Microbiology Research

Columnar cacti do not provide direct economic benefits; they are vital for maintaining the ecological balance of flora and fauna in desert ecosystems. Over the past 20 years, necrotic disease has been observed in the southern part of the peninsula, leading to a decline in populations. The infectious nature of the disease associated with cactus necrosis syndrome (CNS) was determined by estimating the incidence, severity, and dispersion index. The pathogenic fungi were studied based on symptoms, dispersion patterns, morphological features, and molecular analysis. To determine the pathogenicity and severity of the isolated fungi, experimental inoculations were performed on small cacti. Results showed that at least five fungi (Phoma spp., Nigrospora sphaerica, Chaetomium spp., Coniochaeta spp., and Alternaria alternata) may be associated with CNS, with responses varying depending on whether infections are mixed or straightforward. Common symptoms included canker and pustules, with prevalence rates of 78.87% and 85.3%, respectively. An increase in incidence of 9.89% was noted compared to 2019 (74.83%) and 2020 (84.72%). The average severity rate for all observed symptoms was 55.21%. These findings identify the causal agents involved in necrotic diseases, which could influence the severity and progression of CNS in B.C.S. Full article

Campylobacter spp. are common commensals in broiler chickens and certain species are major causes of foodborne illness in humans. However, their on-farm dynamics and environmental dissemination remain poorly understood. This study investigated the occurrence and temporal dynamics of Campylobacter spp. in commercial broiler production systems by integrating faecal and airborne monitoring across three consecutive production cycles in two farms with contrasting productive historical performance. Faecal (n = 24) and air samples (n = 24) were analysed using culture-based methods, quantitative polymerase chain reaction (qPCR), and 16S rRNA gene amplicon sequencing, which were subsequently compared to assess concordance. In faecal samples, Campylobacter spp. colonisation generally occurred from mid-cycle onwards, with earlier and more consistent detection in the farm with suboptimal growth performance. In the optimal growth-performing farm, colonisation was not detected in the first cycle but emerged in subsequent cycles, coinciding with declining productive parameters, which include mortality, average weight at slaughter, Feed Conversion Ratio (FCR), and European Production Efficiency Factor (EPEF). Airborne Campylobacter DNA was intermittently detected by qPCR, in some cases preceding or occurring independently of faecal detection, whereas culture-based methods consistently failed to recover viable Campylobacter from air samples. Microbiome sequencing detected Campylobacter sporadically and at low relative abundances, yielding fewer positive detections across the monitored sampling timepoints than the targeted methods. Overall, qPCR proved to be the most sensitive approach across matrices, while faecal culture provided biologically meaningful data on viable loads. This study also documented temporal changes in Campylobacter detection patterns alongside productive performance indicators under commercial production conditions. These findings highlight the complementary value of faecal and airborne monitoring and underscore the importance of combining targeted molecular and culture-based approaches to characterise Campylobacter dynamics under commercial production conditions. Full article

Candida infections represent a major global public health challenge and remain among the most common opportunistic fungal infections worldwide. Although Candida albicans remains the predominant pathogen, the incidence of infections caused by non-albicans species, particularly Candidozyma auris, has increased substantially in recent years. Candida infections range from superficial mucocutaneous disease to invasive life-threatening infections associated with high morbidity and mortality. In addition to clinical burden, growing evidence indicates a substantial negative impact on health-related quality of life, particularly among patients with recurrent vulvovaginal candidiasis and chronic fungal infections. Full article

Staphylococcus aureus is one of the leading causes of both community- and healthcare-associated infections. Nasal colonization constitutes the primary reservoir for subsequent infection and transmission, while methicillin-resistant Staphylococcus aureus (MRSA) remains a major public health concern because of its resistance to multiple antimicrobial agents. However, data regarding community nasal colonization in rural Portuguese populations remain scarce. The BI-STAPH Project was established to address this knowledge gap through systematic surveillance of rural communities in inland Portugal. To estimate the prevalence of presumptive nasal colonization by Staphylococcus aureus and MRSA among adults living in the municipality of Fundão, Portugal, and to explore potential associations between colonization and demographic, behavioural, occupational, and environmental characteristics. A prospective community-based cross-sectional study was conducted as the second phase of the BI-STAPH Project. A total of 200 adults were recruited from different parishes of the municipality of Fundão. Bilateral nasal swabs were collected and processed using standardized microbiological methods for the presumptive identification of S. aureus. Presumptive MRSA isolates were investigated using a PBP2′ latex agglutination assay. Sociodemographic and exposure-related information was obtained through structured questionnaires. Associations between presumptive colonization and participant characteristics were evaluated using Pearson’s chi-square or Fisher’s exact tests, as appropriate. Presumptive S. aureus nasal colonization was identified in 56 of 200 participants, corresponding to a prevalence of 28.0% (95% CI: 21.8–34.2%). No presumptive MRSA-positive isolates were identified, corresponding to an observed prevalence of 0% (95% CI: 0.0–1.8%). Colonization prevalence was 29.5% among females and 26.8% among males, and ranged from 25.8% to 31.1% across age groups; neither sex nor age was significantly associated with colonization. Participants reporting daily animal contact had a colonization prevalence of 32.3%, compared with 20.5% among those without animal contact, but this difference was not statistically significant (p = 0.075). Overall, no statistically significant associations were identified between presumptive S. aureus colonization and the demographic, behavioural, occupational, or environmental variables evaluated. Presumptive S. aureus nasal colonization was common among adults living in the rural municipality of Fundão, Portugal, whereas no presumptive MRSA-positive isolates were identified in this study population. No statistically significant associations were observed between colonization and the characteristics evaluated. These findings expand the epidemiological evidence generated by the BI-STAPH Project and support continued community-based surveillance of S. aureus in rural Portugal. Future multicentre studies incorporating molecular confirmation, antimicrobial susceptibility testing, and larger populations will be important to better characterize circulating strains and transmission patterns within a One Health framework. Full article

The role of the endometrial microbiome in embryo implantation remains incompletely understood. While most studies have focused on taxonomic composition and Lactobacillus dominance, the ecological organization of microbial communities associated with implantation success has received limited attention. The aim of this study was to investigate whether implantation outcome following euploid embryo transfer is associated with differences in endometrial microbial network structure and community organization. Endometrial biopsies collected during the window of implantation from 95 women undergoing subsequent euploid embryo transfer were analyzed using 16S rRNA gene sequencing. Microbial diversity, co-occurrence networks, community structure, hub taxa, network robustness, and microbial association patterns were evaluated. The Pregnant group demonstrated a more interconnected microbial network with a greater number of significant associations, larger ecological modules, and increased network integration than the Non-pregnant group. Seventeen microbial associations were unique to the Pregnant network, whereas eleven were unique to the Non-pregnant network, indicating implantation-associated ecological rewiring. Lactobacillus-centered association patterns also differed between groups. These findings suggest that successful implantation is associated with coordinated endometrial microbial community organization rather than changes in individual taxa. Microbial network structure may represent a novel dimension of endometrial receptivity assessment. Full article

Short stature is a common pediatric endocrine–metabolic disorder characterized by impaired linear growth and increased risks of adverse health outcomes. Although previous reviews have summarized associations between gut microbiota and childhood health, few have focused on the mechanistic links among microbial composition, microbial-derived metabolites, endocrine regulation, and skeletal growth in short stature. This review provides an integrated framework exploring the potential interactions among gut microbiota composition, microbial-derived metabolites, endocrine regulation, and skeletal development in short stature. We summarize the clinical characteristics and epidemiological features of major short stature subtypes and discuss emerging evidence demonstrating the involvement of gut microbiota alterations and metabolite dysregulation in growth regulation. Particular attention is given to the bidirectional interactions between the gut microbiota and the growth hormone/insulin-like growth factor-1 (GH/IGF-1) axis, as well as the potential role of the gut–liver–bone axis in skeletal growth. Furthermore, this review integrates evidence from metabolomics studies, experimental animal models, and microbiota-targeted interventions to provide mechanistic insights into microbiota-mediated growth regulation. Dietary factors, physical activity, sleep, antibiotic exposure, probiotic interventions, and current clinical treatments are also discussed from the perspective of microbiota modulation. Despite increasing interest in microbiota-based strategies, clinical translation remains limited by insufficient functional validation, unclear causal relationships, and a lack of well-designed intervention trials. Future integration of functional microbiology, multi-omics approaches, and human-based validation platforms may facilitate the development of microbiome-based precision interventions for improving growth outcomes in children with short stature, particularly those with ISS. Full article

During the COVID-19 pandemic, healthcare systems experienced significant disruption, increasing the risk of multidrug-resistant (MDR) pathogen transmission. Acinetobacter baumannii, a critical-priority MDR pathogen, is known for its ability to persist in hospital environments and rapidly acquire resistance. To investigate the genomic characteristics, antimicrobial resistance determinants, and phylogenetic relationships of outbreak-associated Acinetobacter baumannii isolates, whole-genome sequencing (WGS) and comparative genomic analyses on 24 clinical and environmental strains collected during the COVID-19 period were performed. Twenty-four A. baumannii isolates collected between August 2020 and February 2021 from clinical and environmental samples were analyzed by WGS. All isolates displayed an MDR phenotype, with uniform resistance to carbapenems and aminoglycosides, and preserved colistin susceptibility. One environmental strain showed extreme drug resistance. WGS confirmed medium-quality genome assemblies and the clonal spread of a single A. baumannii lineage. Most resistance genes, including OXA-23, ADC-type β-lactamases, and ade efflux pumps, were chromosomally encoded and shared across all isolates. Plasmid-mediated resistance genes were variably distributed. This outbreak of MDR A. baumannii was driven by the clonal dissemination of a genomically stable lineage. Combined genomic and epidemiological analyses underscore the importance of integrated surveillance and environmental decontamination to prevent the spread of MDR pathogens. Full article

Raw-milk and raw dairy products remain a high-sensitivity One Health interface because they bypass a major microbial control step and may carry viable foodborne pathogens, bacteria exhibiting antimicrobial resistance (AMR), and AMR genes from dairy animals, farm environments, milking equipment, handlers, storage systems, and informal or direct-sale chains. This narrative review synthesizes verified scientific evidence on raw milk as a potential vehicle pathway for resistant foodborne pathogens, clinically relevant opportunistic bacteria, indicator organisms, and AMR determinants, and evaluates AMR-related emerging public health risks through a One Health perspective. The review integrates evidence from outbreak investigations, raw milk and raw dairy surveillance, culture-based antimicrobial susceptibility testing, polymerase chain reaction (PCR), whole-genome sequencing (WGS), metagenomics, metaproteomics, risk assessment, and the consumer-risk literature. The synthesis shows that raw-milk-associated AMR evidence should be interpreted by inference level rather than by a single organism or global prevalence estimate. Public health concern becomes stronger when detection or occurrence is supported by viable recovery, plausible consumer exposure, transmission linkage, infection or colonization evidence, source-attribution data, or quantified burden estimates. Evidence is strongest for exposure pathways involving Campylobacter, extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales, methicillin-resistant Staphylococcus aureus (MRSA), Salmonella, Listeria, Enterococcus, Yersinia, and raw-milk resistomes, although causal strength differs across organism groups and study designs. The review distinguishes detection or occurrence, viable recovery, potential exposure, transmission, infection or colonization, source attribution, and attributable AMR burden. One Health control requires mastitis prevention, prudent antimicrobial use, milking hygiene, environmental monitoring, pasteurization or equivalent exposure barriers, WGS-supported outbreak investigation, integrated surveillance, and targeted risk communication. Full article

Pepper (Capsicum annuum L.) is a major vegetable cultivated for seasoning in Korea. Peppers are typically grown as seedlings and transplanted into fields. Infection with Rhizoctonia solani immediately before transplantation can cause significant damage and loss during cultivation. The effectiveness of chemical fungicides is becoming increasingly limited owing to pesticide resistance, emphasizing the need for sustainable agricultural practices. This study aimed to identify a novel biocontrol agent by investigating tidal flat microorganisms capable of controlling damping-off disease in pepper caused by Rhizoctonia solani. Furthermore, we studied the inhibitory effects of different Bacillus species on the mycelial growth of R. solani AG-4 (KACC 40141) for the biological control of damping-off disease. Of the 116 bacterial strains from the tidal flats tested, five (including Bacillus sp. JB005) showed strong inhibitory activity in dual-culture assays against R. solani AG-4. These strains also demonstrated siderophore production, suggesting their potential to suppress damping-off in pepper. We screened useful agricultural traits (e.g., biofilm formation, IAA production, and phosphate solubilizing activity); the most promising strains were used for greenhouse experiments. The results indicated that Bacillus sp. JB005 strongly inhibited damping-off in pepper, suggesting that Bacillus sp. JB005 could serve as a biocontrol agent against R. solani infections. Full article

Replacing chemical compounds with biologically derived bioproducts in agriculture can make a comprehensive contribution to achieving the goals of both the Paris Agreement and the Green Deal. Scientific literature contains a significant amount of data on the use of probiotics in agriculture, which facilitate the supply of nutrients to plants, stimulate physiological processes, and inhibit the development of pathogens. These products do not have a negative impact on the surrounding environment and can therefore be used in sustainable land management. This article analyzes the microbiological composition of a bio-input made from fermented nettle extract and the species diversity of the cultivable bacteria. It was found that this input is rich in bacteria beneficial to plants and soil (Clostridium, Paenibacillus, Frankia, Rhizobium, Bradyrhizobium, Azospirillum, Azotobacter, and others), some of which can be cultured under artificial conditions. Among the cultivable bacteria grown from the tested input, the majority were representatives of the Pseudomonadota (92%), and a small proportion were Bacillota (6%). Among them were a great many different bacteria beneficial to the soil ecosystem. Thus, there is considerable potential here for the use of these bacteria in the production of biological products. Full article

The spread of antimicrobial-resistant bacteria in aquatic environments is a public health concern, especially in areas with anthropogenic activity. Hydroelectric reservoirs may act as interfaces facilitating the dissemination of resistance. Escherichia coli is used as an indicator of environmental contamination and antimicrobial resistance. To investigate the occurrence of E. coli in reservoirs of the Urubupungá Hydroelectric Complex (Paraná River basin, Brazil) and to characterize antimicrobial resistance profiles and ESBL/AmpC-related genes. Methods: Water samples were collected during rainy and dry seasons (2022–2024). A total of 200 E. coli isolates were analyzed by broth microdilution (EUCAST). ESBL and AmpC production were phenotypically assessed, and resistance genes (blaCTX-M, blaTEM, blaSHV, and ampC) were detected by PCR. 26% of isolates showed resistance to at least one antimicrobial, mainly tetracycline (18%), amoxicillin (15%), and ampicillin (15%). All isolates were susceptible to imipenem, meropenem, and norfloxacin. Among the investigated resistance markers, ampC was the most frequently detected gene, whereas blaCTX-M was the predominant ESBL-associated determinant. Significant associations were observed between blaCTX-M and resistance to cefotaxime, ceftazidime, and cefepime, whereas the presence of ampC was significantly associated with cefoxitin resistance. Significant associations were observed between β-lactam resistance and ESBL genes. Hydroelectric reservoirs under anthropogenic influence may serve as environmental reservoirs of antimicrobial-resistant E. coli, particularly ESBL producers. These findings highlight the role of aquatic environments in the dissemination of clinically relevant resistance genes. Full article

The transition toward reusable food packaging driven by European circular economy regulations introduces new food safety challenges related to microbial persistence and cross-contamination. GS-2 is a novel, food-safe antimicrobial formulation developed for use as a coating on reusable packaging materials. In the present study, the intrinsic antimicrobial activity of GS-2 was evaluated in liquid suspension against foodborne bacterial (Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella enterica Agona) and fungal pathogens (Aspergillus flavus and Aspergillus niger), and the transcriptomic response of L. monocytogenes following sublethal GS-2 exposure was investigated. GS-2 exhibited concentration-dependent microbicidal activity, with strong reductions observed at ≥2.8–3.0% against bacterial strains and A. flavus, while A. niger demonstrated resistance. Among bacteria, L. monocytogenes showed the greatest sensitivity, with populations reduced below detection limits at 3% GS-2. To elucidate mechanistic responses, RNA sequencing was performed on L. monocytogenes exposed to sublethal GS-2 concentrations (0.1–1.0%). Transcriptomic analyses using discrete and continuous models revealed a pronounced adaptive stress response at 0.5% GS-2, characterized by coordinated upregulation of pathways involved in carbon, nitrogen, and nucleotide metabolism. At higher sublethal concentrations (1%), transcriptional profiles shifted toward growth arrest and cellular damage management. These findings support GS-2 as a promising antimicrobial for enhancing the microbial safety of reusable food packaging systems. Full article

Nosocomial bronchopneumonia is a severe lung infection that develops more than 48 h after hospital admission and is frequently caused by antibiotic-resistant bacteria. It is often identified postmortem in forensic practice, particularly in patients with severe traumatic injuries requiring prolonged hospitalization and immobilization. Diagnosis is typically based on macroscopic findings and histopathological examination of lung tissue. This study aimed to evaluate the diagnostic value of postmortem microbiological testing by comparison with antemortem microbiological data. Ten patients with a clinical diagnosis of nosocomial bronchopneumonia were selected from forensic cases. During autopsy, tracheal swabs and lung tissue samples were collected and subjected to culture-based and molecular analyses. The results were compared with those obtained from antemortem microbiological investigations. Pathogens characteristic of nosocomial infections were identified; however, concordance with in-hospital microbiological data was highest when using next-generation sequencing (NGS) metagenomic analysis. Tracheal swab culture appears to have limited reliability for postmortem identification of bacterial agents in healthcare-associated bronchopneumonia. In contrast, metagenomic next-generation sequencing (mNGS) of lung tissue obtained at autopsy showed the highest concordance with antemortem microbiological findings and may provide valuable complementary diagnostic information, particularly in polymicrobial infections. Full article

The growing demand for sustainable crop protection has intensified interest in biological control agents. This study characterized a Trichoderma asperellum strain (IDE-10) to assess its suitability for integrated pest and disease management. Key ecophysiological traits, including temperature, pH, and ultraviolet (UV) tolerance, were evaluated, along with compatibility with commonly used fungicides and insecticides. The strain exhibited optimal growth at 28.28 °C and sustained high growth rates up to 35 °C, with a maximum threshold of 39.21 °C, indicating strong adaptation to warm climates. Sporulation was enhanced between 25 and 35 °C, with no growth at 5 °C, and soil viability remained stable from 7 to 21 °C. The IDE-10 strain demonstrated broad pH tolerance (3–7) and high resistance to UV-A and UV-B radiation, distinguishing it from commercial strains. Insecticides had no significant adverse effects, while fungicide compatibility varied, with IDE-10 being compatible with metalaxyl- and copper-based formulations. These findings highlight the robustness and adaptability of T. asperellum IDE-10, supporting its potential as a biocontrol agent for sustainable crop protection strategies, particularly in Mediterranean agricultural systems. Full article

Tomato leaf mold, caused by Passalora fulva, is one of the most destructive fungal diseases affecting greenhouse tomato production and can cause substantial yield losses under conditions of high relative humidity and moderate temperatures that favor pathogen infection and disease development. This study evaluated the in vitro antifungal activity of a commercial fungicide formulation, Priori Top^® (azoxystrobin + difenoconazole), and three essential oils derived from Eucalyptus globulus, Artemisia herba-alba, and Mentha pulegium against two monoconidial isolates of P. fulva. Unlike previous studies, which have mainly focused on mycelial growth, the present work simultaneously evaluated the effects of the tested products on mycelial growth, sporulation, and conidial germination, providing a comprehensive assessment of antifungal efficacy across three key developmental stages of the pathogen. Antifungal activity was quantified by estimating IC₅₀ and IC₉₀ values using Probit regression analysis. The azoxystrobin–difenoconazole formulation consistently exhibited the highest antifungal activity across all evaluated parameters and showed the lowest estimated IC₅₀ and IC₉₀ values for both fungal isolates. Among the tested essential oils, Artemisia herba-alba exhibited the greatest antifungal activity, reducing mycelial growth by 83% and 78% at 500 ppm for isolates 1 and 2, respectively, and consistently outperforming Mentha pulegium and Eucalyptus globulus. Differences in sensitivity were observed between the two fungal isolates, indicating intraspecific variability in their response to the tested treatments. These findings demonstrate the strong antifungal efficacy of the azoxystrobin–difenoconazole formulation against P. fulva and identify A. herba-alba essential oil as the most promising botanical treatment for integrated management of tomato leaf mold. Further greenhouse and field studies are required to validate these findings, optimize formulation strategies, and evaluate the practical application of A. herba-alba essential oil under commercial production conditions. Full article

Acute bronchiolitis is the leading cause of infant hospitalization worldwide, with respiratory syncytial virus (RSV) historically predominating. Prospective virological data for the 2025–2026 epidemic season in Morocco were lacking. A prospective observational cohort study was conducted at the Department of Pediatric Infectious Diseases and Clinical Immunology, Casablanca Mother-Child Hospital, from August 2025 through March 2026. Consecutive infants aged 1–24 months hospitalized with acute viral bronchiolitis underwent nasopharyngeal sampling and multiplex rapid antigen testing for RSV, influenza A, influenza B, and SARS-CoV-2. A total of 131 infants were enrolled (median age 4.8 months; male-to-female ratio 0.84:1). At least one virus was identified in 63 patients (48.1%; 95% CI 39.1–57.3%). RSV predominated: 49 sole infections and 2 co-infections with influenza A, totaling 51 positives (80.9% of virus-positive cases; 38.9% of the cohort). Influenza A totaled 8 cases (12.7%), including the 2 co-infections; influenza B accounted for 2 further cases (3.2%). SARS-CoV-2 was not detected. Epidemic activity peaked in January 2026 (65 admissions), declining through February (34) and March (12). All detected pathogens have licensed preventive options, supporting the introduction of nirsevimab, maternal RSV vaccination, and seasonal influenza vaccination as public health priorities in Morocco. Full article

Mpox remains an important public health threat in several African countries, with recurrent outbreaks highlighting the need for decentralized and scalable diagnostic systems. During the 2024–2025 Mpox outbreak in Burundi, reliance on a single National Reference Laboratory limited timely diagnosis, reduced surveillance efficiency, and delayed outbreak response activities. This study describes and evaluates the implementation of a national strategy for decentralizing and expanding Mpox diagnostic capacity across Burundi. A descriptive implementation study was conducted between August 2024 and July 2025. Burundi implemented a four-phase diagnostic scale-up strategy that expanded Mpox testing services from one centralized laboratory to 56 decentralized GeneXpert-equipped laboratories, including mobile laboratory units. The implementation phases comprised strategic planning and risk mapping, pilot deployment at the national level, regional expansion, and extension to peripheral district laboratories. Key interventions included healthcare workforce training, strengthening laboratory supply chains, deployment of mobile diagnostic units, and integration of laboratory information into the national surveillance system. Program performance was assessed using indicators of laboratory network expansion, testing coverage, diagnostic turnaround time, and confirmed case detection. Following implementation, the number of operational Mpox diagnostic sites increased from 1 to 56, representing a 5500% expansion in testing capacity. National testing coverage approached 100%, substantially improving geographical access to diagnostic services. Weekly confirmed Mpox case detection increased by 496%, reflecting enhanced surveillance sensitivity and improved case identification. Diagnostic turnaround time decreased from 24–72 h under the centralized model to 2–4 h following decentralization. The expanded diagnostic network facilitated earlier case confirmation, more rapid isolation of infected individuals, strengthened surveillance activities, and accelerated implementation of outbreak control measures. The phased decentralization of Mpox diagnostics using existing GeneXpert infrastructure and mobile laboratories substantially improved testing access, reduced diagnostic delays, and strengthened outbreak response capacity in Burundi. This approach demonstrates a practical, scalable, and cost-effective model for enhancing epidemic preparedness and building resilient diagnostic systems in resource-constrained settings. Similar strategies could support improved detection and control of Mpox and other emerging infectious diseases across Africa and comparable low-resource environments. Full article