Search Results (363)

Wastewater treatment plants (WWTPs) are identified as contributors to faecal pollution and the spread of antimicrobial resistance (AMR) in water ecosystems. This research examined the prevalence, profiles of antimicrobial resistance, and pathogenic types of Escherichia coli in effluent from WWTPs and nearby river systems in the Vhembe District. Between May and June 2025, 28 water samples were collected from two WWTP discharge points as well as upstream and downstream locations along the Mvudi, Luvuvhu, and Madadzhe Rivers. The enumeration of E. coli was conducted using Colilert Quanti-Tray method, with isolates obtained via membrane filtration and confirmed using API 20E and VITEK^®2 systems. Antimicrobial susceptibility was assessed using VITEK^®2, while pathotypes were detected through multiplex PCR. E. coli was found at all sampling locations; however, differences in concentrations across sampling sites and sampling periods were not statistically significant (p > 0.05). Out of 26 confirmed isolates, a significant resistance to β-lactam antibiotics was noted, especially ampicillin (100%). Pathotype analysis revealed strains such as ETEC, EAEC, and EPEC. These results underline extensive contamination by antimicrobial-resistant E. coli in rivers affected by WWTP discharge, which poses potential public health concerns and underscores the necessity for enhanced monitoring efforts. Additional research is needed to validate these findings. Full article

Background/Objectives: Globally, the management of infections has been complicated greatly by the rapid emergence of antibiotic resistance among bacterial pathogens, particularly Escherichia coli (E. coli). This bacterium is commonly found in a wide range of vertebrate hosts, including livestock, which can serve as important sources of specific pathogenic or multidrug-resistant strains. Cross-contamination can occur from farm to food, posing public health concerns. Methods: This cross-sectional study examined the antibiotic resistance and virulence gene profiles of E. coli isolated from farm animals, food processing facilities (including meat and contact surfaces), and the surrounding environment (wastewater). Results: Out of 383 samples, 230 samples (60.1%) were positive for E. coli (95% CI: 55.1–64.9). The prevalence rates showed significant variation across different sources, with positive rates of 72.3% (180/249) in animal sources, 33.7% (28/83) in food sources, and 43.1% (22/51) in environmental sources. Over 80% of the isolates across all sources carried the sheA virulence gene, which is associated with hemolytic activity in E. coli. Multidrug resistance (MDR) was commonly observed, with rates of 61.1% in animal samples, 57.1% in food sources, and 50.0% in environmental samples. The E. coli isolates exhibited high levels of antibiotic resistance, particularly to streptomycin (64.9%), ampicillin (58.0%), and tetracycline (57.6%). The most common resistance gene pattern was tetA-strA-bla_TEM (22.6%). Conclusions: These findings indicate widespread occurrence of antibiotic-resistant and virulence gene-carrying E. coli strains across the farm-to-food continuum, underscoring the urgent need for enhanced antimicrobial stewardship and surveillance programs to mitigate transmission from food-producing animals and reduce public health complications. Full article

Shigella spp., and Escherichia coli exhibit notable genomic and phenotypic similarities, including serologically and genetically related somatic antigens. For example, the relationship among pathogenic strains E. coli 64474, O179, O188, and S. boydii O16 suggests a shared clonal origin. To evaluate their genomic proximity, a comparative genomics study was conducted using whole-genome sequencing. Comparative genomics involved rfb gene cluster regions and whole-genome comparisons. Phylogenomic inferences were performed using the virtual genome fingerprint (VGF) method with bootstrap support. The results revealed a high degree of genomic similarity and a close evolutionary relationship among E. coli strains, which also demonstrated genetic associations with clinically relevant pathotypes through the presence of virulence genes. Furthermore, serogroups 64474, O188, and S. boydii O16 exhibited close genetic relationships, suggesting that serotype 64474 could represent a novel serogroup, although its similarity to O188 indicates the influence of divergent factors. These findings support the hypothesis that these E. coli strains originated from a common clonal lineage, enhancing our understanding of serogroup diversity and the evolutionary dynamics within enteric pathogens. Full article

Neonatal meningitis-associated Escherichia coli (NMEC) is a formidable pathogen in veterinary medicine. The emergence of atypical, multidrug-resistant (MDR) variants complicates disease control. An Escherichia coli (E. coli) strain was isolated from the brain tissue of a deceased calf with acute meningitis. Comprehensive characterizations were performed, including whole-genome sequencing (WGS), multi-locus sequence typing (MLST), antimicrobial susceptibility testing (AST), murine pathogenicity assays, and RT-qPCR evaluation of neuroinflammatory cytokines. Results: The isolate (O18ab:H14) was identified as a capsule-deficient NMEC strain belonging to phylogroup A and sequence type ST1434. WGS showed that the genome size of this strain is 5.1 Mb, containing 73 strictly defined antimicrobial resistance genes and 202 virulence factors. These may be involved in the compensatory mechanism for capsule deficiency, and further functional verification is required. Phenotypically, it exhibited a robust MDR profile. In the murine model, the strain demonstrated high lethality, and induced severe multi-organ lesions characteristic of both meningitis and systemic sepsis. While intraperitoneal injection bypasses natural colonization routes, the brain-specific bacterial persistence and neuronal pathology imply neurotropic potential. Furthermore, RT-qPCR confirmed a severe neuroinflammatory response, marked by the significant upregulation of IL-1β, IL-6, and TNF-α in the infected brains. This study characterizes a novel, highly virulent, and MDR capsule-deficient NMEC/SEPEC hybrid strain. The findings emphasize the urgent need for continuous genomic surveillance of atypical E. coli pathotypes in livestock. Full article

Alternaria brown spot, caused by the tangerine pathotype of Alternaria alternata, is a destructive fungal disease affecting citrus production worldwide. Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes constitute a major class of plant immune receptors; however, their genome-wide characteristics and potential association with Alternaria brown spot resistance loci in citrus remain poorly understood. In this study, we performed a comprehensive genome-wide identification and comparative analysis of NBS-LRR genes across representative citrus species. A total of 417 and 326 NBS-LRR genes were identified in Citrus reticulata and Citrus clementina, respectively, and were classified into NL, CNL, TNL, and RNL subfamilies based on domain architecture. Phylogenetic reconstruction, gene structure analysis, conserved motif composition, chromosomal distribution, synteny relationships, and promoter cis-element profiling collectively revealed considerable structural variation and lineage-specific expansion of the NBS-LRR gene family in citrus genomes. By integrating previously reported quantitative trait locus (QTL) data for Alternaria brown spot, we identified several NBS-LRR genes located within a resistance-associated genomic interval on chromosome 3. Among these, a candidate gene, designated LRR2, exhibited differential transcriptional responses upon pathogen inoculation and displayed distinct sequence variations between citrus genotypes. Structural modeling and molecular docking analyses suggested potential binding interfaces between LRR2 and multiple host-selective toxins, although the biological relevance of these interactions requires further experimental validation. Subcellular localization assays in Nicotiana benthamiana showed that LRR2 is distributed in both the nucleus and cytoplasm. Notably, transient overexpression of LRR2 triggered hypersensitive response-like cell death and H₂O₂ accumulation. Collectively, this study provides a comprehensive overview of the citrus NBS-LRR gene family and presents a multifaceted characterization of a QTL-anchored candidate gene. These findings establish a genomic and molecular framework for further functional investigations of citrus–Alternaria interactions. Full article

Salicylic acid (SA) is a key regulator of plant immunity and contributes to defence against Plasmodiophora brassicae, the causal agent of clubroot disease in canola (Brassica napus) and other crucifers. Exogenous SA applications have reduced clubroot severity in some Brassica pathosystems, yet the effectiveness of foliar SA treatment against the predominant resistance-breaking pathotype 3A in western Canada remains unclear. This study evaluated the effects of weekly foliar applications of 0, 1, 5, or 10 mM SA on clubroot development in two B. napus var. napobrassica cultivars under greenhouse and growth chamber conditions. Plants inoculated with pathotype 3A were assessed for disease severity, pathogen resting spore load, plant height, and transcript accumulation of SA-responsive genes. Overall, SA treatments resulted in modest reductions in disease severity and resting spore concentrations; however, treatment effects did not reach statistical significance in most cases. Collectively, foliar SA applications provided limited suppression of clubroot caused by pathotype 3A. Further optimization of SA concentration, timing, and delivery, particularly when targeting the root zone, may be required before SA can be considered a complementary tool in integrated clubroot management. Full article

Wildlife can serve as a potential reservoir and spreader of resistant and pathogenic bacteria. Raptors, occupying the ecological position of apex or mesopredators, integrate exposure across different habitats and therefore serve as bioindicators of environmental dissemination of pathogens. In this study, we isolated 54 Escherichia coli (E. coli) strains from feces sampled from 64 raptors admitted to a wildlife rescue center in Central Italy. Phenotypic antimicrobial susceptibility testing was conducted, followed by molecular screening for resistance genes. Additionally, the presence of intestinal E. coli pathotypes, including STEC, EHEC, EPEC, ETEC, EAEC, EIEC, and NTEC, was evaluated through virulence gene analysis. Results indicated notable resistance to commonly used antimicrobials, with the highest percentages observed for ampicillin (40.74%), fluoroquinolones (31.48%), and tetracycline (25.93%). Molecular analysis of phenotypically resistant isolates identified the presence of several resistance genes, including bla_TEM (13 isolates), bla_CTX-M (4 isolates), bla_CMY-2 (3 isolates), bla_SHV (1 isolate), tet(A) (9 isolates), tet(B) (4 isolates), cat1 (1 isolate), and cmlA (2 isolates). Furthermore, 29.63% of isolates were classified as multidrug-resistant (MDR) and 7.41% as extensively drug-resistant (XDR). Regarding virulence profiles, one isolate harboring eaeA, escV, and astA genes was classified as atypical EPEC, while 27.78% isolates had only the astA gene, preventing precise pathotype assignment. These findings highlight the circulation of antimicrobial-resistant and potentially pathogenic E. coli strains within raptor populations in Central Italy, emphasizing the zoonotic potential and reaffirming the role of raptors as bioindicators within a One Health approach. Full article

Wheat blast, caused by Magnaporthe oryzae pathotype Triticum (MoT), is an emerging fungal disease that poses a serious threat to global wheat production. In Zambia, where wheat is increasingly becoming a vital component for food and nutritional security, the emergence and spread of wheat blast is a growing concern under the influence of climate and agricultural practices changes. This review assesses the risk of wheat blast expansion in Zambia by examining regional climatic trends, future climate projections, crop suitability, and the ecological requirements of MoT. Potential disease hotspots are identified, and integrated management strategies, including chemical, cultural, and biotechnological approaches are evaluated. The review highlights the urgent need for coordinated disease surveillance, the development and deployment of resistant cultivars, and climate-resilient farming practices. By consolidating current knowledge and outlining sustainable management strategies, this paper aims to support effective disease mitigation and safeguard wheat production in Zambia in the face of climate change. Full article

Here, we adopt an historical approach towards reviewing research since the 1970s on the seed-borne virus diseases of cool-season pulses caused by pea seed-borne mosaic virus (PSbMV) in Australia’s grain cropping regions. All relevant investigations concerning the principal cool-season pulse crops infected; field pea, lentil, faba bean, chickpea, and the minor ones, Lathyrus species, vetches and narbon bean, are covered. However, as the PSbMV field pea pathosystem is the most studied, this receives greatest emphasis. The review starts with brief background information, and by describing the disease symptoms caused and the advances in sample testing procedures. Next, findings from past PSbMV studies are covered in greater detail including transmission by aphids, contact and seeds; occurrence in crops and seed stocks; pathotypes and genetic diversity; host resistance; and phytosanitary, cultural and chemical control measures. What these studies found about PSbMV biology, epidemiology and control is emphasized by describing past glasshouse and field experimentation. Then, practical research outcomes identifying PSbMV’s epidemic drivers, forecasting its epidemics and devising an integrated disease management strategy are emphasized. Examples of images that illustrate past investigations and research outputs are provided. Finally, principal research achievements and priorities for future Australian PSbMV cool-season pulse research are highlighted. Full article

Barnyard grass, a widespread and persistent weed in rice paddies, belongs to the same family as rice and may act as a bridge host for the rice blast fungus. This study utilized comparative genomics to analyze six Pyricularia oryzae strains isolated from barnyard grass (Baicao series) and rice (GDYJ7 and ZJX18), integrating pathogenicity assays, whole-genome sequencing, and functional annotation. Pathogenicity tests demonstrated host specificity, as Baicao series strains caused typical lesion symptoms on barnyard grass but not on rice leaves, while GDYJ7 and ZJX18 caused lesions mainly on rice. Genomic analyses indicated that Baicao series strains possessed larger genomes (41.04 Mb to 41.16 Mb) with a higher content of repetitive sequences (6.68% to 7.09%) compared to rice strains GDYJ7 and ZJX18 (38.69 Mb and 39.05 Mb; 3.66% and 3.71% repeats). Phylogenetic analysis confirmed that Baicao series strains represent a grass-infecting pathotype of P. oryzae species, as they were grouped with the established grass-isolated P. oryzae strains, while GDYJ7 and ZJX18 were grouped with rice-isolated P. oryzae strains. However, Baicao series, GDYJ7 and ZJX18 are all relatively distant from P. grisea species. PCR amplification revealed that Baicao series strains harbored significantly fewer avirulence genes (Avr-Pib, Avr-Pizt, PWL3) than GDYJ7 and ZJX18 (Avr-Pib, Avr-Pizt, Avr-Pi9, Avr-Pik, PWL2), with Baicao9 retaining only Avr-Pib. In summary, our results suggested that the genomic sequences of the barnyard grass-isolated strains serve as a valuable resource for the study of P. oryzae strains with differential host preference and provide novel insights into the evolution of pathogen genomes during host adaptation. Full article

Background/Objectives: In food-producing animal (FPA) environments, healthy animals can act as reservoirs of potentially pathogenic Escherichia coli, which can be transmitted through the food chain to humans. This study aimed to evaluate cloacal E. coli in healthy Sicilian lambs subjected to an experimental feeding regimen by assessing bacterial levels, antimicrobial resistance, virulence traits, and the clonal relationships, as well as the impact of a pistachio skin as an agro-industrial by-product supplement during a 58-day feeding trial. Methods: A total of 295 E. coli isolates from the control (CTRL) and treatment (Treated) groups at initial time (T0) and final time (T1) were phenotypically and genotypically characterized using Kirby–Bauer antimicrobial testing, multiplex PCR for virulence genes, and PFGE for clonal analysis. Results: The feeding regimen did not significantly influence the prevalence, abundance, or virulence of the E. coli isolates. Shiga toxin-producing E. coli (STEC) were the most common pathotype, mainly carrying the stx1 gene, while the Enteroinvasive (EIEC) type was detected only sporadically. Enteropathogenic E. coli (EPEC) predominated at T0, while enteroaggregative E. coli (EAEC) at T1, and enterotoxigenic E. coli (ETEC), initially prevalent in Treated samples, disappeared by T1. Antimicrobial resistance profiles varied among isolates, with the highest resistance observed in the CTRL group. However, both groups exhibited high resistance to streptomycin, and 9% of CTRL isolates were multidrug resistant. A notable reduction in overall resistance rates, especially in the Treated group, was observed, indicating a dietary effect on the E. coli resistome. PFGE genotyping showed high genetic diversity, with resistance traits more frequently detected than virulence factors. Conclusions: This study highlights that healthy lambs serve as reservoirs for potentially human-pathogenic E. coli and suggests that dietary regimes could effectively reduce antibiotic resistance. Full article

The emergence of colistin-resistant Escherichia coli (E. coli) in livestock poses a major public health concern due to its zoonotic potential and multidrug resistance (MDR). The study aimed to detect mobilized colistin resistance genes (mcr-1 to mcr-9) in E. coli isolates, along with characterizing their antimicrobial susceptibility, resistance genes, virulence genes, and whole genome sequencing. We investigated E. coli contamination in a swine slaughterhouse in Nakhon Si Thammarat Province, Thailand. A total of 200 fecal samples were collected and screened for E. coli using selective media supplemented with colistin. A total of 200 fecal samples were collected from a swine slaughterhouse and screened for E. coli using selective media supplemented with colistin. Presumptive E. coli isolates were confirmed by PCR, followed by molecular detection of mcr-1 to mcr-9 genes. Antimicrobial susceptibility testing was performed using the disk diffusion method. Selected isolates were further analyzed for additional antimicrobial resistance genes and virulence associated genes by PCR. Whole genome sequencing was conducted on representative isolates exhibiting high levels of antimicrobial resistance. Our results showed that out of 200 fecal samples, 124 presumptive E. coli isolates were recovered from a swine slaughterhouse using selective media containing colistin. PCR confirmation identified 112 isolates (90.32%) as E. coli. Molecular detection of mobilized colistin resistance (mcr) genes (82 isolates, 73.21%) demonstrated that mcr-1 (50.89%) was the most prevalent, followed by mcr-9 (25.89%) and mcr-3 (24.11%). Overall, the 82 mcr E. coli isolates showed the highest level of resistance to ampicillin (97.56%), followed by tetracycline (95.12%), piperacillin (73.17%), and chloramphenicol (65.85%). For non-mcr E. coli isolates, the highest resistance percentage was observed for ampicillin (96.67%), followed by piperacillin (80%) and tetracycline (73.33%). Among the isolates, 75% exhibited MDR phenotypes, showing 22 distinct resistance profiles. The most common MDR pattern was AMP-PIP-TE-C-S (12.5%). Additional antimicrobial resistance genes, including aadA, ampC, and bla_TEM, were detected in over 60% of a subset of 30 tested isolates. The virulence gene analysis revealed that eae (74.10%), associated with enteropathogenic E. coli (EPEC), was the predominant pathotype. Whole genome sequencing of five selected isolates confirmed the presence of multiple antimicrobial resistance and virulence determinants. In conclusion, this study reveals a high prevalence of MDR E. coli harboring colistin resistance genes (mcr-1 to mcr-9) in a swine slaughterhouse in southern Thailand. The findings highlight the potential risk of zoonotic transmission of antimicrobial resistant E. coli through the food production chain and emphasize the importance of continuous genomic surveillance and prudent antimicrobial use in livestock production systems. Full article

Background/Objectives: Bacterial outer membrane vesicles (OMVs) play a role in bacterial communication, virulence, antimicrobial resistance, and host–pathogen interaction. OMV isolation is a key step for studying these particles’ functions; nevertheless, isolation procedures can greatly influence the yield, purity, and structural integrity of OMVs, thereby affecting downstream biological analyses and functional interpretation. Methods: In this study, we compared the efficacy of two OMV isolation techniques, differential ultracentrifugation (dUC) and size-exclusion chromatography (SEC), in separating and concentrating vesicles produced by two Escherichia coli strains belonging to uropathogenic (UPEC) and Shiga toxin-producing (STEC) pathotypes. The isolated OMVs were characterized using a multi-analytical approach including transmission and scanning electron microscopy (TEM, SEM), nanoparticle tracking analysis (NTA), dynamic light scattering (DLS), ζ-potential measurement, and protein quantification to assess the purity of the preparations. Results: Samples obtained by dUC exhibited higher total protein content, broader particle size distributions, and more pronounced contamination by non-vesicular material. In contrast, SEC yielded morphologically homogeneous and structurally well-preserved vesicles, higher particle-to-protein ratios, and lower total protein content, reflecting reduced co-isolation of protein aggregates. NTA and DLS analyses revealed polydisperse populations in samples obtained with both isolation methods, with DLS measurements highlighting the contribution of larger or transient aggregates. ζ-potential values were close to neutrality for all samples, consistent with limited electrostatic repulsion and with the aggregation tendencies observed in some preparations. Conclusions: This study describes features of OMV produced by two relevant E. coli strains considering two isolation strategies which exert method- and strain-dependent effects on vesicle properties, including size distribution and surface charge, and emphasizes the trade-offs between yield, purity, and vesicle integrity. Full article

Escherichia coli is an important human pathogen that is able to cause a variety of infections, which can result in diarrhoea, urinary tract infections, sepsis, and even meningitis, depending on the pathotype of the infecting strain. Like many Gram-negative bacteria, E. coli is becoming increasingly resistant to many frontline antibiotics, including third-generation cephalosporins and carbapenems, which are often considered the antibiotics of last resort for these infections. This is particularly the case in Egypt, where multidrug-resistant (MDR) E. coli is highly prevalent. However, in spite of this, few Egyptian MDR E. coli strains have been fully characterised by genome sequencing. Here, we present the genome sequences of ten highly MDR E. coli strains, which were isolated from children who presented with diarrhoea at the Outpatients Clinic of Assiut University Children’s Hospital in Assiut, Egypt. We report that they carry multiple antimicrobial resistance genes, which includes extended spectrum β-lactamase genes, as well as bla_NDM and bla_OXA carbapenemase genes, likely encoded on IncX3 and IncF plasmids. Many of these strains were also found to be high-risk extra-intestinal pathogenic E. coli (ExPEC) clones belonging to sequence types ST167, ST410, and ST617. Thus, their presence in the Egyptian paediatric population is particularly worrying, and this highlights the need for increased surveillance of high-priority pathogens in this part of the world. Full article

The biomarker landscape in rheumatoid arthritis (RA) is evolving from reliance on traditional markers toward integrated, multimodal strategies enabling precision medicine approaches. To critically evaluate emerging biomarkers across serological, cellular, genetic, imaging, and multi-omic domains, distinguishing those approaching clinical readiness from those requiring further development. In this study, a narrative review of the literature published between 2000 and 2024 relevant to clinical decision-making in RA was conducted. Among novel serological markers, 14-3-3η protein and anti-carbamylated protein antibodies show the strongest validation for seronegative disease and prognostic stratification. Calprotectin demonstrates utility for disease activity monitoring and de-escalation decisions. Multi-biomarker disease activity scores provide an objective assessment but lack outcome trial validation. Musculoskeletal ultrasound offers accessible imaging biomarker capability, while MRI bone marrow edema remains the strongest structural progression predictor. Synovial tissue pathotyping has demonstrated proof-of-concept for treatment stratification. Genetic, epigenetic, and metabolomic approaches remain investigational. Key clinical implications include using 14-3-3η and calprotectin to inform seronegative diagnosis and de-escalation decisions, integrating ultrasound for remission verification, and recognizing that emerging biomarkers for extra-articular complications, including cardiovascular risk and venous thromboembolism, represent important unmet needs. Full article