Search Results (633)

Antimicrobial resistance (AMR) is traditionally discussed in the context of horizontally acquired resistance genes and point mutations at target loci. However, this gene-centred model fails to account for a large number of clinically important modalities of resistance. There is now substantial evidence implicating bacteria in the ability to escape the effects of antibiotics in a variety of non-canonical ways, which are not considered in traditional diagnostic and surveillance pipelines. Among these factors, we can list those arising from global regulatory networks, phase variability, epigenetic tuning, small RNAs, genome structural variability, and phenotypic states like tolerance and persistence. This review will blend the current knowledge on these alternative pathways of resistance and underscore how they intersect with canonical genetic determinants. We will highlight cases where resistance emerges in the absence of known resistance genes, analyse the role of regulatory plasticity in efflux pump expression and membrane remodelling, and examine the contributions of bacterial stress responses and post-transcriptional control. Additionally, we will address methodological gaps in the detection of these mechanisms and their implications for clinical treatment failure, resistance surveillance, and drug development. By integrating insights from molecular microbiology, systems biology, and genomics, this review aims to offer a framework for understanding AMR as a multifaceted, context-dependent phenotype, not merely a genotype. We conclude by identifying knowledge gaps and suggesting priorities for research and diagnostic innovation in this evolving field. Full article

Traumatic brain injury (TBI) remains a major global health problem, contributing significantly to morbidity and mortality worldwide. Despite advances in understanding its complex pathophysiology, current therapeutic strategies are insufficient in addressing the long-term cognitive, emotional, and neurological impairments. While the primary mechanical injury is immediate and unavoidable, the secondary phase involves a cascade of biological processes leading to neuroinflammation, blood–brain barrier (BBB) disruption, and systemic immune activation. The heterogeneity of patient responses underscores the urgent need for reliable biomarkers and targeted interventions. Emerging evidence highlights the gut–brain axis as a critical modulator of the secondary phase, with microbiota-derived extracellular vesicles (MEVs) representing a promising avenue for both diagnosis and therapy. MEVs can cross the intestinal barrier and BBB, carrying biomolecules that influence neuronal survival, synaptic plasticity, and inflammatory signaling. These properties make MEVs promising biomarkers for early detection, severity classification, and prognosis in TBI, while also offering therapeutic potential through modulation of neuroinflammation and promotion of neural repair. MEV-based strategies could enable tailored interventions based on the individual’s microbiome profile, immune status, and injury characteristics. The integration of multi-omics with artificial intelligence is expected to fully unlock the diagnostic and therapeutic potential of MEVs. These approaches can identify molecular subtypes, predict outcomes, and facilitate real-time clinical decision-making. By bridging microbiology, neuroscience, and precision medicine, MEVs hold transformative potential to advance TBI diagnosis, monitoring, and treatment. This review also identifies key research gaps and proposes future directions for MEVs in precision diagnostics and gut microbiota-based therapeutics in neurotrauma care. Full article

Pythiosis is an underestimated and neglected disease in Brazil, both in horse breeders and in horses. The molecular detection of P. insidiosum in horses in the Brazilian Northeast represents a milestone in the epidemiology of equine pythiosis in the country. This study reports novel cases of equine pythiosis, diagnosed by molecular methods, in five states of Northeastern Brazil. Clinical samples were submitted to microbiological culture, DNA extraction, and nested-PCR for molecular detection of P. insidiosum. The nested-PCR successfully detected P. insidiosum in four out of five equine lesion samples, demonstrating higher sensitivity compared to microbiological culture, which confirmed the pathogen in only one case. These findings reinforce the effectiveness of molecular diagnosis for equine pythiosis compared to conventional methods. This is the first molecular confirmation of P. insidiosum in horses from Northeastern Brazil, emphasizing the need for broader surveillance and improved diagnostic approaches in neglected regions. Full article

Background and Clinical Significance: The pathology of the round ligament (RL) is rare and often remains in the shadow of common surgical emergencies. The preoperative diagnosis is challenging, leaving the surgeon perplexed as to whether and when to operate. The presented case deserves attention due to the difficult decision to operate based solely on the clinical picture, despite negative imaging diagnostic results. Case presentation: A 76-year-old woman was admitted to the Emergency Department with 6 h complaints of epigastric pain, nausea, and vomiting. She was afebrile with stable vital signs. The abdomen was slightly tender in the epigastrium, without rebound tenderness or guarding. The following blood variables were beyond the normal range: WBC—13.5 × 109/L; total bilirubin 26 mmol/L; amylase—594 U/L; CRP 11.4 mg/L; ASAT—158 U/L; and ALAT—95 U/L. The ultrasound (US) and multislice computed tomography (MSCT) of the abdomen were normal. A working diagnosis of acute pancreatitis was established, and intravenous infusions were initiated. The next day, the patient became hemodynamically unstable with blood pressure 80/60 mm Hg, heart rate 130/min, chills and fever of 39.5 °C, and oliguria. There was remarkable guarding and rebound tenderness in the epigastrium. The blood analysis revealed the following: WBC—9.9 × 109/L; total bilirubin—76 µmol/L; direct bilirubin—52 µmol/L; amylase—214 U/L; CRP 245 mg/L; ASAT—161 U/L; ALAT—132 U/L; GGT—272 U/L; urea—15.7 mmol/L; and creatinine—2.77 mg/dL. She was taken to the operating room for exploration, which revealed local peritonitis and phlegmon of the RL. Resection of the RL was performed. The microbiological analysis showed Klebsiella varicola. The patient had an uneventful recovery and was discharged on the 5th postoperative day. In the next months, the patients had several readmissions due to mild cholestasis and pancreatitis. The magnetic resonance demonstrated a duodenal diverticulum adjacent to the papilla, located near the junction of the common bile and pancreatic duct. This clinical manifestation and the location of the diverticulum were suggestive of Lemmel’s syndrome, but a papillary dysfunction attributed to the diverticulum or food stasis cannot be excluded. Conclusion: To our knowledge, we report the first association between RL gangrene and Lemmel’s syndrome. We speculate that duodenal diverticulitis with lymphatic spread of the infection or transient bacteriemia in the bile with bacterial translocation due to papillary dysfunction, as well as cholestasis resulting from the diverticulum, could be plausible and unreported causes of the RL infection. The preoperative diagnosis of RL gangrene is challenging because it resembles the most common emergency conditions in the upper abdomen. The present case warrants attention due to the difficult decision to operate based solely on the clinical picture, despite negative imaging results. A high index of suspicion should be maintained in a case of unexplained septic shock and epigastric tenderness, even in negative imaging findings. MSCT, however, is a valuable tool to avert unnecessary operations in conditions that must be managed conservatively, such as acute pancreatitis. Full article

Background/Objectives: The rapid identification of carbapenemase genes directly from positive blood culture (BC) samples shortens the time needed to initiate optimal antimicrobial therapy for Carbapenemase-Producing Enterobacterales (CPE) infections. Several commercial automated PCR systems are available for detecting CPE resistance genes but are expensive. The Xpert^® Carba-R assay (Cepheid GeneXpert System) has high sensitivity and specificity for the detection of carbapenamase genes from bacterial colonies or rectal swabs, with an affordable price. This assay was not used for positive BC testing of CPE resistance genes. Whole-Genome Sequencing (WGS) for resistance genes can be used as the gold standard at a research level. In this study, we evaluated the performance of the Xpert^® Carba-R assay for the early detection of carbapenamase genes directly from positive BCs, using WGS as the gold standard. Methods: A prospective observational study was conducted at Children’s Cancer Hospital-Egypt (CCHE-57357). All positive BCs underwent direct gram staining and conventional cultures. A total of 590 positive BCs containing Gram-negative rods (GNRs) were identified. The Xpert^® Carba-R assay was used to detect carbapenemase genes directly from the positive BC bottle compared with WGS results. Results: Among the 590 GNR specimens, 178 were found to carry carbapenemase genes using the Xpert^® Carba-R assay, with results obtained in approximately one hour. The main genotypes detected were bla_NDM, bla_OXA-48-like, and dual bla_NDM/bla_OXA-48-like at 27%, 29%, and 33%, respectively. The agreement between Xpert^® Carba-R assay and WGS results was almost perfect for the genotype resistance pattern of isolates and individual gene detection. Conclusions: The use of the Xpert^® Carba-R assay directly from BC bottles was an easy-to-use, time-saving, affordable tool with high accuracy in identifying carbapenemase genes and, thus, shortens the time needed to initiate optimal antimicrobial therapy for CPE infections. 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

In neonatal care, donor human milk (DHM) is used when maternal milk is unavailable or insufficient. In several countries, including Germany, raw (i.e., unpasteurised) DHM is occasionally administered under specific clinical conditions. However, the lack of standardised, evidence-based microbiological testing protocols raises concerns about the reliability of safety assessments for this high-risk patient group. The objective of this study was to assess the performance of four culture-based microbiological methods for detecting Enterobacterales in donor human milk, using both spiked samples and raw milk. We compared the detection limits of four culture-based microbiological methods, with and without enrichment, using spiked DHM samples and 93 raw DHM samples from a single donor (limited generalisation). Artificially inoculated samples contained defined concentrations of E. coli, K. pneumoniae, and S. ureilytica. Detection limits varied by several orders of magnitude (2.86 × 10² CFU/mL to 4.90 × 10⁰ CFU/mL). In real samples, enrichment-based methods detected Gram-negative pathogens in four out of ninety-three samples (three S. ureilytica, one P. juntendi); direct plating detected none. Increasing the sample volume and applying enrichment improved detection sensitivity. Whole-genome sequencing confirmed species identity and showed that the S. ureilytica isolates from a single donor were clonally related, indicating a recurring detection pattern and underscoring the need for longitudinal microbiological monitoring. In view of the new EU SoHO Regulation classifying DHM as a Substance of Human Origin, these findings highlight the urgent need for standardised, sensitive protocols to ensure neonatal safety. 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

Background: Purpureocillium lilacinum (P. lilacinum) is an emerging filamentous fungus known to cause opportunistic infections, particularly in immunocompromised patients. Formerly known as Paecilomyces lilacinus, this pathogen is widespread in the environment and can lead to a range of infections, from superficial skin lesions to invasive diseases. This article presents a case of deep cutaneous hyalohyphomycosis caused by P. lilacinum in a liver transplant patient, followed by a review of the literature focusing on new antifungal agents. Methods: We reported a brief case description followed by a narrative review of the literature regarding P. lilacinum cutaneous and lymphangitic infections in immunocompromised patients. Results: We conducted a review of the literature over the past 20 years, focusing on the clinical features, diagnostic challenges, and therapeutic outcomes of cutaneous and lymphangitic P. lilacinum infections in immunocompromised hosts. Conclusions: This review highlights the critical importance of early diagnosis through the analysis of biopsy samples using standard microbiological and histological techniques, complemented by innovative molecular biology methods. We also emphasise the role of appropriate antifungal treatment, despite the absence of an established standard of care, particularly in high-risk patients. Furthermore, we review and discuss the current lack of a standardised therapeutic regimen and the potential of novel antifungal agents as promising treatment options for P. lilacinum infections. Full article

Background: Clostridioides difficile infection (CDI) is the leading cause of nosocomial diarrhea. Current diagnostic tools have difficulty distinguishing between colonization and active infection. This study evaluated the utility of fecal metabolomics in diagnosing CDI in hospitalized patients with acute diarrhea. Methods: We conducted a prospective observational study involving hospitalized adults with new-onset diarrhea during admission. Participants were stratified into groups based on clinical and microbiological findings: controls, C. difficile colonized and C. difficile infected. Fecal samples were analyzed using UPLC-MS/MS and GC-MS to quantify selected short-chain fatty acids, amino acids, and bile acids. Multivariate and univariate statistical analyses included PLS-DA, sPLSDA, and tests with FDR correction. Results: Infected patients exhibited significantly higher concentrations of SCFAs and notable alterations in bile acid profiles. Key discriminative metabolites included isovalerate, propionate, isobutyrate and alpha-aminobutyric acid. ROC curve analyses showed strong diagnostic performance for these markers, with AUC values exceeding 0.85. Conclusions: Fecal metabolomic profiling could effectively differentiate between colonization and infection in CDI among hospitalized patients with diarrhea. These results highlight the potential of metabolomic signatures to enhance the diagnostic precision for CDI. Full article

Pituitary abscess syndrome (PAS) is a rare neurological disorder, typically associated with progressive dysfunction of the cerebrum and brainstem. Reporting PAS in ruminants is essential to broaden the global veterinary understanding of this condition. The present study describes the epidemiological, clinical, laboratory, microbiological, and pathological findings of nine ruminant cases diagnosed with PAS. Neurological signs were the most prominent clinical manifestations and included altered mentation, tongue hypotonia, nystagmus, blindness, ear ptosis, circling, facial hypoalgesia, head pressing, and proprioceptive deficits. Hematological alterations in some animals comprised leukocytosis by neutrophilia, a degenerative left shift, and hyperfibrinogenemia. Serum biochemical abnormalities were inconsistent and varied among cases. Cerebrospinal fluid (CSF) analysis revealed marked variability, ranging from normal parameters to mild or marked pleocytosis, often accompanied by hyperproteinorrachia. Microbiological cultures from CSF samples or abscess material yielded Trueperella pyogenes, Streptococcus spp., and Corynebacterium spp. Gross pathological findings primarily included pituitary hyperemia, abscess formation, or diffuse suppurative inflammation characterized by a creamy yellow to greenish exudate. Histopathological examination revealed severe multifocal suppurative inflammation composed predominantly of neutrophils, occasional histiocytes, abundant bacteria, areas of necrosis, and encapsulated abscesses. This retrospective study provides novel insights into the clinical, laboratory, and pathological characteristics of PAS in ruminants under field conditions, thereby contributing to improved recognition and diagnostic understanding of this uncommon disease. Full article

Carbapenemase-producing Klebsiella pneumoniae (CRKP) is a critical public health threat, particularly in Greece, where high prevalence limits therapeutic options. This retrospective study analyzed 26 CRKP isolates recovered at the General Hospital of Volos between July 2024 and January 2025, aiming to correlate carbapenemase phenotypes with clinical and epidemiological parameters. Demographic, clinical, and microbiological data were extracted from patient records, and isolates underwent phenotypic carbapenemase detection, antimicrobial susceptibility testing, and molecular characterization using real-time PCR; four isolates were further analyzed using whole-genome sequencing. CRKP was detected across multiple hospital departments, notably in the Emergency Department (n = 5) and Intensive Care Unit (n = 6). KPC producers predominated (n = 9), followed by NDM (n = 6), VIM (n = 1), and OXA-48 (n = 6). All VIM- or NDM + VIM-positive cases were associated with mortality. High-risk clones, including ST15, ST11, and ST307, were identified, with one ST15 isolate harboring bla_NDM-1, bla_VIM-1, and chromosomal colistin resistance; this is the first such report in Greece. Colistin and gentamicin were the most active agents in vitro; three isolates were pan-drug-resistant. The findings highlight significant CRKP circulation outside ICUs, the role of horizontal gene transfer in resistance dissemination, and the need to expand screening and rapid diagnostics to non-ICU settings. Enhanced molecular surveillance targeted at infection control and strengthened antimicrobial stewardship programs are essential for limiting the spread of CRKP. Full article

Background: This study aimed to describe cefiderocol prescription and associated patient outcomes at a U.S. academic medical center for various multidrug-resistant organisms (MDRO). Notably, limited real-world data exist on cefiderocol’s clinical use in regions where metallo-β-lactamase (MBL)-producing organisms are prevalent. Methods: A retrospective chart review was conducted on adult inpatients who received ≥24 h of cefiderocol between January 2023 and July 2024. Data collected included microbiology, carbapenemase type (CARBA-5), treatment indication, susceptibility profiles, and clinical outcomes: 30-day mortality, re-infection, and re-admission. Descriptive statistics were used. Results: Seventy-six patients were included, with most receiving cefiderocol for carbapenem-resistant Enterobacterales (CRE) (63%) or P. aeruginosa (17%) infections. Overall, 96% of cases met institutional prescribing criteria. NDM was the predominant carbapenemase (77% of CRE isolates). Cefiderocol was used definitively in 68% of cases. The median duration of therapy was 7 days. Thirty-day mortality was 20%, highest among patients with A. baumannii complex (33%). Re-infection and re-admission occurred in 21% and 32% of patients, respectively. Susceptibility to cefiderocol was highest for P. aeruginosa (100%), Stenotrophomonas (100%), and CRE (88%), but only 50% for A. baumannii complex. Conclusions: Cefiderocol was primarily used in accordance with institutional criteria and demonstrated favorable susceptibility against most target pathogens. However, poor outcomes in A. baumannii complex infections highlight the need for cautious use and the need for rapid diagnostics for early targeted therapy in multidrug-resistant infections. Full article

Background: Native joint septic arthritis is a severe infection associated with considerable morbidity. The data about the microbiological spectrum, treatment methods, and long-term outcomes are heterogeneous. Methods: We performed a decade-long retrospective study encompassing all patients with native joint septic arthritis treated at our institution, a tertiary orthopedic center. Data on demographics, clinical parameters, microbiology, surgical interventions, and antibiotic use were gathered. Outcomes included reoperation, persistent infection and mortality during follow-up. We used logistic regression to identify predictors of adverse outcomes, and Kaplan–Meier analyses to evaluate reoperation-free survival among microbiologic groups. Results: A total of 114 patients (103 adults and 11 children) were included. Cultures yielded positive results in 72 out of 103 (70%) adults and 8 out of 11 (73%) children. Staphylococcus aureus was the primary pathogen in adults (49% of positives) and children (88%), followed by coagulase-negative staphylococci. Antibiotics were administered to all patients, with combinations of at least two molecules in 68% of adults and 91% of children, while surgical intervention predominantly consisted of debridement alone. In adults, an elevated preoperative white blood cell count was associated with unfavorable outcomes in univariate analysis (odds ratio 1.14, 95% confidence interval 1.01–1.30, p = 0.040). The Kaplan–Meier analysis revealed no significant differences in reoperation-free survival across microbiologic groups (log-rank p = 0.361). Conclusions: Over a ten-year period, Staphylococcus aureus remained the predominant cause of native joint septic arthritis; however, culture-negative cases and coagulase-negative staphylococci were also common. Only preoperative leukocytosis was a predictor of poor outcomes, while microbiologic etiology did not significantly influence the risk of reoperation, potentially indicating early and effective therapy. These findings highlight the intricacy of native joint septic arthritis and the necessity for enhanced diagnostics and prognostic stratification. Full article