Mechanism of staphylococcal resistance to clinically relevant antibiotics

Whole genome sequencing-based prediction of antibiotic-resistance of ocular Staphylococcus aureus across six continents

Staphylococcus aureus is a leading cause of ocular infections, resulting in vision loss in severe cases. Understanding the antibiotic resistance profiles of ocular S. aureus can help customize treatments. However, there is a lack of global data on the resistance patterns of ocular isolates and comparative regional analyses. Hence, WGS data from 195 ocular S. aureus isolates across six continents were analysed to identify antibiotic resistance genes (ARGs) and predict antibiotic resistance phenotypes in this study. A total of 40 ARGs were detected, involving resistance mechanisms against aminoglycosides, beta-lactams, macrolide-lacosamide-streptogramin B (MLSB), glycopeptides, tetracyclines, other antibiotic classes, and efflux pump regulators. Notably, the prevalences of ARGs associated with efflux pump regulators and beta-lactams were particularly high (>80 %). Resistance to 45 antibiotics was predicted across the isolates, with 51 % identified as multidrug-resistant (MDR), while only 8 % were predicted to be fully susceptible to all predicted antibiotics. Regional data varied, with isolates from North America and Asia exhibiting the most extensive resistance patterns, showing predicted resistance to 45 and 41 antibiotics, respectively. In contrast, Oceanian isolates were predicted to be resistant to only 14 antibiotics. Beta-lactams showed the highest predicted resistance prevalence among all antibiotic classes. Notably, North American isolates showed markedly higher resistance to MLSB antibiotics. A high proportion of cloud genes highlights the need for monitoring regional resistance. This study provides antibiotic resistance profiles among ocular S. aureus using WGS prediction, emphasizing the importance of regional surveillance and antimicrobial stewardship to suggest effective treatment strategies. It is recommended that WGS of more strains be deposited to overcome limited data, and laboratory tests be performed to analyse the consistency between genetic predicted and phenotypic resistance.

Emergence and spread of ST5 methicillin-resistant Staphylococcus aureus with accessory gene regulator dysfunction: genomic insights and antibiotic resistance

The globally disseminated Staphylococcus aureus ST5 clone poses a major public health threat due to its multidrug resistance and virulence. Here, we identified an agr-dysfunctional (agrA-I238K) ST5 MRSA clone that has spread across East and Southeast Asia, with recent increases in China since its emergence in the 1970s. Comparative genomic analyses identified distinct single-nucleotide polymorphisms and mobile genetic elements linked to enhanced resistance and virulence. This clone exhibits resistance to seven antimicrobial classes, including third-generation tetracyclines and fusidic acid, and shares phenotypic and genetic similarities with the vancomycin-intermediate S. aureus Mu50 strain, including reduced susceptibility to vancomycin, teicoplanin, and daptomycin. The agrA-I238K mutation attenuates hemolytic activity, increases biofilm formation, and reduces daptomycin susceptibility, suggesting a key role in the clone's success. Our results demonstrate the important role of agrA-I238K mutation in the widespread distribution of agr-dysfunctional MRSA and highlight the importance of genomic surveillance in tracking the spread of agr-dysfunctional ST5 MRSA.

Profiling of omadacycline resistance in clinical MRSA: A nationwide genomic survey and in vitro evolutionary analysis

OBJECTIVE

We aimed to evaluate the susceptibility of various clinical methicillin-resistant Staphylococcus aureus (MRSA) lineages to omadacycline and investigate the mechanisms underlying omadacycline resistance.

METHODS

Omadacycline MICs for all MRSA isolates were determined via broth dilution. Representative clinical MRSA isolates of ST59, ST5 and ST9 were exposed to increasing concentrations of omadacycline. Mutants developing omadacycline resistance were isolated, sequenced, and compared using breseq. Molecular cloning was employed to elucidate the mechanisms of omadacycline resistance.

RESULTS

Omadacycline MICs against MRSA ranged from 0.06 to 8 mg/L, with MIC50 and MIC90 values at 0.25 and 4 mg/L, respectively, and an overall resistance rate of 13%. All CC59 isolates were susceptible to omadacycline. Resistant isolates were mainly concentrated in HA-MRSA clones CC5. All 47 isolates with MICs ≥4 mg/L harbored tet(M) and the rpsJ K57M mutation. Cloning experiments demonstrated that both tet(M) and mutated rpsJ reduced susceptibility to omadacycline. The rpsJ gene was a common target in different MRSA lineages for decreased omadacycline susceptibility. Continuous exposure to omadacycline induced novel mutations in rpsJ (H56Y in ST9; H56R, K57M in ST59; and K57M, H56Y in ST5), which cloning experiments confirmed could variably reduce omadacycline susceptibility. Furthermore, mutated mepA also contributed to reduced omadacycline susceptibility.

CONCLUSION

Susceptibility to omadacycline varied among different MRSA lineages, while some CC5 isolates exhibiting the resistance phenotype. The rpsJ gene serves as a general target for the evolution of omadacycline resistance and plays an important role in the refinement of future tetracycline derivatives.

Staphylococcus aureus: A Review of the Pathogenesis and Virulence Mechanisms

Staphylococcus aureus is a formidable human pathogen responsible for infections ranging from superficial skin lesions to life-threatening systemic diseases. This review synthesizes current knowledge on its pathogenesis, emphasizing colonization dynamics, virulence mechanisms, biofilm formation, and antibiotic resistance. By analyzing studies from PubMed, Scopus, and Web of Science, we highlight the pathogen's adaptability, driven by surface adhesins (e.g., ClfB, SasG), secreted toxins (e.g., PVL, TSST-1), and metabolic flexibility in iron acquisition and amino acid utilization. Nasal, skin, and oropharyngeal colonization are reservoirs for invasive infections, with biofilm persistence and horizontal gene transfer exacerbating antimicrobial resistance, particularly in methicillin-resistant S. aureus (MRSA). The review underscores the clinical challenges of multidrug-resistant strains, including vancomycin resistance and decolonization strategies' failure to target single anatomical sites. Key discussions address host-microbiome interactions, immune evasion tactics, and the limitations of current therapies. Future directions advocate for novel anti-virulence therapies, multi-epitope vaccines, and AI-driven diagnostics to combat evolving resistance. Strengthening global surveillance and interdisciplinary collaboration is critical to mitigating the public health burden of S. aureus.

Analysis of bacterial spectrum and construction of a predictive model for postoperative sepsis in patients with upper urinary calculi and positive urinary cultures

BACKGROUND

To analyze bacterial profiles, antibiotic resistance, and urosepsis risk factors in urine culture-positive (UC+) patients post-endoscopic lithotripsy.

RESEARCH DESIGN AND METHOD

Retrospectively, 806 UC+ patients (2016.3-2021.3) were stratified into urosepsis/non-urosepsis groups per Sepsis-3 criteria.

RESULTS

Among 845 isolates (56 species), Escherichia coli dominated (46.8%), followed by Enterococcus faecalis (8.8%). Gram-negative bacteria exhibited high resistance to ampicillin, cefazolin, and cefuroxime. Multivariate analysis identified preoperative multidrug-resistant (MDR) bacteriuria (OR = 2.15), staghorn calculi (OR = 2.23), days of preoperative antibiotics use <3 (OR = 1.87), absence of nephrostomy (OR = 2.30), and postoperative WBC > 9.8 × 109/L (OR = 2.69) as independent sepsis predictors. A nomogram incorporating these factors achieved robust predictive accuracy. Preoperative antibiotic use for ≥3 days was inversely correlated with the risk of urinary sepsis as the duration of antibiotic administration increased.

CONCLUSIONS

Urosepsis incidence was 13.1% post-lithotripsy. Early risk stratification, targeted infection control, and antibiotic stewardship guided by urine susceptibility testing are critical for prevention.

Copper(II) carboxylate complexes inhibit Staphylococcus aureus biofilm formation by targeting extracellular proteins

Three copper(II) complexes of diphenyl acetic acid (DPAA) pyridine (py), 2,2΄-dipyridylamine (dpa), and 4,7-diphenyl, 1,10-phenanthroline (di-phen), [Cu₂(DPAA)₄(py)2] (Cu-1), [Cu(DPAA)₂(dpa)] (Cu-2), and [Cu₂(DPAA)₄(di-phen)₂] (Cu-3) were synthesized and characterized. Their antibacterial activities were evalvated. The minimum inhibitory concentrations (MIC) of these complexes against six tested microbial strains ranged from 1 to 128 μg/mL, and that of vancomycin antibiotic ranged from 0.5 to 2 μg/mL. The bactericidal effects of Cu-1, Cu-2 and Cu-3 and vancomycin against Staphylococcus aureus (S. aureus) were determined by colony count assay. Cu-1, Cu-2, and vancomycin showed relatively weaker antibiofilm formation activities; however, Cu-3 showed enhanced activity against S. aureus proliferation and biofilm formation as confirmed by microscopic analysis. In antibiofilm assays, Cu-1, Cu-2 and Cu-3 demonstrated high inhibition ability (23-75 %), of mature biofilm formation at concentrations of 5 to 15 μg/mL, and vancomycin at 15 μg/mL inhibited only 47 %. Cu-3 also effectively killed S. aureus within biofilms at doses up to 2 × MIC μg/mL. Further analysis of extracellular proteins (ECPs) expression revealed, that Cu-3 had significant potential in suppressing ECPs production. Molecular docking (MD) studies with biofilm associated protein (Bap) and SARS-CoV-2 receptors showed high interactions by several bonding types, where Cu-2 found as potent antiviral agent. Collectively, these findings highlighted the copper complexes potential in antibacterial applications, with Cu-3 emerging as a potent candidate for S. aureus biofilm inhibition.

Developing antibacterial HB43 peptide-loaded chitosan nanoparticles for biofilm treatment

Biofilm-associated infections on medical devices are challenging to treat. Therefore, innovative treatment approaches are needed to penetrate biofilms and eliminate bacteria. With this study, we developed chitosan nanoparticles (CNPs) encapsulating the antibacterial peptide HB43 at increasing CNP/peptide ratios (from 1 to 4 % for P1-CNP, P2-CNP, and P4-CNP, respectively) using the ion gelation method. Our goal was to enhance antibacterial drug delivery inside a methicillin-resistant Staphylococcus aureus (MRSA) biofilm. Our analysis showed a direct correlation between the encapsulation efficacy of HB43 and the physical properties of the CNPs, such as size and zeta potential. P1-CNP was identified as the optimal formulation, characterized by its small size, high encapsulation efficiency, and cationic surface charge. Release studies indicated that HB43 was released in a sustained manner particularly under acidic conditions, which enhanced therapeutic efficacy. We tested the P1-CNP in culture media with pH levels of 7.4 and 5.5 to assess the pH responsiveness of the CNPs and mimic the infection environment. Both conditions showed that the HB43 loaded-CNPs effectively reduced bacterial populations in a dose-dependent manner, with up to a 99.99 % reduction in bacterial load. This study offers a promising new strategy for managing biofilm-associated infections and addressing antibiotic resistance by using CNPs loaded with HB43.

Strategic use of nanomaterials as double-edged therapeutics to control carcinogenesis via regulation of dysbiosis and bacterial infection: current status and future prospects

The human microbiome plays a crucial role in modulating health and disease susceptibility through a complex network of interactions with the host. When the delicate balance of this microbial ecosystem is disrupted, it often correlates with the onset of systemic diseases. An over-abundance of pathogenic microorganisms within the microbiome has been implicated as a driving factor in the development of disease conditions such as diabetes, obesity, and chronic infections. It has been observed that microbiome dysbiosis perturbs metabolic, inflammatory, and immunological pathways, potentially facilitating carcinogenesis. Furthermore, the metabolites associated with microbial dysbiosis exert multifaceted effects, including metabolic interference, host DNA damage, and tumor promotion, further underscoring the microbiome's significance in several of the cancers. This new exploration of microbiome involvement in carcinogenesis needs additional patient sample analysis, which could provide new insights into cancer diagnosis and treatment. However, treating these diseases using drugs, traditional methods, etc. has resulted in multi-drug resistance, and this has eventually made the situation worrisome. This review highlights the importance of nanotechnology, which may tackle these pathogenic conditions simultaneously by targeting common receptors present in bacteria and cancer. Herein, we have explained how nanotechnology may come to the forefront for these treatments. It explores the potential of non-antibiotic disinfectants, i.e., nanoparticles (NPs) with dual targeting capabilities against microbes and cancer cells, using mechanisms such as ROS generation and DNA damage while minimizing the chances of drug resistance.

Disarming Staphylococcus aureus: Review of Strategies Combating This Resilient Pathogen by Targeting Its Virulence

Staphylococcus aureus is a formidable pathogen notorious for its antibiotic resistance and diverse virulence mechanisms, including toxin production, biofilm formation, and immune evasion. This article explores innovative anti-virulence strategies to disarm S. aureus by targeting critical virulence factors without exerting bactericidal pressure. Key approaches include inhibiting adhesion and biofilm formation, neutralizing toxins, disrupting quorum sensing (e.g., Agr system inhibitors), and blocking iron acquisition pathways. Additionally, interventions targeting two-component regulatory systems are highlighted. While promising, challenges such as strain variability, biofilm resilience, pharmacokinetic limitations, and resistance evolution underscore the need for combination therapies and advanced formulations. Integrating anti-virulence strategies with traditional antibiotics and host-directed therapies offers a sustainable solution to combat multidrug-resistant S. aureus, particularly methicillin-resistant strains (MRSA), and mitigate the global public health crisis.

Isolation and assessment of antibiotic resistance of Staphylococcus aureus in the air of an underground hard coal mines

Mine aerosol poses a serious health threat due to its easy access to the human respiratory tract. Damage may be caused by the chemical composition of dust and the substances adsorbed on its surface, including microorganisms that potentially affect human health. Our proposed research aimed to isolate Staphylococcus aureus strains from coal mine bioaerosol and to assess its sensitivity towards selected antibiotics. Bioaerosol samples were collected in three underground hard coal mines located in Upper Silesia in southern Poland. Microbiological tests of the air samples were carried out according to standard microbiological techniques. All tested strains of Staphylococcus aureus were sensitive to oxacillin, which indicated the lack of methicillin-resistant isolates (MRSA) in the tested group. However, antibiotic resistance from macrolide and lincosamide groups was observed among certain strains. 10% of isolates were constitutive MLSB resistance, while 4% of strains were inductive MLSB resistance. Less than 1% of isolates were erythromycin-resistant and clindamycin-sensitive (MSB). Based on the Chi-square test, statistically significant differences were found in the frequency of MSB, MLSB inductive, and MLSB constitutive phenotypes. Almost 30% of the identified strains showed multi-antibiotic resistance. However, the Chi-square test did not reveal any statistically significant differences in the frequency of multidrug-resistant strains in the considered research areas. The analyses carried out constituted the first study related to the isolation and assessment of drug susceptibility of Staphylococcus aureus in the bioaerosol of hard coal mines. Identification of bioaerosol in underground coal mines is a key issue because, due to the presence of pathogens, it plays a significant role in limiting the spread of occupational diseases. For the health of miners, research into microbial communities benefits the promotion of microbiological control of mine air.

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.

Advancements in Antibacterial Therapy: Feature Papers

Antimicrobial resistance (AMR) is a growing global health crisis that threatens the efficacy of antibiotics and modern medical interventions. The emergence of multidrug-resistant (MDR) pathogens, exacerbated by the misuse of antibiotics in healthcare and agriculture, underscores the urgent need for innovative solutions. (1) Background: AMR arises from complex interactions between human, animal, and environmental health, further aggravated by the overuse and inadequate regulation of antibiotics. Conventional treatments are increasingly ineffective, necessitating alternative strategies. Emerging approaches, including bacteriophage therapy, antimicrobial peptides (AMPs), nanotechnology, microbial extracellular vesicles (EVs), and CRISPR-based antimicrobials, provide novel mechanisms that complement traditional antibiotics in combating resistant pathogens. (2) Methods: This review critically analyzes advanced antibacterial strategies in conjunction with systemic reforms such as antimicrobial stewardship programs, the One Health framework, and advanced surveillance tools. These methods can enhance resistance detection, guide interventions, and promote sustainable practices. Additionally, economic, logistical, and regulatory challenges impeding their implementation are evaluated. (3) Results: Emerging technologies, such as CRISPR and nanotechnology, exhibit promising potential in targeting resistance mechanisms. However, disparities in resource distribution and regulatory barriers hinder widespread adoption. Public-private partnerships and sustainable agriculture practices are critical to overcoming these obstacles. (4) Conclusions: A holistic and integrated approach is essential for mitigating the impact of AMR. By aligning innovative therapeutic strategies with global health policies, fostering interdisciplinary collaboration, and ensuring equitable resource distribution, we can develop a sustainable response to this 21st-century challenge.

Silent Carriers: The Hidden Threat of Antibiotic-Resistant Staphylococcus aureus in Retail Seafood Across Poland's Tri-City Area

Background/objectives: Antibiotic-resistant Staphylococcus aureus poses a significant risk to food safety and public health, particularly through the consumption of contaminated seafood. This study aimed to assess the presence and antibiotic resistance of S. aureus in seafood sold in the Tri-City area of Poland, addressing a knowledge gap regarding the region. Methods: Seafood samples (n = 89) were categorized according to their origin: domestic-Poland (PL), European countries (ECs), and Asian countries (ACs). S. aureus was isolated using ISO 6888-1 methods, and antimicrobial susceptibility testing was conducted against three antibiotics: erythromycin, clindamycin, and gentamicin, following CLSI guidelines. Results: Of the 89 samples, 68.5% were contaminated with S. aureus. The highest resistance rates were found for erythromycin (30.5%), with gentamicin showing the lowest resistance (8.3%).No significant correlation (p > 0.05) was found between resistance patterns and fish origin or processing level. Conclusions: The results of this study highlight the widespread occurrence of Staphylococcus aureus in fish sold in the Tri-City area, with a notable prevalence of antibiotic-resistant strains.

Reshaping the battlefield: A decade of clonal wars among Staphylococcus aureus in China

BACKGROUND

Long-term comprehensive studies on the genomic epidemiology of both methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) isolates are limited in China. Here, we aimed to assess the genomic epidemiological characteristics and population dynamics of S. aureus in China.

METHODS

We performed whole-genome sequencing and resistance phenotyping on 3848 S. aureus isolates from bloodstream infections across 72 hospitals in 22 provinces, from 2011 to 2020 in China. We explored the dynamic trends in the resistance/virulence genes and mobile genetic element profiles across lineages, and conducted time-scaled phylogenetic investigation for prevalent lineages.

FINDINGS

The results revealed 315 different sequence types (STs) among all strains, 205 of which were novel. Significant shifts in MRSA population structure were observed, with ST59 replacing ST239 as the dominant lineage, exhibiting widespread inter-hospital transmission and increasing lineage diversity. In contrast, the composition of predominant MSSA lineages, ST188 (11.21 %), ST7 (9.79 %), ST22 (9.10 %), ST5 (8.56 %) and ST398 (7.91 %), remained relatively stable over time, with the diversity among MSSA strains consistently preserved at the population level. Phylogenetic reconstruction showed that ST59, ST398, ST22 and ST188 MSSA could evolve into corresponding MRSA lineages through the acquisition of staphylococcal cassette chromosome mec (SCCmec) elements. Moreover, the distribution patterns of resistance and virulence genes closely correlated with different lineages, where the proportion of PVL+ isolates in MRSA is rising. Concurrently, changes in the MRSA population structure led to an overall decrease in the number of resistance and virulence genes, significantly increased antimicrobial sensitivity.

INTERPRETATION

The shifting genomic landscape of S. aureus in China underscores the need for tailored antimicrobial stewardship and enhances understanding of its epidemiological trends over the past decade.

Investigation of integron classes 1, 2, and 3 among multi-drug resistant Staphylococcus aureus isolates in Iran: a multi-center study

BACKGROUND

Rising methicillin-resistant Staphylococcus aureus (MRSA) poses a global health threat, contributing to serious infections with high mortality rates. Integrons are recognized as significant genetic elements in disseminating multidrug-resistant (MDR) strains. This study focuses on assessing the prevalence of integron classes 1, 2, and 3 in S. aureus strains from four major cities in Iran.

METHODS

This cross-sectional study analyzed 183 S. aureus isolates from Shiraz, Tehran, Isfahan, and Yazd in Iran. The isolates were identified using specific biochemical and molecullar tests. The Kirby-Bauer disc diffusion method and microbroth dilution method were employed to determine the susceptibility of the isolates to relevant antibiotics and vancomycin, respectively. The macrolide-lincosamide-streptogramin B (MLSB) resistance phenotype was also evaluated using the D-test. All isolates were sought for presence of the intI1, intI2, and intI3 genes.

RESULTS

Among 183 S. aureus isolates, high resistance rates were noted: 86.3% for erythromycin, 66.1% for ciprofloxacin, and 61.7% for clindamycin, while all isolates were susceptible to linezolid and vancomycin. Of the 183 isolates, 59.6% were identified as MRSA and 78.1% as MDR. According to the D-test results, 112/183 (61.2%), 29/183 (15.8%), 25/183 (13.7%), and 17/183 (9.7%) of S. aureus isolates showed constitutive resistance-MLSB, inducible resistance-MLSB, sensitive, and resistance to macrolide-streptogramin B (MS) phenotypes, respectively. The intI1 gene was found in 14 out of 183 S. aureus isolates (7.6%), while none were positive for the intI2 or intI3 genes. Notably, 11/14 (78.5%) and 13/14 (92.8%) intI1-positive isolates were MRSA and MDR, respectively.

CONCLUSIONS

The distribution of MRSA and MDR S. aureus isolates in Iran seems concerning. Although the prevalence of intI1 was not as high as in prior studies, almost all S. aureus harbored the intI1 gene were MRSA and MDR.