Microbiology Research

21 pages, 1130 KB

Open AccessReview

Dectin Receptors and Host Defense in Paracoccidioidomycosis

by Aimê Stefany Alves da Fonseca and Aldo Henrique Tavares

Microbiol. Res. 2026, 17(10), 201; https://doi.org/10.3390/microbiolres17100201 - 6 Oct 2026

Paracoccidioidomycosis (PCM) is a neglected tropical disease and the most prevalent systemic mycosis in Latin America. Infection is caused by thermally dimorphic fungi of the genus Paracoccidioides, and disease outcome is largely determined by the nature of the host immune response. Among [...] Read more.

Paracoccidioidomycosis (PCM) is a neglected tropical disease and the most prevalent systemic mycosis in Latin America. Infection is caused by thermally dimorphic fungi of the genus Paracoccidioides, and disease outcome is largely determined by the nature of the host immune response. Among the pattern recognition receptors involved in fungal sensing, the C-type lectin receptors (CLRs) Dectin-1, Dectin-2, and Dectin-3 are critical regulators of antifungal immunity through their recognition of fungal cell wall polysaccharides and activation of Syk-CARD9-dependent signaling pathways. This review summarizes current knowledge regarding the roles of these receptors in immunity to Paracoccidioides. Evidence from murine and human studies shows Dectin-1 and Dectin-2 as major innate sensors that promote fungal control by enhancing phagocyte function, inflammasome activation, and protective adaptive immune responses. In contrast, Dectin-3 demonstrates cell-type and species-specific relevance. The review further discusses fungal immune evasion strategies and Dectin-1 signaling in non-classical phagocytes, with implications for PCM immunopathology and chronicity. Finally, we evaluate emerging translational opportunities, including CLR-targeted vaccine adjuvants, receptor-directed immunotherapies, and Dectin-based antifungal drug-delivery platforms. Full article

(This article belongs to the Section Medical and Veterinary Microbiology)

34 pages, 999 KB

Open AccessReview

Mapping the Neonatal Pathobiont–Resistome Interface Across Four Niches: A Narrative Review of Delivery Mode, Gestational Maturity and the Limits of Current Evidence

by Elena Teona Cosovanu, Ramona Gabriela Ursu, Eric Oliviu Cosovanu, Dorina Adelina Minciuna, Alexandru Carauleanu, Demetra Gabriela Socolov, Luminita Smaranda Iancu and Irina Draga Caruntu

Microbiol. Res. 2026, 17(10), 200; https://doi.org/10.3390/microbiolres17100200 - 4 Oct 2026

Abstract

Cesarean section accounts for 21.1% of births worldwide and 13.4 million infants were born preterm in 2020, yet pathobiont carriage and resistance genes are usually reported separately, from stool alone. This review maps that interface across four anatomical niche groups (an evidence map [...] Read more.

Cesarean section accounts for 21.1% of births worldwide and 13.4 million infants were born preterm in 2020, yet pathobiont carriage and resistance genes are usually reported separately, from stool alone. This review maps that interface across four anatomical niche groups (an evidence map rather than a demonstrated relationship), taking infants born at 32 + 0 to 36 + 6 weeks as the index stratum against term, very preterm and extremely preterm contrasts. Delivery mode is associated with community composition through at least two candidate mechanisms: substitution of the founding inoculum and failure of colonization resistance to be established. Umbilical inoculation at the point of care is treated as mode-independent. Strain sharing across compartments, shown in small series, suggests that single-niche sampling may capture the interface incompletely. Delivery-mode associations are reported less consistently at lower gestational maturity, although biological attenuation cannot be distinguished from differences in care exposure, statistical power and methodology. Within the literature reviewed here, delivery-mode colonization data were not identified for three of the four niche groups; no dataset reported the resistome of this band as a discrete stratum; and the largest intervention evidence base lies outside this population. Breastfeeding support and antibiotic stewardship are the practices best matched to the mechanisms identified. Full article

(This article belongs to the Topic Microbiota Diversity and Its Broader Biological Implications Across Human and Animal Health)

11 pages, 876 KB

Open AccessArticle

Bacteria-Derived Recombinant Interferon-Gamma: Production and In Vitro Activity in Equine Herpesvirus-1 Cell Culture Models

by İlker Şahinkesen, Eda Erdem-Şahinkesen, Veysel Soydal Ataseven, Tarık Fedai, Deniz Arca Çakır, Pınar Erkekoğlu and Seval Bilge-Dağalp

Microbiol. Res. 2026, 17(10), 199; https://doi.org/10.3390/microbiolres17100199 - 4 Oct 2026

Abstract

Equine herpesvirus type 1 (EHV-1) is a major viral pathogen of horses, causing respiratory disease, abortion, and neurological disorders, while current vaccines provide only limited protection. This study aimed to evaluate the in vitro cytoprotective potential of recombinant human interferon-gamma (rhIFN-γ) and its [...] Read more.

Equine herpesvirus type 1 (EHV-1) is a major viral pathogen of horses, causing respiratory disease, abortion, and neurological disorders, while current vaccines provide only limited protection. This study aimed to evaluate the in vitro cytoprotective potential of recombinant human interferon-gamma (rhIFN-γ) and its capacity for the reduction of cytopathic damage in equine dermal cells. The human IFN-γ gene was cloned into a bacterial expression vector, expressed in Escherichia coli, and purified using affinity chromatography. Equine dermal (ED) cells were treated with different concentrations of rhIFN-γ prior to viral challenge. Cytotoxicity was assessed using the MTT assay, and cytoprotective activity was evaluated through cytopathic effect (CPE) observations and TCID₅₀ titration. The results demonstrated that rhIFN-γ reduced EHV-1-induced cytopathic effects in a dose-dependent manner, with the most pronounced protective activity observed at 200 and 400 ng/mL. Additionally, treated cells showed significantly higher viability compared to infected controls (p < 0.05). These findings indicate that bacterially produced rhIFN-γ exhibits both antiviral and cytoprotective effects against EHV-1 in vitro and may represent a promising candidate for the development of alternative potential antiviral strategies targeting EHV-1 infections in horses. These findings indicate that bacterially produced rhIFN-γ exhibits notable cytoprotective activity in vitro by mitigating cellular injury following EHV-1 exposure. Full article

(This article belongs to the Section Medical and Veterinary Microbiology)

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13 pages, 940 KB

Open AccessArticle

Severe Acute Kidney Injury in HIV-Associated Disseminated Histoplasmosis: Clinical Predictors and the Emerging Role of Angiopoietin-2

by Matheus Alves de Lima Mota, Geraldo Bezerra da Silva Junior, Marcos Maciel Sousa, Edla Helena Salles de Brito, Alice Maria Costa Martins, Claudia Maria Costa de Oliveira, Zayra Hellen de Abreu Alexandre, Jacó Ricarte Lima de Mesquita, Lisandra Serra Damasceno, Terezinha do Menino Jesus Silva Leitão, Gdayllon Cavalcante Meneses and Elizabeth De Francesco Daher

Microbiol. Res. 2026, 17(10), 198; https://doi.org/10.3390/microbiolres17100198 - 4 Oct 2026

Abstract

Acute kidney injury (AKI) is a frequent, life-threatening complication in people living with HIV (PLWH), particularly those with disseminated histoplasmosis (DH), yet the determinants of severe AKI and the role of endothelial dysfunction remain poorly understood. We assessed the incidence, predictors, and biomarker [...] Read more.

Acute kidney injury (AKI) is a frequent, life-threatening complication in people living with HIV (PLWH), particularly those with disseminated histoplasmosis (DH), yet the determinants of severe AKI and the role of endothelial dysfunction remain poorly understood. We assessed the incidence, predictors, and biomarker profile of stage 3 AKI in PLWH hospitalized with DH. In this prospective cohort study at a tertiary infectious diseases center in Northeastern Brazil, adults with probable or proven DH were enrolled, and AKI was defined by Kidney Disease: Improving Global Outcomes (KDIGO) criteria. Kidney injury, inflammatory, and endothelial biomarkers, including angiopoietin-2 (Ang-2), were measured early in hospitalization, and predictors were identified using least absolute shrinkage and selection operator (LASSO)-based multivariable logistic regression. Of 58 patients, 24 (41.4%) developed stage 3 AKI, which was associated with intensive care admission, mechanical ventilation, vasoactive drugs, and in-hospital mortality (54.2% vs. 2.9%, p < 0.001) and with lower body mass index (BMI), hepatomegaly, circulating Histoplasma capsulatum-like yeasts, higher inflammatory and liver injury markers, and higher Ang-2. Only BMI remained independently associated: each 1 kg/m² increase was associated with lower odds of stage 3 AKI (odds ratio 0.77; 95% confidence interval 0.60–0.95; p = 0.024). The Ang-2 association suggests that endothelial dysfunction may contribute to severe AKI and warrants further study for early risk stratification. Full article

(This article belongs to the Special Issue Medically Relevant Fungi: Virulence Factors, and New Diagnostic and Treatment Approaches)

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21 pages, 521 KB

Open AccessReview

Axenic and Gnotobiotic Aquatic Models: Methods, Husbandry, and Applications

by Nicolai Crăciun, Ioana Corina Moga, Sergiu Emil Georgescu, Mădălina-Andreea Pop, Abdulhusein Jawdhari and Sergiu Fendrihan

Microbiol. Res. 2026, 17(10), 197; https://doi.org/10.3390/microbiolres17100197 - 2 Oct 2026

Abstract

Axenic and gnotobiotic aquatic animals provide direct experimental access to the causal roles of microorganisms in host physiology, nutrition, immunity and disease. Fish are particularly suitable vertebrate models because fertilization and embryogenesis commonly occur externally, allowing embryos to be disinfected before hatching and [...] Read more.

Axenic and gnotobiotic aquatic animals provide direct experimental access to the causal roles of microorganisms in host physiology, nutrition, immunity and disease. Fish are particularly suitable vertebrate models because fertilization and embryogenesis commonly occur externally, allowing embryos to be disinfected before hatching and maintained under microbiologically controlled conditions. Current approaches combine embryo or egg surface disinfection, sterile water and culture systems, sterilized formulated feeds or axenic live feeds, as well as controlled colonization with defined microorganisms. These systems enable direct testing of microbial effects on immunity, metabolism, pathogen resistance, and nutritional responses. However, their interpretation is constrained by contamination risk, species- and developmental-specific husbandry requirements, changes in feed and water chemistry caused by sterilization, low-biomass limitations in sterility testing, and potential confounding effects of prolonged microbial absence. Zebrafish (Danio rerio) is currently the most studied and well-established axenic or gnotobiotic fish model, but methods have also been established for medaka (Oryzias latipes) and aquaculture species such as Rainbow trout (Oncorhynchus mykiss), European sea bass (Dicentrarchus labrax) and Atlantic cod (Gadus morhua). This narrative review evaluates the practical and conceptual basis of axenic aquatic animal research, with emphasis on fish production, rearing and handling. It compares representative derivation procedures, sterile culture formats, feeding strategies, water-quality constraints and sterility assays, and it examines how these methodological choices affect biological interpretation. A central conclusion is that “axenic” is an operational microbiological state rather than an absolute biological property, as confidence intervals depend on sampling design and orthogonal detection. The review therefore proposes minimum reporting and quality-control practices, including vessel-level replication, longitudinal sterility testing, feed validation, contamination rules and appropriate recolonization controls. These standards are essential if axenic or gnotobiotic aquatic models are to produce reproducible mechanistic results. Future progress will depend on standardized validation and reporting criteria, improved sterile nutrition, water management and longer-term husbandry systems. Full article

(This article belongs to the Special Issue The Animal Microbiome in Health and Disease: From Insights to Innovations)

39 pages, 981 KB

Open AccessReview

Bacteriophage Therapy in Poultry Production: Mechanisms, Applications, and Antimicrobial Stewardship—Review

by Peter Ayodeji Idowu, Deborah Etooluwa Kumoye, Adeola Patience Idowu, Oluwatoyin Victoria Oyekunle, Stephen Olasunkanmi Olawuwo, Ngalula Prudence Kayoka-Kabongo and Lyndy McGaw

Microbiol. Res. 2026, 17(10), 196; https://doi.org/10.3390/microbiolres17100196 - 1 Oct 2026

Abstract

The rapid emergence of antimicrobial resistance (AMR) is a major challenge to sustainable poultry production, food safety, and public health. It reduces the effectiveness of conventional antibiotics and highlights the need for alternative approaches to bacterial disease control. Bacteriophage therapy has re-emerged as [...] Read more.

The rapid emergence of antimicrobial resistance (AMR) is a major challenge to sustainable poultry production, food safety, and public health. It reduces the effectiveness of conventional antibiotics and highlights the need for alternative approaches to bacterial disease control. Bacteriophage therapy has re-emerged as a promising biological approach because of its high specificity, self-amplifying nature, and ability to target multidrug-resistant bacterial pathogens. Phages may also cause less disruption of beneficial intestinal microbiota than broad-spectrum antibiotics, although this effect depends on the phage, target bacterium, treatment conditions, and host context. This review synthesizes current knowledge on bacteriophage biology, mechanisms of action, and therapeutic applications against major poultry pathogens, including Salmonella enterica subsp. enterica, avian pathogenic Escherichia coli (APEC), Campylobacter spp., and Clostridium perfringens. It also examines the challenges associated with commercial implementation. Unlike previous reviews that have mainly focused on pathogen control, this review links bacteriophage therapy with antimicrobial stewardship and the One Health framework to provide a broader perspective on its role in sustainable poultry production. Evidence from experimental, field, and food-chain studies shows that phage therapy can reduce bacterial colonization, biofilm formation, pathogen shedding, and food contamination; and may contribute to antimicrobial stewardship. Recent advances in phage cocktails, genomics-guided phage selection, precision diagnostics, and formulation technologies have further increased their therapeutic potential. However, narrow host range, bacterial resistance, formulation stability, large-scale production, and differences in regulatory requirements continue to limit widespread commercial adoption. Overall, bacteriophage therapy is a promising approach for controlling bacterial diseases in poultry. It may contribute to more targeted antimicrobial use and improved food safety when integrated with other disease-control measures. Although direct reductions in antibiotic use require validation under commercial production conditions. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: New Diagnostic Strategies)

14 pages, 2907 KB

Open AccessArticle

Detection of Avian Infectious Bronchitis Virus Genotype GI-13 in the Almaty Region, Kazakhstan

by Karina Ivanova, Marina Kopochenya, Dinara Naizabayeva and Andrey Zhigailov

Microbiol. Res. 2026, 17(10), 195; https://doi.org/10.3390/microbiolres17100195 - 1 Oct 2026

Abstract

Infectious bronchitis remains one of the most economically significant viral diseases in commercial poultry farming, despite the widespread implementation of vaccination programs. The high genetic variability of the infectious bronchitis virus (IBV) leads to the emergence of genetically and antigenically diverse variants, including [...] Read more.

Infectious bronchitis remains one of the most economically significant viral diseases in commercial poultry farming, despite the widespread implementation of vaccination programs. The high genetic variability of the infectious bronchitis virus (IBV) leads to the emergence of genetically and antigenically diverse variants, including vaccine-related and field variants detected in vaccinated flocks. This study presents a molecular genetic analysis of an IBV variant detected in 2025 at a poultry farm in the Almaty region of Kazakhstan. Samples were collected from seven 35-day-old deceased chickens during an episode of mortality. The reported clinical presentation included diarrhea and signs described as hepatitis, without pronounced respiratory manifestations. Initial molecular screening followed by amplicon sequencing confirmed the presence of IBV RNA in these clinical samples. For detailed genotyping and assessment of genetic variability, an 858-nucleotide fragment of the S1 gene was analyzed. Phylogenetic analysis showed that the detected virus belongs to genotype GI-13 and clusters with the 4/91 vaccine lineage while possessing distinct nucleotide substitutions. Comparison with the 4/91 reference strain identified 17 variable nucleotide positions, including two synonymous and 15 non-synonymous changes, corresponding to 10 unique amino acid substitutions. Broader molecular screening also detected avian leukosis virus (ALV) genotype E and fowl adenovirus type 5 (FAdV-5), whereas the other tested pathogens were not detected. These findings demonstrate the genetic distinctness of the detected GI-13 virus from the 4/91 vaccine reference; however, the available data cannot establish its origin, pathogenic significance, persistence, or sustained circulation. The findings underscore the value of continued molecular surveillance and sequence-based characterization of IBV in vaccinated poultry. Full article

(This article belongs to the Section Medical and Veterinary Microbiology)

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19 pages, 5714 KB

Open AccessArticle

An Integrated Analysis of the Transcriptome and Proteome Reveals Host-Specific Cues in Cordyceps fumosorosea

by Aimin Shi, Muhammad Hamid Bashir, Xingmin Wang and Shaukat Ali

Microbiol. Res. 2026, 17(10), 194; https://doi.org/10.3390/microbiolres17100194 - 28 Sep 2026

Abstract

Cordyceps fumosorosea (Wise) is a prominent entomopathogenic fungus with a broad host spectrum. The specificity of its infection mechanisms across different hosts, especially among lepidopteran species, remains largely enigmatic. This study employed RNA sequencing (RNA-Seq) and Tandem Mass Tag (TMT) proteomics to elucidate [...] Read more.

Cordyceps fumosorosea (Wise) is a prominent entomopathogenic fungus with a broad host spectrum. The specificity of its infection mechanisms across different hosts, especially among lepidopteran species, remains largely enigmatic. This study employed RNA sequencing (RNA-Seq) and Tandem Mass Tag (TMT) proteomics to elucidate the differential pathogenic behavior exhibited by a particular C. fumosorosea isolate when confronting Plutella xylostella and Spodoptera litura. Our analyses revealed 3342 and 2416 differentially expressed genes (DEGs) and 332 and 296 differentially expressed proteins (DEPs) in C. fumosorosea cultured on the cuticles of P. xylostella (PI) and S. litura (SI), respectively. Notably, gene clusters and proteins associated with metabolism, cellular processes, and organismal systems were predominantly upregulated in the strain cultivated on PI compared to that cultivated on SI. In the PI group, significantly enriched metabolic pathways included fatty acid metabolism, nitrogen metabolism, and the metabolism of glycine, serine, threonine, and phenylalanine. Conversely, in the SI group, the upregulated proteins were significantly enriched in pathways related to phenylalanine metabolism, alanine, aspartate and glutamate metabolism, glycerophospholipid metabolism, and peroxisomal activities. These insights shed light on the reasons behind the distinct pathogenicity exhibited by a single C. fumosorosea against diverse hosts, offering prospects for the engineering of fungal strains with enhanced virulence. Full article

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13 pages, 521 KB

Open AccessArticle

Dual Benefits of Opuntia dillenii (Ker Gawl.) Haw. (Cactaceae) Microbiota: Tomato Growth Promotion and Ralstonia solanacearum Mitigation

by Yves Kévin Brun, Agossou Damien Pacôme Noumavo, Marie Epiphane Dossoumou, Julien Colombet, Kouakou Romaric Kouakou, Rachidatou Sikirou and François Lefort

Microbiol. Res. 2026, 17(10), 193; https://doi.org/10.3390/microbiolres17100193 - 26 Sep 2026

Abstract

Tomato production is severely affected by bacterial wilt caused by Ralstonia solanacearum. This study assessed the biocontrol potential of bacterial strains isolated from the cladodes, roots, and rhizosphere of Opuntia dillenii for the sustainable management of bacterial wilt in tomato. An in [...] Read more.

Tomato production is severely affected by bacterial wilt caused by Ralstonia solanacearum. This study assessed the biocontrol potential of bacterial strains isolated from the cladodes, roots, and rhizosphere of Opuntia dillenii for the sustainable management of bacterial wilt in tomato. An in vitro screening identified antagonistic strains, which were subsequently assessed under greenhouse conditions. Among the isolates, Priestia flexa C10 and Bacillus subtilis R6 showed the strongest antagonistic activity against R. solanacearum, with inhibition zones of 22.5 and 20.0 mm, respectively. Under pathogen pressure, the inoculated control exhibited a wilt incidence of 47.5%, whereas B. subtilis R6 and P. flexa C10 reduced disease incidence to 40% and 45%, respectively. Both strains also improved plant growth. Under non-inoculated conditions, B. subtilis R6 showed the greatest growth-promoting effect, increasing plant height (35.9%), leaf number (24.6%), root biomass (94.5%), and root length (59.4%). Under pathogen pressure, P. flexa C10 notably enhanced root biomass (49.8%) and root length (30.6%), while B. subtilis R6 increased root biomass by 80.4%. These findings indicate that while P. flexa C10 and B. subtilis R6 offer limited direct suppression of bacterial wilt, they significantly promote tomato vegetative growth and could serve as valuable plant growth-promoting inoculants to mitigate disease-induced stress. Full article

(This article belongs to the Section Food and Agricultural Microbiology)

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15 pages, 9939 KB

Open AccessArticle

Emerging Pathogens Attention Alert: A Case Report on Isolation and Preliminary Characterization of Escherichia albertii and Kosakonia cowanii from Citrus

by Marcos Vinício Alves, Giselle Santos Silva, Kayque Ordonho Carneiro, Katia Leani Oliveira de Souza Silva, Emília Maria França Lima and Svetoslav Dimitrov Todorov

Microbiol. Res. 2026, 17(10), 192; https://doi.org/10.3390/microbiolres17100192 - 25 Sep 2026

Abstract

Fresh fruits may act as vehicles for microorganisms introduced during cultivation, harvest, and handling, especially in settings where crop production occurs close to animal farming. In this study, three Gram-negative strains incidentally recovered during the screening of lactic acid bacteria from Rangpur limes [...] Read more.

Fresh fruits may act as vehicles for microorganisms introduced during cultivation, harvest, and handling, especially in settings where crop production occurs close to animal farming. In this study, three Gram-negative strains incidentally recovered during the screening of lactic acid bacteria from Rangpur limes (Citrus × limonia) were identified and characterized. Phenotypic and biochemical analyses, rep-PCR, and 16S rRNA gene sequencing identified one strain as Escherichia albertii and two strains as Kosakonia cowanii. The Escherichia albertii and two Kosakonia cowanii strains were further evaluated for β-galactosidase production, antimicrobial susceptibility, hemolytic activity, biogenic amine production, and virulence-associated genes. The three studied strains were hemolytic, positive for β-galactosidase, showed presumptive amino acid decarboxylase activity, and demonstrated resistance to ampicillin, with intermediate susceptibility to nalidixic acid. Classical virulence genes such as eae, cva, iss, iroN, iut, and omp were not detected, whereas fim and hly were observed. These findings indicate that Rangpur limes cultivated at the animal–crop interface may harbor opportunistic and emerging bacteria of relevance to food safety and One Health surveillance. Full article

(This article belongs to the Section Food and Agricultural Microbiology)

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26 pages, 6981 KB

Open AccessReview

Phage–Antibiotic Combinations Against Mature Multidrug-Resistant Biofilms: A Critical Narrative Review of Synergy Determinants, Treatment Sequencing, and Translation

by Touati Abdelaziz, Kirat Hassina and Bellil Zahra

Microbiol. Res. 2026, 17(10), 191; https://doi.org/10.3390/microbiolres17100191 - 24 Sep 2026

Abstract

Background: Phage–antibiotic combinations (PACs) are increasingly proposed for difficult biofilm infections, but planktonic synergy does not reliably predict activity in mature multidrug-resistant (MDR) biofilms. Objective: To identify the biological, pharmacological, evolutionary, methodological, and translational determinants that govern whether phage–antibiotic synergy (PAS) persists in [...] Read more.

Background: Phage–antibiotic combinations (PACs) are increasingly proposed for difficult biofilm infections, but planktonic synergy does not reliably predict activity in mature multidrug-resistant (MDR) biofilms. Objective: To identify the biological, pharmacological, evolutionary, methodological, and translational determinants that govern whether phage–antibiotic synergy (PAS) persists in mature MDR biofilms. Methods: This critical narrative review used a structured evidence map updated through 21 August 2026. Fifty-four primary studies met the final operational core criteria after endpoint-eligibility and publication-status verification and were evaluated for biofilm maturity, phage and antibiotic exposure, treatment sequence, resistance evolution, assay choice, and translational level. Main Results: Twenty of 54 studies (37.0%) included at least one qualifying biofilm/PAC condition aged 48 h or longer, and 14 directly compared treatment order. Interaction direction depended on phage identity, bacterial strain, matrix, absolute phage exposure, antibiotic concentration, timing, and endpoint; the schedule maximizing immediate killing did not necessarily best suppress resistance. Nine core studies reached animal models and four human cases met the defined translational criteria, but uncontrolled cases support feasibility rather than comparative efficacy. Negative, antagonistic, and indeterminate outcomes were retained, and CFU, biomass, metabolic, and lysis-based assays could classify the same regimen differently. Conclusions: PAS should be treated as a context-dependent phenotype requiring direct mature-biofilm validation, factorial dose-sequence testing, longitudinal resistance assessment, and site-matched translational confirmation. Full article

(This article belongs to the Section Antimicrobials and Antimicrobial Resistance)

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20 pages, 1516 KB

Open AccessArticle

Occurrence and Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli in Food-Producing Animals in Burkina Faso: Emphasis on Pigs

by Barthelemy Sibiri Zoma, Evariste Bako, Namwin Siourimè Somda, Modeste Tegawendé Gampene, Djifahamaï Soma, Fatimata B. J. Diarra, Souleymane Sore, Marguerite E. M. Nikiema, Abdoulaye Sana, Souleymane Belem, Nicolas Barro and Isidore Juste Ouindgueta Bonkoungou

Microbiol. Res. 2026, 17(10), 190; https://doi.org/10.3390/microbiolres17100190 - 23 Sep 2026

Abstract

Campylobacter spp. are major foodborne pathogens, and their increasing antimicrobial resistance poses a growing public health concern in sub-Saharan Africa, where surveillance remains limited. This study investigated the occurrence and antimicrobial resistance (AMR) profiles of Campylobacter spp. in food-producing animals, with a particular [...] Read more.

Campylobacter spp. are major foodborne pathogens, and their increasing antimicrobial resistance poses a growing public health concern in sub-Saharan Africa, where surveillance remains limited. This study investigated the occurrence and antimicrobial resistance (AMR) profiles of Campylobacter spp. in food-producing animals, with a particular focus on pigs in Burkina Faso. A cross-sectional study was conducted from June 2024 to July 2025 in Ouagadougou and surrounding areas. A total of 251 fecal samples were collected from pigs (n = 101), sheep (n = 54), goats (n = 51), and cattle (n = 45) and analyzed using standard microbiological methods. Antimicrobial susceptibility testing was performed on freshly recovered colonies immediately after identification, according to the CA-SFM/EUCAST 2024 disk diffusion method. A multiplex PCR targeting the 23S rRNA gene for Campylobacter genus identification and species-specific targets (mapA for C. jejuni, ceuE for C. coli, lpxA-C. lari for C. lari, and lpxA-C. upsaliensis for C. upsaliensis) was used for molecular confirmation. Campylobacter spp. were detected in 18.7% (47/251) of samples, with the highest prevalence observed in pigs (35.6%; 36/101), followed by sheep (11.1%; 6/54), goats (7.8%; 4/51), and cattle (2.2%; 1/45). PCR confirmed C. coli in 80.9% (38/47) and C. jejuni in 17.0% (8/47) of positive samples, while one goat sample showed simultaneous detection of both species (2.1%; 1/47). AMR analysis was performed on the 46 samples yielding a single Campylobacter species; the mixed-species sample was excluded. Resistance was highest to ampicillin (69.6%; 32/46), followed by tetracycline (63.0%; 29/46) and ciprofloxacin (54.3%; 25/46). bla_OXA-61 and tet(O) were the most frequently detected AMR genes. These findings suggest that pigs may represent an important reservoir of antimicrobial-resistant Campylobacter in the study setting and highlight the need for a One Health approach to strengthen surveillance and mitigate transmission risks along the food chain. Full article

(This article belongs to the Section Antimicrobials and Antimicrobial Resistance)

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22 pages, 3064 KB

Open AccessArticle

Development and Analytical Evaluation of a hilA-Targeting TaqMan Real-Time PCR Assay for Salmonella enterica Detection

by Duman Yessimseit, Beck Abdeliyev, Altynai Kassenova, Altyn Rysbekova, Ziyat Abdel, Dana Khaltayeva, Svetlana Issaeva, Nurbol Shaki, Oleg Reva and Aigul Abdirassilova

Microbiol. Res. 2026, 17(10), 189; https://doi.org/10.3390/microbiolres17100189 - 23 Sep 2026

Abstract

Rapid and reliable molecular detection of Salmonella is important for laboratory investigation and infectious disease surveillance. This study compared six candidate molecular targets (hilA, invA, phoP, fimA, rpoS, and spvA) and developed a hilA-targeting TaqMan [...] Read more.

Rapid and reliable molecular detection of Salmonella is important for laboratory investigation and infectious disease surveillance. This study compared six candidate molecular targets (hilA, invA, phoP, fimA, rpoS, and spvA) and developed a hilA-targeting TaqMan real-time PCR assay for Salmonella enterica detection. During conventional PCR screening, the hilA-M1-F/R primer pair demonstrated the most consistent and reproducible amplification across the tested isolate panel under the experimental conditions used and was therefore selected for subsequent assay development. The developed assay showed an amplification efficiency of 93.4% and an R² of 0.9988 over a linear genomic DNA range from 1 ng/μL to 10 fg/μL. Experimentally determined detection limits under the conditions tested were 10² CFU/mL for bacterial suspensions and 10 fg/μL for genomic DNA. All 24 whole-genome sequencing-confirmed S. enterica isolates representing multiple serovars and sequence types were reproducibly detected, whereas no specific amplification was observed within the expanded panel of 15 non-target bacterial strains or isolates. The assay also detected S. enterica DNA in artificially contaminated milk and carrot matrices in preliminary proof-of-concept experiments. These findings demonstrate promising analytical performance of the hilA-targeting TaqMan assay within the evaluated experimental framework. However, broader validation using geographically diverse S. enterica isolate collections, additional non-target organisms, internal amplification controls, naturally contaminated food products, primary clinical, veterinary, and environmental specimens, and independent laboratories is required before routine diagnostic, food-testing, or epidemiological surveillance applications can be established. Full article

(This article belongs to the Special Issue Zoonotic Bacteria: Infection, Pathogenesis and Drugs—Second Edition)

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17 pages, 4365 KB

Open AccessArticle

Comparative Structural Analysis of N-Linked Cell Wall Mannans Among Candida parapsilosis Sensu Stricto, Candida orthopsilosis, and Candida metapsilosis

by Kei Higashijima, Fumie Ito, Takuya Kuraoka, Akihiro Ambo, Norihiko Fujimatsu, Yukiko Ogawa, Masato Sasaki and Hidemitsu Kobayashi

Microbiol. Res. 2026, 17(9), 188; https://doi.org/10.3390/microbiolres17090188 - 21 Sep 2026

Abstract

The Candida parapsilosis complex (CPC), comprising Candida parapsilosis sensu stricto, Candida orthopsilosis, and Candida metapsilosis, is a significant cause of nosocomial candidemia worldwide. Because species-specific drug resistance profiles vary, accurate identification is clinically crucial; however, mainstream molecular diagnostics require expensive instrumentation. [...] Read more.

The Candida parapsilosis complex (CPC), comprising Candida parapsilosis sensu stricto, Candida orthopsilosis, and Candida metapsilosis, is a significant cause of nosocomial candidemia worldwide. Because species-specific drug resistance profiles vary, accurate identification is clinically crucial; however, mainstream molecular diagnostics require expensive instrumentation. To establish a baseline for simple, cost-effective immunochemical diagnostics, we elucidated the cell wall N-linked mannan structures across representative CPC strains. Intact N-linked mannan cores were isolated via the classical Fehling method, which efficiently eliminated confounding O-linked glycans. Contrary to the historical paradigm suggesting a lack of branched side chains in C. parapsilosis, two-dimensional ¹H-¹H total correlation spectroscopy (2D-TOCSY) clearly identified a unique di-substituted branching residue, Manα1-2Manα1-3(Manα1-6)Man, corresponding to antigenic factor 4. Acetolysis and gel filtration demonstrated that the side chains ranged from a degree of polymerization (DP) of 2 to 6, with a tetrasaccharide serving as the structural mainstay. These results redefine the antigenic factor profile of C. parapsilosis as (1, 4, 13b), distinguishing it from C. orthopsilosis and C. metapsilosis (1, 13b). By integrating these N-linked profiles with our recent O-linked data, this study delineates the comprehensive cell wall surface architectures among the CPC. This framework provides a critical molecular foundation for the future development of rapid serological identification kits, while enhancing our understanding of evolutionary diversity and biosynthetic pathways within pathogenic yeasts. Full article

(This article belongs to the Special Issue Medically Relevant Fungi: Virulence Factors, and New Diagnostic and Treatment Approaches)

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13 pages, 4042 KB

Open AccessArticle

Microbe–Metabolite Differential Co-Occurrence Analysis Reveals Interaction-Based Microbial Signatures in Chronic Granulomatous Disease

by Chengcheng Ma, Licheng Liu, Zhi Liu and Zhenyu Wang

Microbiol. Res. 2026, 17(9), 187; https://doi.org/10.3390/microbiolres17090187 - 21 Sep 2026

Abstract

Chronic granulomatous disease (CGD) is a primary immunodeficiency characterized by impaired innate immune responses and frequent gastrointestinal involvement, yet the reorganization of gut microbiome–metabolome interactions in CGD remains poorly understood. This study aimed to characterize disease-associated alterations in microbiome–metabolome interactions using a differential [...] Read more.

Chronic granulomatous disease (CGD) is a primary immunodeficiency characterized by impaired innate immune responses and frequent gastrointestinal involvement, yet the reorganization of gut microbiome–metabolome interactions in CGD remains poorly understood. This study aimed to characterize disease-associated alterations in microbiome–metabolome interactions using a differential microbe–metabolite co-occurrence (DCO) framework. Paired microbiome and metabolome profiles from patients with CGD and healthy controls were used to construct group-specific co-occurrence networks and quantify differential interaction patterns between disease and health states. Microbial features prioritized by differential co-occurrence connectivity discriminated CGD from healthy controls in machine learning models and provided predictive information distinct with abundance-based markers. Functional inference suggested that disrupted interactions were involved in pathways related to regulation and metabolic adaptation. These findings demonstrate that CGD is associated with substantial rewiring of gut microbiome–metabolome interactions and support an interaction-focused, network-based multi-omics framework for characterizing disease-associated microbial alterations. The DCO framework may provide a transferable strategy for investigating microbiome-associated immune disorders and identifying interaction-level biomarkers in addition to conventional abundance-based analyses. Full article

(This article belongs to the Section Medical and Veterinary Microbiology)

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17 pages, 768 KB

Open AccessArticle

Effects of Lactic Acid Bacteria Cultures on Lipid Profile and Volatile Compounds of Reduced–Sodium Fermented Sausages

by Marcello Lima Bertuci, Victoria Diniz Shimizu-Marin, Carlos Alberto Alves Junior, Livia Padilha Lima, Svetoslav Dimitrov Todorov, Suzana Caetano da Silva Lannes, Ana Lúcia Barretto Penna and Andrea Carla da Silva Barretto

Microbiol. Res. 2026, 17(9), 186; https://doi.org/10.3390/microbiolres17090186 - 20 Sep 2026

Abstract

This study evaluated the effect of different lactic acid bacteria (LAB) strains on the fatty acid composition and volatile profile of reduced-sodium fermented sausages. Six treatments were produced: a control with a standard sodium content (Con) and five reduced-sodium treatments, including NAR and [...] Read more.

This study evaluated the effect of different lactic acid bacteria (LAB) strains on the fatty acid composition and volatile profile of reduced-sodium fermented sausages. Six treatments were produced: a control with a standard sodium content (Con) and five reduced-sodium treatments, including NAR and four inoculated with different LAB strains. Fatty acids were analyzed by GC-FID and volatile compounds by HS-SPME/GC–MS, followed by a multivariate analysis. Reduced sodium and LAB inoculation did not significantly affect the total lipid content or the overall fatty acid profile, although minor differences were observed in individual fatty acids. In contrast, both factors markedly influenced the volatile profile. A total of 51 volatile compounds were identified, with carboxylic acids as the predominant class and terpenes as the most diverse. The LAB strains modulated volatile formation in a strain-dependent manner, with Lacticaseibacillus rhamnosus GG showing higher organic acid production. The correlation analysis indicated that polyunsaturated fatty acids were positively associated with aldehydes and alcohols, whereas carboxylic acids were mainly linked to microbial metabolism. These findings demonstrate that selected LAB strains can modulate flavor-related biochemical pathways, representing a promising strategy for improving the aromatic quality of reduced-sodium fermented sausages. Full article

(This article belongs to the Topic Fermented Food: Health and Benefit, 2nd Edition)

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29 pages, 9020 KB

Open AccessReview

Selenium Biotransformation by Food-Relevant Microorganisms: Bacterial and Fungal Differences in Diversified Uptake, Metabolic Partitioning, and Terminal Fate

by Yingqiu Duan, Qinghui Song, Yanqiu Jing, Bo Fu, Xuliang Lu and Dongsheng Luo

Microbiol. Res. 2026, 17(9), 185; https://doi.org/10.3390/microbiolres17090185 - 20 Sep 2026

Abstract

Selenium (Se) biotransformation by microorganisms determines how inorganic selenium is redistributed into organic selenium, selenium nanoparticles (SeNPs), methylated species, and other intracellular or extracellular pools. Although microbial selenium metabolism has been extensively studied, evidence supporting individual mechanisms remains uneven, and bacterial and fungal [...] Read more.

Selenium (Se) biotransformation by microorganisms determines how inorganic selenium is redistributed into organic selenium, selenium nanoparticles (SeNPs), methylated species, and other intracellular or extracellular pools. Although microbial selenium metabolism has been extensively studied, evidence supporting individual mechanisms remains uneven, and bacterial and fungal observations are often compared without sufficient consideration of energetic context, cellular architecture, or evidence strength. This review reorganizes the field around an evidence-graded mechanistic framework. We distinguish direct functional validation from convergent pathway evidence and association-level observations, compare bacterial and fungal selenium handling across uptake, redox metabolism, sulfur assimilation, methylation, compartmentalization, and terminal localization, and introduce cellular selenium loading as a conceptual bridge between uptake and downstream metabolic partitioning. We further emphasize that methylation is not equivalent to volatilization and that terminal selenium fate is best resolved by combining chemical speciation with spatial localization. These mechanisms are integrated into strain-specific selenium-transformation profiles and linked to representative applications and evidence-guided microbial engineering. This synthesis aims to shift microbial selenium research from empirical total-selenium accumulation toward mechanism-resolved, testable, and engineerable selenium biotransformation. Full article

(This article belongs to the Section Food and Agricultural Microbiology)

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16 pages, 3312 KB

Open AccessArticle

Resistant Candida spp. in Healthy Individuals: Mapping a Surveillance Blind Spot

by Anelise Maria Costa Vasconcelos Alves, Laritza Ferreira de Lima, Gabriela Silva Cruz, Ana Caroline Rocha de Melo Leite, Érika Helena Salles de Brito, Nuno Filipe Azevedo and Célia Fortuna Rodrigues

Microbiol. Res. 2026, 17(9), 184; https://doi.org/10.3390/microbiolres17090184 - 17 Sep 2026

Abstract

The prevalence and characteristics of resistant, biofilm-forming Candida strains in healthy individuals remain poorly understood. In this work, Candida strains from 23 healthy volunteers and 11 candidiasis patients (n = 34) were isolated and characterized. Biofilm formation capacity, matrix composition, and antifungal [...] Read more.

The prevalence and characteristics of resistant, biofilm-forming Candida strains in healthy individuals remain poorly understood. In this work, Candida strains from 23 healthy volunteers and 11 candidiasis patients (n = 34) were isolated and characterized. Biofilm formation capacity, matrix composition, and antifungal susceptibility to common drugs (fluconazole, voriconazole, anidulafungin, amphotericin B) were determined. Overall, C. albicans was the predominant species (77%), but non-Candida albicans Candida species were more frequent in clinical infections (45% vs. 11%). Seventy percent of isolates from healthy asymptomatic individuals confirmed resistance to at least one antifungal agent, with only 30% remaining fully susceptible. Among candidiasis patients, 100% showed resistance. Biofilm formation was prevalent in both groups (83% healthy, 82% patients), but the ability to form biofilms did not correlate with resistance patterns (r = 0.274, p = 0.1665), suggesting independent mechanisms. Matrix analysis showed that 50% of strains produced protein-poor, polysaccharide-rich biofilms. This study demonstrates that healthy asymptomatic individuals are key reservoirs of substantial populations of resistant, biofilm-forming Candida strains, which represents a previously underappreciated community harbor. These findings demonstrate a critical gap in current resistance surveillance and underscore the need for WHO One Health approaches incorporating community-based sampling. Full article

(This article belongs to the Topic Multidrug Resistance Across Pathogens: Fungi, Bacteria, Parasites, and Viruses)

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33 pages, 4449 KB

Open AccessReview

Interactions Between the Microbiome and Pharmacotherapy of Allergic Diseases: Current Evidence and Knowledge Gaps

by Miljana Poparić, Borko Milanović, David Strilić, Nebojša Pavlović, Vesna Stojanović, Gordana Vijatov-Đurić and Maja Đanić

Microbiol. Res. 2026, 17(9), 183; https://doi.org/10.3390/microbiolres17090183 - 17 Sep 2026

Abstract

The gut microbiota plays an important role in immune homeostasis, allergic disease pathogenesis, and drug metabolism, potentially influencing therapeutic efficacy and safety. Conversely, pharmacotherapy may modify gut microbial composition and function, creating bidirectional host–drug–microbiome interactions that remain incompletely understood. This narrative review summarises [...] Read more.

The gut microbiota plays an important role in immune homeostasis, allergic disease pathogenesis, and drug metabolism, potentially influencing therapeutic efficacy and safety. Conversely, pharmacotherapy may modify gut microbial composition and function, creating bidirectional host–drug–microbiome interactions that remain incompletely understood. This narrative review summarises current evidence on interactions between the microbiome and therapies for allergic diseases, focusing on antihistamines, corticosteroids, leukotriene receptor antagonists, and biologic agents. Evidence is evaluated from two complementary perspectives: an exposure axis, relevant mainly to orally administered drugs, and a response axis, particularly applicable to biologic therapies. Direct microbial biotransformation has been demonstrated most convincingly for glucocorticoids, with the organosteroid reductase ABC (OsrABC) pathway of Clostridium steroidoreducens reducing systemic prednisolone exposure in a gnotobiotic model. For H₁-antihistamines and leukotriene receptor antagonists, evidence remains limited and inconsistent. The microbiota may also indirectly influence treatment outcomes through effects on epithelial barrier integrity, microbial metabolite production, and immune regulation. Although anti-allergic therapies can alter gut, airway, and skin microbial communities, no validated microbiome signature currently predicts treatment efficacy or safety. Future prospective studies integrating microbiome, metabolome, pharmacokinetic, pharmacodynamic, and clinical data are needed to establish reliable biomarkers and support personalised pharmacotherapy for allergic diseases. Full article

(This article belongs to the Special Issue Gut Microbiome in Disease Pathogenesis)

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