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Geminiviridae are ssDNA plant viruses whose control has both economical and agricultural importance. Their capsids assemble into two distinct architectural forms: (i) a T = 1 icosahedral and (ii) a unique twinned quasi-isometric capsid. Described here are the high-resolution structures of both forms of the maize streak virus using cryo-EM. A comparison of these two forms provides details of the coat protein (CP) and CP–CP and CP–genome interactions that govern the assembly of the architecture of the capsids. Comparative analysis of other representative members of Geminiviridae reveals structural conservation of 60–95% compared to a sequence similarity of 21–30%. This study provides a structural atlas of these plant pathogens and suggests possible antiviral-targetable regions of these capsids. [ABSTRACT FROM AUTHOR]

Nile tilapia (Oreochromis niloticus) and European sea bass (Dicentrarchus labrax) are economically significant species in Mediterranean countries, serving essential roles in the aquaculture industry due to high market demand and nutritional value. They experience substantial losses from bacterial pathogens Vibrio anguillarum and Streptococcus iniae, particularly at the onset of the summer season. The immune mechanisms involved in fish infections by V. anguillarum and S. iniae remain poorly understood. This study investigated their impact through experiments with control and V. anguillarum- and S. iniae-infected groups for each species. Blood samples were collected at 1, 3, and 7 days post bacterial injection to assess biochemical and immunological parameters, including enzyme activities (AST and ALT), oxidative markers (SOD, GPX, CAT, and MDA), and leukocyte counts. Further analyses included phagocyte activity, lysozyme activity, IgM levels, and complement C3 and C4 levels. Muscle tissues were sampled at 1, 3, and 7 days post injection to assess mRNA expression levels of 18 immune-relevant genes. The focus was on cytokines and immune-related genes, including pro-inflammatory cytokines (TNF-α, TNF-β, IL-2, IL-6, IL-8, IL-12, and IFN-γ), major histocompatibility complex components (MHC-IIα and MHC-IIβ), cytokine receptors (CXCL-10 and CD4-L2), antimicrobial peptides (Pleurocidin and β-defensin), immune regulatory peptides (Thymosin β12, Leap 2, and Lysozyme g), and Galectins (Galectin-8 and Galectin-9). β-actin was used as the housekeeping gene for normalization. Significant species-specific responses were observed in N. Tilapia and E. Sea Bass when infected with V. anguillarum and S. iniae, highlighting differences in biochemical, immune, and gene expression profiles. Notably, in N. Tilapia, AST levels significantly increased by day 7 during S. iniae infection, reaching 45.00 ± 3.00 (p < 0.05), indicating late-stage acute stress or tissue damage. Conversely, E. Sea Bass exhibited a significant rise in ALT levels by day 7 in the S. iniae group, peaking at 33.5 ± 3.20 (p < 0.05), suggesting liver distress or a systemic inflammatory response. On the immunological front, N. Tilapia showed significant increases in respiratory burst activity on day 1 for both pathogens, with values of 0.28 ± 0.03 for V. anguillarum and 0.25 ± 0.02 for S. iniae (p < 0.05), indicating robust initial immune activation. Finally, the gene expression analysis revealed a pronounced peak of TNF-α in E. Sea Bass by day 7 post V. anguillarum infection with a fold change of 6.120, suggesting a strong species-specific pro-inflammatory response strategy. Understanding these responses provides critical insights for enhancing disease management and productivity in aquaculture operations. [ABSTRACT FROM AUTHOR]

Simple Summary: This study investigated the gut microbiota of captive Chinese monals across different seasons and age groups. The results revealed significant seasonal fluctuations and age-related factors that shape its composition. Specific biomarkers, including PaeniGlutamicibacter, Pseudarthrobacter, Micrococcaceae, and Micrococcales, were linked to seasonal changes, while mid-aged adults exhibited a higher abundance of Kaistella, Escherichia, Enterobacteriaceae, and Enterobacterales. Furthermore, captive Chinese monals may be more susceptible to bacterial-induced intestinal diseases in spring and summer. This research highlights the dynamic impact of seasonal cycles and age on gut microbiota, offering important findings that support improved conservation strategies and management of captive Chinese monal populations. The Chinese monal (Lophophorus lhuysii) is a large-sized and vulnerable (VU in IUCN) bird from southwestern China. This study applied 16S rRNA high-throughput sequencing to comprehensively examine the gut microbiota of captive Chinese monals (located in Baoxing, Sichuan, China) across varying seasons and life stages. Dominant bacterial phyla identified included Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Significant seasonal and age-associated shifts were observed within specific bacterial groups, particularly marked by seasonal fluctuations in beta diversity. Moreover, linear discriminant analysis effect size (LEfSe) and functional predictions highlighted distinct winter signatures, indicating possible functional shifts in energy metabolism and disease resistance. In mid-aged adults, an expansion of Gamma-Proteobacteria suggested an elevated susceptibility of the gut microbiota of Chinese monals to chronic disorders and microbial imbalance. Putative pathogenic bacteria exhibited increased abundance in spring and summer, likely driven by temperature, host physiological cycles, interspecies interactions, and competition. These findings imply that the diversity, and structure of the gut microbiota in captive Chinese monals are strongly influenced by seasonal and age-related factors. The insights provided here are essential for improving breeding strategies and preventing gastrointestinal diseases in captivity. [ABSTRACT FROM AUTHOR]

The grapevine (Vitis vinifera) is a major fruit crop of economic importance worldwide. Commercial grapevine cultivars are susceptible to infection by pathogenic microorganisms that cause diseases both in leaves and fruits, and it is known that the leaf microbiome plays an important role in plant health and fitness. In this study, shotgun metagenomic sequencing was used to characterize the microbial communities associated with grapevine leaves in three commercial varieties, Cabernet Sauvignon, Garnacha, and Marselan, grown in the same biogeographical unit. Metagenomic data revealed a differential enrichment of the microbial communities living inside grapevine leaves or on the leaf surface in the three varieties. The most abundant fungal taxa associated with grapevine leaves belong to the phylum Ascomycota, which included relevant pathogenic fungi for grapevines, such as Botrytis cinerea, Sclerotinia sclerotium, and Alternaria alternata, as well as several fungal species potentially pathogenic for grapevines (e.g., members of the Colletotrichum, Aspergillus, and Penicillium genera). Basidiomycota constituted a minor fraction of the fungal microbial communities. Grapevine leaves also harbored a diversity of bacterial taxa. At the phylum level, bacterial communities in all three varieties were primarily composed of Pseudomonadata, Bacillota, Bacteroidota, and a lower proportion of Actinomycetota. Differences in the fungal and bacterial community structures were observed between varieties, although they were more important in fungi. In particular, S. sclerotiorum and B. cinerea were found to preferentially colonize leaves in the Marselan and Garnacha varieties, respectively. These findings further support that the host genotype can shape its own microbiome in grapevines. A better understanding of the leaf microbiome in grapevines will provide the basis for the development of tailored strategies to prevent diseases in vineyards while helping to increase sustainability in grapevine production. [ABSTRACT FROM AUTHOR]

Various ingredients are utilized to inhibit the growth of harmful bacteria associated with cavities, gum disease, and bad breath. However, the precise mechanisms by which these ingredients affect the oral microbiome have not been fully understood at the molecular level. To elucidate the molecular mechanisms, a high-throughput bacterial transcriptomics study was conducted, and the gene expression profiles of six common oral bacteria, including two Gram-positive bacteria (Actinomyces viscosus, Streptococcus mutans) and four Gram-negative bacteria (Porphyromonas gingivalis, Tannerella forsythia, Fusobacterium nucleatum, and Prevotella pallens), were analyzed. The bacteria were exposed to nine common ingredients in toothpaste and mouthwash at different concentrations (stannous fluoride, stannous chloride, arginine bicarbonate, cetylpyridinium chloride, sodium monofluorophosphate, sodium fluoride, potassium nitrate, zinc phosphate, and hydrogen peroxide). Across 78 ingredient–microorganism pairs with 360 treatment–control combinations, significant and reproducible ingredient-based transcriptional response profiles were observed, providing valuable insights into the effects of these ingredients on the oral microbiome at the molecular level. This research shows that oral care product ingredients applied at biologically relevant concentrations manifest differential effects on the transcriptomics of bacterial genes in a variety of oral periodontal pathogenic bacteria. Stannous fluoride, stannous chloride, and cetylpyridinium chloride showed the most robust efficacy in inhibiting the growth or gene expression of various bacteria and pathogenic pathways. Combining multiple ingredients targeting different mechanisms might be more efficient than single ingredients in complex oral microbiomes. [ABSTRACT FROM AUTHOR]

Simple Summary: Urban cockroaches raise health concerns due to their association with pathogens. However, their microbial associates can enhance their physiological and reproductive functions. This article details the bacterial community associated with the oriental cockroach Blatta orientalis Linnaeus, 1758 (Blattodea: Blattidae) using metabarcoding for the first time. We analyze bacterial communities on the exoskeleton and within the gut of this cosmopolitan pest. Specimens were collected from the urban area of Santiago, Chile. DNA extraction and metabarcoding were performed for analysis. Our findings reveal a variety of bacterial lineages, including mutualistic symbionts and pathogenic strains. We examined the metabolic functions of these bacterial communities and their implications for B. orientalis as a pathogen reservoir and vector of zoonosis. Lastly, we consider how the microbial diversity in cockroaches might facilitate their adaptation to human-altered environments. Pest cockroaches share urban habitats with us; their prevalence in urban areas prompts concerns regarding their effect on human health, as synanthropic cockroaches often host pathogenic microorganisms. Nonetheless, microbial associates in these insects can also be related to their biology, contributing to their physiological homeostasis and reproductive success. In this article, we present in detail, for the first time, the bacterial community associated with the oriental cockroach Blatta orientalis, one of the world's five most prominent pest cockroaches. We report the composition of the communities of bacteria found over the exoskeleton and inside the gut of this global pest. We collected B. orientalis in Santiago, Chile's capital city, and the urban nucleus in this country. We conducted DNA extractions and metabarcoding analysis. We found diverse bacterial lineages, including mutualist symbiotic strains, and microorganisms considered pathogenic to humans. We also analyzed the metabolic functions of the bacterial communities identified and discussed the role of B. orientalis as a reservoir and vector of pathogens in urban areas. We discuss to what extent the diversity of functions of the microbial community associated with cockroaches may contribute to emergent properties enabling these insects to inhabit human-modified habitats. [ABSTRACT FROM AUTHOR]

Panax plants are known for their significant medicinal and economic value. Being perennial, they are prone to soil-borne diseases during cultivation. However, there has been limited research on the pathogenesis of soil-borne diseases and the diversity of pathogens. While biological control has gained attention for its efficacy and environmental benefits, the factors affecting its efficiency still need thorough evaluation. This review summarizes the influence of biotic factors, such as pathogens and hosts, and environmental factors on the occurrence of soil-borne diseases and pathogen diversity. Additionally, we synthesized bacterial, actinobacterial, and fungal diversity for the biocontrol of soil-borne diseases and their functional mechanisms. Moreover, the review delves into the factors influencing the efficacy of biocontrol, including microbial species, the inoculation method and inoculation volume, and inoculant composition. This article serves as a valuable resource for enhancing the efficiency of biological control and optimizing strategies for managing soil-borne diseases in Panax cultivation in the future. [ABSTRACT FROM AUTHOR]

Fresh produce prone to microbial contamination is a potential reservoir for antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs), posing challenges to food safety and public health. This systematic review aims to comprehensively assess the prevalence of bacterial pathogens and the incidence of ARB/ARGs in fresh produce and agro-ecosystems across South Asia. Twenty-two relevant studies published between 2012 and 2022 from three major scientific databases and the grey literature were identified. The results revealed a wide occurrence of microbial contamination in various types of fresh produce across South Asia, with a predominance of E. coli (16/22), Salmonella spp. (13/22), Staphylococcus spp. (5/22), and Klebsiella spp. (4/22). The agro-ecosystem serves as a complex interface for microbial interactions; studies have reported the prevalence of E. coli (1/4), Salmonella spp. (1/4) and Listeria monocytogenes (1/4) in farm environment samples. A concerning prevalence of ARB has been reported, with resistance to multiple classes of antibiotics. The presence of ARGs in fresh produce underscores the potential for gene transfer and the emergence of resistant pathogens. To conclude, our review provides insights into the requirements of enhanced surveillance, collaborative efforts, implementation of good agricultural practices, and public awareness for food safety and safeguarding public health in the region. [ABSTRACT FROM AUTHOR]

The Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway is highly conserved and essential for numerous biological functions triggered by extracellular signals, including cell proliferation, metabolism, immune response, and inflammation. Defects in STATs, either loss-of-function or gain-of-function defects, lead to a broad spectrum of clinical phenotypes in humans, including a wide range of infectious complications. The susceptibility to pathogens can stem from defects in immune cells within the hematopoietic compartment, impaired barrier functions of non-hematopoietic compartment, or a combination of both, depending on the specific STAT defect as well as the pathogen exposure history. Effective management involves antimicrobial prophylaxis tailored to the patient's infection risk and improving disease control with targeted therapies and/or hematopoietic cell transplantation. [ABSTRACT FROM AUTHOR]

Ageratum conyzoides L. is native to Tropical America, and it has naturalized in many other tropical, subtropical, and temperate countries in South America, Central and Southern Africa, South and East Asia, Eastern Austria, and Europe. The population of the species has increased dramatically as an invasive alien species, and it causes significant problems in agriculture and natural ecosystems. The life history traits of Ageratum conyzoides, such as its short life cycle, early reproductive maturity, prolific seed production, and high adaptive ability to various environmental conditions, may contribute to its naturalization and increasing population. Possible evidence of the molecules involved in the defense of Ageratum conyzoides against its natural enemies, such as herbivore insects and fungal pathogens, and the allelochemicals involved in its competitive ability against neighboring plant species has been accumulated in the literature. The volatiles, essential oils, extracts, residues, and/or rhizosphere soil of Ageratum conyzoides show insecticidal, fungicidal, nematocidal, and allelopathic activity. The pyrrolizidine alkaloids lycopsamine and echinatine, found in the species, are highly toxic and show insecticidal activity. Benzopyran derivatives precocenes I and II show inhibitory activity against insect juvenile hormone biosynthesis and trichothecene mycotoxin biosynthesis. A mixture of volatiles emitted from Ageratum conyzoides, such as β-caryophyllene, β-bisabolene, and β-farnesene, may work as herbivore-induced plant volatiles, which are involved in the indirect defense function against herbivore insects. Flavonoids, such as nobiletin, eupalestin, 5′-methoxynobiletin, 5,6,7,3′,4′,5′-hexamethoxyflavone, and 5,6,8,3,4′,5′-hexamethoxyflavone, show inhibitory activity against the spore germination of pathogenic fungi. The benzoic acid and cinnamic acid derivatives found in the species, such as protocatechuic acid, gallic acid, p-coumaric acid, p-hydroxybenzoic acid, and ferulic acid, may act as allelopathic agents, causing the germination and growth inhibition of competitive plant species. These molecules produced by Ageratum conyzoides may act as defense molecules against its natural enemies and as allelochemicals against neighboring plant species, and they may contribute to the naturalization of the increasing population of Ageratum conyzoides in new habitats as an invasive plant species. This article presents the first review focusing on the defense function and allelopathy of Ageratum conyzoides. [ABSTRACT FROM AUTHOR]

Fungi are diverse organisms with various characteristics and functions. Some play a role in recycling essential elements, such as nitrogen and carbon, while others are utilized in the food and drink production industry. Some others are known to cause diseases in various organisms, including humans. Fungal pathogens cause superficial, subcutaneous, and systemic infections. Consequently, many scientists have focused on studying the factors contributing to the development of human diseases. Therefore, multiple approaches have been assessed to examine the biology of these intriguing organisms. The genome-scale metabolic models (GEMs) have demonstrated many advantages to microbial metabolism studies and the ability to propose novel therapeutic alternatives. Despite significant advancements, much remains to be elucidated regarding the use of this tool for investigating fungal metabolism. This review aims to compile the data provided by the published GEMs of human fungal pathogens. It gives specific examples of the most significant contributions made by these models, examines the advantages and difficulties associated with using such models, and explores the novel approaches suggested to enhance and refine their development. [ABSTRACT FROM AUTHOR]

Background: Diseases of veterinary importance, such as bovine Anaplasmosis, cause significant economic losses. Due to this, the study of various proteins of the causal agent Anaplasma marginale has focused on surface proteins. However, a vaccine for this disease is not yet available. To this end, in this work, moonlighting proteins (MLPs) are presented as an alternative approach for the design of immunogens against A. marginale. Methods: The proteins of the strain MEX-15-099-01 were analyzed, and its MLPs were identified. Subsequently, four virulence-associated MLP genes were selected and identified using PCR. The proteins were analyzed using a structural homology approach and the collection of B-cell epitopes was predicted for each MLP. Finally, a pair of AmEno peptides were synthesized and the antigenic potential was tested using an iELISA. Results: Our bioinformatics analysis revealed the potential of AmEno, AmGroEl, AmEF-Tu, and AmDnaK proteins as promising candidates for designing immunogens. The PCR allowed the gene sequence identification in the genome of the strain MEX-15-099-01. Notably, AmEno-derived synthetic peptides showed antigenicity in an ELISA. Conclusions: Our study has shed light on the potential use of MLPs for immunogen design, demonstrating the antigenic potential of AmEno. [ABSTRACT FROM AUTHOR]

Plant endophytic microbial communities consist of many latent plant pathogens and, also, many pathogen-related species with reduced virulence. Though with a long history of co-evolution, the diversity and composition of the endophytic mycobiota, especially the pathogen-related fungal groups, has been under-investigated in Citrus (C.). Based on the amplicon sequencing of fungal internal transcribed spacer (ITS), the leaf endophytic mycobiota were profiled on citrus varieties from different citrus-producing regions. The pomelo variety shared significantly distinctive leaf mycobiota when compared to the mandarin and sweet orange; these conform to their host genetic relationships. In addition, a data set of 241 citrus-related fungi, including 171 (71%) pathogens and potential pathogens, was summarized from previous studies. Under the criteria of local BLAST (covered ITS nucleotide ≥ 150 bp, sequence identity ≥ 99%), a total of 935 fungal operational taxonomic units (OTUs) were assigned to 62 pathogen-related fungal groups, representing 14.9% of the relative abundance in the whole community. Of which, the top groups consisted of Colletotrichum gloeosporioides (mean relative abundance, 4.3%), Co. citricola and Co. karstii (2.7%), Zasmidium citri-griseum (2.4%), and Z. fructigenum (1.4%). At the genus level, the ratio of the pathogen-related fungal groups in 64% of fungal genera (16 out of 25) exceeded 50%, which are the solely or mainly occurring fungi of their genus in citrus. Our study suggests that the leaf endophytic compartment may be an important place for the growth of latent pathogens. [ABSTRACT FROM AUTHOR]

Simple Summary: Validation of plant pathogens' diagnostic assays requires positive and negative controls. High Throughput Sequencing (HTS) has shown capabilities for detecting multiple pathogens simultaneously. However, accurate pathogen identification from HTS data depends on the bioinformatic pipeline used. There is currently no consensus on the best pipeline, leading to inconsistent results. To address this, standardized artificial HTS datasets are proposed as benchmarks to evaluate the performance of bioinformatic pipelines used in detection scenarios using HTS. These datasets will aid in resolving challenges like unknown sensitivity and specificity of the bioinformatic tool, contributing to advancing plant pathogen detection using HTS. The validation of diagnostic assays in plant pathogen detection is a critical area of research. It requires the use of both negative and positive controls containing a known quantity of the target pathogen, which are crucial elements when calculating analytical sensitivity and specificity, among other diagnostic performance metrics. High Throughput Sequencing (HTS) is a method that allows the simultaneous detection of a theoretically unlimited number of plant pathogens. However, accurately identifying the pathogen from HTS data is directly related to the bioinformatic pipeline utilized and its effectiveness at correctly assigning reads to their associated taxa. To this day, there is no consensus about the pipeline that should be used to detect the pathogens in HTS data, and results often undergo review and scientific evaluation. It is, therefore, imperative to establish HTS resources tailored for evaluating the performance of bioinformatic pipelines utilized in plant pathogen detection. Standardized artificial HTS datasets can be used as a benchmark by allowing users to test their pipelines for various pathogen infection scenarios, some of the most prevalent being multiple infections, low titer pathogens, mutations, and new strains, among others. Having these artificial HTS datasets in the hands of HTS diagnostic assay validators can help resolve challenges encountered when implementing bioinformatics pipelines for routine pathogen detection. Offering these purely artificial HTS datasets as benchmarking tools will significantly advance research on plant pathogen detection using HTS and enable a more robust and standardized evaluation of the bioinformatic methods, thereby enhancing the field of plant pathogen detection. [ABSTRACT FROM AUTHOR]

Background: After the removal of the three-year epidemic control restrictions, Chinese children were confronted with heightened risks of respiratory infections. We aimed to investigate the post-pandemic (2023) epidemiology of respiratory infections among pediatric inpatients in a tertiary hospital in Shanghai, China, and compare it with the pre-pandemic (2019) levels. Methods: A total of 2644 pediatric inpatients were enrolled based on discharge time and divided into group 2019 (n = 1442) and group 2023 (n = 1202). Information on the demographic characteristics, diagnoses, and pathogen test results (Mycoplasma pneumoniae, MP; Chlamydia pneumoniae, CP; Legionella pneumophila, LP; Influenza A, IFA; Influenza B, IFB; Parainfluenza virus, PIV; respiratory syncytial virus, RSV; Coxsackie virus, COX; Adenovirus, ADV; Epstein–Barr virus, EBV) was collected and analyzed. Results: Significant increases were found in the overall test positivity rates (64.6% vs. 46.7%), mixed infection rates (17.4% vs. 9%), and proportion of severe cases (25.5% vs. 3.7%) after the pandemic than those before it. Compared with 2019, the incidences of MP, IFA, LP, RSV, and ADV remarkably increased, while those of IFB and COX decreased, with no obvious differences noted for CP, PIV, and EBV in 2023. A significantly higher MP-positive detection rate was noticed in children aged 1–6 years in 2023 than in 2019. The incidence of RSV infection began to rise in August 2023, earlier than the conventional epidemic season. Conclusions: Compared with the pre-pandemic levels, the overall test positivity rates of atypical pathogens and viruses among pediatric inpatients significantly increased, and alterations in the disease spectrum, epidemic season, and age of prevalence were observed after the COVID-19 pandemic. [ABSTRACT FROM AUTHOR]

Using a pathogenic fungus and selected endophytic fungi of the ash tree, we propose a modified model of fungal dual cultures that allows us to obtain two new parameters particularly useful in the search for fungal pathogen control agents. The first of these, called the vitality parameter, is applicable to the study of both biotic and abiotic factors affecting fungal growth. It is measured as the ratio of fungal growth radius in the direction of a studied factor to the growth radius in the opposite direction. The second parameter, called the inhibition parameter, relates to biofactors and is the ratio of the vitality parameters of the two tested fungi in dual cultures. This parameter combines the information on the growth of both dual culture components, for the first time, as a one value. In order to correctly determine the values of both parameters, a required inoculation configuration in dual cultures and a method for calibrating the duration of such cultures have been developed. All this together creates a new tool for a more sophisticated look at the use of dual cultures in the search for means to control fungal pathogens, including those that threaten the stability of forest ecosystems. [ABSTRACT FROM AUTHOR]

The emergence of infectious disease outbreaks and 'superbugs' related to pollution combined with climate change is a current problem, not just a future threat. In May 2024, an extreme flood hit the Rio Grando Sul State, southern Brazil, triggering an important leptospirosis outbreak in urban settings with deficient sanitation systems. This and other cases discussed in this article exemplify how extreme weather events exacerbate the consequences of environmental pollution by multiple classes of pathogens in the global scenario of increasing anthropogenic pressures on the environment. A combination of actions to combat climate change and improvements in sanitation systems is essential to mitigate this problem. [ABSTRACT FROM AUTHOR]

Airborne pathogens, though a minor fraction of airborne particles, can cause infections, intoxications, or allergic reactions through respiration, dermal contact, or ingestion. The SARS-CoV-2 pandemic has underscored the significance of mitigating airborne microbial threats. Traditional air ionization methods, such as dielectric barrier discharge and metal tip corona discharge, produce ozone, a reactive and potentially harmful byproduct. However, carbon-fiber ionizers (CFIs) generate high concentrations of ions with minimal ozone production, making them a safer alternative. Operating at voltages below 5 kV, CFIs are more efficient than their metallic counterparts. This review focuses on the antimicrobial efficacy of CFIs, which produce unipolar ions that can disrupt microbial membranes, leading to cell death. Compared to ultraviolet light sterilization, CFIs are cost-effective and suitable for small spaces. The literature review highlights the need for comprehensive studies to evaluate the real-world application and effectiveness of CFIs. Many existing studies are limited by small-scale testing and insufficient data reporting, complicating comparative analyses. Our work aims to provide a detailed perspective on CFIs, examining their impact on various microorganisms, ion efficacy, ionization outcomes, and ozone generation levels. By addressing these aspects, the review seeks to offer an updated understanding of CFIs' antimicrobial capabilities and to identify limitations in current research, paving the way for more informed and effective air purification strategies. [ABSTRACT FROM AUTHOR]

Microbial infections caused by bacteria, viruses, and fungi pose significant global health threats in diverse environments. While conventional disinfection methods are effective, their reliance on frequent chemical applications raises concerns about resistance and environmental impact. Photodynamic self-disinfecting surfaces have emerged as a promising alternative. These surfaces incorporate photosensitizers that, when exposed to light, produce reactive oxygen species to target and eliminate microbial pathogens. This review explores the concept and mechanism of photodynamic self-disinfecting surfaces, highlighting the variety and characteristics of photosensitizers integrated into surfaces and the range of light sources used across different applications. It also highlights the effectiveness of these surfaces against a broad spectrum of pathogens, including bacteria, viruses, and fungi, while also discussing their potential for providing continuous antimicrobial protection without frequent reapplication. Additionally, the review addresses both the advantages and limitations associated with photodynamic self-disinfecting surfaces and concludes with future perspectives on advancing this technology to meet ongoing challenges in infection control. [ABSTRACT FROM AUTHOR]

Simple Summary: Bovine tuberculosis is caused by Mycobacterium bovis, which causes tuberculosis in humans and animals. Diagnosis of bovine tuberculosis has relied on examination of immune responses to M. bovis; however, using these methods, disease detection during the earliest phases of infection has been difficult, allowing a window for cattle-to-cattle transmission to occur within a herd. Alternative means of diagnosis could include methods to detect M. bovis or M. bovis DNA in bodily fluids such as nasal secretions, saliva, or blood rather than the animal's response to infection. DNA-from M. bovis was detected in nasal swabs and saliva from a small number of experimentally infected calves during the first 8 weeks after experimental infection. Although DNA from M. bovis could be detected, no culturable M. bovis was recovered from nasal swabs or saliva. Moreover, M. bovis DNA was not found in blood samples collected weekly. Successful infection of all calves was demonstrated using an interferon gamma release assay. Identification of infected animals through the detection of M. bovis will require the use of alternative samples or alternative assays. Bovine tuberculosis is caused by Mycobacterium bovis, a member of the M. tuberculosis complex of mycobacterial species that cause tuberculosis in humans and animals. Diagnosis of bovine tuberculosis has relied on examinations of cell-mediated immune responses to M. bovis proteins using tuberculin skin testing and/or interferon gamma release assays. Even when using these methods, disease detection during the earliest phases of infection has been difficult, allowing a window for cattle-to-cattle transmission to occur within a herd. Alternative means of diagnosis could include methods to detect M. bovis or M. bovis DNA in bodily fluids such as nasal secretions, saliva, or blood. During the first 8 weeks after experimental aerosol infection of 18 calves, M. bovis DNA was detected in nasal swabs from a small number of calves 5, 6, and 8 weeks after infection and in samples of saliva at 1, 7, and 8 weeks after infection. However, at no time could culturable M. bovis be recovered from nasal swabs or saliva. M. bovis DNA was not found in blood samples collected weekly and examined by real-time PCR. Interferon gamma release assays demonstrated successful infection of all calves, while examination of humoral responses using a commercial ELISA identified a low number of infected animals at weeks 4–8 after infection. Examination of disease severity through gross lesion scoring did not correlate with shedding in nasal secretions or saliva, and calves with positive antibody ELISA results did not have more severe disease than other calves. [ABSTRACT FROM AUTHOR]

In this study, we explore how transformer models, which are known for their attention mechanisms, can improve pathogen prediction in pastured poultry farming. By combining farm management practices with microbiome data, our model outperforms traditional prediction methods in terms of the F1 score—an evaluation metric for model performance—thus fulfilling an essential need in predictive microbiology. Additionally, the emphasis is on making our model's predictions explainable. We introduce a novel approach for identifying feature importance using the model's attention matrix and the PageRank algorithm, offering insights that enhance our comprehension of established techniques such as DeepLIFT. Our results showcase the efficacy of transformer models in pathogen prediction for food safety and mark a noteworthy contribution to the progress of explainable AI within the biomedical sciences. This study sheds light on the impact of effective farm management practices and highlights the importance of technological advancements in ensuring food safety. [ABSTRACT FROM AUTHOR]

The study was conducted to identify cluster patterns of enteric microorganisms with potential etiological relevance for infectious gastroenteritis in stool samples of individuals from Ghana, which is a known high-endemicity setting for infectious gastroenteritis. These patterns were compared to previous observations with specimens from Colombian indigenous people in order to assess potentially stable clustering for temporally and spatially distinct populations from high-endemicity regions. By doing so, the study aimed to identify stable clusters as markers of microbial interaction with potential importance for etiological relevance assignment in cases of multiple enteric pathogen detections. Stool samples from 1569 Ghanaian individuals (875 from HIV patients, 30 from HIV-negative control adult patients, and 644 from children < 2 years of age) were assessed for enteric microorganisms by applying real-time PCR. As a result, nucleic acids of bacterial microorganisms were most frequently detected, followed by protozoa, microsporidia, and helminths. Interestingly, the cluster assessment confirmed interaction patterns known from the previous analysis with Colombian indigenous people, demonstrating a high likelihood of Blastocystis hominis for clustering with other microorganisms and a prominent, potentially mediating role of Dientamoeba fragilis for microbial interactions within the clusters. In conclusion, the assessment confirmed conserved clustering of enteric microorganisms with potential etiological relevance for human infectious gastroenteritis over geographically distinct high-endemicity settings. Furthermore, the composition of abundant microorganisms is more important than regional factors for the determination of the interplay of enteric microorganisms in the human gut. Thereby, some microbial pathogens and commensals seem more susceptible to a changing microbial composition in the human gut than others. [ABSTRACT FROM AUTHOR]

Coconut (Cocos nucifera L.) is an important palm species that serves as the mainstay of several industries and contributes to the livelihoods of millions of smallholder farmers. International exchange of coconut germplasm has been undertaken for several decades to facilitate the conservation of selected varieties within global genebanks and for the distribution to farmers and scientists. In vitro systems are a convenient and an efficient method for the exchange of coconut germplasm. However, it is possible that these tissue culture systems can transfer lethal pathogens causing a threat to the importing countries. In this review, the following topics are discussed: the major disease-causing agents of concern, the various tissues that could be used for coconut germplasm exchange, and the techniques available for the detection and elimination of disease-causing agents from various transmission systems. Additionally, the lack of clear, science-backed guidelines to facilitate the exchange of in vitro coconut materials is raised, along with recommendations for future studies to ensure the safe movement of coconut germplasm without biosecurity risks. [ABSTRACT FROM AUTHOR]

The use of double-stranded RNA (dsRNA) for plant protection shows great potential as a sustainable alternative to traditional pesticides. This review summarizes the current state of knowledge on using exogenous dsRNA in plant protection and includes the latest findings on the safety and efficiency of this strategy. The review also emphasizes the need for a cautious and comprehensive approach, considering safety considerations such as off-target effects and formulation challenges. The regulatory landscape in different regions is also discussed, underscoring the need for specific guidelines tailored to dsRNA-based pesticides. The review provides a crucial resource for researchers, regulators, and industry stakeholders, promoting a balanced approach incorporating innovation with thorough safety assessments. The continuous dialog emphasized in this review is essential for shaping the future of dsRNA-based plant protection. As the field advances, collaboration among scientists, regulators, and industry partners will play a vital role in establishing guidelines and ensuring the responsible, effective, and sustainable use of dsRNA in agriculture. [ABSTRACT FROM AUTHOR]

Mild heat (MH) treatment and ascorbic acid (AsA) addition can improve the quality of fresh-cut produce when used individually; however, their combined effect remains unclear. Herein, fresh-cut carrots were used as models to explore the effects of MH (50 °C)–AsA (0.5%) on quality properties including reactive oxygen species (ROS) metabolism, antioxidants, lignin metabolism, naturally present microbes, and inoculated pathogens (Escherichia coli O157: H7 and Salmonella Typhimurium) during storage (0–5 d, 4 °C). The results indicate that the antioxidant properties in the MH–AsA group were consistent with those of single treatments, resulting in a consistent ROS-scavenging effect. From day 3–5, lignin synthesis was significantly inhibited by MH–AsA as compared with single treatments, probably because the two enzymes (phenylalanine ammonia-lyase and peroxidase) responsible for lignin synthesis exhibited lower expressions. Microbial analysis revealed that MH–AsA treatment led to the lowest counts of both pathogens and aerobic mesophilic bacteria at 0–5 d. Conversely, the inhibitory effect of MH–AsA treatment on mold and yeast was consistent with the single treatments. These results suggest that MH–AsA is a low-cost and safe approach to improve the physiological characteristics of fresh-cut produce while reducing microbial risk. [ABSTRACT FROM AUTHOR]

Simple Summary: In the southeastern United States of America, shifts in the environment such as climate change and host availability are pushing tick populations to spread into new areas. It is hypothesized that, as they migrate, tick populations have developed a behavior known as incomplete feeding. With this, ticks feed on more than one host at each life stage, increasing the chance of pathogen transmission. In South Carolina, we found evidence of ticks displaying this behavior. We collected engorged female ticks from stray dogs at animal shelters across the state in 2022. Testing showed that about a third of these ticks had fed on humans. The patterns varied depending on the tick species, where they were found, and the time of collection. This pilot study reflects the growing trend of tick-borne diseases in the southeastern USA. It is crucial to dig deeper into how factors like the season, location, and species are linked to incomplete feeding behavior in South Carolina's tick populations. Dynamic environmental conditions, such as climate change and host availability, have greatly influenced the expansion of medically relevant tick vectors into new regions throughout the southeastern United States of America. As tick populations migrate into new areas, it has been suggested they can exhibit a phenomenon known as incomplete feeding. With this phenomenon, tick vectors feed on more than one host at each life stage, thus increasing the likelihood of pathogen transmission. Although this behavior is not well understood, it presents an important threat to human health. Here we present evidence of incomplete feeding behaviors in multiple tick species in South Carolina. Engorged, blood-fed female ticks were collected from feral dogs at animal shelters across South Carolina in 2022. All ticks were tested for human blood meals using rapid stain identification blood tests. Approximately one third (33.78%) of all ticks tested positive for a human blood meal, with various patterns seen across species, geographic location, and collection month. The results of this pilot study follow the current national trend of increasing rates of tick-borne disease incidence in the southeastern United States of America and warrant further investigation into the relationship between seasonality, geographic distribution, species, and incomplete feeding among tick populations in South Carolina. [ABSTRACT FROM AUTHOR]

Simple Summary: The brown marmorated stink bug, Halyomorpha halys (Stål) (Hemiptera: Pentatomidae), is an invasive pest commonly found in vineyards. This study aimed to investigate the seasonal patterns and distribution of H. halys in vineyards with multiple grape cultivars. We also assessed the damage caused by different levels of pest infestation on grape clusters. Our findings revealed that H. halys populations varied throughout the seasons and were higher on red berry cultivars, such as Cabernet Franc and Merlot, and those ripening later in the season. Additionally, we observed higher pest infestations at the vineyard borders compared to their centers. The study showed that H. halys infestations led to damage to grape berries, with varying susceptibility among different cultivars and phenological stages. Furthermore, the presence of H. halys increased the incidence on clusters of Botrytis cinerea and sour rot, highlighting its significant impact on grapevine health. The brown marmorated stink bug, Halyomorpha halys (Stål) (Hemiptera: Pentatomidae), is an invasive polyphagous pest often observed in vineyards. In Europe, a gap needs to be filled in the knowledge on H. halys seasonal dynamics and damage on grapes. With this study, we described the seasonal dynamics of H. halys and its distribution in multi-cultivar vineyards, and we evaluated the damage on grape clusters induced by different pest densities. In vineyards, the seasonal occurrence of H. halys varied across time and grape cultivars, and the pest was more abundant on Cabernet Franc, Merlot and, to a lesser extent, Pinot gris. Moreover, higher densities of H. halys were found on red berry cultivars than on white ones, and on cultivars ripening late in the season. An edge effect was also detected in pest distribution within vineyards, with more stink bugs observed in the borders. In the study on pest infestation density, H. halys caused damage on berries, showing differences in susceptibility among different cultivars and with regard to the time of infestation (i.e., plant phenological stages). Halyomorpha halys infestation induced an increase in Botrytis cinerea and sour rot incidence, which probably represents the main issue related to the impact of brown marmorated stink bug on grapevine. [ABSTRACT FROM AUTHOR]

The second leading cause of death in children under five years old is diarrheal disease. Probiotics, specifically bifidobacteria, have been associated with a reduction in the number of diarrhea episodes and their severity in babies. In this paper, we summarize the preclinical and clinical evidence of the efficacy of B. longum subsp. infantis IM1® against various gastrointestinal pathogens using in vitro models, animal models, and clinical studies carried out in our laboratory. The preclinical data demonstrate that IM1® effectively inhibits rotavirus replication (by up to 36.05%) in MA-104 and HT-29 cells and from infection (up to 48.50%) through the production of an 11-amino-acid peptide. IM1® displays the capability to displace pathogens from enterocytes, particularly Cronobacter sakazakii and Salmonella enterica, and to reduce the adhesion to the HT29 cells of C. sakazakii and Shigella sonnei. In animal models, the IM1® strain exhibits in vivo protection against rotavirus and improves the clinical symptomatology of bacterial gastroenteritis. A clinical study involving infants under 3 months of age revealed that IM1® reduced episodes of diarrhea, proving to be safe, well tolerated, and associated with a lower prevalence of constipation. B. infantis IM1® emerges as an effective probiotic, diminishing episodes of diarrhea caused by gastrointestinal pathogens. [ABSTRACT FROM AUTHOR]

This study aimed to enhance our understanding of the agreement between two sampling methods for the detection of bovine respiratory disease (BRD) pathogens in calves using high-throughput real-time qPCR (ht-RT-qPCR). In total, 233 paired nasal swab (NS) and non-endoscopic bronchoalveolar lavage (nBAL) samples were collected from 152 calves from 12 Danish cattle herds. In 202 of the observations, the calves were examined using a standardized clinical protocol. Samples were tested for three viruses (bovine respiratory syncytial virus, bovine corona virus, and influenza D virus) and six bacteria (Histophilus somni, Mannheimia haemolytica, Mycoplasma bovis, Mycoplasma species, Pasteurella multocida, and Truepurella pyogenes). The results showed age-related differences in disease and pathogen occurrence, with the highest detection rates in calves aged 35 days or older. Poor to moderate agreement was found between the NS and nBAL results. The presence of Mannheimia haemolytica in both NS and nBAL in younger calves and in nBAL in older calves was associated with clinical BRD. There was a potential link between BRD and influenza D virus in older calves, although it was only found in one herd in a small sample size. Overall, NS was a relatively poor predictor of pathogens in the lower respiratory tract. The present study confirms the complexity of pathogen detection in BRD, with marked influences of age and the sampling method on pathogen detection and disease associations. [ABSTRACT FROM AUTHOR]

Acanthamoeba keratitis (AK) is a severe infection of the cornea. Prevention and treatment are difficult due to the inefficacy of currently available compounds. The impact of many commonly used compounds for routine examinations of Acanthamoeba is unexplored but might offer insight useful in combatting AK. In this study, we demonstrate that sodium metabisulfite, a common preservation constituent of eye care solutions, was found to be active against Acanthamoeba trophozoites at concentrations lower than that commonly found in eye drops (IC50 0.03 mg/mL). We demonstrate that sodium metabisulfite depletes thiamine from growth medium and that Acanthamoeba is a thiamine auxotroph, requiring thiamine salvage for growth. The inhibitory effects of sodium metabisulfite can be overcome by thiamine supplementation. These results are consistent with the lack of key enzymes for thiamine biosynthesis in the genome of Acanthamoeba, an area which might prove exploitable using new or existing compounds. Indeed, this study highlights sodium metabisulfite as a useful inhibitor of Acanthamoeba castellanii trophozoites in vitro and that it acts, at least in part, by limiting available thiamine. [ABSTRACT FROM AUTHOR]

Microplastics contribute to various environmental issues and serve as carriers for a wide range of toxic compounds such as pesticides, pharmaceuticals, and metal ions. Consequently, there is a gradual shift towards replacing them with biodegradable plastics (bioplastics). However, biodegradable plastics require specific conditions for complete biodegradation, and their biodeterioration often leads to the rapid production of smaller fragments, known as microbioplastics. In this review, we summarize selected issues related to the impact of plastic particles on soil properties and the soil microbiome. Findings from numerous studies indicate that both microplastics and microbioplastics induce adverse changes in soil microbiology, potentially increasing the abundance of soil-borne pathogens. Based on these observations, we argue that plastic particles could serve as carriers for colonies of soil-borne pathogens. Furthermore, the use of bioplastics may exacerbate this issue due to their easier and faster formation, increased support for biofilms, and more pronounced adverse effects on soil biota. However, further research is necessary to either substantiate or refute this perspective. [ABSTRACT FROM AUTHOR]

This study aimed to obtain and characterize an oil-in-water nanoemulsion (NE) loaded with an in vitro optimized bactericidal essential oil blend of 50% oregano, 40% thyme, and 10% lemongrass and to evaluate its potential at three different concentrations (0.5%, 1%, and 2%) in the inactivation of Escherichia coli, Staphylococcus aureus, and Salmonella enterica serotype Enteritidis inoculated in rainbow trout fillets stored at 4 °C for 9 days. Regarding the NE, the nanometric size (<100 nm) with low polydispersion (0.17 ± 0.02) was successfully obtained through ultrasound at 2.09 W/cm2. Considering the three concentrations used, S. Enteritidis was the most susceptible. On the other hand, comparing the concentrations used, the NE at 2% showed better activity, reducing S. Enteritidis, E. coli, and S. aureus by 0.33, 0.20, and 0.73 log CFU/g, respectively, in the trout fillets. Thus, this data indicates that this is a promising eco-friendly alternative to produce safe fish for consumption and reduce public health risks. [ABSTRACT FROM AUTHOR]

Due to being sessile, plants develop a broad range of defense pathways when they face abiotic or biotic stress factors. Although plants are subjected to more than one type of stress at a time in nature, the combined effects of either multiple stresses of one kind (abiotic or biotic) or more kinds (abiotic and biotic) have now been realized in agricultural lands due to increases in global warming and environmental pollution, along with population increases. Soil-borne pathogens, or pathogens infecting aerial parts, can have devastating effects on plants when combined with other stressors. Obtaining yields or crops from sensitive or moderately resistant plants could be impossible, and it could be very difficult from resistant plants. The mechanisms of combined stress in many plants have previously been studied and elucidated. Recent studies proposed new defense pathways and mechanisms through signaling cascades. In light of these mechanisms, it is now time to develop appropriate strategies for crop protection under multiple stress conditions. This may involve using disease-resistant or stress-tolerant plant varieties, implementing proper irrigation and drainage practices, and improving soil quality. However, generation of both stress-tolerant and disease-resistant crop plants is of crucial importance. The establishment of a database and understanding of the defense mechanisms under combined stress conditions would be meaningful for the development of resistant and tolerant plants. It is clear that leaf pathogens show great tolerance to salinity stress and result in pathogenicity in crop plants. We noticed that regulation of the stomata through biochemical applications and some effort with the upregulation of the minor gene expressions indirectly involved with the defense mechanisms could be a great way to increase the defense metabolites without interfering with quality parameters. In this review, we selected wheat as a model plant and Zymoseptoria tritici as a model leaf pathogen to evaluate the defense mechanisms under saline conditions through physiological, biochemical, and molecular pathways and suggested various ways to generate tolerant and resistant cereal plants. [ABSTRACT FROM AUTHOR]

In contemporary times, the sustained aspiration of bioengineering and biomedical applications is the progressive advancement of materials characterized by biocompatibility and biodegradability. The investigation of the potential applications of polymers as natural and non-hazardous materials has placed significant emphasis on their physicochemical properties. Thus, this study was designed to investigate the potential of gelatin–chitosan–moringa leaf extract (G–CH–M) as a novel biomaterial for biomedical applications. The wound-dressing G–CH–M biopolymer was synthesized and characterized. The blood haemolysis, anti-inflammatory, antioxidant, and antibacterial activities of the biopolymer were investigated against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacterial isolates. Our results showed that S. aureus swarming motility was drastically affected. However, the biopolymer had no significant effect on the swarming motility of E. coli. In addition, the biopolymer showed high antibacterial capacities, especially against S. aureus. Plasmid DNA was observed to be effectively protected from oxidative stresses by the biopolymer. Furthermore, the biopolymer exhibited greatly suppressed haemolysis (lower than 2%), notwithstanding the elevated concentration of 50 mg/mL. These results indicated that this novel biopolymer formulation could be further developed for wound care and contamination prevention. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic was a challenge for the whole world, and it had major secondary effects on humans and environmental health. The viral infection induced, in many situations, secondary bacterial infections, especially enteric infections, by destabilizing the balance of the gastrointestinal microbiota. The large-scale use of antibiotics and biocides for both curative and preventive purposes has resulted in an increase in bacterial resistance, and at the same time, the possibility of pathogenic microorganism multiplication and their dissemination to natural environments. Wastewater is the main vector of fecal microorganisms that favors their dissemination into natural aquatic ecosystems. The present paper aims to analyze the effect of the COVID-19 pandemic on the microbiological quality of wastewater from sewage treatment plants in Romania and its impact on receiving rivers. In order to highlight different and important areas in Romania, three cities from the east, center and west were selected for a microbiological evaluation of their WWTP influents and effluents from the pre-COVID-19 period and during the COVID-19 pandemic peak period, when the COVID-19 pandemic had a direct impact on WWTP microbial compositions. Our study shows that a higher level of contamination with fecal bacteria is linked to a higher COVID-19 incidence. The increased usage of pharmaceutical compounds, in turn, increases the number of resistant bacteria reaching the environment via WWTP effluents. [ABSTRACT FROM AUTHOR]

Staka is a traditional Greek sour cream made mostly from spontaneously fermented sheep milk or a mixture of sheep and goat milk. At the industrial scale, cream separators and starter cultures may also be used. Staka is sometimes cooked with flour to absorb most of the fat. In this study, we employed culture-based techniques, amplicon sequencing, and shotgun metagenomics to analyze the Staka microbiome for the first time. The samples were dominated by Lactococcus or Leuconostoc spp. Most other bacteria were lactic acid bacteria (LAB) from the Streptococcus and Enterococcus genera or Gram-negative bacteria from the Buttiauxella, Pseudomonas, Enterobacter, Escherichia-Shigella, and Hafnia genera. Debaryomyces, Kluyveromyces, or Alternaria were the most prevalent genera in the samples, followed by other yeasts and molds like Saccharomyces, Penicillium, Aspergillus, Stemphylium, Coniospotium, or Cladosporium spp. Shotgun metagenomics allowed the species-level identification of Lactococcus lactis, Lactococcus raffinolactis, Streptococcus thermophilus, Streptococcus gallolyticus, Escherichia coli, Hafnia alvei, Streptococcus parauberis, and Enterococcus durans. Binning of assembled shotgun reads followed by recruitment plot analysis of single reads could determine near-complete metagenome assembled genomes (MAGs). Culture-dependent and culture-independent analyses were in overall agreement with some distinct differences. For example, lactococci could not be isolated, presumably because they had entered a viable but not culturable (VBNC) state or because they were dead. Finally, several LAB, Hafnia paralvei, and Pseudomonas spp. isolates exhibited antimicrobial activities against oral or other pathogenic streptococci, and certain spoilage and pathogenic bacteria establishing their potential role in food bio-protection or new biomedical applications. Our study may pave the way for additional studies concerning artisanal sour creams to better understand the factors affecting their production and the quality. [ABSTRACT FROM AUTHOR]

In response to the pressing need for continuous monitoring of emergence and circulation of pathogens through genomics, it is imperative to keep developing bioinformatics tools that can help in their rapid characterization and classification. Here, we introduce ReporType, a versatile bioinformatics pipeline designed for targeted loci screening and typing of infectious agents. Developed using the snakemake workflow manager, ReporType integrates multiple software for read quality control and de novo assembly, and then applies ABRicate for locus screening, culminating in the production of easily interpretable reports for the identification of pathogen genotypes and/or screening of specific genomic loci. The pipeline accommodates a range of input formats, from Illumina or Oxford Nanopore Technology (ONT) reads (FASTQ) to Sanger sequencing files (AB1), or FASTA files, making it flexible for application in multiple pathogens and with different purposes. ReporType is released with pre-prepared databases for some viruses and bacteria, yet it remains easily configurable to handle custom databases. ReporType performance and functionality were validated through proof-of-concept exercises, encompassing diverse pathogenic species, including viruses such as measles, Newcastle disease virus (NDV), Dengue virus (DENV), influenza, hepatitis C virus (HCV) and Human T-Cell Lymphotropic virus type 1 (HTLV-1), as well as bacteria like Chlamydia trachomatis and Legionella pneumophila. In summary, ReporType emerges as a simple, dynamic and pan-pathogen tool, poised to evolve in tandem with the ever-changing needs of the fields of pathogen genomics, infectious disease epidemiology, and one health bioinformatics. ReporType is freely available at GitHub. [ABSTRACT FROM AUTHOR]

Epidemics of infectious diseases threaten human health and society stability. Pharmacophagous plants are rich in bioactive compounds that constitute a safe drug library for antimicrobial agents. In this study, we have deciphered for the first time antibacterial ingredients and modes of the methanol-phase extract (MPE) from the fruit of Amomum villosum Lour. The results have revealed that the antibacterial rate of the MPE was 63.64%, targeting 22 species of common pathogenic bacteria. The MPE was further purified by high performance liquid chromatography (Prep-HPLC), and three different constituents (Fractions 1–3) were obtained. Of these, the Fraction 2 treatment significantly increased the cell membrane fluidity and permeability, reduced the cell surface hydrophobicity, and damaged the integrity of the cell structure, leading to the leakage of cellular macromolecules of Gram-positive and Gram-negative pathogens (p < 0.05). Eighty-nine compounds in Fraction 2 were identified by ultra HPLC-mass spectrometry (UHPLC-MS) analysis, among which 4-hydroxyphenylacetylglutamic acid accounted for the highest 30.89%, followed by lubiprostone (11.86%), miltirone (10.68%), and oleic acid (10.58%). Comparative transcriptomics analysis revealed significantly altered metabolic pathways in the representative pathogens treated by Fraction 2 (p < 0.05), indicating multiple antibacterial modes. Overall, this study first demonstrates the antibacterial activity of the MPE from the fruit of A. villosum Lour., and should be useful for its application in the medicinal and food preservative industries against common pathogens. [ABSTRACT FROM AUTHOR]

The gastrointestinal tract is an environment that hosts various microorganisms, including pathogens. Generally, pathogenic bacteria enter the host body through food and the gastrointestinal tract. These pathogenic bacteria can colonize or infiltrate host cells and tissues, causing various infectious diseases. In recent years, the protective role of probiotic bacteria against gastrointestinal pathogens has been carefully investigated. Probiotics have been found to modulate intestinal microbial flora and play a significant role in the gastrointestinal tract's function, especially by inhibiting the growth of pathogenic bacteria. However, the mechanism of action of probiotics has yet to be sufficiently proven and recognized. Several important mechanisms support the antagonistic effects of probiotics on various microorganisms, which is achieved, for example, through the production of different antimicrobial compounds, such as bacteriocins, various organic acids, antibiotics, antimicrobial proteins, and exopolysaccharides; mucosal barriers with mucosa and bacteria binding blockers; competition for nutrient uptake; and strengthening of the immune system. Accordingly, this review summarizes the recent studies that have examined the mechanism of action of probiotic bacteria and their beneficial effects in preventing pathogenic bacterial growth and improving gastrointestinal functions. Comprehending their mechanisms of action allows the selection of appropriate probiotic strains for specific applications in gastrointestinal dysfunction. [ABSTRACT FROM AUTHOR]

Simple Summary: This study has investigated the presence of Leptospira bacteria in urine, kidney, and blood samples from African giant pouched rats (Cricetomys spp.) in the Ngorongoro Conservation Area (NCA), Tanzania. The giant rat is an important maintenance host of leptospires; understanding their abundance and distribution in this environment is important to help prevent the transmission of the bacteria from rodents to other animals and humans co-existing in the area. This study demonstrates that Cricetomys spp. in the NCA are infected with the spirochete, and are hence a potential threat to public health. This study calls for an enhanced awareness of the presence of Leptospira spp. in Cricetomys spp. and calls for a one-health approach to protect both humans and animals from the pathogens. Leptospirosis, also known as Weil's disease, is a febrile tropical disease of humans and diverse animals. The maintenance hosts of the infectious pathogen, Leptospira spp., are primarily rodents, while other warm-blooded animals and some reptiles are secondary or transient hosts of this pathogen. African giant pouched rats (Cricetomys spp.) have been identified to be important maintenance hosts of pathogenic leptospires in the tropical and subtropical regions of the world. This study assessed the seroprevalence of Leptospira spp. in the African giant pouched rats of the Ngorongoro Conservation Area (NCA), Tanzania, where there is close human, domestic animal, and wildlife interaction. A total of 50 African giant pouched rats were sampled between July 2020 and December 2021. Blood sera were screened for specific leptospiral antibodies using a microscopic agglutination test (MAT), while urine and kidney tissues were examined for the pathogen and pathogen-specific genes using cultures and polymerase chain reactions (PCR), respectively. The pathogen detection varied from 0% in cultures to 6% via the MAT and 20% via PCR. The Fisher exact test was applied to compare positive cases detected through the diagnostic tests, and showed a significant difference in the indirect and direct detection of Leptospira serovars via the MAT and PCR. We conclude that pathogenic Leptospira serovar are found in the NCA and recommend that the NCA authority raises awareness of the existence of the Leptospira serovar in giant African pouched rats, and possibly other rodents. The NCA should initiate appropriate management strategies, including the guided disposal of household garbage, which is the major attractant of rodents to residential areas. Where necessary, the NCA should carry out limited rodent control and periodic monitoring of the pathogen carrier (rodent) populations. [ABSTRACT FROM AUTHOR]

Aquaculture is a growing industry worldwide, but it faces challenges related to animal health. These challenges include infections by parasites, bacteria, and viral pathogens. These harmful pathogens have devastating effects on the industry, despite efforts to control them through vaccination and antimicrobial treatments. Unfortunately, these measures have proven insufficient to address the sanitary problems, resulting in greater environmental impact due to the excessive use of antimicrobials. In recent years, probiotics have emerged as a promising solution to enhance the performance of the immune system against parasitic, bacterial, and viral pathogens in various species, including mammals, birds, and fish. Some probiotics have been genetically engineered to express and deliver immunomodulatory molecules. These promote selective therapeutic effects and specific immunization against specific pathogens. This review aims to summarize recent research on the use of probiotics in fish aquaculture, with a particular emphasis on genetically modified probiotics. In particular, we focus on the advantages of using these microorganisms and highlight the main barriers hindering their widespread application in the aquaculture industry. [ABSTRACT FROM AUTHOR]

The emergence of infectious diseases presents a significant global health, economic, and security risk. Climate change can unexpectedly lead to the spread of pathogens, vectors, or hosts into new areas, contributing to the rise of infectious diseases. Surveillance plays a crucial role in monitoring disease trends and implementing control strategies. In this study, we document the first discovery of Heterobilharzia americana, a parasitic schistosome of mammals and its intermediate hosts Galba cubensis and Galba humilis along the banks of the Colorado River in California. We conducted multiple samplings of snails from various locations in the region with a previous history of canine schistosomiasis. Nucleotide sequencing of the multiple regions of the snails' and parasites' DNA revealed the coexistence of G. cubensis and G. humilis, both infected with H. americana. Phylogenetic analyses further validate the presence of H. americana in California, suggesting a wider distribution than previously reported. Our findings have implications for public health, veterinary medicine, and biodiversity conservation, contributing to developing effective control strategies to prevent the spread of this emerging infectious disease. [ABSTRACT FROM AUTHOR]

Vermicomposting stands as a sustainable and environmentally friendly waste management practice, leveraging the metabolic prowess of earthworms to facilitate the decomposition of organic matter into nutrient-rich compost. The aim of this experiment was to study the influence of Eisenia fetida on the density and the tropic structure of a nematode community during the vermicomposting process over a period of 3 months. Sewage sludge and green waste served as composting substrates. Overall, six compost variants were prepared consisting of three variants incorporating E. fetida and three control variants lacking E. fetida. Throughout the investigation, samples were gathered on a monthly basis, with each variant undergoing three repetitions. The aim was to isolate nematodes, determine the population density of the five trophic groups, and identify the dominant community. The anaysis was conducted employing both microscopic examination and molecular metabarcoding (NGS). It was shown that the bacterial-feeding community maintained dominance. The introduction of E. fetida into the compost led to a significant rise in the abundance of Diplogasteridae. In the variant without E. fetida, the amount of Diplodasteridae exceeded 0.1% only after the 30th (C3) or the 60th (C1, C2) day of composting, while in the compost with E. fetida, they were present in large amounts (ranging from 11.0% to 28.0%) already on the 30th day of composting. The introduction of Eisenia fetida also led to a notable reduction in H. gingivalis with significant implications for mitigating the risk of halicephalobiosis. The introduction of E. fetida resulted in reducing H. gingivalis to levels below 0.1% in all compost variants. [ABSTRACT FROM AUTHOR]

Macadamia decline poses a serious economic threat to the macadamia industry. It exhibits either a slow decline due to infection by Kretzschmaria clavus or Ganoderma lucidum, or a quick decline caused by pathogens like Phytophthora spp., Lasiodiplodia spp., Neofusiccocum spp., Nectria rugulosa, Xylaria arbuscula, Phellinus gilvus, Acremonium recifei, and Rosellinia spp. Chemical strategies, resistant cultivars, and agronomic measures have been widely adopted to control macadamia decline, but effective biological control measures have rarely been applied. This paper proposes two key steps for implementing biological control strategies, i.e., the isolation and selection of biological control agents from healthy plants, or from the disease-suppressive soil for the construction of synthetic microbial communities, and the integration of synthetic microbial communities with various strategies, including seed coating, root dipping, seedling substrate, soil drenching, foliar spraying, and application as a bio-organic fertilizer. By adopting these strategies, we aim to provide proactive and efficient approaches for combating macadamia decline and safeguarding the health of macadamia orchards. [ABSTRACT FROM AUTHOR]

A significant part of freshwater mussel populations has strongly declined and many species are severely threatened nowadays. Captive breeding programs often form a central part of conservation strategies. As the life cycles of many mussel species include an obligate parasitic phase, host fish health is a crucial component of successful mussel breeding efforts. However, information about the safe application of fish therapeutants in mussel captive breeding is scarce. This article summarizes information about practical experiences in Europe. In total, eight different therapeutants were used to treat infestations of eight pathogens. Treatment success varied depending on pathogen and prevalence when treatments were initiated. Mussels did not seem to be affected by treatments, especially as long as they remained encysted. In a second step, Virkon S was applied to treat a fungal infection in tanks with brown trout (Salmo trutta) carrying encysted freshwater pearl mussel (Margaritifera margaritifera) glochidia and to disinfect juvenile mussel rearing containers. In both cases, mussels were not harmed and treated fish fully recovered. Results indicate that certain therapeutants can be used safely and successfully at different stages of breeding cycles. Nevertheless, there is still a lack of standard protocols, which would improve efficiency and the safety of treatments. [ABSTRACT FROM AUTHOR]

Healthcare-associated infections caused by multi-drug-resistant pathogens are increasing globally, and current antimicrobial options have limited efficacy against these robust species. The WHO details the critically important bacterial and fungal species that are often associated with medical device HAIs. The effective sterilization of medical devices plays a key role in preventing infectious disease morbidity and mortality. A lack of adherence to protocol and limitations associated with each sterilization modality, however, allows for the incidence of disease. Furthermore, issues relating to carcinogenic emissions from ethylene oxide gas (EtO) have motivated the EPA to propose limiting EtO use or seeking alternative sterilization methods for medical devices. The Food and Drug Administration supports the sterilization of healthcare products using low-temperature VH2O2 as an alternative to EtO. With advances in biomaterial and medical devices and the increasing use of combination products, current sterilization modalities are becoming limited. Novel approaches to disinfection and sterilization of medical devices, biomaterials, and therapeutics are warranted to safeguard public health. Bacteriophages, endolysins, and antimicrobial peptides are considered promising options for the prophylactic and meta-phylactic control of infectious diseases. This timely review discusses the application of these biologics as antimicrobial agents against critically important WHO pathogens, including ESKAPE bacterial species. [ABSTRACT FROM AUTHOR]

Escherichia coli is a major player in foodborne illnesses, capable of forming biofilms on dairy facilities, leading to milk contamination. Thus, we examined the capacity of E. coli strains from raw milk bulk tanks to form biofilms on surfaces made of polystyrene, stainless steel, and silicone; the potential links between biofilm formation with genes responsible for fimbriae and virulence factors of extra-intestinal E. coli (ExPEC); and the susceptibility of biofilm-forming isolates to iodine and chlorhexidine digluconate. Out of 149 E. coli strains, 42.28% (63/149) formed biofilm on polystyrene, 56.38% (84/149) on silicone, and 21.48% (32/149) on stainless steel. The frequency of genes was: fimH (100%), hlyA (5.4%), irp2 (2.7%), sitA (10.7%), ompT (43.6%), and traT (98%). No biofilm developed when disinfectants were used prior to biofilm formation. However, iodine and chlorhexidine digluconate allowed 25.40% (16/63) of isolates displaying growth after a mature biofilm was formed. The presence of biofilm on different surfaces emphasizes the vital need for thorough equipment cleaning, both in farms and in industrial dairy settings. Rapid disinfection is crucial, given the reduced susceptibility of potentially pathogenic E. coli after biofilm maturity. [ABSTRACT FROM AUTHOR]

Bacterial membrane vesicles (BMVs) are produced by most bacteria and participate in various cellular processes, such as intercellular communication, nutrient exchange, and pathogenesis. Notably, these vesicles can contain virulence factors, including toxic proteins, DNA, and RNA. Such factors can contribute to the harmful effects of bacterial pathogens on host cells and tissues. Although the general effects of BMVs on host cellular physiology are well known, the underlying molecular mechanisms are less understood. In this study, we introduce a vesicle quantification method, leveraging the membrane dye FM4-64. We utilize a linear regression model to analyze the fluorescence emitted by stained vesicle membranes to ensure consistent and reproducible vesicle–host interaction studies using cultured cells. This method is particularly valuable for identifying host cellular processes impacted by vesicles and their specific cargo. Moreover, it outcompetes unreliable protein concentration-based methods. We (1) show a linear correlation between the number of vesicles and the fluorescence signal emitted from the FM4-64 dye; (2) introduce the "vesicle load" as a new semi-quantitative unit, facilitating more reproducible vesicle-cell culture interaction experiments; (3) show that a stable vesicle load yields consistent host responses when studying vesicles from Pseudomonas aeruginosa mutants; (4) demonstrate that typical vesicle isolation contaminants, such as flagella, do not significantly skew the metabolic response of lung epithelial cells to P. aeruginosa vesicles; and (5) identify inositol monophosphatase 1 (SuhB) as a pivotal regulator in the vesicle-mediated pathogenesis of P. aeruginosa. [ABSTRACT FROM AUTHOR]

Biofilms in water distribution lines strongly affect water safety as they are the main carriers of pathogens. The current study investigated the biofilm formation and identification of selected pathogens in different distribution pipeline materials and their disinfection method in an annular reactor (AR). Initially, the quality of the flowing water from each pipeline material was analyzed, i.e., pH, TDS, EC, turbidity, and salinity; then, the biofilm formation was monitored for each material, i.e., ABS, PC, PVC, PP, and HDPE. Further, the disinfection kinetics of biofilm at different chlorine doses, i.e., 0.5, 1.0, 1.5, and 2.0 mg/L, was investigated. The selected pathogens, i.e., E. coli, Pseudomonas, Shigella, Salmonella sp., and Vibrio sp. were identified in biofilms formed in different pipeline materials. The disinfection kinetics results showed that a chlorine dose of 2.0 mg/L was the most effective in disinfecting selected pathogens. Following the disinfection kinetics, it was observed that Salmonella sp. was disinfected within 7 days, whereas other pathogenic biofilms were disinfected within 14 days. The efficacy of chlorine disinfection was affected by the types of pipeline materials. The study outcomes could provide insights into biofilms' disinfection method and the selection of suitable pipeline materials to ensure drinking water safety. [ABSTRACT FROM AUTHOR]

The thrip (Megalurothrips usitatus) damages the flowers and pods of the cowpea, causing "black-heads and black-tails" (BHBT) symptoms and negatively affecting its economic value. However, the mechanism by which BHBT symptoms develop is still unknown. Our results showed that the microstructure of the pod epidermis was altered and the content of the plant's resistance-related compounds increased after a thrip infestation. However, the contents of protein and free amino acids did not change significantly, suggesting that the nutritional value was not altered. Pathogens were found not to be involved in the formation of BHBT symptoms, as fungi and pathogenic bacteria were not enriched in damaged pods. Two herbivory-induced flavonoids—7,4′-dihydroxyflavone and coumestrol—were found to exert insecticidal activity. Our study clarified that BHBT symptoms are directly caused by the thrip. Thresholds for pest control need to be reconsidered as thrip herbivory did not degrade cowpea nutrition. [ABSTRACT FROM AUTHOR]