Search Results (2,456)

Environmental DNA (eDNA) analysis has emerged as a transformative tool in environmental monitoring, enabling non-invasive detection of species and microbial communities across diverse ecosystems. This study systematically reviews the role of bioinformation technology in eDNA analysis, focusing on methodologies and applications across air, soil, groundwater, sediment, and aquatic environments. Advances in molecular biology, high-throughput sequencing, bioinformatics tools, and field-deployable detection systems have significantly improved eDNA detection sensitivity, allowing for early identification of invasive species, monitoring ecosystem health, and tracking pollutant degradation processes. Airborne eDNA monitoring has demonstrated potential for assessing microbial shifts due to air pollution and tracking pathogen transmission. In terrestrial environments, eDNA facilitates soil and groundwater pollution assessments and enhances understanding of biodegradation processes. In aquatic ecosystems, eDNA serves as a powerful tool for biodiversity assessment, invasive species monitoring, and wastewater-based epidemiology. Despite its growing applicability, challenges remain, including DNA degradation, contamination risks, and standardization of sampling protocols. Future research should focus on integrating eDNA data with remote sensing, machine learning, and ecological modeling to enhance predictive environmental monitoring frameworks. As technological advancements continue, eDNA-based approaches are poised to revolutionize environmental assessment, conservation strategies, and public health surveillance. Full article

Coastal ecosystems are increasingly threatened by climate change and anthropogenic pressures, which can disrupt microbial communities and favor the emergence of pathogenic organisms. In this study, we applied metagenomic analysis to characterize fungal communities in sediment samples from an urban mangrove subjected to environmental stress. The results revealed a fungal community with reduced richness—28% lower than expected for similar ecosystems—likely linked to physicochemical changes such as heavy metal accumulation, acidic pH, and eutrophication, all typical of urbanized coastal areas. Notably, we detected an increase in potentially pathogenic genera, including Candida, Aspergillus, and Pseudoascochyta, alongside a decrease in key saprotrophic genera such as Fusarium and Thelebolus, indicating a shift in ecological function. The fungal assemblage was dominated by the phyla Ascomycota and Basidiomycota, and despite adverse conditions, symbiotic mycorrhizal fungi remained present, suggesting partial resilience. A considerable fraction of unclassified fungal taxa also points to underexplored microbial diversity with potential ecological or health significance. Importantly, this study does not aim to compare pristine and contaminated environments, but rather to provide a sanitary alert by identifying the presence and potential proliferation of pathogenic fungi in a degraded mangrove system. These findings highlight the sensitivity of mangrove fungal communities to environmental disturbance and reinforce the value of metagenomic approaches for monitoring ecosystem health. Incorporating fungal metagenomic surveillance into environmental management strategies is essential to better understand biodiversity loss, ecological resilience, and potential public health risks in degraded coastal environments. Full article

Contaminated seeds pose a major risk in hydroponic systems, as a single contaminated seed can compromise the entire setup. Effective decontamination strategies are essential to control seed-borne pathogens. Pecan shells, a byproduct comprising nearly 50% of the nut’s weight, have demonstrated antimicrobial properties against key pathogens. This study evaluated pecan shell extract (PSE) as a treatment to inactivate Listeria monocytogenes, Escherichia coli O157:H7, and Pseudomonas spp. on lettuce seeds and its effect on germination. Lettuce seeds were inoculated with L. monocytogenes strains (101 M, V7, LCDC, and Scott A) and treated with PSE (1:10 w/v) either by coating in sodium alginate or priming for 6 h (4 °C or room temperature). Hydropriming was used as a control. Additional trials with E. coli and Pseudomonas spp. tested PSE at 1:10, 1:20, and 1:30 w/v ratios. Priming at refrigeration significantly reduced Listeria levels. E. coli priming treatments showed significant reductions at 1:20 and 1:30 w/v. For Pseudomonas, priming at 1:20 showed the highest reduction. PSE priming also enhanced germination (88.3%), outperforming other treatments. These findings suggest PSE is a sustainable and effective seed treatment to reduce microbial contamination and enhance seed germination in hydroponic systems. Full article

This investigation examines the influence of P. dabryanus density on the growth performance of P. nigromaculatus and the structural and functional dynamics of paddy soil microbial communities within a rice–frog–loach integrated aquaculture system. Field experiments were conducted with five density gradients of P. dabryanus (0.5, 1.0, 1.5, 2.0, and 2.5 × 10⁴ individuals/667 m²), designated as RFLS0.5, RFLS1.0, RFLS1.5, RFLS2.0, and RFLS2.5, respectively. Control treatments included rice monoculture (RM) and rice–frog co-culture (RFS). These findings demonstrated that as the density of loach increased, the weight gain ratio of P. nigromaculatus showed a unimodal pattern, reaching its peak in RFLS1. Metagenomic analysis on paddy soil revealed that the RFLS1 facilitated the enrichment of nitrogen-fixing bacteria (Proteobacteria), while concurrently suppressing proliferation of the potential pathogen Pseudomonas aeruginosa and microbial markers in metal-contaminated environments of Usitatibacter rugosus. Further, functional profiling indicated that RFLS1 group reached a peak activity in amino acid metabolism (14.52 ± 0.09%) and carbohydrate metabolism (14.44 ± 0.06%) and showed a higher proportion of glycosyltransferase (GT) abundance (41.93 ± 0.02%) than other groups. In summary, the optimal stocking density of P. dabryanus in rice–frog–loach integrated systems was determined to be 1.0 × 10⁴ individuals/667 m². This density not only promotes the growth of P. nigromaculatus but also improves the structure of paddy soil microbial communities. Full article

The demand for wild animal meat, popularly called “bushmeat”, serves as a driving force behind the emergence of infectious diseases, potentially transmitting a variety of pathogenic bacteria to humans through handling and consumption. This study investigated the microbial load and bacterial diversity in bushmeat sourced from a prominent bushmeat market in Kumasi, Ghana. Carcasses of 61 wild animals, including rodents (44), antelopes (14), and African civets (3), were sampled for microbiological analysis. These samples encompassed meat, intestines, and anal and oral swabs. The total aerobic bacteria plate count (TPC), Enterobacteriaceae count (EBC), and fungal counts were determined. Bacterial identification was conducted using MALDI-TOF biotyping. Fungal counts were the highest across all animal groups, with African civets having 11.8 ± 0.3 log₁₀ CFU/g and 11.9 ± 0.2 log₁₀ CFU/g in intestinal and meat samples, respectively. The highest total plate count (TPC) was observed in rodents, both in their intestines (10.9 ± 1.0 log₁₀ CFU/g) and meat (10.9 ± 1.9 log₁₀ CFU/g). In contrast, antelopes exhibited the lowest counts across all categories, particularly in EBC from intestinal samples (6.1 ± 1.5 log₁₀ CFU/g) and meat samples (5.6 ± 1.2 log₁₀ CFU/g). A comprehensive analysis yielded 524 bacterial isolates belonging to 20 genera, with Escherichia coli (18.1%) and Klebsiella spp. (15.5%) representing the most prevalent species. Notably, the detection of substantial microbial contamination in bushmeat underscores the imperative for a holistic One Health approach to enhance product quality and mitigate risks associated with its handling and consumption. Full article

Objectives: Burkholderia cepacia complex (Bcc), a Gram-negative organism, is a well-recognized cause of hospital outbreaks, often linked to a contaminated shared source, such as multidose medications. In this study, we report an outbreak of Bcc infections in a tertiary care hospital, associated with the intrinsic contamination of a prepared solution used in interventional radiology (IR) procedures. Additionally, we provide a detailed explanation of the interventions implemented to control and interrupt the outbreak. Methods: Records from the infection control committee from 1 January 2023 to 31 October 2024 were screened to identify cases with Bcc growth in cultured blood, urine, or respiratory samples. Clinical and laboratory data were collected in March 2025. Bacterial identification was performed using conventional methods and MALDI-TOF (Bruker Daltonics, Bremen, Germany). Controls were matched to cases by ward, date of initial growth, and duration of hospitalization. Demographic and clinical data of these patients were systematically collected and analyzed. Microbiological cultures were obtained from environmental objects of concern and certain medications. Results: A total of 82 Burkholderia species were identified. We enrolled 77 cases and 77 matched controls. The source of contamination was identified in ready-to-use intravenous medications (remifentanil and magnesium preparations) in the IR department. These preparations were compounded in advance by the team and were used repeatedly. Although the outbreak originated from contaminated IV medications used in IR, secondary transmission likely affected 28 non-IR patients via fomites, shared environments, and possible lapses in isolation precautions. The mortality rate among the cases was 16.9%. Infection with Bcc was associated with prolonged intensive care unit stays (p = 0.018) and an extended overall hospitalization duration (p < 0.001); however, it was not associated with increased mortality. The enforcement of contact precautions and comprehensive environmental decontamination successfully reduced the incidence of the Bcc outbreak. No pathogens were detected in cultures obtained after the disinfection. Conclusions: The hospital transmission of Bcc is likely driven by cross-contamination, invasive medical procedures, and the administration of contaminated medications. Implementing stringent infection control measures such as staff retraining, updated policies on medication use, enhanced environmental decontamination, and strict adherence to isolation precautions has proven effective in curbing the spread of virulent and transmissible Bcc. Full article

Biosecurity measures applied on poultry farms, with a recent history of highly pathogenic avian influenza virus infection, were monitored using 24 h/7 days-per-week video monitoring. Definition of biosecurity breaches were based on internationally acknowledged norms. Farms of four different production types (two broiler, two layer, two breeder broiler, and one duck farm) were selected. Observations of entry to and exit from the anteroom revealed a high degree of biosecurity breaches in six poultry farms and good biosecurity practices in one farm in strictly maintaining the separation between clean and potentially contaminated areas in the anteroom. Hand washing with soap and water and/or using disinfectant lotion was rarely observed at entry to the anteroom and was almost absent at exit. Egg transporters did not disinfect fork-lift wheels when entering the egg-storage room nor change or properly disinfect footwear. The egg-storage room was not cleaned and disinfected after egg transport by the farmer. Similarly, footwear and trolley wheels were not disinfected when introducing young broilers or ducklings to the poultry unit. Biosecurity breaches were observed when introducing bedding material in the duck farm. This study shows a need for an engaging awareness and training campaign for poultry farmers and their co-workers as well as for transporters to promote good biosecurity practices. Full article

Background: Polymerase chain reaction (PCR) is highly sensitive and specific for the rapid diagnosis of invasive fungal disease (IFD) but is not yet widely implemented due to concerns regarding limited standardisation between assays, the lack of commercial options and the absence of clear guidance on interpreting results. Objectives and Methods: This review provides an update on technical and clinical aspects of PCR for the diagnosis of the most pertinent fungal pathogens, including Aspergillus, Candida, Pneumocystis jirovecii, Mucorales spp., and endemic mycoses. Summary: Recent meta-analyses have demonstrated that quantitative PCR (qPCR) offers high sensitivity for diagnosing IFD, surpassing conventional microscopy, culture and most serological tests. The reported specificity of qPCR is likely underestimated due to comparison with imperfect reference standards with variable sensitivity. Although the very low limit of detection of qPCR can generate false positive results due to procedural contamination or patient colonisation (particularly in pulmonary specimens), the rates are comparable to those observed for biomarker testing. When interpreting qPCR results, it is essential to consider the pre-test probability, determined by the patient population, host factors, clinical presentation and risk factors. For patients with low to moderate pre-test probability, the use of sensitive molecular tests, often in conjunction with serological testing or biomarkers, can effectively exclude IFD when all tests return negative results, reducing the need for empirical antifungal therapy. Conversely, for patients with high pre-test probability and clinical features of IFD, qPCR testing on invasive specimens from the site of infection (such as tissue or bronchoalveolar lavage fluid) can confidently rule in the disease. The development of next-generation sequencing methods to detect fungal infection has the potential to enhance the diagnosis of IFD, but standardisation and optimisation are essential, with improved accessibility underpinning clinical utility. Full article

Yeasts possess a range of environmental adaptations that allow them to colonize soil and sand. They can circulate seasonally between different components of lake ecosystems, including beach sand, water, and the coastal phyllosphere. The accumulation of people on beaches promotes the development and transmission of yeasts, posing an increasing sanitary and epidemiological risk. The aim of this study was to determine the species and quantitative composition of potentially pathogenic and pathogenic yeasts for humans present in the sand of supervised and unsupervised beaches along the shores of lakes in the city of Olsztyn (northeastern Poland). The study material consisted of sand samples collected during two summer seasons (2019; 2020) from 12 research sites on sandy beaches of four lakes located within the administrative boundaries of Olsztyn. Standard isolation and identification methods used in diagnostic mycological laboratories were applied and are described in detail in the following sections of this study. A total of 259 yeast isolates (264, counting species in two-species isolates separately) belonging to 62 species representing 47 genera were obtained during the study. Among all the isolates, five were identified as mixed (two species from a single colony). Eight isolated species were classified into biosafety level 2 (BSL-2) and risk group 2 (RG-2). The highest average number of viable yeast cells was found in sand samples collected in July 2019 (5.56 × 10² CFU/g), August, and September 2020 (1.03 × 10³ CFU/g and 1.94 × 10³ CFU/g, respectively). The lowest concentrations were in samples collected in April, September, and October 2019, and October 2020 (1.48 × 10² CFU/g, 1.47 × 10² CFU/g, 1.40 × 10² CFU/g, and 1.40 × 10² CFU/g, respectively). The results indicate sand contamination with yeasts that may pose etiological factors for human mycoses. In light of these findings, continuous sanitary-epidemiological monitoring of beach sand and further studies on its mycological cleanliness are warranted, along with actions leading to appropriate legal regulations. Full article

Foodborne pathogenic bacteria critically threaten public health and food industry sustainability, serving as a predominant trigger of food contamination incidents. To mitigate these risks, the development of rapid, sensitive, and highly specific detection technologies is essential for early warning and effective control of foodborne diseases. In recent years, biosensors have gained prominence as a cutting-edge tool for detecting foodborne pathogens, owing to their operational simplicity, rapid response, high sensitivity, and suitability for on-site applications. This review provides a comprehensive evaluation of critical biorecognition elements, such as antibodies, aptamers, nucleic acids, enzymes, cell receptors, molecularly imprinted polymers (MIPs), and bacteriophages. We highlight their design strategies, recent advancements, and pivotal contributions to improving detection specificity and sensitivity. Additionally, we systematically examine mainstream biosensor-based detection technologies, with a focus on three dominant types: electrochemical biosensors, optical biosensors, and piezoelectric biosensors. For each category, we analyze its fundamental principles, structural features, and practical applications in food safety monitoring. Finally, this review identifies future research priorities, including multiplex target detection, enhanced processing of complex samples, commercialization, and scalable deployment of biosensors. These advancements are expected to bridge the gap between laboratory research and real-world food safety surveillance, fostering more robust and practical solutions. Full article

Beach Sand Mycobiome is currently among the most important health challenges for viticulture in the world. Remarkably, the study of fungal communities in coastal beach sand and recreational waters remains underexplored despite their potential implications for human health. This research aimed to assess the prevalence of fungal species and the antifungal susceptibility profiles of fungi recovered from the beaches of the Persian Gulf and the Sea of Oman. Sand and seawater samples from 39 stations distributed within 13 beaches along the coastline were collected between May and July 2023. The grown isolates were identified at the species level based on morphological characteristics and DNA sequencing. Antifungal susceptibility testing was performed according to the Clinical Laboratory Standards Institute guidelines. Of 222 recovered isolates, 206 (92.8%) filamentous fungi and 16 (7.2%) yeast strains were identified. Sand-recovered fungi comprised 82.9%, while water-originated fungi accounted for 17.1%. The DNA sequencing technique categorized 191 isolates into 13 genera and 26 species. The most recovered genus was Aspergillus (68.9%), and Aspergillus terreus sensu stricto was the commonly identified species (26.14%). Voriconazole was the most effective antifungal drug against Aspergillus species. Research on fungal contamination levels at these locations could provide a foundation for establishing regulatory frameworks to diminish fungal risks, thereby enhancing public health protection. The ecological significance of fungal communities in sandy beaches to human infections remains to be explored, and earlier reports in the literature may motivate researchers to focus on detecting this mycobiome in natural environments where further investigation is warranted. Ultimately, our discovery serves as a reminder that much remains to be learned about pathogenic fungi and underscores the need for vigilance in areas where emerging pathogens have not yet been identified. Full article

Mycotoxins represent a group of highly toxic secondary metabolites produced by diverse fungal pathogens. Mycotoxin contaminations frequently occur in foods and feed and pose significant risks to human and animal health due to their carcinogenic, mutagenic, and immunosuppressive properties. Notably, deoxynivalenol, zearalenone, fumonisins (mainly including fumonisins B1, B2, and FB3), aflatoxin B1 (AFB1), and T-2/HT-2 toxins are the major mycotoxin contaminants in foods and feed. Undoubtedly, exposure to these mycotoxins can disrupt gut health, particularly damaging the intestinal epithelium in humans and animals. In this review, we summarized the detrimental effects caused by these mycotoxins on the intestinal health of humans and animals. The fundamental molecular mechanisms, which cover the induction of inflammatory reaction and immune dysfunction, the breakdown of the intestinal barrier, the triggering of oxidative stress, and the intestinal microbiota imbalance, were explored. These signaling pathways, such as MAPK, Akt/mTOR, TNF, TGF-β, Wnt/β-catenin, PKA, NF-kB, NLRP3, AHR, TLR2, TLR4, IRE1/XBP1, Nrf2, and MLCK pathways, are implicated. The abnormal expression of micro-RNA also plays a critical role. Finally, we anticipate that this review can offer new perspectives and theoretical foundations for controlling intestinal health issues caused by mycotoxin contamination and promote the development of prevention and control products. Full article

Water buffalo (Bubalus bubalis) are a primary source of milk in Pakistan, where bovine mastitis is a significant health issue among cattle, leading to substantial economic losses. Staphylococcus aureus is a predominant pathogen associated with mastitis; however, a detailed molecular characterization of the strains in the country remains limited. We previously characterized mastitis strains from the Hazara division of Khyber Pakhtunkhwa, Pakistan. In this study, we investigated mastitis cases in the Peshawar division, including samples from both animals and human farm workers for comparison. Higher rates of mastitis (67.27% of animals) and sub-clinical mastitis (91.03% of positive animals) were identified in Peshawar than for those (34.55% and 75.31%, respectively) previously observed in Hazara. Methicillin-susceptible S. aureus (MSSA) belonging to clonal complex 9 (ST2454) were predominant. Methicillin-resistant S. aureus (MRSA) belonging to ST22 and ST8 were also detected in the Nowshera district. While no S. aureus colonization was observed among animal handlers, evidence of hand contamination suggests a potential route for pathogen spread. Low levels of antibiotic resistance were noted amongst isolates, but higher rates were seen in MRSA. This study presents only the second comprehensive molecular investigation of S. aureus isolated from buffalo mastitis in Pakistan and indicates a concerning rise in mastitis within the province. Full article

Foodborne diseases are the most common causes of illness worldwide. Bacterial pathogens, including Staphylococcus aureus, are often involved in foodborne disease and pose a serious threat to human health. S. aureus is commonly found in humans and a variety of animal species. Staphylococcal enteric disease, specifically staphylococcal food poisoning (SFP), accounts for numerous gastrointestinal illnesses, through the contamination of food with its enterotoxins, and its major impact on human health imposes a heavy economic burden in society. Commonly, antibiotics and antimicrobials are used to treat SFP. However, a range of complications may arise with these treatments, impeding the control of S. aureus diseases specifically caused by methicillin-resistant S. aureus (MRSA). Natural alternative options to control S. aureus diseases, such as bacteriophages, plant-based antimicrobials, nanoparticle-based or light-based therapeutics, and probiotics, are promising in terms of overcoming these existing problems as they are environmentally friendly, abundant, unlikely to induce resistance in pathogens, cost-effective, and safe for human health. Recent findings have indicated that these alternatives may reduce the colonization and infection of major foodborne pathogens, including MRSA, which is crucial to overcome the spread of antibiotic resistance in S. aureus. This review focuses on the present scenario of S. aureus in foodborne disease, its economic importance and current interventions and, most importantly, the implications of natural antimicrobials, especially probiotics and synbiotics, as alternative antimicrobial means to combat pathogenic microorganisms particularly, S. aureus and MRSA. Full article

The demand for unpasteurized fruit juices has grown due to their natural nutritional benefits, but this also increases the risk of foodborne illnesses. This study evaluated the transfer of three pathogens (Salmonella enterica, Escherichia coli O157:H7, and Listeria monocytogenes) from different surfaces (cutting boards, knives, and gloves) to produce and subsequently across different juice batches. Cutting boards and gloves showed the highest pathogen transfer rates (ranging from 2.03 ± 4.36 to 70.69 ± 23.58% for cutting boards, and from 0.04 ± 0.05 to 70.61 ± 23.51% for gloves), while knives exhibited the lowest (from 1.27 ± 1.35 to 7.87 ± 5.33%), when surface-to-produce transference was evaluated. Among the tested produce, beetroot had the highest pathogen transfer for all the tested pathogens (for the cutting board, from 48.55 ± 21.66 to 70.69 ± 23.58%, for the knife from 7.17 ± 6.17 to 7.87 ± 5.33%, and for the gloves from 48.85 ± 21.66 to 70.61 ± 23.51%). Beetroot juice provided the most favorable conditions for bacterial transfer (δ = 0.53–0.56; k_max1 = 3.09–3.20), whereas strawberry juice led to the fastest microbial decrease (δ = 1.10–1.26; k_max1 = 2.08–2.28) throughout processed juices. Apple juice demonstrated intermediate bacterial decline rates (δ = 0.75–1.10; k_max1 = 2.20–2.61). These findings highlight the need for improved hygiene practices and contamination control in juice processing to minimize food safety risks associated with unpasteurized fruit or vegetable juices. Full article