Search Results (97)

Typhoid fever, caused by Salmonella enterica subsp. enterica serovar Typhi (S. typhi), remains a major public health concern, particularly in low-resource settings with poor sanitation. The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains have significantly complicated treatment, especially in vulnerable pediatric populations. This study aimed to characterize the genetic profiles of drug resistance in MDR and XDR S. typhi isolates from pediatric patients. Methods: A cross-sectional study was conducted on 800 blood samples from pediatric typhoid patients. S. typhi isolates were identified using the BacT/ALERT 3D system, followed by culture on MacConkey and blood agar. Antimicrobial susceptibility was assessed using the disk diffusion method according to CLSI 2022 guidelines. Whole-genome sequencing (WGS) was performed on 29 isolates using Illumina MiSeq technology, and resistance genes and mutations were analyzed. Results: Antimicrobial susceptibility testing revealed that 68 (48.57%) of S. typhi isolates were XDR and 61 (43.57%) were MDR, exhibiting widespread resistance to ciprofloxacin, ampicillin, chloramphenicol, ceftriaxone, and co-trimoxazole. WGS identified key resistance genes across all 29 isolates, including bla_CTX-M-15, bla_TEM-1B, qnrS1, aac(6′)-Iaa, catA1, dfraA7, sul1, qacEΔ1, and the gyrA-S83F mutation. Notably, gyrA-S83F and qnrS1 were detected in all isolates and strongly correlated with ciprofloxacin resistance. Virulence genes were consistently present in all isolates, indicating a high pathogenic potential. The IncY plasmid, found in four (14%) isolates, was linked to resistance against third-generation cephalosporins, including ceftriaxone. Conclusion: This study underscores the alarming prevalence of MDR and XDR S. typhi isolates among pediatric patients, driven by resistance genes such as bla_CTX-M-15, bla_TEM-1B, and gyrA-S83F. These findings highlight the urgent need for targeted therapeutic strategies and robust surveillance systems to combat the growing threat of drug-resistant typhoid fever. Full article

Background/Objectives: The COVID-19 pandemic significantly disrupted healthcare systems worldwide, leading to increased healthcare-associated infection rates, particularly in the intensive care unit (ICU) setting. Little is known about the evolution of this phenomenon in subsequent years. Methods: This retrospective analysis of prospectively collected data (January 2020–December 2024) examined central line-associated bloodstream infections (CLABSI) in the Wroclaw Medical University hospital’s ICU during and after the COVID-19 pandemic. Results: Ninety CLABSI cases were observed in 3149 ICU patients across 39,837 patient-days and 36,038 central-vascular-catheter-days (CVC-D). The mean CLABSI frequency was 2.97 per 100 admissions, with an incidence density of 2.49 per 1000 CVC-D. CLABSI occurred more frequently in males than in females (3.51% vs. 1.69%, p = 0.003) and in patients with concomitant SARS-CoV-2 infection than in individuals without such coinfection (6.06% vs. 1.88%, p = 0.00037). Microbiological analysis revealed Staphylococcus epidermidis as the most frequent etiological factor of CLABSI (33.3%). Alert pathogens constituted 34.26% of all CLABSI etiological factors, with higher prevalence during the pandemic than afterward (51.16% vs. 23.08%, p = 0.005437). Patients with CLABSI had significantly longer ICU stays (53.57 vs. 11.62 days, p = 0.001). After adjusting for immortal time bias using matched cohort analysis, CLABSI was not associated with increased mortality (p = 0.735). The overall compliance level of adherence to CLABSI prevention measures was 86.9%, with no statistically significant difference between the pandemic and post-pandemic periods, p = 0.417. The study did not systematically collect data on catheter types, insertion sites, or clinical circumstances (emergency vs. elective), which are known risk factors that may have influenced the observed CLABSI incidence rates. Conclusions: Despite increased patient volume post-pandemic, CLABSI metrics remained stable, possibly due to the successful adaptation of infection prevention protocols. However, interpretation of incidence data should consider unmeasured confounding factors. These findings address knowledge gaps regarding how the pandemic affected CLABSI epidemiology and antimicrobial resistance patterns, with implications for infection control practices during future healthcare crises. Full article

Coastal ecosystems are increasingly threatened by climate change and anthropogenic pressures, which can disrupt microbial communities and favor the emergence of pathogenic organisms. In this study, we applied metagenomic analysis to characterize fungal communities in sediment samples from an urban mangrove subjected to environmental stress. The results revealed a fungal community with reduced richness—28% lower than expected for similar ecosystems—likely linked to physicochemical changes such as heavy metal accumulation, acidic pH, and eutrophication, all typical of urbanized coastal areas. Notably, we detected an increase in potentially pathogenic genera, including Candida, Aspergillus, and Pseudoascochyta, alongside a decrease in key saprotrophic genera such as Fusarium and Thelebolus, indicating a shift in ecological function. The fungal assemblage was dominated by the phyla Ascomycota and Basidiomycota, and despite adverse conditions, symbiotic mycorrhizal fungi remained present, suggesting partial resilience. A considerable fraction of unclassified fungal taxa also points to underexplored microbial diversity with potential ecological or health significance. Importantly, this study does not aim to compare pristine and contaminated environments, but rather to provide a sanitary alert by identifying the presence and potential proliferation of pathogenic fungi in a degraded mangrove system. These findings highlight the sensitivity of mangrove fungal communities to environmental disturbance and reinforce the value of metagenomic approaches for monitoring ecosystem health. Incorporating fungal metagenomic surveillance into environmental management strategies is essential to better understand biodiversity loss, ecological resilience, and potential public health risks in degraded coastal environments. Full article

Monitoring infectious diseases is essential for safeguarding equine health and ensuring the sustainability of the horse industry. In 2019, the Royal Veterinary Association of the Netherlands (KNMvD) and Royal GD (GD Animal Health) launched SEIN (Surveillance of Equine Infectious diseases in the Netherlands), a voluntary surveillance system for laboratory-confirmed outbreaks of equid alphaherpesvirus 1 (EHV-1), equid alphaherpesvirus 4 (EHV-4), equine influenza virus (EIV), and Streptococcus equi subsp. equi. This retrospective study analyzed 364 confirmed outbreaks reported through SEIN between June 2019 and April 2023. S. equi was the most commonly reported pathogen overall (64%). Among outbreaks involving respiratory disease, S. equi accounted for 74% of cases, followed by EHV-4 (16%), EIV (6%), and EHV-1 (4%). The geographical distribution of outbreaks covered 80 of the 90 postal code regions (89%), and approximately half of all participating practices generated at least 1 alert. Vaccination data revealed low coverage against EHV-1/4, EIV, and S. equi among both affected horses and premises. Clinical signs overlapped between pathogens, but some were more pathogen-specific, e.g., coughing in EIV, and abscessation in S. equi. The SEIN system provided spatiotemporal information on confirmed outbreaks. These results underscore the importance of quick diagnostics and structured surveillance systems in guiding prevention strategies. Full article

The results of our recent research revealed that biologically synthesized silver nanoparticles (bio-AgNPs) applied to several-day-old pea (Pisum sativum L.) plants or used for seed nanopriming protected pea plants against selected fungal pathogens. However, the susceptibility of pea to bio-AgNPs during seed germination remains mostly unknown. Therefore, in this study, we investigated the cells’ viability, ROS generation, total antioxidant capacity, the activity of selected antioxidant enzymes, and changes in the polar metabolite profiles of 4-day-old pea seedlings developed in water (control) and water suspensions of bio-AgNPs (at 50 and 200 mg/L). The bio-AgNPs did not negatively affect pea seeds’ germination, early seedlings’ growth, and root tips cells’ viability (at both tested concentrations). In the root, the bio-AgNPs at a lower concentration (50 mg/L) stimulated ROS generation. Nanoparticles enhanced peroxidase activity in root and the total antioxidant capacity in epicotyl. Increased levels of malate, phosphoric acid, proline, GABA, and alanine were observed in root and epicotyl of pea seedlings developed at 50 mg/L of bio-AgNPs. A higher concentration affected the tricarboxylic acid cycle and nitrogen metabolism. Bio-AgNPs alerted oxidative homeostasis and primary metabolism of pea seedlings but did not exceed a certain threshold limit and thus did not injure pea at an early stage of seedling development. Full article

Tourism plays an important role in the economic and social development of many countries and regions. Tourists buy food, such as canned food, alcohol, and spices, which increases the value of a trip, fulfilling a cultural, sentimental, educational, and marketing role whilst documenting the trip, or they become gifts for family and friends. However, spices may not be of the appropriate quality or may even be harmful to health due to contamination or adulteration. Therefore, the aim of the paper was to present spices as culinary souvenirs and to indicate some risks that may arise from their consumption. To date, only few such studies have been published in this area. A literature review was conducted and data from Eurostat, Rapid Alert System for Food and Feed (RASFF) and Web of Science were used. The most serious hazards in spices are pathogens, pesticides, and mycotoxins in products from Asia. Adequate awareness needs to be built among tourists and tour operators about where to buy spices that are risk-free and not adulterated. It will contribute to the development of sustainable food tourism. Further research may look at specific types of spices and where they are purchased highlighting the issue of authenticity and traceability. Full article

Diabetes mellitus (DM) and tuberculosis (TB) are two global health challenges that significantly impact population health, with DM increasing susceptibility to TB infections. However, early risk prediction methods for DM patients complicated with TB (DM–TB) are lacking. This study mined transcriptome data of DM–TB patients from the GEO database (GSE181143 and GSE114192) and used differential analysis, weighted gene co-expression network analysis (WGCNA), intersecting immune databases, combined with ten machine learning algorithms, to identify immune biomarkers associated with DM–TB. An early alert model for DM–TB was constructed based on the identified core differentially expressed genes (DEGs) and validated through a prospective cohort study and reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) for gene expression levels. Furthermore, we performed a detailed immune status analysis of DM–TB patients using the CIBERSORT algorithm. We identified 1090 DEGs associated with DM–TB and further pinpointed CETP (cholesteryl ester transfer protein) (AUC = 0.804, CI: 0.744–0.864), TYROBP (TYRO protein tyrosine kinase binding protein) (AUC = 0.810, CI: 0.752–0.867), and SECTM1 (secreted and transmembrane protein 1) (AUC = 0.811, CI: 0.757–0.864) as immune-related biomarkers for DM–TB patients. An early alert model was developed based on these three genes (AUC = 0.86, CI: 0.813–0.907), with a sensitivity of 0.80829 and a specificity of 0.75758 at a Youden index of 0.56587. External validation using the GSE114192 dataset showed an AUC of 0.901 (CI: 0.847–0.955). Population cohort research and RT-qPCR verified the expression levels of these three genes, demonstrating consistency with trends seen in the training set. KEGG enrichment analysis revealed that NF-κB and MAPK signaling pathways play crucial roles in the DM–TB pathogenic mechanism, and immune infiltration analysis showed significant suppression of certain adaptive immune cells and activation of inflammatory cells in DM–TB patients. This study identified three potential immune-related biomarkers for DM–TB, and the constructed risk assessment model demonstrated significant predictive efficiency, providing an early screening strategy for DM–TB. Full article

Background/Objectives: Continuous monitoring blood culture systems (CMBCSs) are revolutionary automated instruments that facilitate the rapid identification of pathogens in blood samples from patients with sepsis. However, with only a few CMBCSs being widely used as references, user dependency on these limited options has grown. In response, a new CMBCS was developed and compared with existing systems to evaluate microbial growth. Methods: HubCentra84 was compared to BacT/Alert^® 3D and BACTEC™ FX. Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Bacteroides fragilis, and Candida albicans were selected as representative clinically infectious microorganisms. Colonies from pure cultures were diluted with 0.9% saline to create simulated sepsis specimens (SSSs). The SSSs were injected into dedicated culture bottles for each instrument. Thirty paired tests were performed for each strain. Results: Colony-forming units of the added SSSs were consistent according to bacteria, and all strains demonstrated robust growth in three CMBCSs. Time-to-positivity was uniformly observed according to the instruments used. The novel CMBCS detected the growth of the clinically significant bacteria S. aureus, S. pneumoniae, E. coli, and P. aeruginosa approximately 2 h faster than the other two systems. However, it was approximately 200 min slower for C. albicans and 3000 min for B. fragilis. Conclusions: The novel CMBCS demonstrates advantages in detecting the growth of common clinical bacteria. Although slow growth was detected for certain microorganisms, it successfully captured the growth of all tested microorganisms. Full article

The European Green Deal attaches great importance to sustainability, including food security, which is also linked to food safety. This is particularly relevant in such a sensitive region as the Mediterranean. The goal of this study was to investigate Rapid Alert System for Food and Feed (RASFF) notifications of hazards reported in 1997–2021 (a 25-year period) in products from northern Mediterranean countries considering products and other variables. A two-way joining cluster analysis was used. The most notable hazards in the latter years of the reported period were as follows: ochratoxin A and pesticide residues in fruits and vegetables imported from Turkey and ethylene oxide in various products, as well as Salmonella in chicken, Listeria in cheese, Escherichia coli in cheese and mussels from France, mercury in swordfish from Spain, and Anisakis in seafood from France and Morocco. The increasing number of notifications of ochratoxin A and pathogenic micro-organisms in recent years may be caused by climate change. This also results in the need to use more pesticides and the appearance of related hazards, i.e., residues of such compounds in food products. It is, therefore, vitally important that border posts and control authorities in particular European Union countries are vigilant. Full article

Oropouche virus (OROV) is an orthobunyavirus endemic in the Brazilian Amazon that has caused numerous outbreaks of febrile disease since its discovery in 1955. During 2024, Oropouche fever spread from the endemic regions of Brazil into non-endemic areas and other Latin American and Caribbean countries, resulting in 13,014 confirmed infections. Similarly to other orthobunyaviruses, OROV can undergo genetic reassortment events with itself as well as other viruses. This occurred during this current outbreak, resulting in novel strains with increased pathogenicity and levels of transmission. For the first time, pregnant women with Oropouche fever have sustained poor perinatal outcomes, including miscarriage, fetal demise, stillbirths and malformation syndromes including microcephaly. In July 2024, PAHO issued an Epidemiological Alert warning of the association of OROV with vertical transmission. OROV has now been identified in the fetal blood, cerebrospinal fluid, placenta and umbilical cords, and fetal somatic organs including the liver, kidneys, brain, spleen, heart, and lungs using nucleic acid and antigen testing. Perinatal autopsy pathology has confirmed central nervous system infection from OROV in infants with congenital infection including microcephaly, ventriculomegaly, agenesis of corpus callosum, and neuronal necrosis. The latest data from Brazil show 3 confirmed cases of OROV vertical transmission; 2 cases of fetal death; 1 case of congenital malformation; and ongoing investigations into the role of OROV in 15 cases of fetal death, 3 cases of congenital malformations and 5 spontaneous miscarriages. This Commentary discusses the mechanisms and significance of development of novel reassortant strains of OROV during the current outbreak and their recent recognition as causing vertical infection and adverse perinatal outcomes among pregnant women with Oropouche fever. Full article

MyD88 deficiency is a rare inborn error of immunity (IEI) characterized by susceptibility to pyogenic infections without overt signs of inflammation. Half of the reported patients belong to Roma descent, an itinerant ethnic group living mostly in Europe, with an increased risk of childhood mortality due to limited access to healthcare services. We describe three unrelated patients from the Campania region in Italy with MyD88 deficiency, all belonging to Roma descent and displaying severe or recurrent infections in early infancy. They underwent a comprehensive immunological work-up including targeted next-generation sequencing for IEIs that identified a homozygous pathogenic in-frame deletion c.157_159del p.(Glu53del) in MYD88 gene, already described in this ethnic group, suggesting a founder effect. A high level of alert should be kept in patients of Roma ethnicity with early onset severe infections. Moreover, being associated with increased Immunoglobulin E (IgE) levels, this condition should be included in the differential diagnosis of Hyper-IgE syndromes. Full article

Background/Objectives: Hypophosphatasemia (HPE) may be temporary (tHPE) in the context of severe diseases, such as sepsis or trauma, or it may persist (pHPE), indicating an adult form of hypophosphatasia (HPP; OMIM 171760), a rare metabolic bone disorder caused by pathogenic nucleotide variants (PNVs) in the ALPL gene. The aim of this study was to analyze the role of auxiliary general biomarkers in verifying low alkaline phosphatase (ALP) serum activity level as an alert parameter for PNVs in the ALPL gene, which are indicative of HPP. In this retrospective analysis, we examined adult patients with an ALP serum activity level below 21 U/L. The cohort comprised 88 patients with temporary HPE (tHPE group) and 20 patients with persistent HPE who underwent re-examination. Genetic analysis performed on 12 pHPE patients identified PNV in the ALPL gene in 11 cases (ALPL group). Hemoglobin [HB], aspartate aminotransferase [AST], gamma-glutamyl transferase [GGT], calcium, phosphate, thyrotropin [TSH], albumin, total protein, and C-reactive protein [CRP] levels represented basic biomarkers. A comparative analysis between groups employed a Student’s t-test, and a Student’s t-test with bootstrap sampling (n = 10.000) was performed. Results: The mean HB, ALP, calcium, albumin, and total protein levels were lower in the tHPE group compared with the ALPL group (p < 0.01). AST and CRP were increased in the tHPE group (p < 0.01). The model showed an accuracy of 90% and an AUC of 0.94, which means that it can discern the two groups ~94% of the time. Conclusions: Basic biomarker evaluation effectively supports the interpretation of a decreased ALP serum activity level in the context of suspected HPP. In patients with laboratory HPE and biomarkers within reference, a PNV in the ALPL gene is highly suspected. Full article

The SARS-CoV-2 pandemic significantly affected the epidemiology of Streptococcus pyogenes, a pathogen associated with various clinical presentations such as pharyngitis, scarlet fever, and invasive diseases. This study analyzed the incidence and characteristics of S. pyogenes infections between 2018 and 2023, examining 915 cases categorized as either respiratory or non-respiratory. Respiratory infections predominantly affected children, accounting for 76% of cases, with a median age of 5 [3, 8] years, while non-respiratory infections were more common in adults, with a median age of 46.5 [34, 64] years. Invasive respiratory infections, such as pneumonia and empyema, were more frequent in children (54.8%), whereas invasive non-respiratory infections, such as primarily cellulitis, were predominantly seen in adults (90.5%). A sharp decline in S. pyogenes infections was observed during the pandemic, with respiratory cases decreasing tenfold in 2020 compared to the previous year, and non-respiratory cases experiencing a twofold reduction. However, infection rates returned to pre-pandemic levels by 2022 and 2023, with a notable resurgence of invasive respiratory infections in children following a public health alert in the United Kingdom in late 2022. These findings highlight distinct infection patterns between pediatric and adult populations and emphasize the significant impact of the pandemic on respiratory infections, particularly in children. Full article

Symbiosis establishment between Trichoderma atroviride and plant roots triggers the priming of defense responses, among other effects. Currently, there is no clear evidence regarding the molecular mechanisms that allow the plant to remain alert to future stimulus, either by pathogen attack or any other abiotic stress. Epigenetic modifications have emerged as a strategy to explain the increased defense response of plants in a priming state conferred by Trichoderma. Recently, various non-canonical structures of nucleic acids, especially G-quadruplex structures (G-quadruplexes or G4s), have been identified as potential targets during the establishment or maintenance of plant signals. In the present study, we developed a screening test for the identification of putative G4-forming sequences (PQSs) in previously identified Z. mays priming genes. Bioinformatic analysis revealed the presence of PQSs in the promoter region of five essential genes playing a critical role in priming in maize. Biophysical and spectroscopy studies showed the formation of G4s by these PQSs in vitro, and ChIP assays demonstrate their formation in vivo. Therefore, G4 formation could play a role as an epigenetic regulatory mechanism involved in the long-lasting primed state in maize plants. Full article

The epidemic of avian influenza outbreaks, especially high-pathogenicity avian influenza (HPAI), which causes respiratory disease and death, is a disaster in poultry. The outbreak of HPAI in 2014–2015 caused the loss of 60 million chickens and turkeys. The most recent HPAI outbreak, ongoing since 2021, has led to the loss of over 50 million chickens so far in the US and Canada. Farm biosecurity management practices have been used to prevent the spread of the virus. However, existing practices related to controlling the transmission of the virus through wild birds, especially waterfowl, are limited. For instance, ducks were considered hosts of avian influenza viruses in many past outbreaks. The objectives of this study were to develop a machine vision framework for tracking wild birds and test the performance of deep learning models in the detection of wild birds on poultry farms. A deep learning framework based on computer vision was designed and applied to the monitoring of wild birds. A night vision camera was used to collect data on wild bird near poultry farms. In the data, there were two main wild birds: the gadwall and brown thrasher. More than 6000 pictures were extracted through random video selection and applied in the training and testing processes. An overall precision of 0.95 (mAP@0.5) was reached by the model. The model is capable of automatic and real-time detection of wild birds. Missed detection mainly came from occlusion because the wild birds tended to hide in grass. Future research could be focused on applying the model to alert to the risk of wild birds and combining it with unmanned aerial vehicles to drive out detected wild birds. Full article