover, the controversial role of phages in AMR transmission is discussed alongside the potential of phage therapy as a promising alternative to conventional antibiotic treatment.

The epidemiology of antimicrobial resistant bacterial infection in Qatar: A systematic review and meta-analysis

BACKGROUND

Antimicrobial resistance (AMR) is the current silent pandemic responsible for approximately five million deaths annually. According to the WHO, antimicrobial resistance is one of the top global public health threats and the third leading cause of death worldwide.

METHOD

This systematic review and meta-analyses aims to provide Qatar's first comprehensive epidemiological assessment of AMR. We conducted extensive search of three databases (PubMed, Embase and Web of Science) using broad search terms with no restrictions. The meta-analysis of prevalence was done using the Freeman-Turkey transformation and random effects models. Subgroup analysis was performed for three categories; the composite isolates, otherwise responsive isolates, and otherwise resistant isolates.

RESULTS

The search yielded a total of 1258 publications, of which 55 publications were included. The overall prevalence of all isolates was 13.64 % (95 %CI: 6.80 - 22.11, I2=99 %), all the studies were cross-sectional of convenience sampling, conducted in healthcare settings. The subgroup prevalence for the composite isolates was 8.87 % (95 %CI: 2.72 - 17.77, I2=98.7), otherwise responsive isolates was 11.37 % (95 %CI: 4.31 - 20.72, I2=98.3 %), otherwise resistant isolates was 23.55 % (95 %CI: 10.12 - 40.14, I2=99.1). The otherwise resistant isolates stratified analyses revealed that ESBL prevalence was 38.94 % (95 %CI: 21.63 - 57.79, I2=99.2 %), MDR was 15.99 % (95 %CI: 2.46 - 37.00, I2=99 %), MRSA was 52.37 % (95 %CI: 13.91 - 89.50, I2=88 %), Nosocomial infections prevalence was 23.55 % (95 %CI: 10.12 - 40.14, I2=98.2 %). The ESKAPE bacterial strains accounted for the majority of resistance.

CONCLUSION

Qatar's AMR overall prevalence is close to the global estimates, however the resistant isolates prevalence is higher than average according to the global estimates for high-income countries. The AMR public health response including national action plan to combat AMR and antimicrobial stewardship programs need to be orchestrated. AMR epidemiological research needs improvement in expanding coverage across diverse population groups to ensure greater clarity and precision in identifying bacterial infections and antibiotic classifications.

Light-based therapy of infected wounds: a review of dose considerations for photodynamic microbial inactivation and photobiomodulation

Significance

Chronic or surgical wound infections in healthcare remain a worldwide problem without satisfying options. Systemic or topical antibiotic use is an inadequate solution, given the increase in antimicrobial-resistant microbes. Hence, antibiotic-free alternatives are needed. Antimicrobial photodynamic inactivation (aPDI) has been shown to be effective in wound disinfection. Among the impediments to the wide utility of aPDI for wounds is the high variability in reported photosensitizer and light dose to be effective and unintentional detrimental impact on the wound closure rates. Additionally, the time required by the healthcare professional to deliver this therapy is excessive in the present form of delivery.

Aim

We reviewed the dose ranges for various photosensitizers required to achieve wound disinfection or sterilization while not unintentionally inhibiting wound closure through concomitant photobiomodulation (PBM) processes.

Approach

To allow comparison of aPDI or PBM administered doses, we employ a unified dose concept based on the number of absorbed photons per unit volume by the photosensitizer or cytochrome C oxidase for aPDI and PBM, respectively.

Results

One notes that for current aPDI protocols, the absorbed photons per unit volume for wound disinfection or sterilization can lead to inhibiting normal wound closure through PBM processes.

Conclusion

Options to reduce the dose discrepancy between effective aPDI and PBM are discussed.

Degradation of plasmid-mediated resistance genes in poultry slaughterhouse wastewater employing a UV/H2O2 process: A metagenomic approach

Poultry slaughterhouse effluents are important hotspots for the spread of both antibiotic-resistant bacteria (ARBs) and antibiotic resistance genes (ARGs), contributing to the antimicrobial resistance (AMR). This study reports a novel investigation to assess the effects of UV/H2O2 treatment on the removal of metaplasmidome-mediated ARGs from poultry slaughterhouse effluents. The effluent samples were subjected at 0.005-0.15 mol L-1 of H2O2 and pH conditions (3, 5, 7 and 9). Bacterial community (rrs 16S rRNA), Escherichia coli (uidA) antimicrobial resistance (sul1 and int1) and metagenomic plasmid DNA removal were assessed. The UV/H2O2 treatment employing H2O2 = 0.01 mol L-1 at pH 3 resulted in decreased of several markers (uidA, sul1 and int1). A metaplasmidome indicated the persistence of Burkholderiales order. The UV/H2O2 process reduced plasmid-associated ARGs by 92.5% and 90.4% at pH 3 and 7, respectively. Persistent genes were mainly composed of genes associated with efflux pumps and resistance to beta-lactams and fluoroquinolones. These findings contribute to mitigate the spread of AMR in the agricultural sector, especially through the implementation of more efficient treatments, and reducing the use of antibiotics in livestock farming.

Genetic Determinants of Carbapenem and Fluoroquinolone Resistance in Escherichia coli Isolates of Clinical Origin

BACKGROUND

Antimicrobial resistance has emerged as a global public health challenge, leading to higher mortality rates from infections that were once treatable with antibiotics. In this study, we assessed the susceptibility of Escherichia coli strains isolated from clinical samples to carbapenems and fluoroquinolones and screened for genetic determinants mediating resistance.

MATERIALS AND METHODS

This retrospective study included 46 E. coli isolates retrieved from the stock culture collection at the Molecular Biology and Biotechnology Department of the Nigerian Institute of Medical Research. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disc diffusion method, and molecular techniques were employed to detect genetic determinants of antimicrobial resistance.

RESULTS

The E. coli isolates exhibited high resistance to fluoroquinolones, with 72% resistant to ciprofloxacin and 52% to levofloxacin. Resistance to carbapenems was relatively low, with 4% resistant to imipenem and 11% to meropenem. The prevalence of the genetic determinants gyrA, gyrB, and parC, which mediate fluoroquinolone resistance, was 26%, 24%, and 15%, respectively. blaOXA-48 and blaNDM, which mediate carbapenem resistance, were detected in only two isolates. Some isolates harbored plasmids ranging from 5 kb to 16 kb; however, no plasmid-mediated genetic determinants conferring fluoroquinolone resistance were identified.

CONCLUSION

This study revealed a high level of resistance to fluoroquinolones, emphasizing the need for judicious use of antibiotics, particularly those with low resistance rates. Continuous surveillance is essential to monitor emerging trends in resistance among bacterial pathogens.

Current trends in the epidemiology of multidrug-resistant and beta-lactamase-producing Pseudomonas aeruginosa in Asia and Africa: a systematic review and meta-analysis

Pseudomonas aeruginosa continues to be a significant contributor to high morbidity and mortality rates worldwide, particularly due to its role in severe infections such as hospital-acquired conditions, including ventilator-associated pneumonia and various sepsis syndromes. The global increase in antimicrobial-resistant (AMR) P. aeruginosa strains has made these infections more difficult to treat, by limiting the effective drug options available. This systematic review and meta-analysis aim to provide an updated summary of the prevalence of AMR P. aeruginosa over the past 5 years. A systematic search was performed across three major electronic databases-PubMed, ScienceDirect, and Web of Science-yielding 40 eligible studies published between 2018 and 2023. Using a random-effects model, our meta-analysis estimated that the overall prevalence of P. aeruginosa in Asia and Africa over the past 5 years was 22.9% (95% CI [14.4-31.4]). The prevalence rates for multidrug-resistant (MDR) and extensively drug-resistant (XDR) P. aeruginosa strains were found to be 46.0% (95% CI [37.1-55.0]) and 19.6% (95% CI [4.3-34.9]), respectively. Furthermore, the prevalence rates of extended-spectrum β-lactamase- and metallo-β-lactamase-producing P. aeruginosa were 33.4% (95% CI [23.6-43.2]) and 16.0% (95% CI [9.8-22.3]), respectively. Notably, resistance rates to β-lactams used for treating pseudomonal infections were alarmingly high, with rates between 84.4% and 100.0% for cephalosporins, and over 40% of P. aeruginosa isolates showed resistance to penicillins. Our analysis identified the lowest resistance rates for last-resort antimicrobials, with 0.3% (95% CI [0.0-1.3]) resistance to polymyxin B and 5.8% (95% CI [1.5-10.2]) to colistin/polymyxin E. The low resistance rates to polymyxins suggest that these antibiotics remain effective against MDR P. aeruginosa. However, the findings also highlight the critical public health threat posed by antimicrobial-resistant P. aeruginosa, particularly concerning β-lactam antibiotics. This underscores the need for effective and carefully planned intervention strategies, including the development of new antibiotics to address the growing challenge of resistance. Developing robust antibiotic treatment protocols is essential for better management and control of pseudomonal infections globally. Therefore, continued research and international collaboration is vital to tackle this escalating public health challenge. This study protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO), under registration number CRD42023412839.

Investigating the Link Between Biofilm Formation and Antibiotic Resistance in Clinical Isolates of Acinetobacter baumannii

Background: Acinetobacter baumannii has become a significant problem in hospitals worldwide during the last decades. Biofilm formation is a virulence factor that may affect antibiotic resistance. This study aimed to elucidate the correlation between biofilm formation and biofilm-related and oxacillinase genes in A. baumannii clinical isolates. Methods: This study was conducted on 53 A. baumannii isolates collected from hospitals affiliated with Babol University of Medical Sciences (Babol, Iran) from April to October 2023. Kirby-Bauer disc diffusion was used to determine antibacterial resistance. Biofilm formation was examined using crystal violet staining. Polymerase chain reaction was used to detect oxacillinase (bla OXA-23, bla OXA-24, bla OXA-51, and bla OXA-58) and biofilm-encoding (bap and bla PER-1) genes using specific primers. Results: The strains showed the highest resistance to trimethoprim/sulfamethoxazole and ciprofloxacin (98.11%) and the lowest resistance to ampicillin/sulbactam (66.03%). All isolates formed biofilms. Also, 67.92%, 18.86%, and 11.32% were strong, moderate, and weak biofilm producers, respectively. The frequencies of bla OXA-23, bla OXA-24, bla OXA-51, bap, and bla PER-1 genes were 92.45%, 71.69%, 100%, 73.58%, and 58.49%, respectively. None of the isolates harbored bla OXA-58. Conclusions: A high prevalence of antibiotic-resistant strains was found among A. baumannii clinical isolates. There was no significant correlation between the clinical sample type and biofilm formation, but a notable link was found between antimicrobial resistance and biofilm formation, except for ciprofloxacin. Oxacillinase genes were not significantly correlated with biofilm formation, but biofilm production was associated with bap rather than bla PER-1. Understanding the A. baumannii biofilm formation process is crucial for effective control of associated infections by targeting this mechanism.

Staphylococcus epidermidis: Antimicrobial Resistance Profiles of Biofilm-Forming Isolates From Pediatric Bacteremia in Pakistan

Background: Staphylococcus epidermidis is an important cause of nosocomial infections in children. The study undertaken identified antibiotic resistance markers among biofilm-forming S. epidermidis. Methods: A total of 105 bacteremia-positive samples from hospitalized children were processed for identification of S. epidermidis using species-specific rdr gene. Phenotypic antibiotic resistance was checked through Kirby-Bauer disc diffusion method. 96-well microtiter plate assays and PCR were used for biofilm production and antibiotic-resistant genes, respectively. Results: Among 105 clinical isolates, rdr gene was detected in 34 (32.38%) isolates. The rdr detected isolates exhibited biofilm formation (n = 34; 100%). Multidrug-resistant (MDR) pattern was observed among S. epidermidis, while the frequency of MDR was higher in very strong biofilm-forming S. epidermidis (n = 18; 52.9%, p ≤ 0.002) as compared to weak biofilm-forming S. epidermidis (n = 6; 17.6%). All S. epidermidis strains were resistant to cefoxitin, penicillin, and augmentin (n = 34; 100%). High resistance was observed against erythromycin (n = 29; 85.29%) and ciprofloxacin (n = 25; 73.5%). S. epidermidis displayed complete susceptibility (n = 34; 100%) toward vancomycin, tetracycline, and linezolid. Among the S. epidermidis isolates, the methicillin resistance gene (mecA, n = 29; 85.2%, p ≤ 0.000), the erythromycin resistance gene (msrA, n = 19; 55.7%) and the beta-lactamase resistance gene (blaZ, n = 17; 50%) were detected. Detection of mecA (n = 17; 94.4%), msrA (n = 8; 44.4%) and blaZ (n = 11; 61.1%) significantly (p ≤ 0.0052) correlated with very strong biofilm-forming S. epidermidis. Conclusion: Biofilm formation is significantly associated with antibiotic resistance. The study's result will help to understand the molecular mechanism of antimicrobial resistance in biofilm-forming S. epidermidis among pediatric patients.

Effect of non-antibiotic factors on conjugative transfer of antibiotic resistance genes in aquaculture water

Aquaculture water with antibiotic resistance genes (ARGs) is escalating due to the horizontal gene transfer. Non-antibiotic stressors specifically found, including those from fishery feed and disinfectants, are potential co-selectors. However, the mechanisms underlying this process remains unclear. Intragenus and intergenus conjugative transfer systems of the antibiotic-resistant plasmid RP4 were established to examine conjugative transfer frequency under exposure to five widely used non-antibiotic factors in aquaculture water: iodine, oxolinic acid, NO2-N, NO3-N and H2O2 and four different recipient bacteria: E. coli HB101, Citrobacter portucalensis SG1, Vibrio harveyi and Vibrio alginolyticus. The study found that low concentrations of non-antibiotic factors significantly promoted conjugative transfer, whereas high concentrations inhibited it. Moreover, the conjugation transfer efficiencies were significantly different with different bacterial species within (E. coli HB101 ∼ 10-3 %) or cross genera (C. portucalensis SG1 ∼10-5 %, V. harveyi ∼1 %). Besides, excessive exposure concentrations inhibited the expression of related genes and the generation of reactive oxygen species (ROS). Regulation of multiple related genes and ROS-induced SOS responses are common primary mechanisms. However, the mechanisms of non-antibiotic factors differ from those of standard antibiotics, with direct changes in cell membrane permeability potentially playing a dominant role. Additionally, variations among non-antibiotic factors and the specific characteristics of bacterial species contribute to differences in conjugation mechanisms. Notably, this study found that non-antibiotic factors could increase the frequency of intergeneric conjugation beyond that of intrageneric conjugation. Furthermore, non-antibiotic factors influenced by multiple transport systems may raise the risk of unintended cross-resistance, significantly amplifying the potential for resistance gene spread. This study underscores the significance of non-antibiotic factors in the propagation of ARGs, highlighting their role in advancing aquaculture development and protecting human health.

Isolation of Acanthamoeba Species and Bacterial Symbiont Variability in Puna Salt Plains, Argentina

Acanthamoeba spp. are widespread protists that feed on bacteria via phagocytosis. This predation pressure has led many bacteria to evolve strategies to resist and survive inside these protists. The impact of this is not well understood, but it may limit detection and allow survival in extreme environments. Three sites in the Puna salt plains, Catamarca province, Argentina, were sampled for Acanthamoeba spp., verified using PCR and Sanger sequencing. The intracellular microbiome was analysed with 16S rRNA gene sequencing and compared to the overall site microbiome. Acanthamoeba were found at all locations, and their intracellular microbiome was similar across samples but differed from the overall site microbiome. Pseudomonas spp., a clinically relevant genus, was most abundant in all isolates. This study suggests Acanthamoeba can protect bacteria, aiding their detection avoidance and survival in harsh conditions.

Current scenario of emerging pollutants in farmlands and water reservoirs: Prospects and challenges

Globally, roughly more than 400 million metric tons of plastics are produced annually. Similarly, the pharmaceuticals business is rising exponentially yearly, 5.8 %. It is expected to increase from USD 714 billion to USD 1454 billion by 2029. Beyond their intended uses, these substances are released into the environment as contaminants due to improper usage and management practices. Therefore, pharmaceuticals and microplastics (MPs) are classified as emerging pollutants (EPs), and their existence in agricultural ecosystems adversely affects soil and environmental health, ultimately impacting both ecological and human well-being. Pharmaceuticals and MP-loaded organic amendments (especially manure) are a primary cause of emerging soil pollutants. The increasing application of treated wastewater or biosolids as irrigation water or soil conditioners, mainly when derived from untreated sewage sludge, can introduce pharmaceuticals and MPs into the farmlands, merging these pollutants within the soil medium. The co-occurrence of MPs and pharmaceuticals leads to prolonged environmental presence and gradual bioaccumulation in organisms over time, contributing to persistent contamination and long-lasting effects on ecosystems. Moreover, these EPs have the potential to alter the composition of soil biogeochemistry and disrupt overall soil health and productivity. Numerous methods have been developed to address this emerging issue, including electrochemical degradation, advanced oxidation processes, photocatalytic degradation, biosurfactants, micro- and nano-bubble systems, ultrasonic cavitation, nanotechnology, constructed wetlands, and many hybrid approaches. This review explores the extent of EPs, their interactions, and management strategies in EPs-contaminated environments.

Unveiling the Resistome Landscape in Peri-Implant Health and Disease

Background: The human oral microbiome is a critical reservoir for antibiotic resistance; however, subgingival peri-implant biofilms remain underexplored in this context. We aimed to explore the prevalence and distribution of antibiotic resistance genes (ARGs) in metagenomes derived from saliva and subgingival peri-implant biofilms. Methods: A total of 100 metagenome datasets from 40 individuals were retrieved from the Sequence Read Archive (SRA) database. Of these, 20 individuals had exclusively healthy implants and 20 had both healthy and affected implants with peri-implantitis. ARGs and their taxonomic assignments were identified using the ABRicate tool, and plasmid detection was performed with PlasmidFinder. Results: Four plasmid replicons were identified in 72 metagenomes, and 55 distinct ARGs from 13 antibiotic classes were detected in 89 metagenomes. ARGs conferring resistance to macrolides-lincosamides-streptogramins, tetracyclines, beta-lactams, and fluoroquinolones were the most prevalent. The msr(D) and mef(A) genes showed the highest prevalence, except in saliva samples from individuals with healthy implants, where mef(A) ranked fourth. A pairwise PERMANOVA of principal coordinate analysis based on Jaccard distances revealed that saliva samples exhibited significantly greater ARG diversity than subgingival biofilm samples (p < 0.05). However, no significant differences were observed between healthy and peri-implantitis-affected subgingival biofilm groups (p > 0.05). The taxonomic origins of ARGs were also analyzed to understand their distribution and potential impact on oral microbial communities. Conclusions: Resistome profiles associated with both peri-implant health and disease showed no significant differences and higher salivary abundance of ARGs compared to subgingival biofilm samples.

Antibacterial and antibiofilm activities of kaffir lime essential oils and their active constituents against Staphylococcus aureus focusing on sortase A

Staphylococcus aureus biofilm has become a global medical concern due to rising antibiotic resistance. This study aimed to evaluate the potential activities of kaffir lime essential oils and their active compounds as alternative anti-S. aureus biofilm agents. The compositions of the essential oils were identified by gas chromatography/mass spectrometry (GC/MS), and their antibacterial activity was determined through broth-microdilution and time-kill assays. Antibiofilm activities were assessed using Congo red agar (CRA) well diffusion method, pre-biofilm inhibition resazurin assay, and post-biofilm inhibition assay. Sortase A (SrtA) inhibition was also investigated using in silico and in vitro approaches. This is followed by morphological studies to observe change in biofilm formations using light and scanning electron microscopy (SEM). Phytochemical analysis revealed that the kaffir lime essential oils from leaves (KLL) and peels (KLP) were primarily composed of the monoterpene aldehyde citronellal (59.13 %) and the monoterpene hydrocarbon (-)-limonene (25.69 %). However, the monoterpenoid alcohols, β-citronellol and terpinen-4-ol, which were the third most abundant compounds in KLL (5.35 %) and KLP (10.87 %), respectively, were selected for further study. All test compounds exhibited anti-Staphylococcal activity with a minimum inhibitory concentration (MIC) range of 0.1-0.3 % v/v. Their inhibition above the MIC levels showed time- and concentration-independence. Among the test compounds, terpinen-4-ol revealed good antibiofilm activity by inhibiting biofilm formation rather than eradicating the established biofilm. However, terpinen-4-ol exhibited weak SrtA inhibition with docking score of 32.58 and in vitro SrtA inhibition of 46.14 ± 3.58 % at 1 % v/v. Interestingly, terpinen-4-ol caused visible damage to the bacterial cell barrier, as revealed by SEM micrographs. These findings suggest the potential use of kaffir lime oils and their active compounds to combat biofilm-forming S. aureus infection.

Silver Nanoparticles as Antimicrobial Agents in Veterinary Medicine: Current Applications and Future Perspectives

Silver nanoparticles (AgNPs) have gained significant attention in veterinary medicine due to their antimicrobial properties and potential therapeutic applications. Silver has long been recognized for its ability to combat a wide range of pathogens, and when engineered at the nanoscale, silver's surface area and reactivity are greatly enhanced, making it highly effective against bacteria, viruses, and fungi. This narrative review aimed to summarize the evidence on the antimicrobial properties of AgNPs and their current and potential clinical applications in veterinary medicine. The antimicrobial action of AgNPs involves several mechanisms, including, among others, the release of silver ions, disruption of cell membranes and envelopes, induction of oxidative stress, inhibition of pathogens' replication, and DNA damage. Their size, shape, surface charge, and concentration influence their efficacy against bacteria, viruses, and fungi. As a result, the use of AgNPs has been explored in animals for infection prevention and treatment in some areas, such as wound care, coating of surgical implants, animal reproduction, and airway infections. They have also shown promise in preventing biofilm formation, a major challenge in treating chronic bacterial infections. Additionally, AgNPs have been studied for their potential use in animal feed as a supplement to enhance animal health and growth. Research suggested that AgNPs could stimulate immune responses and improve the gut microbiota of livestock, potentially reducing the need for antibiotics in animal husbandry. Despite their promising applications, further research is necessary to fully understand the safety, efficacy, and long-term effects of AgNPs on animals, humans, and the environment.

First whole genome report of Mangrovibacter phragmitis PSU-3885-11 isolated from a patient in Thailand

Mangrovibacter phragmitis is a Gram-negative bacterium typically found in plant roots that supports nitrogen fixation in nutrient-poor environments such as mangrove ecosystems. Although primarily found in environmental niches, an unusual case in Thailand of M. phragmitis strain PSU-3885-11 isolated from the sputum of a 29-year-old female patient with spinal tuberculosis. This isolate was initially misidentified as part of the Enterobacter cloacae complex (ECC) by MALDI-TOF. However, WGS subsequently confirmed its correct identity as M. phragmitis. The genome contains 4,651 coding sequences, along with 72 tRNA genes and 1 tmRNA. Moreover, comparative genomic analysis showed 99.32 % average nucleotide identity (ANI) similar to M. phragmitis MP23, and several antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were identified in the PSU-3885-11 genome which may contribute to its ability to survive in diverse environments, including human hosts. The PSU-3885-11 displayed resistance to beta-lactam antibiotics such as ampicillin and cefotaxime, while remaining sensitive to a wide range of other antibiotics. Key virulence genes including ompA, hcp/tssD, and rpoS, were identified which may play a role in its persistence in human hosts as an opportunistic pathogen. The presence of ribosomally synthesized and post-translationally modified peptides (RiPPs) and bacteriocins indicates the antimicrobial properties that may provide a competitive advantage in both environmental and clinical settings of this strain. Therefore, this study provides valuable insights into the genomic features, antibiotic resistance, and potential pathogenicity of M. phragmitis PSU-3885-11. The findings also emphasize the importance of continued surveillance and genomic analysis of environmental bacteria that may emerge as opportunistic pathogens in human infections.

Design, synthesis, antimicrobial activity, stability, and mechanism of action of bioresorbable ceragenins

Device-related infections (DRIs) from bacterial/fungal biofilms that form on surfaces are a major cause of death in first-world countries. DRIs and the increasing prevalence of antibiotic resistant strains require development of new antimicrobials for improved antimicrobial prophylaxis. New antimicrobial prophylaxis practices necessitate novel agents to combat a broad spectrum of both fungi and bacteria, to be less toxic to patients, and to be locally administrable to prevent perturbations to a patient's microbiome. A class of antimicrobials that we have previously developed to fit these criteria is ceragenins. Here we describe the design, synthesis, and characterization of a new series of ceragenins that is composed of and degrades into endogenous compounds: cholic acid, B alanine, and glycerides. From this series we identify an optimized bioresorbable ceragenin that has comparable antimicrobial activities to other ceragenins, degrades rapidly through the action of lipase and at pH 7.2, and has a similar mechanism of action to previously developed ceragenins.

Intra- and Interspecies Conjugal Transfer of Plasmids in Gram-Negative Bacteria

Background/Objectives: Plasmid-mediated resistance is a significant mechanism that contributes to the gradual decrease in the efficacy of antibiotics from various classes, including carbapenems. The aim of this study is to investigate the frequency of transfer of carbapenemase-encoding plasmids from K. pneumoniae to E. coli and P. aeruginosa. Methods: Matings were performed on agar with subsequent isolation of transconjugant, recipient, and donor colonies. The frequency of conjugation (CF) and minimum inhibitory concentrations (MICs) of meropenem were determined for the PCR-confirmed transconjugants. A pharmacodynamic study was conducted using a hollow-fiber infection model on E. coli transconjugant in order to evaluate its viability in the presence of therapeutic concentrations of meropenem. Results: CF for K. pneumoniae-K. pneumoniae was similar to that for K. pneumoniae-E. coli and was higher the higher was meropenem MIC of the K. pneumoniae donor. The meropenem MICs for K. pneumoniae and E. coli transconjugants were higher (0.25-4 μg/mL) compared to recipients (0.03-0.06 μg/mL). P. aeruginosa did not acquire plasmids from K. pneumoniae. In pharmacodynamic experiments, an E. coli transconjugant with MIC of 2 mg/L within the "susceptibility range", failed to respond to meropenem treatment. Conclusions: The frequency of conjugation between K. pneumoniae and E. coli falls within a similar range. A higher permissiveness of K. pneumoniae for plasmids from K. pneumoniae, i.e., within the same species, was observed. Conjugation did not occur between K. pneumoniae and P. aeruginosa. The transconjugants with meropenem MICs with borderline susceptibility may pose a potential threat to the efficacy of meropenem.

A novel broad-spectrum bacteriophage cocktail against methicillin-resistant Staphylococcus aureus: Isolation, characterization, and therapeutic potential in a mastitis mouse model

Bovine mastitis is a considerable challenge within the dairy industry, causing significant financial losses and threatening public health. The increased occurrence of methicillin-resistant Staphylococcus aureus (MRSA) has provoked difficulties in managing bovine mastitis. Bacteriophage therapy presents a novel treatment strategy to combat MRSA infections, emerging as a possible substitute for antibiotics. This study evaluated the therapeutic potency of a novel bacteriophage cocktail against MRSA mastitis. Two new bacteriophages (vB_SauR_SW21 and vB_SauR_SW25) with potent lytic activity against MRSA were isolated and characterized. The one-step growth curve displayed a rapid latent period (20-35 min) and substantial burst size (418 and 316 PFU/ cell). In silico analyses have confirmed the absence of antimicrobial resistance or virulence factor-encoding genes within their genomes. According to the results, combining these phages augmented their host range and virulence. The phage cocktail significantly reduced bacterial burden in a BALB/c mastitis model, demonstrating efficacy comparable to antibiotic treatment. Moreover, its administration led to decreased concentrations of IL-1β and TNF-α compared to the negative control group. The bacteriophage cocktail (SW21-SW25) exhibits a promising profile for therapeutic applications and may represent a novel substitute to antibiotics for managing MRSA bovine mastitis.

NIR-Activated Hydrogel with Dual-Enhanced Antibiotic Effectiveness for Thorough Elimination of Antibiotic-Resistant Bacteria

Antibiotic resistance has become a critical health crisis globally. Traditional strategies using antibiotics can lead to drug-resistance, while inorganic antimicrobial agents can cause severe systemic toxicity. Here, we have developed a dual-antibiotic hydrogel delivery system (PDA-Ag@Levo/CMCS), which can achieve controlled release of clinical antibiotics levofloxacin (Levo) and classic nanoscale antibiotic silver nanoparticles (AgNPs), effectively eliminating drug-resistant P. aeruginosa. Benefiting from the photothermal (PTT) effect of polydopamine (PDA), the local high temperature generated by PDA-Ag@Levo/CMCS can quickly kill bacteria through continuous and responsive release of dual-antibiotics to restore sensitivity to ineffective antibiotics. Moreover, AgNPs could significantly improve the efficiency of traditional antibiotics by disrupting bacterial membranes and reducing their toxicity to healthy tissues. A clever combination of PTT and drug-combination therapy can effectively eliminate biofilms and drug-resistant bacteria. Mechanism studies have shown that PDA-Ag@Levo might eliminate drug-resistant P. aeruginosa by disrupting biofilm formation and protein synthesis, and inhibit the resistance mutation of P. aeruginosa by promoting the expression of related genes, such as rpoS, dinB, and mutS. Collectively, the synergistic effect of this dual-antibiotic hydrogel combined with PTT provides a creative strategy for eliminating drug-resistant bacteria in chronic infection wounds.

Anti-Biofilm Agents to Overcome Pseudomonas aeruginosa Antibiotic Resistance

Pseudomonas aeruginosa is one of world's most threatening bacteria. In addition to the emerging prevalence of multi-drug resistant (MDR) strains, the bacterium also possesses a wide variety of virulence traits that worsen the course of the infections. Particularly, its ability to form biofilms that protect colonies from antimicrobial agents is a major cause of chronic and hard-to-treat infections in immune-compromised patients. This protective barrier also ensures cell growth on abiotic surfaces and thus enables bacterial survival on medical devices. Hence, as the WHO alerted to the need to develop new treatments, the use of anti-biofilm agents (ABAs) appeared as a promising approach. Given the selection pressure imposed by conventional antibiotics, a new therapeutic strategy has emerged that aims at reducing bacterial virulence without inhibiting cell growth. So-called anti-virulence agents (AVAs) would then restore the efficacy of conventional antibiotics (ATBs) or potentiate the effectiveness of the immune system. The last decade has seen the development of ABAs as AVAs against P. aeruginosa. This review aims to highlight the design strategy and critical features of these molecules to pave the way for further discoveries of highly potent compounds.

Investigating Past, Present, and Future Trends on Interface Between Marine and Medical Research and Development: A Bibliometric Review

The convergence of marine sciences and medical studies has the potential for substantial advances in healthcare. This study uses bibliometric and topic modeling studies to map the progression of research themes from 2000 to 2023, with an emphasis on the interdisciplinary subject of marine and medical sciences. Building on the global publication output at the interface between marine and medical sciences and using the Hierarchical Dirichlet Process, we discovered dominating research topics during three periods, emphasizing shifts in research focus and development trends. Our data show a significant rise in publication output, indicating a growing interest in using marine bioresources for medical applications. The paper identifies two main areas of active research, "natural product biochemistry" and "trace substance and genetics", both with great therapeutic potential. We used social network analysis to map the collaborative networks and identify the prominent scholars and institutions driving this research and development progress. Our study indicates important paths for research policy and R&D management operating at the crossroads of healthcare innovation and marine sciences. It also underscores the significance of quantitative foresight methods and interdisciplinary teams in identifying and interpreting future scientific convergences and breakthroughs.

Unveiling the nanoworld of antimicrobial resistance: integrating nature and nanotechnology

A significant global health crisis is predicted to emerge due to antimicrobial resistance by 2050, with an estimated 10 million deaths annually. Increasing antibiotic resistance necessitates continuous therapeutic innovation as conventional antibiotic treatments become increasingly ineffective. The naturally occurring antibacterial, antifungal, and antiviral compounds offer a viable alternative to synthetic antibiotics. This review presents bacterial resistance mechanisms, nanocarriers for drug delivery, and plant-based compounds for nanoformulations, particularly nanoantibiotics (nAbts). Green synthesis of nanoparticles has emerged as a revolutionary approach, as it enhances the effectiveness, specificity, and transport of encapsulated antimicrobials. In addition to minimizing systemic side effects, these nanocarriers can maximize therapeutic impact by delivering the antimicrobials directly to the infection site. Furthermore, combining two or more antibiotics within these nanoparticles often exhibits synergistic effects, enhancing the effectiveness against drug-resistant bacteria. Antimicrobial agents are routinely obtained from secondary metabolites of plants, including essential oils, phenols, polyphenols, alkaloids, and others. Integrating plant-based antibacterial agents and conventional antibiotics, assisted by suitable nanocarriers for codelivery, is a potential solution for addressing bacterial resistance. In addition to increasing their effectiveness and boosting the immune system, this synergistic approach provides a safer and more effective method of tackling future bacterial infections.

Point mutations in functionally diverse genes are associated with increased natural DNA transformation in multidrug resistant Streptococcus pneumoniae

DNA transformation is key for phenotypic diversity and adaptation of Streptococcus pneumoniae including in the emergence of multidrug resistance (MDR). Under laboratory conditions, DNA transformation is facilitated by the artificial triggering of competence by the competence stimulating peptide (CSP). In ongoing DNA transformation work, we observed that exogenous CSP was dispensable depending on the combination of strains and culture media. Here, we carried out a chemogenomic screen to select for S. pneumoniae mutants capable of natural transformation in medium that normally would not sustain natural transformation. Our chemogenomic screen relied on chemical mutagenesis followed by selection of mutants with increased DNA transformation capacities. Sequencing the genome of these mutants revealed an abundance and diversity of mutated genes proven experimentally to increase natural transformation. A genome wide association study between MDR and sensitive clinical isolates revealed gene mutations associated with MDR, many of which intersected with those pinpointed by our chemogenomic screens and that were proven to increase natural transformation. S. pneumoniae has adopted DNA transformation as its lifestyle and can select for mutations facilitating DNA transformation.

The "best practices for farming" successfully contributed to decrease the antibiotic resistance gene abundances within dairy farms

Introduction

Farms are significant hotspots for the dissemination of antibiotic-resistant bacteria and genes (ARGs) into the environment and directly to humans. The prevalence of ARGs on farms underscores the need for effective strategies to reduce their spread. This study aimed to evaluate the impact of a guideline on "best practices for farming" aimed at reducing the dissemination of antibiotic resistance.

Methods

A guideline focused on prudent antibiotic use, selective therapy, and hygienic and immune-prophylactic practices was developed and provided to the owners of 10 selected dairy farms and their veterinarians. Fecal samples were collected from lactating cows, dry cows, and calves both before and after the implementation of the guideline. ARGs (bla TEM, ermB, sul2, and tetA) were initially screened by end-point PCR, followed by quantification using digital droplet PCR. ARG abundance was expressed in relative terms by dividing the copy number of ARGs by the copy number of the 16S rRNA gene.

Results

The ARG abundances were higher in lactating cows compared to other categories. Despite similar levels of antibiotic administration (based on veterinary prescription data from the sampled farms) in both sampling campaigns, the total abundance of selected ARGs, particularly bla TEM and tetA, significantly decreased after the adoption of the farming guidelines.

Discussion

This study highlights the positive impact of prudent antibiotic use and the implementation of farming best practices in reducing the abundance of ARGs. The lactating cow category emerged as a crucial point of intervention for reducing the spread of antibiotic resistance. These findings contribute to ongoing efforts to address antibiotic resistance in farm environments and strengthen the evidence supporting the adoption of good farming practices.

Genomic Characterization of Carbapenemase-Producing Enterobacteriaceae from Clinical and Epidemiological Human Samples

Background/Objectives: Infections caused by multidrug-resistant (MDR)bacteria pose a significant public health threat by worsening patient outcomes, contributing to hospital outbreaks, and increasing health and economic burdens. Advanced genomic tools enhance the detection of resistance genes, virulence factors, and high-risk clones, thus improving the management of MDR infections. In the Autonomous Community of Aragon, the diversity and incidence of carbapenemase-producing Enterobacteriaceae (CPE) have increased during the last years. This study analyses CPE trends at a tertiary hospital in Spain from 2021 to 2023, aiming to optimize personalized medicine. Methods: CPE isolates were the first isolate per patient, year, species, and carbapenemase from January 2021 to December 2023. Additional metadata were collected from the laboratory's information system. Antibiotic susceptibility testing was performed by broth microdilution. Whole-genome sequencing (WGS) was performed using Illumina short reads. De novo assembly was used to generate draft genomes in order to determine their complete taxonomic classification, resistome, plasmidome, sequence type (ST), core-genome multilocus sequence typing (cgMLST), and phylogenetic relationships using a suite of bioinformatics tools and in-house scripts. Results: Between 2021 and 2023, 0.4% out of 38,145 Enterobacteriaceae isolates were CPE. The CPE rate tripled in 2022 and doubled again in 2023. The most common species was Klebsiella pneumoniae (51.8%) and the most common carbapenemase was blaOXA-48. WGS revealed concordant species identification and the carbapenemase distribution in detail. Resistance rates to critical antibiotics, such as carbapenems, were variable, but in most cases were above 70%. Genetic diversity was observed in WGS and phylogenetic analyses, with plasmids often mediating carbapenemase dissemination. Conclusions: The increasing rate of CPE in healthcare settings highlights a critical public health challenge, with limited treatment options. Genomic characterization is essential to understanding resistance mechanisms, aiding therapy, limiting outbreaks, and improving precision medicine.

Biofilm formation mechanisms of mixed antibiotic-resistant bacteria in water: Bacterial interactions and horizontal transfer of antibiotic-resistant plasmids

Over 95 % of bacteria on water supply pipeline surfaces exist in biofilms, which are hotspots for antibiotic resistance gene (ARG) transmission. This study established mixed biofilm culture systems on a metal iron substrate using Escherichia coli: antibiotic-sensitive bacteria (ASB) and antibiotic-resistant bacteria (ARB). The growth rate and extracellular polymeric substances (EPS) content of mixed biofilm surpassed single-species biofilms due to synergistic interactions among different bacteria. However, the composition of mixed biofilms formed by ASB and ARB became unstable after 72 h, linked to reduced polysaccharide proportions in EPS and inter-bacterial competition. The bacterial composition and conjugative transfer frequency of ARGs in mixed biofilms indicate that biofilm formation significantly enhances horizontal transfer of ARGs. Notably, the conjugative transfer frequency of the mixed biofilm formed by two ARB increased 100-fold within five days. In contrast, the conjugative transfer frequency in the mixed biofilm formed by ASB and ARB was unstable; inter-bacterial competition led to plasmid loss associated with horizontal transfer of ARGs, ultimately resulting in biofilm shedding. Furthermore, genes associated with ARG transfer and biofilm growth up-regulated by 1.5 - 6 and 2 - 7 times, respectively, in mixed biofilm. These findings highlight a mutually reinforcing relationship between biofilm formation and horizontal ARG transmission, with significant environmental implications.

Biochemistry of Bacterial Biofilm: Insights into Antibiotic Resistance Mechanisms and Therapeutic Intervention

Biofilms, composed of structured communities of bacteria embedded in a self-produced extracellular matrix, pose a significant challenge due to their heightened resistance to antibiotics and immune responses. This review highlights the mechanisms underpinning antibiotic resistance within bacterial biofilms, elucidating the adaptive strategies employed by microorganisms to withstand conventional antimicrobial agents. This encompasses the role of the extracellular matrix, altered gene expression, and the formation of persister cells, contributing to the recalcitrance of biofilms to eradication. A comprehensive understanding of these resistance mechanisms provides a for exploring innovative therapeutic interventions. This study explores promising avenues for future research, emphasizing the necessity of uncovering the specific genetic and phenotypic adaptations occurring within biofilms. The identification of vulnerabilities in biofilm architecture and the elucidation of key biofilm-specific targets emerge as crucial focal points for the development of targeted therapeutic strategies. In addressing the limitations of traditional antibiotics, this review discusses innovative therapeutic approaches. Nanomaterials with inherent antimicrobial properties, quorum-sensing inhibitors disrupting bacterial communication, and bacteriophages as biofilm-specific viral agents are highlighted as potential alternatives. The exploration of combination therapies, involving antimicrobial agents, biofilm-disrupting enzymes, and immunomodulators, is emphasized to enhance the efficacy of existing treatments and overcome biofilm resilience.

Phage-Derived Endolysins Against Resistant Staphylococcus spp.: A Review of Features, Antibacterial Activities, and Recent Applications

Antimicrobial resistance is a significant global public health issue, and the dissemination of antibiotic resistance in Gram-positive bacterial pathogens has significantly increased morbidity, mortality rates, and healthcare costs. Among them, Staphylococcus, especially methicillin-resistant Staphylococcus aureus (MRSA), causes a wide range of diseases due to its diverse pathogenic factors and infection strategies. These bacteria also present significant issues in veterinary medicine and food safety. Effectively managing staphylococci-related problems necessitates a concerted effort to implement preventive measures, rapidly detect the pathogen, and develop new and safe antimicrobial therapies. In recent years, there has been growing interest in using endolysins to combat bacterial infections. These enzymes, which are also referred to as lysins, are a unique class of hydrolytic enzymes synthesized by double-stranded DNA bacteriophages. They possess glycosidase, lytic transglycosylase, amidase, and endopeptidase activities, effectively destroying the peptidoglycan layer and resulting in bacterial lysis. This unique property makes endolysins powerful antimicrobial agents, particularly against Gram-positive organisms with more accessible peptidoglycan layers. Therefore, considering the potential benefits of endolysins compared to conventional antibiotics, we have endeavored to gather and review the characteristics and uses of endolysins derived from staphylococcal bacteriophages, as well as their antibacterial effectiveness against Staphylococcus spp. based on conducted experiments and trials.

Biofilm battleground: Unveiling the hidden challenges, current approaches and future perspectives in combating biofilm associated bacterial infections

A biofilm is a complex aggregation of microorganisms, either of the same or different species, that adhere to a surface and are encased in an extracellular polymeric substances (EPS) matrix. Quorum sensing (QS) and biofilm formation are closely linked, as QS genes regulate the development, maturation, and breakdown of biofilms. Inhibiting QS can be utilized as an effective approach to combat the impacts of biofilm infection. The impact of biofilms includes chronic infections, industrial biofouling, infrastructure corrosion, and environmental contamination as well. Therefore, a deep understanding of biofilms is crucial for enhancing public health, advancing industrial processes, safeguarding the environment, and deepening our knowledge of microbial life as well. This review aims to offer a comprehensive examination of challenges posed by bacterial biofilms, contemporary approaches and strategies for effectively eliminating biofilms, including the inhibition of quorum sensing pathways, while also focusing on emerging technologies and techniques for biofilm treatment. In addition, future research is projected to target the challenges associated with the bacterial biofilms, striving to develop new approaches and improve existing strategies for their effective control and eradication.

Prevalence and Antibiotic Susceptibility of Pathogenic Enterobacteria Strains from Three Biotopes in the City of Ouagadougou (Burkina Faso)

Purpose

The emergence of antibiotic resistance in pathogenic Enterobacteriaceae is a public health problem in tropical countries such as Burkina Faso. Antibiotic resistance could be identified using a variety of approaches. This study aimed to estimate the prevalence of pathogenic enterobacteria strains from three sources, as well as their antibiotic resistance profile to biotope and climatic season.

Material and Methods

The methodological approach consisted of identifying Enterobacteriaceae from human (urine, stool), animal (eggs, milk, fish), and environmental (soil, lettuce) samples, followed by assessing their antibiotic susceptibility. Samples were collected from February to December 2023. Bacterial species were isolated and phenotypically identified (morphologically, culturally, biochemically, and antigenically) using standard methods. The prevalence of bacterial susceptibility to ten antibiotics was determined using the agar disk diffusion method. The collected data were analyzed with IBM SPSS Statistics 25 software.

Results

A total of 615 Enterobacteriaceae isolates were collected, including 300, 168, and 147 samples from human, animal, and environmental sources respectively. Phenotypic characteristics allowed to partially identify 43 species, among these 29.76% belonged to Escherichia coli, 24.72% to Enterobacter cloacae, 13.82% to Klebsiella pneumoniae, 3.41% to Enterobacter sakazakii and 2.6% to Klebsiella oxytoca. Bacterial resistance rates were: aminopenicillins (54.8%), first-generation cephalosporins (35.3%), sulfonamides (33.3%), third-generation cephalosporins (30.7%), fourth-generation cephalosporins (22.5%), fluoroquinolones (21.8%), phenicols (16.8%), and carbapenems (16.2%). The distribution of antibiotic resistance was 45.3% from human sources, 19.3% from animal sources, and 13.8% from environmental sources.

Conclusion

The results indicate that resistant bacteria can come from any of the three biotopes, with human origin being the most frequent. The high prevalence of resistance to the antibiotics tested in isolated bacteria raises interest in investigating the genetic factors responsible.

Prevalence of Antibiotic Resistance Genes in Differently Processed Smoothies and Fresh Produce from Austria

Plant-derived foods are potential vehicles for microbial antibiotic resistance genes (ARGs), which can be transferred to the human microbiome if consumed raw or minimally processed. The aim of this study was to determine the prevalence and the amount of clinically relevant ARGs and mobile genetic elements (MGEs) in differently processed smoothies (freshly prepared, cold-pressed, pasteurized and high-pressure processed) and fresh produce samples (organically and conventionally cultivated) to assess potential health hazards associated with their consumption. The MGE ISPps and the class 1 integron-integrase gene intI1 were detected by probe-based qPCR in concentrations up to 104 copies/mL in all smoothies, lettuce, carrots and a single tomato sample. The highest total (2.2 × 105 copies/mL) and the most diverse ARG and MGE loads (16/26 targets) were observed in freshly prepared and the lowest prevalences (5/26) and concentrations (4.1 × 103 copies/mL) in high-pressure-processed (HPP) smoothies. BlaCTX-M-1-15 (1.2 × 105 c/mL) and strB (6.3 × 104 c/mL) were the most abundant, and qacEΔ1 (95%), blaTEM1 (85%), ermB and sul1 (75%, each) were the most prevalent ARGs. QnrS, vanA, sat-4, blaKPC, blaNDM-1 and blaOXA-10 were never detected. HPP treatment reduced the microbial loads by ca. 5 logs, also destroying extracellular DNA potentially encoding ARGs that could otherwise be transferred by bacterial transformation. The bacterial microbiome, potential pathogens, bacterial ARG carriers and competent bacteria able to take up ARGs were identified by Illumina 16S rRNA gene sequencing. To reduce the risk of AMR spread from smoothies, our data endorse the application of DNA-disintegrating processing techniques such as HPP.