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Relationship Between Human Microbiome and Helicobacter pylori
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Sex Differences and Pathogen Patterns in Surgically Treated Aortic Valve Endocarditis over 15 Years
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Transcriptomic Response of Balamuthia mandrillaris to Lippia graveolens Extract Fractions
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Broad Spectrum Antimicrobial Activity of Bacteria Isolated from Vitis vinifera Leaves
Journal Description
Microbiology Research
Microbiology Research
is an international, scientific, peer-reviewed open access journal published monthly online by MDPI (from Volume 11 Issue 2-2020).
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, ESCI (Web of Science), Embase, and other databases.
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 15.4 days after submission; acceptance to publication is undertaken in 2.7 days (median values for papers published in this journal in the second half of 2024).
- Recognition of Reviewers: APC discount vouchers, optional signed peer review, and reviewer names published annually in the journal.
Impact Factor:
2.1 (2023);
5-Year Impact Factor:
2.0 (2023)
Latest Articles
Detoxification of Ustiloxin A by Hydroxylation of Endophytic Fungus Petriella setifera Nitaf10
Microbiol. Res. 2025, 16(5), 93; https://doi.org/10.3390/microbiolres16050093 (registering DOI) - 29 Apr 2025
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Ustiloxins are a kind of cyclopeptide mycotoxins produced by rice false smut pathogen Villosiclava virens, which seriously threatens the safe production of rice and health of humans and animals. Hydroxylation, a biotransformation reaction that regio- and stereoselectively introduces a hydroxyl group into
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Ustiloxins are a kind of cyclopeptide mycotoxins produced by rice false smut pathogen Villosiclava virens, which seriously threatens the safe production of rice and health of humans and animals. Hydroxylation, a biotransformation reaction that regio- and stereoselectively introduces a hydroxyl group into the molecule catalyzed by the hydroxylase produced by organisms, has been considered an efficient way to detoxify mycotoxins. In this study, the endophytic fungus Petriella setifera Nitaf10 was found to be able to detoxify ustiloxin A, the main toxic component in V. virens. In addition to the two main transformed products previously identified, ustiloxins A1 and A2, an additional transformed product was obtained by using cell-free extract (CFE) of P. setifera Nitaf10 prepared with 5 mmol/L of pH 9.0 carbonate-buffered solution (CBS). It was structurally characterized as a novel ustiloxin analog named 13-hydroxy ustiloxin A (1) by analysis of the 1D and 2D NMR and HRESIMS spectra as well as by comparison with known ustiloxins. Biotransformation reaction of ustiloxin A was found to proceed via hydroxylation, and was possibly catalyzed by the intracellular hydroxylase in the CFE. The cytotoxic and phytotoxic activities of 13-hydroxy ustiloxin A (1) were much weaker than those of ustiloxin A. Detoxification of ustiloxin A by hydroxylation of P. setifera will be an efficient strategy.
Full article
Open AccessReview
Gut Bacteria-Based Cancer Therapy and Anti-Solid Tumor Mechanisms
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Tianzhu Zhang, Xiao-Mei Yu, Shang-Tian Yang and Wen-Wen Zhou
Microbiol. Res. 2025, 16(5), 92; https://doi.org/10.3390/microbiolres16050092 (registering DOI) - 26 Apr 2025
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Cancer constitutes a significant global health challenge, ranking among the leading contributors to worldwide mortality. The inherent limitations of conventional oncologic interventions, particularly their frequent inability to induce durable remissions in advanced malignancies, continue to drive transformative explorations into novel therapeutic paradigms. In
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Cancer constitutes a significant global health challenge, ranking among the leading contributors to worldwide mortality. The inherent limitations of conventional oncologic interventions, particularly their frequent inability to induce durable remissions in advanced malignancies, continue to drive transformative explorations into novel therapeutic paradigms. In recent years, bacteria-based therapies have gained recognition in the management of solid tumors. Compared to traditional therapeutic modalities, extensive research has demonstrated that bacteria possess remarkable anticancer properties. Gut bacteria, which naturally coexist within the human body, represent a unique category of living cells with inherent advantages for solid tumor treatment. These microorganisms are characterized by their relative safety, ease of cultivation, and potential for use in precision medicine through genetic modifications. Furthermore, gut bacteria exhibit diverse mechanisms of action against tumor cells, with different bacterial species potentially exerting synergistic effects. However, the precise anticancer mechanisms of these bacteria, particularly those of gut microbiota, require further detailed investigation. This review categorizes anticancer gut bacteria according to their effects on cancer cells and elucidates their anticancer mechanisms across five domains: modification of the tumor microenvironment, competitive inhibition, activation of immune cells, vectors for gene therapy, and production of bacterial anticancer biomolecules. Additionally, we discuss the potential challenges of utilizing different gut bacteria for cancer treatment, highlight their anticancer advantages, and suggest promising directions for future research. Ultimately, this review serves as a comprehensive guide for utilizing both natural and engineered gut bacteria as therapeutic agents against solid tumors in cancer treatment.
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Open AccessArticle
In Utero Exposure to 2,3,7,8-Tetrachlorodibenzo-p-dioxin Impairs the Ability of Mice to Clear a Pseudomonas aeruginosa Infection in Adulthood
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Victoria R. Stephens, Julia K. Bohannon, Kaylon L. Bruner-Tran, Xenia D. Davis, Mary A. Oliver, Margaret A. McBride, Sharareh Ameli, Jelonia T. Rumph, Jennifer A. Gaddy, Edward R. Sherwood and Kevin G. Osteen
Microbiol. Res. 2025, 16(5), 91; https://doi.org/10.3390/microbiolres16050091 (registering DOI) - 26 Apr 2025
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Exposure to endocrine-disrupting chemicals (EDCs) has been linked to several pathologies in human health, especially those involving the immune system. The vast majority of studies have focused on cells and functions of the adaptive immune system with little investigation of the impact of
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Exposure to endocrine-disrupting chemicals (EDCs) has been linked to several pathologies in human health, especially those involving the immune system. The vast majority of studies have focused on cells and functions of the adaptive immune system with little investigation of the impact of EDCs on innate immunity. While EDC exposure remains a threat throughout the lifetime of an individual, the most detrimental effects on human health occur during critical stages of development, such as in utero. Fetal development is not only associated with growth and tissue remodeling but also with the establishment of key processes, including those of the immune system. Unfortunately, due to fetal plasticity, developmental exposure to certain EDCs, including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), can affect mammalian health well into adulthood by altering fetal programming. Herein, we hypothesize that in utero exposure to TCDD induces developmental reprogramming of the innate immune system that subsequently impacts the adult response to infection. To interrogate our hypothesis, we challenged adult mice with and without a history of in utero TCDD exposure with 1 × 108 CFU Pseudomonas aeruginosa via intraperitoneal injection. Results revealed a significant decrease in the number of innate leukocytes at the site of infection six hours after inoculation in toxicant-exposed mice compared to unexposed mice. The reduction in the number of phagocytes correlated with a reduction in bacterial clearance in toxicant-exposed mice. We also noted a decreased ability of peritoneal immune cells from toxicant-exposed mice to produce chemokines necessary for immune cell recruitment. Taken together, our results indicate that in utero EDC exposure impairs the innate immune response to a bacterial infection in adult offspring, particularly in males.
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Open AccessArticle
The Presence of an ESBL-Encoding Plasmid Reported During a Klebsiella pneumoniae Nosocomial Outbreak in the United Kingdom
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Stephen Mark Edward Fordham, Anna Mantzouratou and Elizabeth Sheridan
Microbiol. Res. 2025, 16(5), 90; https://doi.org/10.3390/microbiolres16050090 - 25 Apr 2025
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An EBSL-encoding plasmid, pESBL-PH, was identified during a nosocomial outbreak of Klebsiella pneumoniae ST628 at a United Kingdom general district hospital in 2018. The plasmid from the earliest 2018 K. pneumoniae strain discovered during the outbreak was assembled using both Oxford nanopore long
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An EBSL-encoding plasmid, pESBL-PH, was identified during a nosocomial outbreak of Klebsiella pneumoniae ST628 at a United Kingdom general district hospital in 2018. The plasmid from the earliest 2018 K. pneumoniae strain discovered during the outbreak was assembled using both Oxford nanopore long reads and illumina short reads, yielding a fully closed plasmid, pESBL-PH-2018. pESBL-PH-2018 was queried against the complete NCBI RefSeq Plasmid Database, comprising 93,823 plasmids, which was downloaded on 16 July 2024. To identify structurally similar plasmids, strict thresholds were applied, including a mash similarity ≥0.98. This returned 61 plasmids belonging to 13 unique sequence types (STs) hosts. The plasmids were detected from 13 unique countries, dating from 2012 to 2023. The AMR region of the plasmids varied. Interestingly IS26-mediated tandem amplification of resistance genes, including the ESBL gene blaCTX-M-15 was identified in two independent strains, raising their copy number to three. Furthermore, the genomic background of strains carrying a pESBL-PH-2018-like plasmid were analyzed, revealing truncation of the chromosomal ompK36 porin gene and carbapenem resistance gene carriage on accessory plasmids in 17.85% and 26.78% of strains with a complete chromosome available. This analysis reveals the widespread dissemination of an ESBL-encoding plasmid in a background of resistance-encoding strains, requiring active surveillance.
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Open AccessEssay
Diversity Analysis of Rhizosphere Microorganisms in Helichrysum arenarium (L.) Moench and Screening of Growth-Promoting Bacteria in Xinjiang, China
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Xiaoyan Xin, Wei He, Junhui Zhou, Yong Chen, Xin Huang, Jinyu Yang, Jianjun Xu and Suqin Song
Microbiol. Res. 2025, 16(5), 89; https://doi.org/10.3390/microbiolres16050089 (registering DOI) - 25 Apr 2025
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Rhizosphere microorganisms effectively exploit nutrient resources within the rhizosphere, while growth-promoting bacteria in this environment play a vital role in regulating soil fertility and enhancing plant health. In this study, we utilized a comprehensive approach that included the isolation, purification, and identification of
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Rhizosphere microorganisms effectively exploit nutrient resources within the rhizosphere, while growth-promoting bacteria in this environment play a vital role in regulating soil fertility and enhancing plant health. In this study, we utilized a comprehensive approach that included the isolation, purification, and identification of dominant microorganisms, alongside high-throughput sequencing technology. This methodology was employed to analyze the primary microbial groups and their diversity within the rhizosphere soil of Helichrysum arenarium (L.) Moench in Altay, Xinjiang, China. By isolating bacterial strains from the rhizosphere soil using a dilution coating method, we successfully obtained 43 distinct strains. Subsequently, selective media were employed to screen for growth-promoting characteristics among these isolated strains derived from the rhizosphere soil of H. arenarium (L.) Moench. The results, obtained through high-throughput amplification sequencing, revealed diverse bacterial communities belonging to 35 phyla, 93 orders, 215 families, 324 genera, and 231 species associated with H. arenarium (L.) Moench, as well as fungal communities comprising 14 phyla, 47 orders, 96 families, 204 genera, and 571 species present in the rhizosphere soil. Among these identified communities, Actinobacteriota emerged as the predominant bacterial phylum while Ascomycetes and Mortieromycetes were recognized as the principal fungal phyla found in the rhizospheric soil of H. arenarium (L.) Moench. Analysis of culturable bacteria’s promotion activity within this rhizospheric environment indicated that three strains—S16, S31, and S29—exhibited the highest solubility index for inorganic phosphorus; additionally, the screened strains S7 and S10 demonstrated nitrogen-fixing capabilities. Furthermore, ten strains exhibiting excellent iron-bearing capacities were identified; notably, strain S16 displayed the highest D/d value indicating, its superior iron-bearing capacity. The growth-promoting bacteria were identified as Kocuria rosea, Priestia megaterium, Bacillus mobilis, Bacillus bataviensis, three variants of Bacillus mycoides, Bacillus paramobilis, Bacillus sonorensis, and Alcaligenes faecalis. This study provides a foundational understanding of how microorganisms in the rhizosphere of H. arenarium (L.) Moench influence soil nutrient release and offers valuable insights into enhancing yield and quality cultivation by isolating, screening, and identifying growth-promoting bacteria from rhizosphere soil.
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Open AccessArticle
Tick Dispersal and Borrelia Species in Ticks from Migratory Birds: Insights from the Asinara National Park, Sardinia, Italy
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Valentina Chisu, Laura Giua, Piera Bianco, Cipriano Foxi, Giovanna Chessa, Giovanna Masala and Ivana Piredda
Microbiol. Res. 2025, 16(5), 88; https://doi.org/10.3390/microbiolres16050088 - 23 Apr 2025
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Rapid environmental changes driven by human activities are contributing to a significant decline in global biodiversity, with avian species being particularly affected due to their migratory behavior. As highly mobile hosts, birds facilitate the geographic dispersal of ectoparasites, including ticks, which serve as
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Rapid environmental changes driven by human activities are contributing to a significant decline in global biodiversity, with avian species being particularly affected due to their migratory behavior. As highly mobile hosts, birds facilitate the geographic dispersal of ectoparasites, including ticks, which serve as vectors for numerous zoonotic pathogens. This study, conducted in collaboration with the Faunistic Observatory of the Asinara National Park between 2021 and 2023, aimed to investigate the potential role of migratory birds in tick dispersal and the presence of Borrelia spp. DNA. Birds were captured using mist nets during pre-breeding (April–May) and post-breeding (October–November) migration periods. Ticks were systematically collected and identified at the species level, and molecular analyses were performed using real-time and conventional PCR to detect the presence of Borrelia spp. DNA. Results showed a distinct seasonal variation in tick species composition. In autumn, Ixodes ricinus was predominant (99%), whereas Hyalomma species were more frequently observed in spring (78%). Molecular screening revealed Borrelia spp. DNA in 26.1% of the collected ticks, with Borrelia garinii being the most prevalent species. These findings underscore the ecological significance of migratory birds in the dissemination of ticks and tick-borne pathogens, highlighting their potential role in shaping disease transmission dynamics across different geographic regions. This study provides valuable insights into the seasonal fluctuations in tick populations associated with migratory avifauna and the epidemiological risks posed by these interactions. Continued surveillance of migratory birds as vectors of zoonotic pathogens is essential for informing public health strategies and mitigating the risks of emerging infectious diseases, but further investigation is needed to clarify the actual role of migratory birds in the transmission of Borrelia spp.
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Open AccessArticle
Dual Detection of Pathogenic tdh and trh Genes of Vibrio parahaemolyticus in Oysters Using Multienzyme Isothermal Rapid Amplification (MIRA) Combined with Lateral-Flow Dipstick (LFD) Assay
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Seong Bin Park, Sam K. C. Chang, Lin Bi, Yunim Cha and Yan Zhang
Microbiol. Res. 2025, 16(5), 87; https://doi.org/10.3390/microbiolres16050087 - 22 Apr 2025
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Vibrio parahaemolyticus is a foodborne pathogen commonly associated with the consumption of contaminated seafood, particularly oysters. While PCR and real-time PCR are widely used to detect its pathogenicity through tdh and trh gene detection, these methods may not be practical in resource-limited settings
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Vibrio parahaemolyticus is a foodborne pathogen commonly associated with the consumption of contaminated seafood, particularly oysters. While PCR and real-time PCR are widely used to detect its pathogenicity through tdh and trh gene detection, these methods may not be practical in resource-limited settings such as field environments. To address this limitation, a rapid, sensitive, and specific duplex detection method was developed using the multienzyme isothermal rapid amplification (MIRA) assay in combination with lateral flow dipstick (LFD) technology. The assay utilized specific primer sets and probes to simultaneously amplify tdh and trh fragments tagged with 3′-FAM and 5′-Digoxigenin or Biotin during MIRA amplification, enabling the detection via respective antibody capture on the LFD strip. This duplex MIRA-LFD assay demonstrated a detection limit of 100 fg of DNA, 300 CFU/reaction for bacterial culture, and 3000 CFU/reaction for seeded oyster samples at 40 °C within 20 min. Notably, the assay exhibited no cross-reactivity with nine other Vibrio species or 18 foodborne pathogens, confirming its high specificity. Due to its simplicity, rapid turnaround time, and high sensitivity, this duplex MIRA-LFD assay offers a valuable tool for the surveillance of V. parahaemolyticus pathogenicity, aiding in public health protection and supporting the local seafood industry.
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Open AccessReview
The Genus Clonostachys (Bionectria) as a Potential Tool Against Agricultural Pest and Other Biotechnological Applications: A Review
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Manuela Reyes-Estebanez and Pedro Mendoza-de Gives
Microbiol. Res. 2025, 16(4), 86; https://doi.org/10.3390/microbiolres16040086 - 19 Apr 2025
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The Clonostachys genus is a saprophytic soil microfungus (Ascomycota). It exhibits significant ecological adaptability and plays a crucial role in maintaining the balance of soil microorganisms. Species within this genus are natural antagonists of insects and nematodes, and they also combat phytopathogenic fungi
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The Clonostachys genus is a saprophytic soil microfungus (Ascomycota). It exhibits significant ecological adaptability and plays a crucial role in maintaining the balance of soil microorganisms. Species within this genus are natural antagonists of insects and nematodes, and they also combat phytopathogenic fungi through mycoparasitism. This process involves producing lytic enzymes and competing for space and nutrients. Clonostachys species are effective biocontrol agents in agriculture and have been utilized to manage pests affecting many high-value commercial crops, acting as a natural biopesticide. They inhabit plant tissues, boosting plant defenses and activating genes for water and nutrient uptake, enhancing plant performance. Additionally, they produce enzymes and bioactive metabolites with antimicrobial, antifungal, nematocidal, anticancer, and antioxidant properties. Clonostachys species can degrade plastic waste and remove hydrocarbons from crude oil-contaminated sites when functioning as endophytes, positioning Clonostachys as a promising candidate for reducing environmental pollution. There are still challenges and limitations, such as the continuous surveillance of the safety of Clonostachys species on plants, the establishment of commercial applications, formulation viability, and variability due to field conditions. These issues will have to be addressed. This review provides an overview of Clonostachys ecology, morphology, classification, and biotechnological applications, emphasizing its significance in various fields.
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Open AccessReview
The Complexities of Canine Monocytic Ehrlichiosis: Insights into Ehrlichia canis and Its Vector Rhipicephalus sanguineus
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Joana Ferrolho, Sandra Antunes, Hugo Vilhena, Sofia Anastácio, Sérgio Ramalho de Sousa, Gonçalo Frouco, Bárbara Ferreira and Ana Domingos
Microbiol. Res. 2025, 16(4), 85; https://doi.org/10.3390/microbiolres16040085 - 17 Apr 2025
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Canine monocytic ehrlichiosis (CME) is a highly infectious disease with zoonotic potential. Ehrlichia canis, the causative agent, is primarily transmitted by Rhipicephalus sanguineus. Tick infestation and tick-borne diseases (TBDs) are serious human and veterinary health problems due to the lack of
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Canine monocytic ehrlichiosis (CME) is a highly infectious disease with zoonotic potential. Ehrlichia canis, the causative agent, is primarily transmitted by Rhipicephalus sanguineus. Tick infestation and tick-borne diseases (TBDs) are serious human and veterinary health problems due to the lack of efficient control measures. This review aims to provide information about CME, detailing epidemiology, pathogenesis, clinical manifestations, and current strategies for diagnosis, treatment, and prevention. The review delves into the biology of R. sanguineus, exploring its lifecycle, habitat, and mechanisms of E. canis transmission. Ehrlichia canis infection follows a three-phase transition: acute, subclinical, and chronic, with distinct clinical signs, from mild to severe and even life-threatening in some cases, with the potential for asymptomatic long-term carriers acting as reservoirs. Pathogenesis involves complex interactions between the pathogen and host immune responses, influencing disease severity and progression. Additionally, the review highlights challenges in controlling CME due to the widespread distribution of R. sanguineus. Genetic diversity within R. sanguineus populations and their varying vector competence further complicate control efforts. The role of environmental changes in tick distribution aligns the control of CME within the One Health concept, integrating approaches to improve outcomes for humans, animals, and the environment. Preventive measures on tick control and potential vaccine development are also reviewed.
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Open AccessArticle
YKL-40 and Lysosome-Associated Membrane Proteins as Potential Discriminative Biomarkers in Central Nervous System Infections
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Maria Kazakova, Yordan Kalchev, Valentin Dichev, Petya Argirova, Kiril Simitchiev, Mariana Murdjeva and Victoria Sarafian
Microbiol. Res. 2025, 16(4), 84; https://doi.org/10.3390/microbiolres16040084 - 11 Apr 2025
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The aim of our study was to evaluate the discriminative value of gene and protein expression levels of the inflammatory marker (YKL-40) and lysosome-associated membrane protein 1 and 2 (LAMP-1 and LAMP-2) in patients with central nervous system (CNS) infections. Thirty hospitalized patients
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The aim of our study was to evaluate the discriminative value of gene and protein expression levels of the inflammatory marker (YKL-40) and lysosome-associated membrane protein 1 and 2 (LAMP-1 and LAMP-2) in patients with central nervous system (CNS) infections. Thirty hospitalized patients with CNS infections and undefined etiology, and 22 healthy subjects as a control group, were included in the study. Gene expression levels of YKL-40, LAMP-1 and LAMP-2 were determined by qPCR. Plasma and CSF concentrations of the tree proteins of interest were detected by ELISA. Our results showed that mRNA levels of YKL-40 were significantly downregulated in WBCs of patients compared to controls, while plasma YKL-40 concentrations were higher. LAMP-1 significantly increased in patients’ plasma and CSF was found. Patients were subdivided depending on the confirmed or presumed etiological agent into two subgroups groups—patients with bacterial or with viral neuroinfection. Differences between plasma levels of YKL-40 in the subgroups when matched with controls were detected. The concentrations of the glycoprotein were higher in patients with bacterial infections compared to those with the viral ones. We revealed that LAMP-1 plasma levels were also significantly increased in patients with viral infections in comparison to healthy individuals. We could speculate that YKL-40 plasma levels might serve as a fast discriminative tool to support the presence of viral or bacterial CNS infections.
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Open AccessArticle
Antimicrobial Resistance in Swine and Cattle Farms
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Bruna F. Pinto, Sara A. M. Silva, Inês C. Rodrigues, J. M. Lopes-Jorge, J. Niza-Ribeiro, Joana C. Prata and Paulo Martins da Costa
Microbiol. Res. 2025, 16(4), 83; https://doi.org/10.3390/microbiolres16040083 - 9 Apr 2025
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Antimicrobial resistance is increasingly becoming a serious public health issue. There is scientific evidence linking the use of antibiotics in livestock production to the emergence and spread of resistance in bacteria that are important for human health. To assess the prevalence of antimicrobial
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Antimicrobial resistance is increasingly becoming a serious public health issue. There is scientific evidence linking the use of antibiotics in livestock production to the emergence and spread of resistance in bacteria that are important for human health. To assess the prevalence of antimicrobial resistance in Escherichia coli and Enterococcus spp., fecal and slurry wastewater samples were collected from various cattle and swine farms, mainly located in the northern and central regions of Portugal. Samples from each farm were pooled for microbiological processing to isolate Escherichia coli and Enterococcus spp., followed by specific antibiotic susceptibility testing for each species using the disk diffusion method. The results of these analyses indicated a significant issue with tetracycline resistance in E. coli and Enterococcus spp. Furthermore, a notably higher frequency in resistant strains was observed in the majority of slurry samples compared to those derived from swine feces. This observation led to the hypothesis that slurry may provide a comprehensive historical perspective for studying the antibiotic resistance patterns present on a farm.
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Open AccessArticle
Epidemiological, Clinical and Phylogenetic Characteristics of West Nile Virus in Bulgaria, 2024
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Kim Ngoc, Ivan Stoikov, Ivelina Trifonova, Elitsa Panayotova, Iva Trifonova and Iva Christova
Microbiol. Res. 2025, 16(4), 82; https://doi.org/10.3390/microbiolres16040082 - 4 Apr 2025
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West Nile Virus (WNV), a mosquito-borne pathogen, is a growing public health challenge across Europe. Environmental and anthropogenic factors have led to the spread of the virus to higher geographic latitudes, as well as to increased viral circulation and genetic diversity. Aims: This
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West Nile Virus (WNV), a mosquito-borne pathogen, is a growing public health challenge across Europe. Environmental and anthropogenic factors have led to the spread of the virus to higher geographic latitudes, as well as to increased viral circulation and genetic diversity. Aims: This study aimed to describe the epidemiological, clinical, and laboratory characteristics of WNV cases in Bulgaria during 2024 and to investigate WNV phylogenetics. Epidemiological, clinical and laboratory data from 32 patients with confirmed or probable WNV infections were collected and analysed. Complete viral genomes were obtained from two samples using whole genome sequencing (WGS). Phylogenetic analysis was performed using the Nextstrain WNV analysis pipeline. Severe disease was observed in 21 patients, with three fatalities reported in older males with comorbidities. Phylogenetic analysis revealed that Bulgarian strains clustered within the Central/Southern European clade of lineage 2, closely related to Greek strains. Evidence suggested localised viral evolution following cross-border introduction from Greece. Our study provides a detailed clinical and laboratory characterization of the human WNV cases detected in Bulgaria in 2024. Improved diagnostic workflows, expanded laboratory resources and increased molecular surveillance are essential to better understand the burden of WNV infections in Bulgaria, as well as to follow the evolution and spread of the virus.
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Open AccessArticle
Molecular and Epidemiological Analysis of Carbapenem-Resistant Klebsiella pneumoniae in a Greek Tertiary Hospital: A Retrospective Study
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Alexandra Myari, Petros Bozidis, Efthalia Priavali, Eleni Kapsali, Vasilios Koulouras, Georgia Vrioni and Konstantina Gartzonika
Microbiol. Res. 2025, 16(4), 81; https://doi.org/10.3390/microbiolres16040081 - 4 Apr 2025
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Carbapenemase-producing Klebsiella pneumoniae is responsible for multiple serious infections with high mortality rates. K. pneumoniae carbapenemases (KPCs) are the most commonly isolated carbapenemases worldwide. To study the epidemiological and molecular characteristics of KPC-producing K. pneumoniae (KPC-KP), we conducted a retrospective study at the
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Carbapenemase-producing Klebsiella pneumoniae is responsible for multiple serious infections with high mortality rates. K. pneumoniae carbapenemases (KPCs) are the most commonly isolated carbapenemases worldwide. To study the epidemiological and molecular characteristics of KPC-producing K. pneumoniae (KPC-KP), we conducted a retrospective study at the University General Hospital of Ioannina, Greece. A total of 177 K. pneumoniae clinical strains from the period 2014–2015 were confirmed as KPC producers by polymerase chain reaction (PCR) and were further examined for the presence of blaVIM, blaNDM, blaTEM, blaSHV, and blaCTX-M genes. Using the amplification refractory mutation system (ARMS) method, we identified the presence of the KPC-2 allele in 130 strains and the KPC-9 allele in 47. Strains from both allele groups belonged to the sequence type 258 (ST258). KPC-9 was responsible for a distinct outbreak, considered part of the broader KPC-2 outbreak. Molecular characterization of selected KPC-KP isolates from the period 2021–2022 revealed their continued presence in our hospital. Comparison of the antimicrobial susceptibility profiles of the two alleles showed a statistically significant increase in minimum inhibitory concentration (MIC) for ceftazidime (p = 0.03) and higher resistance to amikacin (p = 0.012) and colistin (p < 0.001) for KPC-9 compared to the KPC-2 allele. The two KPC alleles had similar mortality rates. This study demonstrates the heterogeneity of resistance genes in carbapenem-resistant K. pneumoniae (CR-KP) within a single-hospital setting and underscores the need for immediate containment measures.
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Open AccessArticle
Enhancing Diagnostic Resilience: Evaluation of Extraction Platforms and IndiMag Pathogen Kits for Rapid Animal Disease Detection
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Anne Vandenburg-Carroll, Douglas G. Marthaler and Ailam Lim
Microbiol. Res. 2025, 16(4), 80; https://doi.org/10.3390/microbiolres16040080 - 3 Apr 2025
Abstract
The United States is facing outbreaks of highly pathogenic avian influenza H5N1 in birds and dairy cattle, along with threats of African swine fever, classical swine fever, and foot-and-mouth disease. While the National Animal Health Laboratory Network (NAHLN) depends on high-throughput testing, the
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The United States is facing outbreaks of highly pathogenic avian influenza H5N1 in birds and dairy cattle, along with threats of African swine fever, classical swine fever, and foot-and-mouth disease. While the National Animal Health Laboratory Network (NAHLN) depends on high-throughput testing, the KingFisher Duo Prime, IndiMag 48s, and IndiMag 2 are viable alternatives to aid in outbreak assessments. This study evaluates extraction platforms and the IndiMag Pathogen Kit for detecting the previous listed pathogens. Samples and reference materials were extracted using the MagMAX Viral RNA Isolation Kit, MagMAX CORE Nucleic Acid Purification Kit, and IndiMag Pathogen Kit. Real-time RT-PCR was performed following NAHLN protocols to assess analytical and diagnostic performance. Comparable limits of detection across extraction chemistries, instrumentation, and pathogens were demonstrated, with PCR efficiency ranging between 82.5% and 107.6%. The precision variability was low, with the coefficient of variation ranging from 0.16% to 1.76%. Diagnostic sensitivity and specificity were 100%, with a kappa coefficient of 1.0, indicating strong agreement between methods. These findings support the KingFisher Duo Prime, IndiMag 48s, IndiMag 2, and IndiMag Pathogen Kits as reliable options for NAHLN-approved testing, increasing equipment and reagent alternatives to enhance diagnostic resilience and improve response capabilities to emerging animal health threats.
Full article
(This article belongs to the Special Issue Veterinary Microbiology and Diagnostics)
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Open AccessArticle
Bacterial Profile and Antimicrobial Resistance Pattern from Different Clinical Specimens at Uttara Adhunik Medical College Hospital, Dhaka
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Mahfuza Nasrin, Fahmida Begum, Mohammad Julhas Sujan, Hridika Talukder Barua, Zakir Hossain Habib, S M Shahriar Rizvi, Aninda Rahman, Alina Shaw, Abul Hasnat, Soo Young Kwon, Rezina Karim, Md. Shah Alam, Noshin Nawal, Mohammad Moniruzzaman Bhuiyan, Ahmed Taha Aboushady, Adam Clark, John Stelling, Sanjay Gautam, Florian Marks and Nimesh Poudyal
Microbiol. Res. 2025, 16(4), 79; https://doi.org/10.3390/microbiolres16040079 - 2 Apr 2025
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Introduction: Antimicrobial resistance (AMR) is a critical global public health issue, leading to prolonged illness, increased morbidity and mortality, and rising healthcare costs. The effectiveness of antibiotics is diminishing due to the emergence of resistant bacterial strains. This study aimed to determine the
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Introduction: Antimicrobial resistance (AMR) is a critical global public health issue, leading to prolonged illness, increased morbidity and mortality, and rising healthcare costs. The effectiveness of antibiotics is diminishing due to the emergence of resistant bacterial strains. This study aimed to determine the bacterial profile and AMR patterns of clinical isolates at Uttara Adhunik Medical College Hospital (UAMCH), Dhaka. Methods: A retrospective study was conducted at UAMCH from January 2017 to December 2019. A total of 32,187 clinical specimens (urine, blood, stool, wound swabs/pus, and sputum) were processed, of which 4232 yielded positive cultures. Bacterial identification followed standard bacteriological methods, and antibiotic susceptibility was assessed using the Kirby–Bauer disc diffusion method per CLSI guidelines. Data analysis was conducted using WHONET and QAAPT. Results: The highest proportion of positive cultures was from urine (47.5%), followed by blood (35.0%) and wound swabs/pus (10.1%). The most common isolates were Escherichia coli (37.2%), Salmonella typhi (25.7%), and Klebsiella sp. (11.5%). Gram-negative bacteria showed high resistance to commonly used antibiotics such as amoxicillin/clavulanic acid, cefixime, and ceftriaxone, while the resistance rates were lower for gentamicin, amikacin, and meropenem. However, Acinetobacter sp. exhibited alarming resistance to all tested antibiotics. Conclusions: This study highlights concerning resistance patterns among bacterial isolates, emphasizing the need for ongoing AMR surveillance to inform treatment strategies and improve patient care in Bangladesh.
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Open AccessReview
Bacterial Foodborne Diseases in Central America and the Caribbean: A Systematic Review
by
Nicole Severino, Claudia Reyes, Yumeris Fernandez, Vasco Azevedo, Luis Enrique De Francisco, Rommel T. Ramos, Luis Orlando Maroto-Martín and Edian F. Franco
Microbiol. Res. 2025, 16(4), 78; https://doi.org/10.3390/microbiolres16040078 - 1 Apr 2025
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Foodborne diseases (FBDs) represent a significant public health concern, particularly in regions like Central America and the Caribbean (CAC), where surveillance gaps due to a lack of resources, knowledge, and technical abilities hinder control over outbreaks. This review investigates the bacterial pathogens responsible
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Foodborne diseases (FBDs) represent a significant public health concern, particularly in regions like Central America and the Caribbean (CAC), where surveillance gaps due to a lack of resources, knowledge, and technical abilities hinder control over outbreaks. This review investigates the bacterial pathogens responsible for FBDs, their prevalence, management challenges, and prevention strategies. This systematic review followed PRISMA guidelines, focusing on bacterial FBDs in CAC from 2000 to 2024. PubMed and Google Scholar were used as primary databases, supported by other sources to identify relevant studies. Inclusion criteria encompassed studies focusing on bacterial pathogens, prevalence, risk factors, and surveillance practices. Out of the 509 studies initially identified, 35 met the inclusion criteria. The most prevalent pathogens were Salmonella spp., Escherichia coli, Campylobacter spp., and Aliarcobacter spp., with contamination often associated with poultry, eggs, and vegetables. Key challenges included inadequate surveillance systems, limited resources, and inconsistent reporting practices. A more significant investment in pathogen monitoring, documentation, and education, along with technologies like whole-genome sequencing (WGS), is crucial. Institutional and governmental funding is vital to improve surveillance and strengthen regional risk analysis.
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Open AccessArticle
Antiprotozoal Activity and Selectivity Index of Organic Salts of Albendazole and Mebendazole
by
Miriam Guadalupe Barón-Pichardo, Janeth Gómez-García, David Durán-Martínez, Oscar Torres-Angeles, Jesús Rivera-Islas and Blanca Estela Duque-Montaño
Microbiol. Res. 2025, 16(4), 77; https://doi.org/10.3390/microbiolres16040077 - 27 Mar 2025
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Infections from the protozoa Entamoeba histolytica (E. histolytica), Giardia lamblia (G. lamblia), and Trichomonas vaginalis (T. vaginalis) pose a public health issue, with albendazole and mebendazole serving as the second-line medications for treating these parasitic infections. However,
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Infections from the protozoa Entamoeba histolytica (E. histolytica), Giardia lamblia (G. lamblia), and Trichomonas vaginalis (T. vaginalis) pose a public health issue, with albendazole and mebendazole serving as the second-line medications for treating these parasitic infections. However, the low aqueous solubility of these compounds has led to the exploration of new strategies to enhance their solubility, with the formation of salts being a commonly employed strategy. The sulfonates A1, A2, and A3 of albendazole, along with M1, M2, and M3 of mebendazole, were synthesized. The antiparasitic activity in vitro was assessed against the trophozoites of E. histolytica, G. lamblia, and T. vaginalis. The salts A2, A3, M2, and M3 demonstrated a greater antiparasitic effect (IC50 37.95–125.53 µM) compared to the positive controls albendazole and mebendazole. The salts A1, A3, M2, and M3 do not exhibit cytotoxic effects at concentrations of 500 µM on the Vero cell line. Taken together, these findings indicate that the formation of these new solid saline phases enhances the antiparasitic effects in vitro, which is crucial in the current search for improved, safe, and effective antiparasitic agents.
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Open AccessReview
Rabbit Models for Infectious Diseases Caused by Staphylococcus aureus
by
Minghang Zeng, Yadong Wang, Fang Liu, Jinzhao Long and Haiyan Yang
Microbiol. Res. 2025, 16(4), 76; https://doi.org/10.3390/microbiolres16040076 - 27 Mar 2025
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Staphylococcus aureus (S. aureus) is a disreputable symbiotic bacterium that is responsible for a range of diseases, including life-threatening pneumonia, endocarditis, septicemia, and others, which has led to an immense loss in both public health and economy, imposing a significant burden
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Staphylococcus aureus (S. aureus) is a disreputable symbiotic bacterium that is responsible for a range of diseases, including life-threatening pneumonia, endocarditis, septicemia, and others, which has led to an immense loss in both public health and economy, imposing a significant burden on society. To investigate the pathogenic mechanism of S. aureus and develop new treatment methods for infectious diseases caused by S. aureus, various rabbit models have been developed to simulate different infections by S. aureus, such as pneumonia models, meningitis models, and endocarditis models, etc. In this review, we summarized the application of rabbit models in S. aureus-induced infectious diseases.
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Open AccessReview
The Role of Microbial Dynamics, Sensorial Compounds, and Producing Regions in Cocoa Fermentation
by
Sofia de M. Campos, Walter J. Martínez-Burgos, Guilherme Anacleto dos Reis, Diego Yamir Ocán-Torres, Gabriela dos Santos Costa, Fernando Rosas Vega, Beatriz Alvarez Badel, Liliana Sotelo Coronado, Josilene Lima Serra and Carlos Ricardo Soccol
Microbiol. Res. 2025, 16(4), 75; https://doi.org/10.3390/microbiolres16040075 - 26 Mar 2025
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Cocoa fermentation is a critical step in chocolate production, influencing the flavor, aroma, and overall quality of the final product. This review focuses on the microbial dynamics of cocoa fermentation, emphasizing the roles of yeasts, lactic acid bacteria (LAB), and acetic acid bacteria
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Cocoa fermentation is a critical step in chocolate production, influencing the flavor, aroma, and overall quality of the final product. This review focuses on the microbial dynamics of cocoa fermentation, emphasizing the roles of yeasts, lactic acid bacteria (LAB), and acetic acid bacteria (AAB). These microorganisms interact in a well-defined succession, producing organoleptic compounds such as alcohols, organic acids, and esters, which are key to the sensory profile of cocoa. This article examines the impact of different fermentation methods, including spontaneous fermentation and the use of starter cultures, on microbial communities and flavor development. Advances in starter culture technology are highlighted, demonstrating how microbial control can enhance fermentation efficiency, reduce fermentation time, and improve the consistency of chocolate flavor. Patents related to cocoa fermentation further emphasize the growing interest in microbial management to meet market demands for high-quality, distinct chocolate. This review also outlines future research directions, including the identification of new microbial strains, optimization of fermentation conditions, and the potential of biotechnological advancements to improve the fermentation process. Understanding microbial dynamics in cocoa fermentation offers significant potential for enhancing chocolate quality, sustainability, and the development of new, region-specific flavor profiles.
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Open AccessArticle
Frequency, Resistance Patterns, and Serotypes of Salmonella Identified in Samples from Pigs of Colombia Collected from 2022 to 2023
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Stefany Barrientos-Villegas, Juana L. Vidal, Nidia Gomez, Fernando L. Leite, Sara López-Osorio and Jenny J. Chaparro-Gutiérrez
Microbiol. Res. 2025, 16(4), 74; https://doi.org/10.3390/microbiolres16040074 - 25 Mar 2025
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The objective of this study was to determine the frequency of Salmonella in pig samples analyzed at the Veterinary Diagnostic Unit of the Faculty of Agricultural Sciences of the University of Antioquia, Colombia, between 2022 and 2023. Out of 5820 serum samples analyzed
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The objective of this study was to determine the frequency of Salmonella in pig samples analyzed at the Veterinary Diagnostic Unit of the Faculty of Agricultural Sciences of the University of Antioquia, Colombia, between 2022 and 2023. Out of 5820 serum samples analyzed using indirect enzyme-linked immunosorbent assay, 63.76% were positive. Additionally, Salmonella was isolated and identified in a separate group of 848 samples (feces, tissues, etc.) with a positivity rate of 23.47%. Eight serotypes were identified, with the most common being Salmonella enterica subsp. enterica serotype Typhimurium (49.2%), followed by its monophasic variant I 4,[5],12:i:- (23%), and serotype Choleraesuis (18%). Antimicrobial susceptibility profiles of 105 isolates were evaluated using the Kirby–Bauer method, which demonstrated higher resistance (100%) to ampicillin, tiamulin, penicillin, tylosin, and erythromycin (these were the least tested), followed by florfenicol (44/54), doxycycline (4/5), spectinomycin (18/25), amoxicillin (32/46), chloramphenicol (2/3), tetracycline (2/3), and enrofloxacin (34/64), with lower resistance observed for fosfomycin (2/38) and ceftiofur (5/35). Multi-drug resistance was observed in 59% (62/105) of the isolates. The high proportion of Salmonella and the levels of resistance to various drugs raise significant concerns, indicating potential deficiencies in responsible antimicrobial use and management practices on pig farms in the region.
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