Search Results (547)

Antimicrobial resistance (AMR) poses a critical global health threat. Wastewater surveillance has recently emerged as a valuable public health tool for monitoring AMR in communities and healthcare settings. This narrative review comprehensively examines the role of hospital wastewater surveillance (HWWS) in monitoring antimicrobial resistance. Methods to detect resistant bacteria and antimicrobial resistance genes (ARGs) in wastewater systems, ranging from culture-based techniques to advanced molecular approaches, including polymerase chain reaction (PCR) and next-generation sequencing (NGS), are explored. The review synthesizes data on key antimicrobial resistance genes commonly detected in hospital effluents and explores how HWWS contributes to understanding the dynamics of resistance within healthcare settings. Furthermore, it identifies methodological challenges and inconsistencies in data reporting and outlines necessary standardization steps to enhance the effectiveness of HWWS programs. Opportunities for integrating HWWS with clinical and public health frameworks are presented, emphasizing the need for robust metadata and transparent reporting. This review provides a comprehensive approach to HWWS strategies, which could complement robust infection control and antibiotic stewardship interventions to combat AMR. Full article

Bovine respiratory disease (BRD) is a multifactorial syndrome and a leading cause of morbidity and economic loss in global cattle production. Next-generation sequencing (NGS) platforms, including Illumina and Oxford Nanopore Technologies (ONT), have enabled high-resolution profiling of the bovine respiratory microbiome and virome, revealing novel viral contributors such as bovine rhinitis A virus (BRAV) and influenza D virus (IDV). Transcriptomic approaches, including RNA sequencing (RNA-Seq) and microRNA (miRNA) profiling, provide insights into host immune responses and identify potential biomarkers for disease prediction. Traditional diagnostic methods—culture, ELISA, and immunohistochemistry—are increasingly complemented by PCR-based and metagenomic techniques, improving sensitivity and specificity. Despite technological progress, gaps remain in virome characterization, miRNA function, and the integration of multi-omics data. Standardized protocols and longitudinal studies are needed to validate microbial signatures and support field-deployable diagnostics. Advances in bioinformatics, particularly network-based integrative pipelines, are becoming essential for harmonizing multi-omics datasets and revealing complex host–pathogen interactions. The objective of this comprehensive review was to synthesize current understanding of the bovine transcriptomic response to BRD as well as the respiratory microbiome and virome, emphasizing how advanced sequencing technologies have transformed microbial profiling and molecular diagnostics in BRD. Full article

Wound healing is a complex and multistage process that incorporates precise cellular and molecular coordination. The presence of biofilms in chronic wounds adversely affects the wound healing process, as it prolongs the closure of the wound, thus sustaining chronic inflammation. Current data suggest that biofilms are present in almost all chronic wounds, which leads to significant challenges in diagnosis and treatment. Traditional detection methods, such as cultures and light microscopy, often fail to detect biofilms; however, sophisticated molecular and imaging techniques are constrained by their expense and accessibility. Chronic wound management, therefore, has progressed from conventional antimicrobial application to integrated methodologies that incorporate biofilm debridement, antibiofilm dressing, negative pressure wound therapy, and innovative enzyme or nanoparticle interventions. This review highlights the clinical significance of biofilm presence as a barrier in chronic wound healing, assesses diagnostic and therapeutic innovations, and stresses the urgent need to improve patient outcomes. Full article

Primordial germ cells (PGCs) are the unipotent precursors of sperm and ova, responsible for transmitting hereditary information across generations. Their ability to be isolated and cultured in vitro has opened new horizons for avian biotechnology, species conservation, and fundamental developmental research. In birds, the unique migratory pattern of PGCs—originating in the epiblast and traveling via the bloodstream to the gonads—enables their collection and manipulation during embryogenesis. Long-term in vitro culture systems have been successfully established in chickens, where defined media allow for stable proliferation and genetic modification. Applications include germline chimeras, generation of transgenic lines, recombinant protein production, and cryobanking of genetic resources. However, translating these advances to other species remains challenging due to interspecies variability in signaling requirements. Recent work in geese, ducks, quails, and zebra finches underscores the need for tailored media formulations and a better understanding of molecular regulation. This review summarizes established techniques, highlights key interspecies differences, and outlines future directions for the standardization and expansion of avian PGC culture systems to support conservation and biotechnology. Full article

Apple represents one of the most economically significant fruit crops worldwide, and the performance of its scion is largely determined by the physiological and genetic characteristics of the rootstock. Despite their superior ecological adaptability and growth-controlling attributes, many dwarfing apple rootstocks exhibit inherently poor rooting competence, which poses a critical limitation to their large-scale clonal propagation and commercial utilization. Adventitious root (AR) formation is a pivotal yet highly intricate developmental process that governs the success of asexual propagation. It is orchestrated by a complex network of hormonal signaling, transcriptional regulation, metabolic reprogramming, and environmental cues. Over the past decade, remarkable advances have elucidated the physiological, biochemical, and molecular frameworks underpinning AR formation in apple rootstocks. This review provides an integrative synthesis of current progress in vegetative propagation techniques—including cutting, layering, and tissue culture—and systematically dissects the endogenous and exogenous factors influencing AR development. Particular emphasis is placed on the regulatory interplay among phytohormones, carbohydrate and nitrogen metabolism, phenolic compounds, transcription factors (such as WUSCHEL-RELATED HOMEOBOX (WOX), LATERAL ORGAN BOUNDARIES DOMAIN (LBD), and RESPONSE FACTOR (ARF families), and epigenetic modulators that collectively coordinate root induction and emergence. Furthermore, emerging insights into multi-omics integration and genotype-specific molecular regulation are discussed as strategic pathways toward enhancing propagation efficiency. Collectively, this review establishes a comprehensive theoretical framework for optimizing the asexual propagation of apple rootstocks and provides critical molecular guidance for breeding novel, easy-to-root genotypes that can drive the sustainable intensification of global apple production. Full article

Nonunions and fracture-related infections represent a significant complication in orthopedic and trauma care, with their incidence rising due to an aging, more comorbid global population and the escalating threat of multi-resistant pathogens. This narrative review highlights pivotal advancements in diagnostics and therapeutic approaches, while also providing an outlook on future directions. Diagnostic methodologies have significantly evolved from traditional cultures to sophisticated molecular techniques like metagenomic next-generation sequencing and advanced imaging. Simultaneously, therapeutic strategies have undergone substantial refinement, encompassing orthoplastic management for infected open fractures and the innovative application of antibiotic-loaded bone substitutes for local drug delivery. The effective integration of these possibilities into daily patient care critically depends on specialized centers. These institutions play an indispensable role in managing complex cases and fostering innovation. Despite considerable progress over the past 25 years, ongoing research, interdisciplinary collaboration, and a steadfast commitment to evidence-based practice remain crucial to transforming management for the future. Full article

Cannabis plants are susceptible to microbial contamination, including fungi capable of producing harmful mycotoxins. The presence of these toxins in cannabis products poses serious health risks, especially when used for medical purposes in immunocompromised people. This study evaluated the presence of fungi and mycotoxins in dried cannabis buds following gamma irradiation, using culture-based techniques, PCR/qPCR, and ELISA. Irradiation significantly reduced fungal and bacterial loads, eliminating culturable bacteria but did not achieve complete sterilization. Viable spores of toxigenic fungal genera, such as Aspergillus, Penicillium, and Fusarium, persisted. Sequencing of ITS amplicons revealed dominant mycotoxigenic fungi in non-irradiated (NR), irradiated (IR) and licensed producer (LP) samples, while next-generation sequencing (NGS) revealed additional non-culturable toxigenic species. PCR/qPCR detected biosynthetic genes for aflatoxins, trichothecenes, ochratoxins, and deoxynivalenol across all samples, with gene copy numbers remaining stable post-irradiation, suggesting DNA damage without full degradation. ELISA confirmed aflatoxin, ochratoxin, DON, and T2 toxins in both IR and LP samples at variable concentrations. While LP samples showed lower microbial counts and gene abundance, residual DNA and toxins were still detected. Our study shows that while irradiation decreases microbial loads, it does not completely remove toxigenic fungi or their metabolites. Ensuring the safety of cannabis products necessitates a multifaceted assessment that incorporates cultural, molecular, and immunological techniques, in parallel with more stringent microbial standards during production stage. Full article

Background: Acute lymphoblastic leukemia (ALL) is a genetically heterogeneous malignancy driven by structural variants (SVs) that impact diagnosis, prognosis, and treatment. Traditional methods such as karyotyping, FISH, and PCR often fail to detect cryptic or complex rearrangements, which are critical for accurate risk stratification. Methods: Optical Genome Mapping (OGM) is a technology that directly analyzes ultra-high-molecular-weight DNA, enabling the identification of balanced and unbalanced SVs, copy number variations (CNVs), and gene fusions with high resolution. This review compares the advantages and limitations of OGM versus standard techniques in ALL. Results: OGM improves ALL diagnosis by detecting clinically relevant alterations such as IKZF1 deletions, cryptic KMT2A rearrangements, and kinase fusions, especially in cases with normal or uninformative karyotypes. It reduces artifacts by eliminating cell culture and shortens reporting times. OGM resolves complex events like intrachromosomal amplifications and chromothripsis, enhancing classification and therapy decisions. Limitations include reduced sensitivity in repetitive regions, challenges in detecting Robertsonian translocations, difficulties with complex ploidies, and lower sensitivity for low-frequency subclones. Conclusions: Integrating OGM with next-generation sequencing (NGS) allows comprehensive genomic profiling, improving diagnosis, prognosis, and personalized treatment in ALL. Future advancements promise to further enhance the clinical utility of OGM. Full article

Background: Molecular techniques for microbial identification have highlighted the relevance of polymicrobial infections in humans, such as those affecting the urinary tract. Although in vitro investigations have demonstrated connections between co-infections and microbial interaction, their role is unclear in clinics, given the overlap with host conditions. Objective: We aimed to separate the roles of organisms and patient conditions in human polymicrobial urinary samples by performing a relevant epidemiological analysis. Methods: We analyzed retrospective results from urine cultures performed during one year in a 1200 beds Italian hospital. Patients were grouped as uncompromised and compromised and positive urine cultures were grouped as monomicrobial and polymicrobial. We assessed associations between single microorganisms and the groups of positive samples and between single microorganisms and the group of patients through a multivariate logistic regression model, adjusting by the confounding effect of seven variables. Results: We enrolled 24,067 urine samples, among which 7208 were positive, 75% monomicrobial and 25% polymicrobial. We found that the polymicrobial samples had a microbial scenario wider than the monomicrobial ones and the organisms most sampled had the highest number of different pairwise associations. Certain organisms shown having absolute numerical advantages in the polymicrobial urine cultures with respect to the monomicrobial ones, independently of host’s conditions. Conclusions: The numerical advantage shown by certain organisms in polymicrobial urine samples over monomicrobial samples supports the hypothesis of microbial synergies favouring the occurrence of certain co-infections. Full article

The Mycobacterium tuberculosis complex (MTBC) represents one of the most significant bacterial pathogen groups affecting both animals and humans worldwide. This review provides a comprehensive analysis of MTBC species distribution across different animal hosts and evaluates current laboratory diagnostic methodologies for pathogen detection and identification. The complex comprises seven primary species: Mycobacterium bovis, M. caprae, M. tuberculosis, M. microti, M. canettii, M. africanum, and M. pinnipedii, each exhibiting distinct host preferences, geographical distributions, and pathogenic characteristics. Despite sharing >99% genetic homology, these species demonstrate variable biochemical properties, morphological features, and pathogenicity profiles across mammalian species. Current diagnostic approaches encompass both traditional culture-based methods and advanced molecular techniques, including whole genome sequencing. This review emphasises the critical importance of rapid, accurate detection methods for effective tuberculosis surveillance and control programmes in veterinary and public health contexts. Full article

Periprosthetic joint infection (PJI) remains a major complication in orthopedic surgery, with accurate and timely diagnosis being essential for optimal patient management. Traditional culture-based diagnostics are often limited by suboptimal sensitivity, especially in biofilm-associated and low-virulence infections. In recent years, non-culture-based methodologies have gained prominence. Molecular techniques, such as polymerase chain reaction (PCR) and next-generation sequencing (NGS), offer enhanced detection of microbial DNA, even in culture-negative cases, and enable precise pathogen identification. In parallel, extensive research has focused on biomarkers, including systemic (e.g., C-reactive protein, fibrinogen, D-dimer), synovial (e.g., alpha-defensin, calprotectin, interleukins), and pathogen-derived markers (e.g., D-lactate), the latter reflecting metabolic products secreted by microorganisms during infection. The development of multiplex platforms now allows for the simultaneous measurement of multiple synovial biomarkers, improving diagnostic accuracy and turnaround time. Furthermore, the integration of artificial intelligence (AI) and machine learning algorithms into diagnostic workflows has opened new avenues for combining clinical, molecular, and biochemical data. These models can generate probability scores for PJI diagnosis with high accuracy, supporting clinical decision-making. While these technologies are still being validated for routine use, their convergence marks a significant step toward precision diagnostics in PJI, potentially improving early detection, reducing diagnostic uncertainty, and guiding targeted therapy. Full article

Background/Objectives: Urinary tract infections (UTIs) represent a considerable challenge within the field of clinical medicine, as they are responsible for significant morbidity and intensify the operational pressures encountered by healthcare systems. Conventional diagnostic approaches, which include symptom evaluation, dipstick urinalysis, and standard urine culture, often demonstrate inadequacies in identifying atypical clinical manifestations, infections with low bacterial counts, or pathogens that show growth difficulties under typical laboratory conditions. These limitations undermine diagnostic accuracy and hinder timely therapeutic measures. Methods: The present manuscript is a systematic review conducted in accordance with PRISMA guidelines. A structured search was performed in PubMed, Scopus, and Google Scholar, yielding 573 records, of which 107 studies were included for qualitative synthesis. The primary aim of this systematic review is to evaluate both conventional and emerging diagnostic methods for UTIs, with specific objectives of assessing their clinical applicability, limitations, and potential to improve patient outcomes. Results: Recent progress in diagnostic technologies offers promising alternatives. Molecular-based assays, such as multiplex polymerase chain reaction, matrix-assisted laser desorption ionization mass spectrometry, and next-generation sequencing, have substantially improved both the precision and efficiency of pathogen identification. Furthermore, contemporary techniques for evaluating antimicrobial susceptibility, including microfluidic systems and real-time phenotypic resistance assays, enable clinicians to execute targeted therapeutic strategies with enhanced efficacy. Results of this synthesis indicate that while conventional diagnostics remain the cornerstone for uncomplicated cases, innovative molecular and phenotypic approaches demonstrate superior performance in detecting low-count bacteriuria, atypical pathogens, and resistance determinants, particularly in complicated and recurrent infections. These innovations support antimicrobial stewardship by reducing dependence on empirical antibiotic treatment and lessening the risk of resistance emergence. Conclusions: Nonetheless, the incorporation of these technologies into clinical practice requires careful consideration of implementation costs, standardization protocols, and the necessary training of healthcare professionals. In conclusion, this systematic review highlights that emerging molecular diagnostics and resistance-profiling tools offer substantial promise in complementing or enhancing traditional methods, but their widespread adoption will depend on robust validation, cost-effectiveness, and integration into clinical workflows. Full article

Hepatic actinomycosis (HA) and IgG4-related inflammatory pseudotumors are rare and often overlooked causes of liver mass, which can easily be misdiagnosed as primary liver cancer or metastasis. Diagnosis is arduous due to unspecified clinical and radiological features and the fact that histology is not always conclusive. In cases of actinomycosis, the use of molecular diagnostic techniques—such as polymerase chain reaction (PCR) for bacterial DNA—can aid in establishing a definitive diagnosis, especially when conventional cultures are non-diagnostic. We present a case report of one of our patients who was incidentally diagnosed with a hepatic lesion presenting aspecific radiological features. Since radiological imaging was inconclusive, a biopsy was performed, and a diagnosis of IgG4 related hepatic inflammatory pseudotumor was then made. Because of the disease progression, during immunosuppressive therapy, our diagnosis was questioned and a new liver biopsy was carried out. At the end, it took three consequent biopsies to finally find out the presence of an actinomyces infection. Full article

Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a global health problem. One of the characteristic features of mycobacteria is their exceptional resistance to environmental factors and their slow growth rate, both of which significantly prolong microbiological diagnostics. Due to the mortality rate and the rising prevalence of multidrug-resistant (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB), early detection and prompt initiation of treatment are extremely important. Traditional diagnostic methods, such as microscopic examination and culture on solid and liquid media, are still important, but are time-consuming and resource-intensive. However, the dynamic development of nucleic acid amplification techniques (NAATs), genotyping assays, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has accelerated the identification of mycobacteria and the detection of drug resistance. Early and precise diagnosis is essential for effective disease control and improved treatment outcomes. This paper reviews the current state of knowledge on tuberculosis; including biological and structural characteristics of mycobacteria; the epidemiology of the disease; and the role of the main diagnostic methods; with a particular focus on molecular methods and MALDI-TOF MS. This paper highlights their advantages and limitations and discusses their implications for the future of TB diagnosis and control Full article

The nymphaeum originated as a monument dedicated to the nymphs and defined as a natural cave with a water source. Over time, it has been transformed into an artificial cave with the presence of fountains, statues and wall paintings. The nymphaeum is exposed to specific environmental conditions, leading to biodeterioration caused by vegetal organisms that find an ideal environment for their growth. This study aimed to document the vegetation present inside and outside the Carolei’s Nymphaeum, as well as the biofilm on the interior walls, particularly the painted walls. The biological work is part of a large-scale project involving building materials, thermo-hygrometric parameters, and partial pilot restoration work. Multiple approaches were used for biological analysis by combining microscopic, culture, and molecular techniques. We identified Pteridophytes, Angiosperms, and mosses, as well as fungal taxa, cyanobacteria, and chlorophytes in the biofilms. The results indicate that there is a very heterogeneous organism composition with significant biodeterioration potential. Biodeterioration is one of the major problems in the prevention, conservation, and restoration of cultural heritage, and the data gathered in this research may help to enhance the understanding of issues and develop suitable strategies for restoration, upkeep, and accessibility and usability. Full article