Resistant Pathogens Research Articles

Pathogen Identification and Resistance Screening of Fusarium Basal Rot in Taşköprü Garlic in Türkiye

ABSTRACTFusarium basal rot (FBR), caused by Fusarium spp., is a significant threat to garlic production globally, including in Türkiye, where the unique Taşköprü garlic is highly valued. This study investigated the diversity and aggressiveness of 77 Fusarium isolates obtained from disease surveys of FBR in Taşköprü garlic and evaluated the yield and resistance of 20 garlic accessions, including 18 local landraces, the locally developed ‘Taşköprü 56’, and the commercial Chinese variety ‘ASCG’. Molecular identification using translation elongation factor 1‐α (TEF1) and second largest RNA polymerase II B‐subunit (RPB2) genes revealed F. oxysporum (67.5%) as the dominant species, followed by F. proliferatum (15.6%), F. solani (9.1%), F. redolens (5.2%) and F. clavum (2.6%), respectively. All isolates were pathogenic, but aggressiveness varied, with F. solani being the most aggressive, followed by F. redolens and F. oxysporum. While ‘ASCG’ exhibited the highest yield (3.15 ton/ha), it was highly susceptible to FBR (DSI = 97.50%). Conversely, the landrace ASTK2 displayed the highest resistance (DSI = 53.13%), but lower yield. Promisingly, several Taşköprü landraces, such as ASTK6 and ASTK13, demonstrated both moderate resistance and promising yield potential. Surprisingly, ‘Taşköprü 56’, despite being a locally developed variety, exhibited high susceptibility to FBR (DSI = 93.75%) and did not outperform many landraces in terms of yield. This study provides the first reports of F. redolens and F. clavum infecting garlic in Türkiye, and the first molecular characterisation of F. solani as a garlic pathogen in the country, highlighting the potential of local landraces for breeding FBR‐resistant, high‐yielding cultivars.

Evaluation of biogenic bismuth oxide nanoparticles from Rubus niveus leaves and fruits extract for antimicrobial and photocatalytic activity

The present study focused on producing bismuth oxide nanoparticles (Bi2O3 NPs) using methanolic extracts from Rubus niveus fruits and leaves. These extracts were used as both a capping and reducing agent. The properties of the Bi2O3 NPs were determined using advanced characterization methods such as XRD, FTIR, SEM, TEM, XPS, and UV–Vis spectroscopy. The findings demonstrated the formation of spherical and rod-shaped structures in Bi2O3 nanoparticles synthesized using methanol extracts derived from leaves and fruits, respectively. The average diameters of the crystallites were measured as 69.39 nm for RNF-NPs and 62.85 nm for RNL-NPs in Bi2O3 nanoparticles. The grain sizes were observed to be 130 ± 0.25 nm for RNF-NPs and 320 ± 1.22 nm for RNL-NPs, with corresponding D-spacings of 0.314 nm and 0.617 nm. Additionally, the presence of a weak band in the FTIR spectra at 717.29 cm−1 for RNL-NPs and 715.25 cm−1 for RNF-NPs indicated the monoclinic morphology of the synthesized α-Bi2O3 nanoparticles. The antibacterial activity of the samples was assessed using the agar well diffusion technique for bacteria and the poisoned food method for fungus. The antibacterial findings demonstrate that the nanoparticles derived from the methanolic extract of leaves (Methicillin resistance S. aureus [ZOI: 23 ± 0.57 mm] and fruits (MDR P. aeruginosa [ZOI: 26.5 ± 0.57 mm]) exhibit comparable zone of inhibition against multi-drug resistant pathogens. Moreover, the antifungal efficacy of Bi2O3 nanoparticles derived from the methanol extract of the fruits (R. necatrix [59.29 ± 0.80 %]) was shown to be superior to that of nanoparticles obtained from the methanol extract of the leaves. Addition, the methanol extract of the flower demonstrated a superior photocatalytic activity, specifically 94.44 %, using Bi2O3 nanoparticles.

Multi-resistant bacteria - epidemiological trends and new treatment options

Multi-resistant bacteria such as Escherichia coli and Klebsiella pneumoniae are a growing threat worldwide. The spread of Carbapenemase-producing strains is particularly worrying. New antibiotics and combination therapies offer treatment options, but the development of resistant pathogens remains a major challenge.

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis – update from 2017 to 2023

Antimicrobial resistance (AMR) is a critical global health concern. A previous systematic review showed that migrants in Europe are at increased risk of AMR. Since the COVID-19 pandemic there have been rapid changes in patterns of antibiotic use, AMR, and migration. We aimed to present an updated evidence synthesis on the current distribution of AMR among migrants in Europe. We carried out a systematic review and meta-analysis in accordance with PRISMA guidelines (PROSPERO ID: CRD42022343263). We searched databases (MEDLINE, Embase, PubMed and Scopus) from 18 January 2017 until 18 January 2023 to identify primary data from observational studies reporting any laboratory-confirmed AMR among migrants in the European Economic Area (EEA) and European Union-15 (EU-15) countries using over 7 key search terms for migrants and over 70 terms for AMR and countries in Europe. Outcomes were infection with, or colonisation of AMR bacteria. Methodological quality was assessed using Joanna Briggs Institute Critical Appraisal Checklist for Observational Studies. We meta-analysed the pooled-prevalence of infection and/or colonisation of AMR organisms. Among 630 articles, 21 observational studies met the inclusion criteria and were included in this review. The pooled prevalence for any detected AMR was 28.0% (95% CI 18.0%-41.0%, I 2 =100%) compared to a 25.4% seen in the previous review; gram-negative bacteria 31.0% (95% CI 20.0%-44.0%, I 2 =100%), and methicillin-resistant staphylococcus aureus 10.0% (95% CI 5.0%-16.0%, I 2 =99%). Drug-resistant bacteria were more prevalent in community settings in large migrant populations (pooled prevalence: 41.0%, 95% CI 24.0%-60.0%, I 2 =99%) than in hospitals (21.0%, 95% CI 12.0%-32.0%, I 2 =99%). AMR estimates in 'other' migrants were 32.0%, (95% CI 12.0%-57.0%, I 2 =100%) and 28.0% (95% CI 18.0%-38.0%, I 2=100%) in forced migrants. No firm evidence of AMR acquisition with arrival time or length of stay in the host country was found. Studies investigating AMR in migrants are highly heterogenous. However, since the COVID-19 pandemic, migrants may be at higher risk of acquiring resistant bacteria, particularly gram-negative bacteria, within community settings such as refugee camps and detention centres in Europe. Our study highlights the importance of infrastructure and hygiene measures within these settings, to mitigate transmission of resistant pathogens. Policy-makers should screen for AMR in migrants prior to departure from countries of origin, where feasible, and upon arrival to a new country to ensure optimal health screening, infection control and effective treatment. There was no funding source for this study.

Interventions based on alternative and sustainable strategies for postharvest control of anthracnose and maintain quality in tropical fruits.

Colletotrichum spp. is a phytopathogen causing anthracnose in a variety of tropical fruits. Strategies used to control postharvest diseases in tropical fruits typically rely on the use of synthetic fungicides, which have stimulated the emergence of resistant pathogens. Safer alternative strategies to control anthracnose in tropical fruits have been described in the literature. This review presents and discusses the main innovative interventions concerning the application of sustainable alternative strategies in the postharvest control of pathogenic Colletotrichum species in tropical fruits, with a particular emphasis on the studies published in the last 5 years. The available studies have shown the use of various methods, including physical barriers, natural antimicrobials, and biological control with antagonistic microorganisms, to reduce anthracnose lesion severity and incidence in tropical fruits. The available literature showed high inhibitory activity in vitro, reduced anthracnose incidence and lesion diameter, and total disease inhibition in tropical fruits. Most studies focused on the inhibition of Colletotrichum gloeosporioides on avocado, papaya, and mango, as well as of Colletotrichum musae on banana; however, the inhibition of other Colletotrichum species was also demonstrated. The application of emerging sustainable alternative methods, including natural antimicrobial substances, also stimulated the induction of defense systems in tropical fruits, including enzymatic activity, such as polyphenol oxidase, peroxidase, and phenylalanine ammonia-lyase. The retrieved data helped to understand the current state of the research field and reveal new perspectives on developing efficient and sustainable intervention strategies to control pathogenic Colletotrichum species and anthracnose development in tropical fruits.

Formononetin derivatives containing benzyl piperidine: A brand new, highly efficient inhibitor targeting Xanthomonas spp

IntroductionPlant bacterial diseases take an incalculable toll on global food security. The indiscriminate use of chemical synthetic pesticide not only facilitates pathogen resistance of pathogenic bacteria, but also poses a major threat to human health and environmental protection. Therefore, it is of great economic value and scientific significance to develop a new antibacterial drug with environmental friendliness and unique mechanism of action. ObjectivesTo design and synthesize formononetin derivatives based on natural products, evaluate their in vitro and in vivo antibacterial activities and elucidate the mechanisms involved. MethodsThe synthesis was carried out by classical active group splicing method. The antibacterial activities were evaluated using turbidimetry and pot experiments. The antibacterial mechanism was further investigated using scanning electron microscopy (SEM), virulence factors, defense enzymes activities, proteomics and metabolomics. Results40 formononetin derivatives containing benzyl piperidine were designed and synthesized. The antibacterial results demonstrated that H32 exhibited the most potent inhibitory effect against Xanthomonas oryzae pv. Oryzae (Xoo) with the EC50 of 0.07 μg/mL, while H6 displayed the highest inhibitory activity against Xanthomonas axonopodis pv. Citri (Xac) with the EC50 of 0.24 μg/mL. Furthermore, the control efficacy of H32 against rice bacterial leaf blight (BLB) and H6 against citrus canker (CC) was validated through pot experiments. SEM, virulence factors and host enzyme activities assay indicated that H32 could not only reduce the virulence of Xoo, but also activate the activities of defense enzymes and improve the disease resistance of host plants. The proteomics and metabolomics analysis demonstrated that H32 could inhibit the synthesis of branched-chain amino acids, make Xoo cells in a starvation state, inhibit its proliferation, weaken its virulence and reduce its colonization and infection of host cells. ConclusionFormononetin derivatives containing benzyl piperidine could be used as potentially effective inhibitors against Xanthomonas spp.

Caprylic Acid From Vitex mollis Pulp Alters Colletotrichum gloeosporioides Plasma Membrane and Reduces Anthracnose Development on Papaya Fruit

ABSTRACTSynthetic fungicides are used to control anthracnose caused by Colletotrichum gloeosporioides; however, their frequent application increases the risk of pathogen resistance, environmental damage, and health concerns. It has been reported that caprylic acid (CA) inhibits the in vitro development of C. gloeosporioides; however, its antifungal mechanism and in vivo antifungal potential are still unknown. Therefore, the present work aims to analyse the effect of a CA‐enriched sub‐fraction (CAES) extracted from Vitex mollis fruit on the fungal microstructure by confocal fluorescence microscopy and morphometric analysis. Moreover, the effect of CAES on anthracnose development and quality parameters in papaya fruit was evaluated. The confocal microscopy images confirmed that CAES damaged the cell wall of conidia, given their decreased width. The increased fluorescence intensity in the CAES and CA‐treated mycelium suggested they were attached to the plasma membrane. These treatments produced structural alterations of the vacuoles and septa in mycelium, while in the fungicide thiabendazole (TBZ) treatment, apoptotic bodies appeared. CAES at 1.0 g L−1 had the best effect against anthracnose incidence and severity in papaya fruit, whereas TBZ was only effective on anthracnose severity. None of the applied treatments affected the fruit quality parameters. Therefore, CAES may be develop as an effective option to suppress anthracnose on papaya fruit.

Molecular Dynamics Simulation Studies of Beta-Glucogallin and Dihydro Dehydro Coniferyl Alcohol from Syzygium cumini for its Antimicrobial Activity on Staphylococcus aureus.

With the escalating threat of antimicrobial resistance (AMR), discovering novel therapeutic agents against resistant pathogens like Staphylococcus aureus is crucial. This study explores phytochemicals from Syzygium cumini for their potential efficacy against AMR S. aureus infections, elucidating their mechanisms through in silico methods. We investigated 83 compounds from S. cumini, sourced from PubMed, using rigorous docking analysis against the ATP binding domain AgrC of S. aureus with AMdock with Autodock Vina v1.5.2. Drug-likeness predictions were assessed using SwissADME v2023 and Pass online v2.0. Molecular dynamics (MD) simulations identified promising compounds, focusing on stability and interaction dynamics. Beta-Glucogallin (BEG) and Dihydro Dehydro Coniferyl alcohol (DIH) emerged as significant hits. MD simulations with GROMACS v2020.6 revealed stable BEG and DIH complexes with AgrC, forming six hydrogen bonds with six key amino acids (Arg-303, Asp-338, Glu-342, Glu-384, Lys-389, Gly-396), indicating strong and stable bonding. The binding affinities for DIH and BEG are -73.474 ± 11.104 kJ/mol and -6.319 ± 18.823 kJ/mol with 4BXI, respectively. Our findings highlight BEG and DIH as promising candidates against AMR S. aureus infections, showing favourable binding affinities and stable interactions with AgrC. This study underscores the importance of natural products in combating AMR and demonstrates the utility of computational methodologies in drug discovery. Further experimental validation is warranted to fully exploit these phytochemicals' therapeutic potential.

Antimicrobial metabolites from Probiotics, Pleurotus ostreatus and their co-cultures against foodborne pathogens isolated from ready-to-eat foods

BackgroundThe incidence of foodborne pathogens in ready- to-eat (RTE) can be attributed to various foodborne diseases. Most of the isolated microorganisms from RTE foods are resistant to common antibiotics and thus, resulted to treatment failure when commercially available antibiotics are administered. However, the secondary metabolites secreted by microorganisms can serve as alternative therapy that are reliable and safe. Secondary metabolites obtained from mono- and co-culture microorganisms can inhibit the growth of antibiotic-resistant microorganisms. Bioactive compounds in the secreted metabolites can be identified and utilized as sources of new antibiotics. In this study, antimicrobial activity of secondary metabolites from Lactobacillus fermentum, Saccharomyces cerevisiae, Pleurotus ostreatus, and their co-cultures were tested against foodborne pathogens isolated from RTE foods using agar well diffusion. The bioactive compounds in the metabolites were identified using gas chromatography-mass spectrometry.ResultsFrom a total of 100 RTE foods examined, Salmonella enterica, Shigella dysenteriae, Escherichia coli, Klebsiella pneumoniae (subsp ozaenae), Pseudomonas fluorescens, Clostridium perfringes, Bacillus cereus, Listeria monocytogens, and Staphylococcus aureus, Penicillium chrysogenum, Aspergillus flavus, and Aspergillus niger were isolated and displayed multiple antibiotic resistance. The secondary metabolites secreted by co-culture of L. fermentum + P. ostreatus + S. cerevisiae, and co-culture of P. ostreatus + S. cerevisiae have the highest (P ≤ 0.05) zones of inhibition (23.70 mm) and (21.10 mm) against E. coli, respectively. Metabolites from mono-cultured L. fermentum, P. ostreatus, and S. cerevisiae showed zones of inhibition against indicator microorganisms with values ranging from 8.80 to 11.70 mm, 9.00 to 14.30 mm, and 9.30 to 13.00 mm, respectively. Some of the bioactive compounds found in the metabolites of co-cultured microorganisms were alpha-linolenic acid (25.71%), acetic acid 3-methylbutyl ester (13.83%), trans-squalene (12.39%), pentadecylic acid (11.68%), 3- phenyllactic acid (30.13%), linolelaidic acid methyl ester (15.63%), and 4-O-methylmannose (53.74%).ConclusionRTE foods contain multiple antibiotics resistance pathogens. The pronounced antimicrobial activity of the secondary metabolites against microorganisms from RTE foods could be attributed to the presence of bioactive compounds in the metabolites. These metabolites can be exploited as alternative food preservatives, biopharmaceuticals and can be used towards better health delivering systems.

Epinecidin-1 and lactic acid synergistically inhibit Aeromonas hydrophila through membrane disruption

Epinecidin-1 (Epi-1) is an antimicrobial peptide originated from fish with various pharmacological activities but carries the risk of acquiring resistance with long-term use. In the present study, we use L-lactic acid to enhance the antibacterial activity of synthesized Epi-1 against the aquaculture and food pathogen Aeromonas hydrophila. The results showed that 5.5 mmol/L lactic acid increased the inhibitory and bactericidal activity of 25 μmol/L Epi-1 against two strains of A. hydrophila. The laser confocal images proved that lactic acid pre-treatment improved the attachment efficiency of Epi-1 in A.hydrophila cells. In addition, lactic acid enhanced the damaging effect of Epi-1 on the cell membrane of A. hydrophila, evidenced by releasing more nucleic acids, proteins, and transmembrane pH ingredients decrease and electromotive force dissipation. SEM images showed that compared with the single Epi-1 treatment, the co-treatment of Epi-1 and lactic acid caused more outer membrane vesicles (OMVs) and more severe cell deformation. These findings proved that lactic acid could enhance the efficiency of Epi-1 against A. hydrophila and shed light on new aspects to avoid resistance of pathogens against Epi-1.

Green fabrication of silver nanoparticles with Syzygium aromaticum leaf extract: Characterization and applications as a biocontrol agent for multidrug resistant pathogens

The current study looks into the physical, chemical, and antimicrobial potential of the biogenic Silver Nanoparticles(AgNPs) using Syzygium aromaticum leaf extract.Synthesis parameters were altered to figure out optimum synthesis conditions. Optimum synthesis was observed with 9 mL of 1 mM silver nitrate and 1 mL leaf extract at 55 °C and pH 9 with 24 h incubation.Characterization was performed using UV–vis spectroscopy, X-ray diffraction, Transmission Electron Microscopy, Scanning Electron Microscopy, Fourier Transform Infrared, and Zeta Potential. Average particle size was found to be 37.5 nm. Nanoparticles synthesized exhibited strong antibacterial activity against tested multidrug-resistant pathogens(MDR) pathogens affirming their therapeutic potential.

Investigation of Flagellum genes FleN and FlgE and Gene Expression of FleN Gene in Pseudomonas Aeruginosa Clinical Isolates

The opportunistic multidrug resistance pathogen Pseudomonas aeruginosa has one or several flagella, and the numbers of these sophisticated machines are regulated by the flagellar regulator gene FleN. The flagellar hook gene FlgE is important for its synthesis, motility and tolerance to antibiotics. Bacteriahave resistance to antibiotics, especially to cephalosporin beta-lactam antibiotics. For the current study, 102 clinical specimens were collected and identified using routine laboratory tests and confirmed by Vitek-2 compact system. A total of 33 isolates of P. aeruginosa were identified. The antibiotic susceptibility test was done by the Vitek 2 Compact system. Flagellar gene detected by conventional PCR revealed that the FleN gene existed in 26 (78.8%), of which fifteen isolates were MDR. Whereas the FlgE gene existed in 20 (60.6%), of which fourteen isolates were MDR bacteria. The FleN gene expression in five isolates done by RT-qPCR revealed that four isolates were down regulated, and one isolate was up regulated in FleN gene expression when treated with ceftazidime at sub-MIC. While all isolates were downregulated when treated with amikacin at sub-MIC.

Chitosan-carrageenan microbeads containing nano-encapsulated curcumin: Nano-in-micro hydrogels as alternative-therapeutics for resistant pathogens associated with chronic wounds

Antimicrobial resistance is an issue of global relevance for the treatment of chronic wound infections. In this study, nano-in-micro hydrogels (microbeads) of chitosan and κ-carrageenan (CCMBs) containing curcumin-loaded rhamnosomes (Cur-R) were developed. The potential of Cur-R-CCMBs for improving the antibacterial activity and sustained release of curcumin was evaluated. Curcumin-loaded rhamnosomes (rhamnolipids functionalized liposomes) had a mean particle size of 116 ± 7 nm and a surface-charge of −24.5 ± 9.4 mV. The encapsulation efficiency of curcumin increased from 42.83 % ± 0.69 % in Cur-R to 95.24 % ± 3.61 % respectively after their embedding in CCMBs. SEM revealed smooth surface morphology of Cur-R-CCMBs. FTIR spectroscopy confirmed the presence of weak electrostatic and hydrophobic interactions among curcumin, rhamnosomes, and microbeads. Cur-R-CCMBs had demonstrated significant antibacterial activity against multi-drug resistant chronic wound pathogens including Staphylococcus aureus and Pseudomonas aeruginosa. Cur-R-CCMBs also exhibited significantly higher anti-oxidant (76.85 % ± 2.12 %) and anti-inflammatory activity (91.94 % ± 0.41 %) as well as hemocompatibility (4.024 % ± 0.59 %) as compared to pristine microbeads. In vivo infection model of mice revealed significant reduction in the viable bacterial count of S. aureus (∼2.5 log CFU/mL) and P. aeruginosa (∼2 log CFU/mL) for Cur-R-CCMBs after 5 days. Therefore, nano-in-micro hydrogels can improve the overall efficacy of hydrophobic antimicrobials to develop effective alternative-therapeutics against resistant-pathogens associated with chronic wound infections.

Polymyxin resistance in Enterobacter cloacae complex in Brazil: phenotypic and molecular characterization.

Enterobacter cloacae complex isolates have been reported as an important nosocomial multidrug resistance pathogen. In the present study, we investigated antimicrobial susceptibility and the colistin-resistance rates,their genetic determinants and clonality among clinical E. cloacae complex isolates from different Brazilian states. For this, an initial screening was carried out on 94 clinical isolates of E. clocacae complex received between 2016 and 2018 by LAPIH-FIOCRUZ, using EMB plates containing 4μg/mL of colistin, followed MIC determination, resulting in the selection of 26 colistin-resistant isolates from the complex. The presence of carbapenemases encoding genes (blaKPC, blaNDM and blaOXA-48), plasmidial genes for resistance to polymyxins (mcr1-9) and mutations in chromosomal genes (pmrA, pmrB, phoP and phoQ) described as associated with resistance to polymyxin were screened by PCR and DNA sequencing. Finally, the hsp60 gene was sequenced to identify species of the E. cloacae complex and genetic diversity was evaluated by PFGE and MLST. The results have shown that among 94 E. cloacae complex isolates, 19 (20.2%) were colistin-resistant. The resistant strains exhibited MIC ranging from 4 to 128µg / mL and E. hormaechei subsp. steigerwaltii was the prevalent species in the complex (31,6%), followed by E. cloacae subsp. cloacae (26,3%). The antimicrobials with the highest susceptibility rate were gentamicin (21%) and tigecycline (26%). Carbapenemases encoding genes (blaKPC n = 5, blaNDM n = 1) were detected in 6 isolates and mcr-9 in one. Among the modifications found in PmrA, PmrB, PhoP e PhoQ (two-component regulatory system), only the S175I substitution in PmrB found in E. cloacae subsp cloacae isolates were considered deleterious (according to the prediction of PROVEAN). By PFGE, 13 profiles were found among E. cloacae complex isolates, with EcD the most frequent. Furthermore, by MLST 10 ST's, and 1 new ST, were identified in E. cloacae. In conclusion, no prevalence of clones or association among carbapenemase production and polymyxin resistance was found between the E. cloacae. Thereby, the results suggest that the increased polymyxin-resistance is related to the selective pressure exerted by the indiscriminate use in hospitals. Lastly, this study highlights the urgent need to elucidate the mechanism involved in the resistance to polymyxin in the E. cloacae complex and the development of measures to control and prevent infections caused by these multiresistant bacteria.

Estimating the value of new antibiotic treatment strategies in Zhejiang province, China: cost-effectiveness analysis based on a validated dynamic model

ObjectivesThis analysis aims to better reflect the value of new antibiotic treatment strategies, thereby informing clinical antibiotic use, antimicrobial reimbursement and/or hospital formulary decision-making in China.DesignWe adapted a published and...

Exploring the interactions between Nosema ceranae infection and the honey bee gut microbiome

Managed colonies of the European honey bee, Apis mellifera, have faced considerable losses in recent years. A widespread contributing factor is a microsporidian pathogen, Nosema ceranae, which occurs worldwide, is increasingly resistant to antibiotic treatment, and can alter the host’s immune response and nutritional uptake. These obligate gut pathogens share their environment with a natural honey bee microbiome whose composition can affect pathogen resistance. We tested the effect of N. ceranae infection on this microbiome by feeding 5 day-old adult bees that had natural, fully developed microbiomes with live N. ceranae spores (40,000 per bee) or a sham inoculation, sterile 2.0 M sucrose solution. We caged and reared these bees in a controlled lab environment and tracked their mortality over 12 d, after which we dissected them, measured their infection levels (gut spore counts), and analyzed their microbiomes. Bees fed live spores had two-fold higher mortality by 12 d and 36.5-fold more spores per bee than controls. There were also strong colony effects on infection levels, and 9% of spore-inoculated bees had no spore counts at all (defined as fed-spores-but-not-infected). Nosema ceranae infection had significant but subtle effects on the gut microbiomes of experimentally infected bees, bees with different infection levels, and fed-spores-but-not-infected vs. bees with gut spores. Specific bacteria, including Gilliamella ASVs, were positively associated with infection, indicating that multiple strains of core gut microbes either facilitate or resist N. ceranae infection. Future studies on the interactions between bacterial, pathogen, and host genotypes would be illuminating.

Genomics‐based plant disease resistance prediction using machine learning

AbstractPlant disease outbreaks continuously challenge food security and sustainability. Traditional chemical methods used to treat diseases have environmental and health concerns, raising the need to enhance inherent plant disease resistance mechanisms. Traits, including disease resistance, can be linked to specific loci in the genome and identifying these markers facilitates targeted breeding approaches. Several methods, including genome‐wide association studies and genomic selection, have been used to identify important markers and select varieties with desirable traits. However, these traditional approaches may not fully capture the non‐linear characteristics of the effect of genomic variation on traits. Machine learning, known for its data‐mining abilities, offers an opportunity to enhance the accuracy of the existing trait association approaches. It has found applications in predicting various agronomic traits across several species. However, its use in disease resistance prediction remains limited. This review highlights the potential of machine learning as a complementary tool for predicting the genetic loci contributing to pathogen resistance. We provide an overview of traditional trait prediction methods, summarize machine‐learning applications, and address the challenges and opportunities associated with machine learning‐based crop disease resistance prediction.

Diverse RNA viruses discovered in multiple seagrass species.

Seagrasses are marine angiosperms that form highly productive and diverse ecosystems. These ecosystems, however, are declining worldwide. Plant-associated microbes affect critical functions like nutrient uptake and pathogen resistance, which has led to an interest in the seagrass microbiome. However, despite their significant role in plant ecology, viruses have only recently garnered attention in seagrass species. In this study, we produced original data and mined publicly available transcriptomes to advance our understanding of RNA viral diversity in Zostera marina, Zostera muelleri, Zostera japonica, and Cymodocea nodosa. In Z. marina, we present evidence for additional Zostera marina amalgavirus 1 and 2 genotypes, and a complete genome for an alphaendornavirus previously evidenced by an RNA-dependent RNA polymerase gene fragment. In Z. muelleri, we present evidence for a second complete alphaendornavirus and near complete furovirus. Both are novel, and, to the best of our knowledge, this marks the first report of a furovirus infection naturally occurring outside of cereal grasses. In Z. japonica, we discovered genome fragments that belong to a novel strain of cucumber mosaic virus, a prolific pathogen that depends largely on aphid vectoring for host-to-host transmission. Lastly, in C. nodosa, we discovered two contigs that belong to a novel virus in the family Betaflexiviridae. These findings expand our knowledge of viral diversity in seagrasses and provide insight into seagrass viral ecology.

AUDIT OF INFECTION CONTROL EFFECTIVENESS AND ANTIMICROBIAL DRUGS ADMINISTRATION IN UKRAINE: A PROSPECTIVE FOLLOW-UP

Indicators of antibiotic resistance in the world and in Ukraine are steadily increasing. As of 2021, there is a national standard in Ukraine that recognizes the deescalation of antibiotic therapy, but the war in Ukraine has significantly disrupted the supply of essential services. War-related infections and antimicrobial resistance are seriously affecting the health of people in Ukraine and beyond, forming a great reservoir of multidrug-resistant gram-negative infections Aims: monitor the effectiveness of infection control and antibiotic administration in the Public Health Department of Ukraine. Methods: Based on the Department of Surgery, Anesthesiology and Intensive Care of the PDO National Medical University named after O.O. Bogomolets, a prospective observational study was carried out - an anonymous audit of doctors, anesthesiologists and doctors of other specialties who work at the Public Health Service of Ukraine from the beginning of 2024. The investigation was carried out on the online platform Google-form. After the completion of the tracking period, all completed data was transferred to an Excel table and analyzed using additional descriptive statistics for parametric data. Results: The results of 214 participants from different regions of Ukraine were collected. Half of the respondents reported that the department of infection control functions effectively - 105 (49.2 %), formally important - 85 (39.9 %), and does not function in 3 (1.5 %) Cefazolin as the first choice AB (57.7 %), using of Ceftriaxone (18.6 %) or Cefuroxime (7.9 %) as the 1st line of AB prophylaxis. About not using the protocol tell for us the choice of AB 2-line AB prevention and treatment of Gram+ and Gram-infection. The most common resistant pathogens in the Ukrainian health care sector were: Klebsiella pneumonia 140 (65.4 %) and Pseudomonas aeruginosa 99 (46.3 %) species. Most respondents also reported the expansion of three courses of AB therapy: 7-10 days in 97 (45.5 %) and 10 days and more – 85 (39.9 %) types. Conclusion: most health protection regulations in Ukraine today include the creation of infection control and approval of local documents (new clinical protocols, patient routes) from infection control and administration Instruction of AB. However, wider problems are avoided without the continuation of specific protocols, the use of AB group reserve for AB prophylaxis, the choice of non-optimal empirical AB therapy, the wider acceptance of combination therapy without indications, trivial courses therapy and type of de-escalation.

Contributions of Long-Read Sequencing for the Detection of Antimicrobial Resistance.

In the context of increasing antimicrobial resistance (AMR), whole-genome sequencing (WGS) of bacteria is considered a highly accurate and comprehensive surveillance method for detecting and tracking the spread of resistant pathogens. Two primary sequencing technologies exist: short-read sequencing (50-300 base pairs) and long-read sequencing (thousands of base pairs). The former, based on Illumina sequencing platforms (ISPs), provides extensive coverage and high accuracy for detecting single nucleotide polymorphisms (SNPs) and small insertions/deletions, but is limited by its read length. The latter, based on platforms such as Oxford Nanopore Technologies (ONT), enables the assembly of genomes, particularly those with repetitive regions and structural variants, although its accuracy has historically been lower. We performed a head-to-head comparison of these techniques to sequence the K. pneumoniae VS17 isolate, focusing on blaNDM resistance gene alleles in the context of a surveillance program. Discrepancies between the ISP (blaNDM-4 allele identified) and ONT (blaNDM-1 and blaNDM-5 alleles identified) were observed. Conjugation assays and Sanger sequencing, used as the gold standard, confirmed the validity of ONT results. This study demonstrates the importance of long-read or hybrid assemblies for accurate carbapenemase resistance gene identification and highlights the limitations of short reads in the context of gene duplications or multiple alleles. In this proof-of-concept study, we conclude that recent long-read sequencing technology may outperform standard short-read sequencing for the accurate identification of carbapenemase alleles. Such information is crucial given the rising prevalence of strains producing multiple carbapenemases, especially as WGS is increasingly used for epidemiological surveillance and infection control.