Search Results (2,648)

Background/Objectives: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is of great concern because of the difficulties encountered in the management of infections it may cause. This study aims to identify possible difficulties in the management of K. pneumoniae infections in the current context of antibiotic resistance, particularly regarding carbapenem resistance. Methods: This is a retrospective, cross-sectional study that analyses epidemiological, clinical and bacteriological features identified in all patients with CRKP infections/colonization admitted during 2024 in an infectious diseases hospital. Results: Carbapenemase-producing K. pneumoniae isolates were co-harboring NDM+OXA-48 in 55.2% of cases. NDM+OXA-48-producing K. pneumoniae (116 isolates, 55.2%) was correlated with high resistance to aztreonam (100%, p = 0.01), ceftazidime–avibactam (100%, p < 0.01), trimethoprim–sulfamethoxazole (99.1%, p < 0.01), gentamycin (94.8%, p < 0.01), amikacin (93.8%, p < 0.01), colistin (79.8%, p < 0.01). OXA-48-producing K. pneumoniae (29 isolates, 13.8%) was correlated with lower resistance to ceftazidime–avibactam (11.5%, p < 0.01), amikacin (48.1%, p < 0.01), colistin (51.7%, p = 0.01), and gentamycin (65.5%, p < 0.01). We found in vitro synergistic effects of ceftazidime/avibactam + aztreonam for 32/32 CRKP isolates and of colistin + tigecycline for 12/14 CRKP isolates. Higher recurrence of CRKP infections was recorded in patients with urinary tract conditions (RR = 11.58, 95%CI: 1.58–81.91) and upper urinary tract devices (RR = 3.53, 95% CI: 1.72–7.22). In this study, adequate antibiotic treatment, compared to excessive antibiotic treatment in CRKP infections, was associated with shorter treatment duration (p = 0.02) and shorter length of hospitalization (p = 0.04). Conclusions: In our study, CRKP is frequently coharboring NDM+OXA-48, having limited treatment options. Implementing new treatment strategies, testing antibiotic synergies for older antibiotics in order to identify alternative treatment options and avoiding unnecessary carbapenem consumption are essential for decreasing the burden of CRKP infections. Full article

Plant-parasitic nematodes (PPNs) rank among the most economically destructive soilborne pathogens worldwide, causing annual crop losses estimated at USD 125–175 billion. Traditional management of plant parasitic nematodes has depended significantly on synthetic nematicides; however, increasing regulatory constraints, environmental pollution, and the rise of resistant nematode populations have generated an urgent need for sustainable alternatives. Humic substances (HS), comprising humic acids, fulvic acids, and humins derived primarily from leonardite and lignite, represent biologically active components of soil organic matter. Their different functional groups, like carboxylic, phenolic, and carbonyl groups, have direct nematicidal and nematostatic effects by stopping eggs from hatching, slowing down juvenile development, and lowering infectivity. They also indirectly improve soil structure, nutrient bioavailability, and the composition of the rhizosphere microbiome. Plant growth-promoting rhizobacteria (PGPR), particularly Bacillus spp. and Pseudomonas spp., suppress PPN populations through antibiotic biosynthesis, cuticle-degrading hydrolytic enzymes, nematostatic volatile organic compounds, and elicitation of induced systemic resistance (ISR). This review methodically analyzes the individual and synergistic processes by which HS and PGPR inhibit PPNs and enhance plant growth. Humic compounds strongly promote PGPR rhizosphere colonization, augmenting microbial metabolic activity and bioinoculant stability, hence producing combinatorial suppressive effects unattainable by either input independently. The combined HS-PGPR approach is reliable and environmentally sustainable for comprehensive nematode control, requiring multidisciplinary research to achieve global sustainable agriculture. Full article

Verticillium wilt, caused by Verticillium dahliae, is a devastating disease that severely threatens cotton production worldwide. The long-term survival of the pathogen in soil and the limited availability of resistant cultivars make effective control strategies challenging. Although the fungal cross-kingdom RNA VdsR-1 has been reported to delay floral transition and prolong vegetative growth, the underlying plant regulatory mechanisms remain largely unclear. Here, we show that the transcription factor AtTOE1, a target of ath-miR172b-3p, displays altered expression in response to changes in ath-miR172b-3p levels during V. dahliae inoculation, coinciding with coordinated changes in plant immune-related and developmental responses. Increased AtTOE1 expression is correlated with enhanced disease resistance, reduced pathogen colonization, and delayed floral transition. Furthermore, our results indicate that the VdsR-1/AtSPL13A module is associated with modulation of AtTOE1 expression via ath-miR172b-3p, suggesting the involvement of a cross-kingdom RNA-related regulatory framework linking plant immunity and development. Notably, this regulatory relationship is also observed in cotton, indicating evolutionary conservation across plant species. Together, our findings highlight TOE1 as a potential integrator of defense and growth-related processes during pathogen challenge and provide insights that may inform strategies to improve resistance to V. dahliae in cotton and other crops. Full article

Inflammatory bowel disease (IBD) is a chronic inflammatory condition resulting from complex interactions between the immune system, genetic predisposition, and the gut microbiota. In this context, Escherichia coli (E. coli) plays a dual role in the human gut, ranging from harmless commensal strains to pathobionts capable of promoting intestinal inflammation. A growing body of evidence suggests that specific E. coli pathotypes, such as adherent-invasive E. coli (AIEC) and diffusely adherent E. coli (DAEC), contribute to the development and progression of IBD. This narrative review critically examines the microbiological, immunological, and clinical evidence supporting the role of E. coli in IBD, with particular emphasis on mechanisms of mucosal colonization, host–microbe interactions, and persistence within the inflamed intestinal environment. Furthermore, the lack of a standardized operational definition and the limited reproducibility of the AIEC phenotype are addressed, as well as uncertainty about the role played by E. coli as a primary initiator of the disease or as an opportunistic amplifier of intestinal inflammation, and the varying strength of evidence supporting associations with Crohn’s disease versus ulcerative colitis. Diagnostic implications, antimicrobial resistance, and therapeutic aspects are addressed as downstream and context-dependent consequences of E. coli–host interactions, with relevance for disease management and therapeutic response in patients with established IBD. By integrating data from experimental models, clinical studies, and translational research, the review identifies areas of consensus, ongoing controversy, and major knowledge gaps in IBD pathophysiology and clinical practice. Full article

Background/Objectives: Escherichia coli (E. coli) spans commensal, intestinal pathogenic, and extraintestinal pathogenic lineages distributed across human, animal, and environmental reservoirs, yet the extent to which virulence architectures are shared across these compartments remains incompletely understood. Using a One Health framework, we profiled putative virulence determinants in pooled multidrug-resistant (MDR) E. coli source groups representing human, animal, and environmental sectors. Methods: Virulence genes were predicted with VirulenceFinder, and presence–absence profiles were integrated to define functional composition, sector overlap, source-group distribution breadth, and pathotype-associated signatures. Predicted pathogenic potential was assessed with PathogenFinder and compared with pathogenic family richness. Results: Overall, 114 putative virulence genes were detected, with adhesion/colonization functions dominating the virulome (33/114), followed by toxin-associated genes (12/114). A conserved core of 50 virulence genes was shared across all three sectors, including determinants linked to serum resistance (iss, ompT, traT), adhesion (csgA, fimH), stress adaptation (terC), and iron acquisition (sitA, iutA, fyuA). ExPEC-associated determinants were most numerous in environmental source groups (n = 52), whereas diarrheagenic E. coli markers were most frequent in animal-associated groups (n = 42). LEE-associated effectors were infrequent and largely absent from human source groups. Despite ecological differences in virulence composition, pathogenicity scores remained consistently high across sectors (0.83–0.92) and showed no significant association with pathogenic family richness (Spearman’s ρ = 0.197, p = 0.392). Conclusions: Within the limits of pooled source-group analysis, these findings suggest that MDR E. coli across One Health compartments shares a broadly distributed, ExPEC-associated virulence repertoire overlaid with sector-specific pathotype signals, underscoring the value of integrated genomic surveillance while highlighting the need for isolate-resolved analysis. Full article

Recently, a strain of Streptococcus agalactiae serotype Ia sequence type 7 clonal complex 1 (SaIa ST7 CC1) has emerged in Latin American tilapia aquaculture as an international threat. This study evaluated outbreaks of acute streptococcosis occurring between 2021 and 2025 on commercial Nile tilapia (Oreochromis niloticus) farms in six Latin American countries, aiming to integrate molecular, clinical, pathological, and environmental data. In total, 360 moribund or recently dead fish at various production stages (larvae/fry, pre-grow-out, and grow-out) were examined, and 25 S. agalactiae isolates were serotyped and subjected to real-time PCR analysis, multilocus sequence typing (MLST), virulence and antimicrobial resistance gene profiling, and antimicrobial susceptibility testing. All isolates belonged to SaIa and shared the same ST7 CC1 MLST profile, forming a highly homogeneous cluster with reference SaIa ST7 CC1 strains previously isolated from tilapia farms in Asia. These results are consistent with the regional spread of a single clonal line. At the larval and fry stages, SaIa ST7 CC1 was associated with hyperacute septicemia, gastrointestinal hemorrhage, and frequent intestinal intussusception, whereas in pre-grow-out and grow-out fish, neurological signs were more prominent, followed by ocular signs, systemic hemorrhages, and coelomic lesions. Histopathological examination showed profuse colonization of the brain, spleen, liver, and intestine by Gram-positive cocci, accompanied by marked acute circulatory and inflammatory lesions and few chronic granulomatous responses, consistent with a rapidly progressing, highly aggressive infectious process. All outbreaks occurred during extended periods of warm water (>32 °C), with large day–night thermal gradients and reduced dissolved oxygen, suggesting that thermal stress may exacerbate disease expression in affected systems. All SaIa ST7 CC1 strains exhibited phenotypic susceptibility to florfenicol and amoxicillin, whereas 84% (21/25) and 100% (25/25) exhibited intermediate susceptibility to oxytetracycline and enrofloxacin, respectively. In total, 5 of the 21 isolates (23.8%) with intermediate susceptibility to oxytetracycline carried tetracycline resistance genes (tetM, tetO). These findings identify SaIa ST7 CC1 as a clinically significant emerging threat associated with thermally facilitated and geographically expanding streptococcosis in tilapia production in Latin America. Immediate priorities include screening imported broodstock using MLST or whole-genome sequencing (WGS), harmonized regional molecular surveillance, climate-adaptive farm management practices, prudent antimicrobial use, and serotype-matched vaccination and breeding strategies that improve both disease and heat resilience. Full article

Synthetic polymers are widely used in stone conservation, yet their long-term biological stability remains insufficiently evaluated. This study investigates the microbial susceptibility of three commonly used acrylic consolidants, Paraloid B-72, B-66, and B-44, applied to deteriorated limestone. Bacteria, fungi, and actinomycetes were isolated from a deteriorated limestone false door and screened for acid production. From each microbial group, only the strong acid-producing isolates were selected for further investigation, including evaluation of their ability to utilize the three Paraloid resins as sole carbon sources and their deterioration potential on limestone cubes before and after consolidation. Deterioration was assessed by weight loss, compressive strength testing, stereomicroscopy, scanning electron microscopy (SEM), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR). All selected strong acid-producing isolates demonstrated the ability to grow on the tested polymers, confirming their biodegradation potential. Mixed microbial cultures caused greater weight loss and compressive strength reduction than single isolates, attributed to synergistic metabolic interactions. Among the consolidants, Paraloid B-72 showed the highest susceptibility to microbial attack, while Paraloid B-66 exhibited comparatively greater resistance, attributed to the steric hindrance of its isobutyl side groups and higher surface hydrophobicity. FTIR and XRD analyses confirmed ester bond hydrolysis, progressive gypsum formation, and structural alteration of the limestone substrate. These findings demonstrate that acrylic consolidants commonly used in stone conservation are not biologically inert and may actively contribute to biodeterioration under microbial colonization, highlighting the need for developing bio-resistant conservation materials. Full article

The genus Bacillus is widely recognized for its metabolic versatility, enabling it to colonize extreme environments, including sites contaminated with metals. In this study, we report the genome of B. velezensis strain HM1, isolated from sulfur-rich mine tailings from silver mining activities in southwestern Mexico. Isolation was performed by heat treatment followed by selective cultivation in a medium enriched with mine tailings extract (metals and sulfates), resulting in a single dominant morphotype corresponding to strain HM1. Whole-genome sequencing was carried out using the Illumina NovaSeq platform (2 × 250 bp). The assembled genome of strain HM1 has a size of 4,044,128 bp, distributed across 20 contigs, with an N50 of 700,388 bp and an L50 of 3, and an average coverage of 66.8×. The GC content was 46.31%, with an estimated completeness of 99.81% and contamination of 0.01%. Genome analyses indicate that the assembly corresponds to a single chromosome, with no evidence of plasmid replicons. Genome annotation identified 3950 coding sequences (CDSs), 83 tRNAs, 11 rRNAs, 26 ncRNAs, and 4 sORFs. Phylogenomic analysis, together with genomic similarity metrics (ANI > 98.6%, AAI > 98.8%, dDDH > 87%), confirms its classification as Bacillus velezensis. Functionally, the genome encodes multiple genes involved in resistance to metals and metalloids (including ABC transporters, efflux pumps, and biotransformation enzymes), as well as a complete pathway for sulfate assimilation. Collectively, these genomic features reveal a broad repertoire of adaptive strategies employed by strain HM1 to thrive in metal-contaminated environments. Full article

To prevent the spread of antibiotic resistance, bacteriophages have gradually become the most promising alternative to antibiotics for treating bacterial infectious diseases. In this study, using E. coli DC1 as the host strain, we isolated a bacteriophage named Escherichia coli phage XJA18 from farm sewage. We conducted morphological identification, host range determination, biological characteristic analysis, genomic feature analysis, and evaluation of in vitro and in vivo antibacterial effects. Electron microscopy revealed that phage XJA18 belongs to the class Caudoviricetes, with an icosahedral head and a non-contractile long tail. Whole-genome sequencing revealed that the phage has dsDNA with a length of 50,572 bp, with a GC content of 45.33%. The genome does not contain any antibiotic resistance genes or virulence genes, indicating good safety. XJA18 showed lytic activity against 24% of clinically isolated E. coli strains. The optimal multiplicity of infection (MOI) was 0.001, with a latent period of 10 min, a burst period of 30 min, and a burst size of 2.22 × 10² PFU/cell. It remained stable at 4–50 °C and pH 4–12. In vitro antibacterial results revealed that XJA18 had the most pronounced initial bacterial growth suppression at MOI = 0.001 during the first 4 h. In vivo experiments demonstrated that both prophylactic and therapeutic administration of XJA18 could protect against E. coli infection, significantly reducing inflammatory cytokine levels and bacterial loads in the livers and spleens of mice (p < 0.001), significantly increasing body weight (p < 0.05), and reducing histopathological damage to the colon, liver, and lungs. In summary, phage XJA18 can effectively inhibit E. coli and is safe and stable. These characteristics indicate that phage XJA18 has great potential as a novel biological agent to replace antibiotics for treating bacterial infectious diarrhea in calves. Full article

Background: The in vivo efficacy and mechanisms of matrine (MT) in reversing β-lactam resistance in E. coli remain unclear. Methods: β-lactam-resistant E. coli strains were treated with MT both in vitro and in a murine intestinal colonization model. Phenotypic changes (MIC, morphology, growth, biofilm, β-lactamase) were evaluated, and transcriptomic profiles were analyzed. Results: MT at sub-inhibitory concentrations significantly and concentration-dependently reduced the MICs of β-lactam-resistant E. coli strains by 2- to 32-fold in vitro. This reduction was also confirmed in vivo, and its magnitude became more pronounced as the number of doses increased. MT treatment dispersed bacterial aggregates and dissipated extracellular matrix, but did not alter the morphology of individual bacteria. At concentrations above 1024 μg/mL, MT significantly inhibited bacterial growth; lower concentrations (≤512 μg/mL) had no effect. Notably, MT inhibited biofilm formation and β-lactamase production both in vitro and in vivo. Conclusions: MT restored the susceptibility of β-lactam-resistant E. coli to cefepime and cefquinome. This effect was associated with suppression of biofilm formation and β-lactamase production, which correlated with the downregulation of key genes (ycgR, pgaB, pgaD, bla_TEM and bla_CTX-M). Full article

Chronic wounds represent a major complication of underlying conditions such as diabetes mellitus, arterial ischemia, surgical wound and burns. This study aimed at the phenotypic and molecular characterization of antimicrobial resistance for a selection of bacterial isolates, originating from wounds harvested from patients hospitalized in the Vascular Surgery and Plastic Surgery wards. The microbiological diagnosis of wound infections was established according to the laboratory’s working protocol. PCR screening of antibiotic resistance genes was performed using a real-time PCR, while the microtiter plate assay was used to determine the biofilm-forming capacity. Testing of biofilm susceptibility to meropenem and amikacin was performed on Calgary biofilm device. Of the 88 bacterial isolates studied, 78.40% were Gram-negative bacilli (GNB)—Klebsiella pneumoniae (K.P), Pseudomonas aeruginosa (P.A), Proteus mirabilis (P.M), Acinetobacter baumannii (A.B), while the remaining 21.60% were Gram-positive cocci (GPC)—Staphylococcus aureus (S.A). All A.B isolates and 92.59% of K.P were carriers of β-lactamase- and carbapenemase-encoding genes, while 57.89% of S. aureus isolates were carriers of mecA (methicillin-resistant). Strong biofilm-forming isolates (B+++) were more frequent in P.A than in K.P (p = 0.002) and P.M (p = 0.02), with a frequency comparable to that of A.B strains (p = 0.212). When analyzing the biofilm reaction to meropenem, a significantly lower susceptibility was detected in the biofilm for K.P isolates, compared to the planktonic ones. Most GNB have been extensively multidrug-resistant, particularly K.P and A.B. Isolates from chronic wounds are major biofilm-formers. A strong and statistically significant association has been identified in the case of K.P and P.M between the presence of resistance genes and the biofilm-forming capacity. These findings highlight the need for a customized therapeutic approach for each chronic wound, considering the mechanisms underlying treatment resistance. These include bacterial virulence factors and the wound microenvironment colonized by the biofilm and the relative contribution of each to the overall resistance profile. Full article

Induced resistance primes host immunity for enhanced protection; however, how pathogens respond to this primed state remains poorly understood. Here, we investigated the molecular responses of the rice blast fungus Magnaporthe oryzae during infection of benzothiadiazole (BTH)-primed rice. Seed priming with BTH conferred long-lasting resistance against M. oryzae at the four-leaf stage. Time-course transcriptomic analyses (12–48 hpi) identified 699 differentially expressed genes (DEGs) in M. oryzae, revealing a distinct temporal transition during infection of BTH-primed rice. The fungal transcriptional response shifted from early growth and environmental sensing to enhanced protein turnover, metabolic repression, energy depletion, and genomic instability, indicating progressive impairment of fungal fitness by host immunity. From these DEGs, eight BTH-suppressed candidate virulence genes (MoBVG1–8) were selected for functional characterization. Gene overexpression analyses showed that two genes, MoBVG2 and MoBVG6, significantly increased pathogenicity on BTH-primed rice, while knockout analyses confirmed that both are required for full pathogenicity on non-primed control plants. MoBVG2 encodes a reactive oxygen species (ROS)-scavenging effector, and MoBVG6 encodes an environmental sensor, highlighting the importance of ROS detoxification and environmental perception for successful host colonization. Functional analyses further revealed that MoBVG2 contribute to vegetative growth, while MoBVG6 is required for proper appressorium development. Together, these findings suggest that BTH-induced resistance restricts blast disease by impairing fungal metabolic fitness and suppressing key virulence genes, providing novel insights into the pathogen-side molecular mechanisms underlying chemically induced resistance in plants. Full article

Shallow lakes in the Yangtze River Delta are characterized by fragile ecosystems, strong sediment–water interactions, and poor resistance to pollution shocks; they are prone to shift from macrophyte-dominated clear-water states to phytoplankton-dominated turbid states under intensive human disturbance. To improve the efficacy of aquatic ecological restoration, this study takes a typical shallow urban lake—Kuilei Lake in Kunshan—as the research object, and establishes a two-dimensional hydrodynamic and water quality model to simulate the temporal and spatial variations in flow fields, flow circulations, and water quality indicators (TP, NH₃-N, COD_Mn) throughout the year. The results are as follows: (1) The hydrodynamic regime of Kuilei Lake is dominated by wind-driven currents, with seasonal flow circulations regulating pollutant migration and the suitability for submerged macrophyte growth; (2) Intense circulations in summer (July–September) enhance sediment resuspension and endogenous nutrient release, which are unfavorable for submerged plant colonization; (3) April–June is the optimal window for ecological restoration, with a mean flow velocity of 2.0–2.5 cm/s, TP ≤ 0.06 mg/L, NH₃-N ≤ 0.20 mg/L, COD_Mn ≤ 3.0 mg/L, and water temperature of 15–25 °C, providing favorable thresholds for submerged macrophyte recovery. This study reveals the coupled hydrodynamic–water environmental thresholds for shallow lake restoration, and offers a scientific basis for flow field regulation and ecological reconstruction of shallow lakes in the Yangtze River Delta. Full article

Background: Fluoroquinolone prophylaxis during autologous stem cell transplantation (aSCT) reduces the risk of fever but raises the risk of bloodstream infection (BSI) with fluoroquinolone-resistant Enterobacterales (FRE). We performed a prospective cohort study to detect the presence and potential gain or loss of colonic FRE colonization using serial sampling before and after aSCT in a uniform population of patients with a diagnosis of multiple myeloma. Methods: Eligible subjects underwent aSCT after conditioning with dose-intense melphalan, 200 mg/m². Peri-anal swabs were obtained before aSCT, upon hospital discharge, and 12–16 weeks after transplantation. Samples were cultured in tryptic soy broth supplemented with either ciprofloxacin or ceftriaxone with subsequent plating onto selective chromogenic agar designed to facilitate recovery and differentiation of Enterobacterales. Results: FRE colonization on pre-transplant sampling was detected for 23 of 117 subjects (19.7%) and 29 of 98 (29.6%) subjects at hospital discharge after a course of fluoroquinolone (116/117 subjects) prophylaxis (p < 0.001) and 28 of 92 (30.4%) subjects at 12–16 weeks. Including all three sampling time points, 48 of 117 subjects (41.0%) tested positive for FRE colonization. In total, 58 of the 90 FRE isolates (64.4%) from 48 subjects expressed extended-spectrum beta-lactamase (ESBL). Three FRE-colonized subjects developed FRE BSI. Bloodstream isolates for two subjects were identical to the organisms identified on pre-transplant sampling. Conclusions: We hypothesize that fluoroquinolone prophylaxis of subjects with undetected low levels of FRE colonization allows the expansion of the FRE population, placing subjects at risk of BSI with fluoroquinolone-resistant (and ESBL-expressing) Enterobacterales. Pre-transplant testing for FRE colonization permits patient-specific design of prophylactic and empiric antibiotic regimens. Full article

Avibacterium paragallinarum (A. paragallinarum) is the primary causative agent of infectious coryza in chickens. Infection often leads to growth retardation in broilers and a 10% reduction in egg production, reaching over 40% in laying hens. The problem is particularly severe under intensive farming conditions, significantly jeopardizing global poultry health and farming profitability. From a ‘One Health’ perspective, this not only disrupts the stability of the food supply chain, but also increases antibiotic usage due to disease prevention and control needs, thereby aggravating antimicrobial resistance (AMR) and posing a global public health challenge. This review systematically summarizes advances in the pathogenesis of A. paragallinarum and the protective immunity induced by subunit vaccines. It focuses on the infection mechanisms of A. paragallinarum, emphasizing its colonization strategies in the infraorbital sinus and nasal epithelium of chickens, and analyzes the roles of key virulence factors such as hemagglutinin and capsule in adhesion, colonization, and immune evasion. We integrate the tissue-specific pathogenesis of A. paragallinarum with the role of respiratory commensal microbiota in facilitating infection, providing an in-depth analysis of the bacterium’s key immune evasion strategies, thus offering novel insights into host–pathogen-microbiome interactions. Concurrently, to the best of our knowledge, this review provides the first comprehensive overview of current developments in subunit vaccines and their immunoprotective properties, with special attention to limitations in eliciting mucosal immune responses. By delving into the pathogen-host interaction mechanisms, this review aims to inform the optimization of subunit vaccine design and immunization strategies. Ultimately, it seeks to establish a theoretical basis and practical framework for precise control of A. paragallinarum. Full article