Search Results (371)

Background/Objectives: Antimicrobial resistance (AMR) is a major global public health threat, particularly in intensive care units (ICUs), where critically ill patients are exposed to high antimicrobial pressure. ESKAPE pathogens play a central role in healthcare-associated infections and are frequently associated with multidrug resistance. This study aimed to evaluate the microbiological profiles and antimicrobial resistance patterns of bacterial isolates from an adult ICU in a tertiary hospital in Brazil. Methods: A retrospective, observational, cross-sectional study was conducted using microbiological culture data from patients admitted during 2024 to the adult intensive care unit of a tertiary hospital in Brazil. Bacterial isolates from clinical specimens were included, and antimicrobial susceptibility testing was performed according to routine laboratory procedures. Descriptive statistics were used to summarize microorganism frequency and antimicrobial resistance rates. Results: A total of 1869 isolates were analyzed, with predominance of Gram-negative bacteria. The most frequent pathogens were Klebsiella pneumoniae (287/1869; 15.33%), Staphylococcus haemolyticus (164/1869; 8.76%), Enterococcus faecalis (144/1869; 7.69%), and Acinetobacter baumannii (135/1869; 7.21%). A high proportion of isolates belonged to the ESKAPE group. Gram-negative bacteria, particularly Klebsiella pneumoniae and Acinetobacter baumannii, showed high resistance to β-lactams, cephalosporins, carbapenems, and quinolones. Among Gram-positive organisms, resistance was high for macrolides, oxacillin, and clindamycin, while glycopeptides and linezolid remained effective. Conclusions: These findings highlight the importance of continuous microbiological surveillance and robust antimicrobial stewardship strategies. The present study adds novel local epidemiological evidence from a Brazilian ICU by integrating species-level distribution, antimicrobial-specific resistance, and resistance patterns by pharmacological class, with particular emphasis on ESKAPE pathogens. Full article

To promote the sustainable management of marine aquaculture waste, this study investigated the effect of corn stover biochar (300 °C, 400 °C, and 500 °C) on the mesophilic anaerobic digestion (37 ± 1 °C) of particulate matter from seawater aquaculture wastewater. Batch experiments evaluated biochar’s effects on methane production, microbial succession, and antibiotic resistance genes (ARGs), and the correlation between ARG abundance and microbial taxa. Biochar addition significantly enhanced biogas production and shortened the lag phase. During 60 h fermentation, the optimal treatment achieved a methane yield of 291 mL, which was 164.55% higher than the control. Metagenomic sequencing revealed that biochar altered microbial community structure and ARG profiles, reducing the 11 most prevalent ARG types. Glycopeptide resistance genes showed the greatest reduction (15.02%). Correlation analysis identified Enterococcus, Peptostreptococcus, and Clostridium as major ARG hosts, accounting for 64.78–69.81% of total ARG abundance in the control and 68.14–76.17% in the biochar-amended group, confirming that Firmicutes are key potential ARG carriers in marine aquaculture particulate waste. From the perspective of sustainable development, biochar addition improves energy recovery from aquaculture waste and mitigates ARG dissemination risk. This study provides practical guidance for material selection and process optimization in sustainable aquaculture biogas projects, supporting the transition toward a circular bioeconomy. Full article

Kennel-housed dogs may experience chronic stress affecting cognition. This study compared the effects of Lycium barbarum polysaccharides (LBP) and glycopeptide (LbGP) on cognitive function in laboratory-kenneled poodles. Eighteen dogs were assigned to CON, LBP, or LbGP groups for 42 days. Cognitive tests were performed and serum, saliva, and feces were collected for subsequent analysis. Both supplements improved cognitive performance (e.g., increased the correct rate in the cylinder test by approximately 40.0%, both p < 0.001). LBP enriched beneficial bacteria (Faecalibacterium and Bacteroides, p < 0.05), reduced pathogens (Romboutsia and Terrisporobacter, p < 0.05), and predominantly influenced the indole pathway of tryptophan metabolism. LbGP specifically decreased Escherichia-Shigella and Corynebacterium, increased fecal SCFAs, and mainly targeted the 5-HT pathway. Both treatments regulated immune function (i.e., elevated IL-6 and IL-10) and antioxidant capacity; LBP significantly increased serum superoxide dismutase (SOD) levels by 6.8% (p < 0.01) and BDNF levels by 13.5% (p < 0.05), while LbGP elevated (p < 0.01) glutathione peroxidase (GSH-Px) levels by 20.9% and reduced salivary cortisol levels by 14.2% (p < 0.01). Overall, LBP and LbGP support canine cognition through distinct microbiota-related mechanisms, likely via the microbiota–gut–brain axis, suggesting their potential as functional feed additives for cognitive health. Full article

Fabrazyme (agalsidase beta) is a therapeutic enzyme whose clinical efficacy is contingent upon its complex N-glycosylation patterns. Nevertheless, comprehensive glycosylation profiling remains challenging due to high site-specific heterogeneity. To address this, three orthogonal liquid chromatography–mass spectrometry (LC-MS) approaches were employed: (1) released N-glycan analysis with fluorescence detection and MS annotation, (2) site-specific glycopeptide mapping, and (3) intact protein MS. The released glycan profiling method was validated for reproducibility, intermediate precision, and inter-laboratory transferability, thereby enabling reliable separation and quantification of neutral, phosphorylated, and sialylated species. Glycopeptide mapping revealed distinct site-specific distributions: N108 was found to predominantly carry sialylated complex glycans; N161 was enriched in phosphorylated oligomannose structures; and N184 displayed the highest heterogeneity, including bisphosphorylated and sialylated glycans. Intact protein analysis was performed on both intact and desialylated Fabrazyme, thereby enabling confirmation of glycan assignments. Desialylation reduced spectral complexity, thereby facilitating accurate mass matching with a combinatorial library generated from glycopeptide-level data. The complementary use of these three analytical levels provides a comprehensive view of Fabrazyme glycosylation, offering a robust reference for quality control and biosimilar development. Full article

The surface of cancer cells is covered in abnormal carbohydrate antigens that facilitate tumor growth, immune evasion and metastasis. Overexpressed and often specific to cancer cells, these tumor-associated carbohydrate antigens (TACAs) offer a valuable handle for targeted immunotherapy and were soon targeted by TACA–protein conjugate vaccines. Despite good initial results, sTn-KLH conjugate Theratope^® failed in clinical trials fifteen years ago for failure to improve life expectancy. This has been attributed to poor immunogenicity, inhomogeneous expression of TACAs within tumors, and vaccine carrier interference. This review covers the two decades of subsequent effort to overcome these limitations and the now large toolbox available to vaccine researchers to improve the outcome of anticancer vaccines: analogues and conformation-locked mimics of TACAs, monomolecular multivalent vaccines, more biologically relevant presentation of TACAs through clusters and glycopeptides, and a new generation of vaccine carriers to reduce carrier interference, immune reaction, or provide simple modular vaccine delivery platforms. Full article

The gut microbiota is a crucial component of a tiger’s health and plays a significant role in adapting to changes in food and the environment. Although extensive studies have been carried out on the gut microbiota of tigers, investigating the responses of gut microbial composition and function to preadaptation to wild predation patterns under captive conditions is particularly significant for South China tigers, given that it is the only tiger subspecies existing solely in captive settings at present. Here, we performed shotgun metagenomic sequencing for a comprehensive analysis of the gut microbiota of South China tigers assigned to two dietary groups (live prey group, LP group; frozen meat group, FM group), thereby generating abundant valuable data for this endangered subspecies. The results indicated that the core intestinal microbial composition was similar between the two dietary groups. Differential analysis revealed associations between dietary treatments and microbial abundance in the intestines of South China tigers. Functional gene analysis revealed that the LP group exhibited upregulation of genes and pathways related to antimicrobial resistance, bacterial infection-related disease, cell motility and proliferation, while the FM group displayed efficient energy metabolism. A total of 1251 antibiotic resistance genes (ARGs) were identified in the gut microbiome of South China tigers. The core resistome mainly included resistance to peptides, glycopeptides, tetracyclines, fluoroquinolones, and macrolides. In addition, the differences in ARGs between the LP group and FM group may be related to a broader range of animal tissues of live prey and the processing conditions of frozen meat. In summary, although feeding live prey did not change the core framework of the gut microbiota in South China tigers, it was associated with differences in microbial abundance, metabolic pathways, and antibiotic resistance gene profiles. Full article

Rates of foodborne infectious disease are increasing globally. The One Health zoonoses report shows increasing cases of shigatoxigenic Escherichia coli, campylobacteriosis, salmonellosis and listeriosis in the last 5 years. The ESKAPE pathogens are the top priority due to their alarming rate of resistance to broad-spectrum beta-lactams, carbapenems, glycopeptides, fluoroquinolones, aminoglycosides and biocide solutions. Research assessing alternative biocontrol options highlight the advantages of bacteriophages in the control of resistant bacterial species. Phage formulations including ListShield^TM and SalmoFresh^TM have gained FDA approval for food production. As biocontrol agents, however, phages are limited by their specificity in a multispecies environment, the presence of environmental variables and bacterial resistance mechanisms. Genetic modification and the use of phage cocktails aim to overcome such limitations. Future research is warranted in a harmonised approach supported by a defined legal framework to establish best formulation and exposure protocols. This review discusses phages as biocontrol agents in the control of high-risk pathobionts associated with foodborne illness. Pathobionts associated with bovine livestock are discussed due to the morbidity and incidence of disease associated with such pathogens. Full article

Streptococcus suis is an emerging zoonotic pathogen that typically causes bacteremia or meningitis in humans, whereas vertebral osteomyelitis with epidural abscess is exceedingly rare and may be missed. We describe a 65-year-old farmer with fever and severe low back pain after long-term bare-handed handling of raw pig lungs. Pre-treatment blood cultures yielded S. suis identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). After transient improvement on empirical therapy, fever recurred with worsening lumbar pain. Contrast-enhanced magnetic resonance imaging (MRI) demonstrated multilevel thoracolumbar pyogenic spondylitis with an epidural abscess and a sub-ligamentous abscess beneath the posterior longitudinal ligament (PLL) extending from L2 to L5. Computed tomography-guided lumbar biopsy followed by tissue metagenomic next-generation sequencing (mNGS) detected S. suis, providing concordant evidence supporting pathogen involvement at the vertebral focus. The bloodstream isolate (SS-JX2025-01) was serotype 2, sequence type 7 (ST7). It remained susceptible to β-lactams and glycopeptides but was resistant to macrolide–lincosamide and tetracycline classes, consistent with erm(B), tet(O), tet(40), and ant(6)-Ia detected by whole-genome sequencing (WGS). Virulence profiling revealed an epf⁺/sly⁺/mrp⁻ pattern with multiple adhesins and immune-evasion factors, whereas canonical 89K pathogenicity island markers were absent. Core-genome phylogeny placed SS-JX2025-01 within the Chinese ST7 lineage associated with previous outbreaks. This biopsy-supported case expands the clinical spectrum of invasive S. suis infection, highlights the value of tissue mNGS as an adjunct for supporting deep-seated foci in zoonotic infections, and underscores the importance of occupational prevention in small-scale farming households. Full article

Background: Antimicrobial resistance (AMR) is a growing global health concern, driven in part by antibiotic use in animal production systems. Despite its relevance, the microbiome and resistome of small ruminant farm environments remain largely underexplored. Methods: In this study, shotgun metagenomics was applied to environmental samples from 46 sheep, goat and mixed-species farms across 14 municipalities in central Portugal. Results: Microbial profiling revealed a well-preserved microbiome with Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota (syn. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes respectively) as the most dominant phylum across different farm types. Regarding AMR, a total of 706 unique antimicrobial resistance genes (ARGs), covering 15 antibiotic classes, were detected. Tetracycline, aminoglycoside and macrolide resistance genes dominated across all samples, forming a conserved core resistome. While overall resistome profiles were broadly similar among farm types, significant differences were observed in specific ARG classes, such as pleuromutilin and fosfomycin. Conclusions: These findings highlight small ruminant farm environments as potential reservoirs of clinically relevant ARGs, including WHO highest priority critically important antimicrobial (HPCIA) resistance genes for macrolides (mph(c), erm(f), erm(b)) and fluoroquinolones (qnrD1), as well as critically important antimicrobial (CIA) resistance genes for glycopeptides (vanR-SC, vanR-O) and aminoglycosides (str, aadA), supporting the need to incorporate these environments into surveillance strategies. Full article

Lung cancer is the leading cause of cancer-related mortality worldwide. This editorial accompanies the Special Issue “Lung Cancer: From Mechanisms of Action and Risk Factors in Disease Onset to Management” published in Cancers (MDPI), and introduces the twenty-one research and review articles included in the collection. The contributions span a wide spectrum of topics, from risk factors such as allostatic load and telomere biology, to molecular biomarkers including DNA methylation and serum glycopeptides, to advances in low-dose CT screening and the management of incidental findings, to targeted therapy, immunotherapy, surgical techniques, and health economics. Together, the papers highlight the multifactorial and clinically complex nature of lung cancer, and reinforce the importance of integrated, evidence-based strategies to reduce its global burden. Full article

Albumen transparency is an important quality trait of pigeon eggs that directly influences consumer preference and market value; however, its molecular basis remains unclear. This study aimed to characterize the key molecular differences between transparent and opaque pigeon egg albumen from an N-glycoproteomic perspective and to explore their associations with macroscopic textural properties. Transparent and opaque pigeon eggs were selected, and N-glycoproteomic analysis combined with texture profile analysis was conducted to compare glycosylation modifications and textural characteristics between the two groups. The results showed that transparent pigeon egg albumen exhibited significantly lower hardness, fracturability, gumminess, and chewiness than opaque albumen. Comparative glycoproteomic analysis revealed that the abundance of 122 glycopeptides was significantly lower in the transparent group, primarily originating from ovalbumin-related proteins and transferrin. Functional enrichment and protein–protein interaction analyses indicated that these proteins are closely associated with the extracellular space and serine-type endopeptidase inhibitor activity, and form a functional interaction module dominated by ovalbumin family proteins and transferrin. Overall, reduced N-glycosylation of key egg white proteins may influence protein aggregation behavior and gel network formation during heating, thereby contributing to differences in albumen textural properties and transparency. These findings provide glycoproteomic insights into the molecular mechanisms underlying transparency differences in pigeon egg albumen and identify specific glycosylation-related targets that may be exploited to modulate gel properties during thermal processing. This knowledge may support precision quality control of pigeon eggs and facilitate the development of transparent protein-based foods and functional gel products in the food industry. Full article

Immunodeficiency is a global health concern, partly due to disrupted rhythms and drugs. Marine glycopeptides, with immunomodulatory and intestinal barrier protective activities, show great potential in dietary supplements and functional foods. Here, a marine glycopeptide, SC2-3, with a molecular weight of 5061 Da, was isolated and purified from Nereis succinea. Monosaccharide composition, NMR data, amino acid composition analysis, and SDS-PAGE analyses identified SC2-3 as a glycopeptide. The N-glycome results of SC2-3 collected by MALDI-TOF-MS revealed that SC2-3 contains fucosylated N-glycans with shorter glycan chains compared to human-derived N-glycans. SC2-3 exerted a significant immune-enhancing effect on macrophages in vitro. In vivo, in cyclophosphamide-induced immunocompromised mice, SC2-3 at different concentrations elevated organ indices, blood cell counts, and serum levels of IL-1β, TNF-α, and IL-6, while repairing cyclophosphamide-damaged/atrophied tissues. Mechanistically, SC2-3 induced the differentiation of RAW264.7 cells toward an M1-like activation profile, significantly promoting the release of NO and ROS, upregulating the secretion of pro-inflammatory cytokines (IL-1β, TNF-α, and IL-6), and activating the TLR4/NF-κB signaling pathway. Additionally, SC2-3 upregulated intestinal epithelial tight junction proteins and normalized the overexpression of MUC-2, thereby maintaining intestinal barrier integrity. These findings indicated the potential efficacy of the glycopeptide SC2-3 derived from natural marine sources in immunomodulation and protection of intestinal health. Full article

Background: Lupus nephritis (LN) is a severe manifestation of systemic lupus erythematosus (SLE), characterised by unpredictable outcomes due to the absence of reliable biomarkers. This hypothesis-generating study aimed to evaluate whether changes in the N-glycosylation of IgG, C3, AGP, and the serum proteins over one year of treatment correlate with clinical and histological features of LN and predict renal outcomes. Methods: Serum samples from 19 treatment-naïve patients with LN were collected at baseline and 12 months post-treatment, in conjunction with per-protocol repeat kidney biopsy. IgG (Fc, Fab, and total), C3, AGP, and total serum glycoproteins were isolated and analysed as either released N-glycans or N-glycopeptides using high-throughput glycomic approaches. Clinical and histological data were obtained at both time points, along with assessments of clinical and histological response at 12 months and long-term renal function. Results: In total, we identified 24/243 increased N-glycosylation traits (2 total IgG, 5 IgG Fc, 7 IgG Fab, 5 serum glycoproteins, 4 AGP, and 1 C3) and 10/243 decreased N-glycosylation traits (7 total IgG, 2 IgG Fc, 1 IgG Fab) following treatment. Baseline AGP IORMIF1N5H6S2F1 showed a positive correlation with eGFR both at baseline (r = 0.64, p = 0.005) and at 12 months (r = 0.51, p = 0.032). Among AGP N-glycosylation traits, IVORMI1N7H8S3 (r = 0.66, p = 0.002; r = 0.48, p = 0.041, respectively), VORMI1N8H9S4 (r = 0.51, p = 0.029; r = 0.49, p = 0.038, respectively), and VORMI1N8H9S4F1 (r = 0.48, p = 0.039; r = 0.49, p = 0.034, respectively) significantly correlated with activity index (AI) at baseline and at 12 months. Presence of cellular crescents at baseline positively correlated with three AGP N-glycosylation traits: IORMISORMIIA1N4H5S2 (r = 0.49, p = 0.036), VORMII1N5H6S3F1 (r = 0.63, p = 0.006), and VORMII1N4H5S2 (r = 0.48, p = 0.046). Total serum N-glycan (structure) N5H4F1 at 12 months was associated with both clinical and histological response to treatment. Delta of total serum N-glycan structure N5H5S1 was independently associated with poor long-term outcome. Conclusions: This study suggests that glycosylation changes over one year of treatment are associated with specific clinical and histological features and both short- and long-term renal outcomes in LN. Given the small cohort size, results should be considered hypothesis-generating warranting further investigation in independent cohorts. Full article

Efficient and reproducible protein extraction is a critical prerequisite for high-quality proteomic and glycoproteomic analyses. In this study, four commonly used lysis buffers, sodium dodecyl sulfate (SDS), guanidine hydrochloride (GuHCl), urea (UA), and mammalian protein extraction reagent (MPER), were systematically evaluated within an integrated proteomic and N-glycoproteomic workflow. Using HeLa and HEK293T cells as model systems, we assessed buffer performance in terms of protein and intact N-glycopeptide identification depth, quantitative reproducibility, subcellular coverage, and glycan type distribution. Across both cell lines, SDS consistently achieved the deepest proteome and N-glycoproteome coverage, yielding the highest numbers of identified proteins, N-glycopeptides, glycoproteins, and glycosylation sites. Quantitative analysis demonstrated that SDS provided superior reproducibility, with approximately 85% of quantified proteins exhibiting coefficients of variation below 5%. Subcellular localization analysis at the global proteome level showed that SDS enabled more comprehensive extraction of proteins from multiple cellular compartments, including the nucleus, cytoplasm, mitochondria, and plasma membrane, indicating reduced extraction bias toward specific subcellular regions. Consistently, subcellular localization analysis of identified glycoproteins revealed enhanced coverage of membrane-associated compartments, particularly the plasma membrane, endoplasmic reticulum, Golgi apparatus, and lysosome. In addition, the analysis of glycan type classification for intact N-glycopeptides revealed that the SDS lysis buffer demonstrated the most comprehensive identification capability for glycopeptides with multiple glycosylation modifications in both cell lines. MPER and UA showed a highly consistent distribution across various glycosylation types, whereas the guanidine hydrochloride method was comparatively least effective. Overall, these results establish SDS as a robust lysis buffer for comprehensive, reproducible, and quantitatively stable proteomic and N-glycoproteomic analyses, providing practical guidance for buffer selection in quantitative glycosylation-focused studies. Full article

Background: Commercial broiler farms produce a large amount of litter that must be removed. Anaerobic digestion (AD) is animal manure management technology with the added benefit of producing reusable energy. Our team previously showed that the micro-aeration and sound treatment of animal manure during AD increase biogas production. However, their influence on antimicrobial resistance genes (ARGs) and bacterial virulence factor genes (VFGs) is unknown. Therefore, the objective of this study was to evaluate the effect of AD on the resistome and VFGs in poultry litter (PL) and see if the effect is modified by micro-aeration and/or sound treatments. Methods: A field experiment was conducted in four anaerobic digesters that consisted of a control (a standard AD system with no air or sound), micro-aeration, sound, and combined micro-aeration and sound treatments. Overall, 21 samples were collected and analyzed with shotgun metagenomic sequencing. The samples included digestate samples (n = 12) from the four digesters obtained at 6 (baseline, i.e., before beginning of micro-aeration and sound treatments), 23 and 42 weeks, raw PL samples (n = 4), two disks comprised of the same wood as the bedding material, an initial digestate seed sample, and two initial week 0 mix samples. Results: Across all sequence reads (n = 3190) obtained from 21 samples, over 80% of the resistome was composed of four antimicrobial classes: macrolides–lincosamides–streptogramins, tetracyclines, aminoglycosides, and glycopeptides. While the total number of ARGs declined in the control digestor, it increased over time in micro-aerated or sound-treated digesters, and their combination greatly increased the number of ARGs detected. This is a new finding, and it clearly shows that micro-aeration, sound, and their combination treatment during the anaerobic digestion of PL enriches ARGs. In contrast, sound-treated AD by itself significantly (p = 0.035) reduced the mean total ARG abundance compared to the control. The number and abundance of ARGs detected in the initial digestate and PL were lower than those in the AD samples, indicating their enrichment during the AD process. On the other hand, although the AD samples had a lower frequency and abundance of VFGs than the PL, AD did not completely remove the VFGs, and their detection frequency increased over time. While micro-aeration increased the abundance of VFGs compared to the control, this effect was countered by its combination with sound treatment, offering a good animal manure treatment strategy to reduce bacterial VFGs. Conclusions: Although additional research may be required, it was shown that while sound treatment may enrich the occurrence of ARGs, it seems promising to reduce the abundance of ARGs and VFGs during the AD of PL. On the other hand, micro-aeration, alone or when combined with sound treatment, increases the abundance of both ARGs and VFGs. Moreover, the study showed that AD, with or without micro-aeration and sound treatment, is not effective for the complete removal of ARGs and VFGs from poultry litter. Rather, AD systems may act as a hotspot for ARGs, and post-AD treatments such as composting need to be evaluated. Full article