Search Results (116)

Metagenomic next-generation sequencing (mNGS) is transforming infectious disease diagnostics by enabling simultaneous, hypothesis-free detection of a broad array of pathogens—including bacteria, viruses, fungi, and parasites—directly from clinical specimens such as cerebrospinal fluid, blood, and bronchoalveolar lavage fluid. Unlike traditional culture and targeted molecular assays, mNGS serves as a powerful complementary approach, capable of identifying novel, fastidious, and polymicrobial infections while also characterizing antimicrobial resistance (AMR) genes. These advantages are particularly relevant in diagnostically challenging scenarios, such as infections in immunocompromised patients, sepsis, and culture-negative cases. Despite its potential, mNGS remains underutilized in clinical microbiology due to persistent gaps between its technical capabilities and routine diagnostic adoption. This review addresses key translational challenges that limit the broader implementation of mNGS, especially in resource-constrained and critical care settings. We provide a comprehensive overview of the entire workflow—from sample processing and host DNA depletion to sequencing platforms and downstream bioinformatics—and highlight sources of variability, including contamination, human DNA interference, and inconsistencies in resistance gene annotation. Additionally, we explore the ethical, legal, and privacy implications of host genomic data, as well as economic and regulatory obstacles hindering mNGS integration into standard clinical practice. To illustrate clinical relevance, we examine real-world evidence from large-scale trials such as MATESHIP, GRAIDS, DISQVER, and NGS-CAP. Finally, we outline future directions involving artificial intelligence, multi-omics integration, cloud-based analytics, and portable sequencing technologies for point-of-care diagnostics. By addressing both current limitations and emerging innovations, this review offers a translational framework for integrating mNGS into precision diagnostics and infection management across diverse healthcare environments. Full article

Schaalia canis is a Gram-positive, facultatively anaerobic, rod-shaped bacterium originally isolated from the mucosa and skin of dogs. While it is a part of the normal canine oral flora, it has rarely been implicated in human disease, with only one prior case of cellulitis reported following a dog bite. Case Presentation: We present the case of a 57-year-old immunocompetent man who developed osteomyelitis of the left index finger following a delayed presentation after a dog bite. Despite initial conservative management with empirical oral antibiotics, the infection progressed, eventually requiring surgical debridement and the terminalisation of the finger at the proximal interphalangeal joint. Cultures from intraoperative bone specimens yielded the growth of Schaalia canis, with no other pathogenic organisms identified on the extended culture. Conclusions: This is the first documented case of Schaalia canis-associated osteomyelitis in a human and the first to necessitate a surgical intervention, expanding the known clinical spectrum of this organism. This case underscores the risks of delayed intervention in polymicrobial animal bite wounds and highlights the emerging role of Schaalia species as opportunistic zoonotic pathogens, particularly in the setting of deep, refractory infections. Full article

Background/Objectives: The porcine respiratory disease complex (PRDC) is a multifaceted, polymicrobial syndrome resulting from a combination of environmental stressors, primary infections (e.g., PRRSV) and secondary infectious agents (viruses and bacteria). PRDC causes severe lung pathology, leading to reduced performance, increased mortality rates, and higher production costs in the global pig industry. Our goal was to conduct a comprehensive study correlating both the anti-PRRSV immune response and 21 secondary infectious agents with PRDC severity. Methods: To this end, PRRSV-negative weaners were vaccinated with a PRRSV-2 MLV and put into a farm with a history of PRDC. Subsequently, anti-PRRSV cellular and antibody responses were monitored pre-vaccination, at 28 days post vaccination (dpv) and during PRDC outbreak (49 dpv). NanoString was used to quantify 21 pathogens within the bronchoalveolar lavage (BAL) at the time of necropsy (51 dpv). PRRSV-2 was present in 53 out of 55 pigs, and the other five pathogens (PCMV, PPIV, B. bronchiseptica, G. parasuis, and M. hyorhinis) were detected in BAL samples. Results: Although the uncontrolled settings of field trials complicated data interpretation, multivariate correlation analyses highlighted valuable lessons: (i) high weaning weight predicted animal resilience to disease and high weight gains correlated with the control of the PRRSV-2 field strain; (ii) most pigs cleared MLV strain within 7 weeks, and the field PRRSV-2 strain was the most prevalent lung pathogen during PRDC; (iii) all pigs developed a systemic PRRSV IgG antibody response which correlated with IgG and IgA levels in BAL; (iv) the induction of anti-field strain-neutralizing antibodies by MLV PRRSV-2 vaccination was both late and limited; (v) cellular immune responses were variable but included strong systemic IFN-γ production against the PRRSV-2 field strain; (vi) the most detected lung pathogens correlated with PRRSV-2 viremia or lung loads; (vii) within the six detected pathogens, two viruses, PRRSV-2 and PCMV, significantly correlated with the severity of the clinical outcome. Conclusions: While a simple and conclusive answer to the multifaceted nature of PRDC remains elusive, the key lessons derived from this unique study provide a valuable framework for future research on porcine respiratory diseases. Full article

Introduction: Clostridioides difficile (C. difficile) is primarily associated with colonic disease, including pseudomembranous colitis. However, in rare instances, it may cause extraintestinal infectious and non-infectious manifestations, particularly in immunocompromised patients or those with significant underlying conditions. Search Methods: A literature review was performed using PubMed, Embase, and Researchgate databases up to 15 February 2025. The following search strings were used: “extraintestinal manifestations”, “extracolonic manifestations”, “extraintestinal infections”, “extracolonic infections”, “Clostridium difficile”, and “Clostridioides difficile”. Results: Extraintestinal manifestations of C. difficile appear to represent fewer than 1% of all reported infections. The most frequently reported infectious complications include bacteremia and abdominopelvic infections and abscesses, often involving polymicrobial cultures, with the isolation of C. difficile alongside microorganisms typically found in the normal intestinal microbiota. Rare non-infectious cases, such as reactive arthritis, have also been described. The underlying pathogenetic mechanism is believed to involve disruption of the intestinal barrier and translocation of bacteria or toxins to sterile sites. Conclusions: Though rare, extraintestinal C. difficile manifestations pose important clinical challenges. Better understanding of their mechanisms is essential for early recognition and appropriate management. Further research is warranted to define potential mechanisms and therapeutic approaches. Full article

Cystic fibrosis (CF) is a life-limiting autosomal recessive disorder affecting a large number of individuals in Europe. The disease arises from mutations in the CFTR gene encoding the cystic fibrosis transmembrane conductance regulator, a chloride ion channel crucial for maintaining epithelial ion and fluid homeostasis. Dysfunctional CFTR disrupts mucociliary clearance, particularly in the respiratory tract, resulting in persistent bacterial colonization, chronic inflammation, and progressive pulmonary damage—ultimately leading to respiratory failure, the principal cause of mortality in CF patients. Early diagnosis and advances in therapy have substantially improved both survival and quality of life. A hallmark of CF pathology is the establishment of polymicrobial infections within the thickened airway mucus. Pseudomonas aeruginosa is the dominant pathogen in chronic CF lung infections and demonstrates a remarkable capacity for adaptation via biofilm formation, metabolic reprogramming, and immune evasion. Biofilms confer increased tolerance to antimicrobial agents and facilitate long-term persistence in hypoxic, nutrient-limited microenvironments. P. aeruginosa exhibits a wide range of virulence factors, including exotoxins (e.g., ExoU, ExoS), pigments (pyoverdine, pyochelin), and motility structures (flagella and pili), which contribute to tissue invasion, immune modulation, and host damage. During chronic colonization, P. aeruginosa undergoes significant genotypic and phenotypic changes, such as mucoid conversion, downregulation of acute virulence pathways, and emergence of hypermutator phenotypes that facilitate rapid adaptation. Persistent cells, a specialized subpopulation characterized by metabolic dormancy and antibiotic tolerance, further complicate eradication efforts. The dynamic interplay between host environment and microbial evolution underlies the heterogeneity of CF lung infections and presents significant challenges for treatment. Elucidating the molecular mechanisms driving persistence, hypermutability, and biofilm resilience is critical for the development of effective therapeutic strategies targeting chronic P. aeruginosa infections in CF. Full article

Fungal prosthetic joint infection (fPJI) is one of the orthopaedic pathologies where there is no clear evidence, guidelines or algorithm to guide the surgeon in its management. This is in addition to the difficulty with which these infections are diagnosed, isolated and treated. Fungi form notorious biofilms that are difficult to eradicate once formed and that display resistance to antimicrobial agents. These biofilms have been shown to act synergistically with biofilms of bacteria, further adding to medical treatment resistance. We have reviewed the literature for reports that describe the results of different methods in surgically treating fPJI. We found that surgical management with two stages remains the gold standard for treatment of fPJI, as is the case for bacterial PJI (bPJI). We have investigated medical treatment, debridement with implant retention (DAIR) and staged revisions and whether a reasonable recommendation can be made based on the best knowledge and practice available. From the data on bPJI, there exists a role for conservative management of acute PJI with debridement, antibiotics and implant retention (DAIR). While fPJI and bPJI both represent infections, the differences in our ability to detect these infections clinically, culture the pathogens and treat them with proper antimicrobial agents, along with the difference in the reported results of the surgical treatment, make us believe that these two types of infections should not be treated in the same manner. With all this in mind, we reviewed several reports in the literature on fPJI to determine the efficacy of current treatment modalities, including DAIR, which followed current guidelines for PJI. Data show an overall treatment success rate of 64.4% [range 17.4–100%]. Subgroup analysis revealed a success rate of 11.6% [range 0–28.7%] in patients treated with DAIR. There is no doubt that DAIR should not be encouraged as it consistently has a bad record. Although there are not enough studies or numbers of patients to show an evidence-based preference over one- or two-staged revisions, the two-stage revision of fPJI consistently shows better results and should be considered as the gold standard of management in cases of revision fPJI. This should also be coupled with proper expertise, follow-ups and recommended lengths of medical treatment, which should not be less than six months. From the review of these data, we have developed reasonable recommendations for the management of fPJI. These recommendations center on staged surgical debridement along with medical management. Medical treatment should be for at least 6 months under the guidance of an infectious disease team and based on intraoperative cultures. In the case of local antimicrobial treatment reported in the literature, many patients with fPJI were found to have a polymicrobial infection. As a result, it is our recommendation that antifungals as well as antibacterials should be incorporated into the cement spacer mix of these cases. Fungal PJI remains an exceedingly difficult pathology to treat and should be managed by experienced surgeons in a well-equipped institution. Full article

Objectives: Fosfomycin is an old antibiotic that has recently gained attention owing to its preserved activity against multidrug-resistant (MDR) bacteria. Data on its use in real life are limited. Thus, we evaluated the efficacy and safety of fosfomycin disodium in the context of our hospital clinical practice. Methods: Single-center, retrospective, observational study on 56 patients who received fosfomycin disodium from September 2016 to July 2023, focusing on clinical and microbiological outcomes and adverse events. Results: Included in this study were 56 patients. Fosfomycin disodium was administered for a median duration of 10 days [5–13.5] and was always used in combination with other antibiotics, more frequently with meropenem (16 cases, 28.6%) and colistin (11 cases, 19.6%). It was mostly used for treating pneumonia (41%), followed by bloodstream infections (19.6%), urinary tract infections (16.1%), bone infections (16.1%), and surgical site infections (7.1%). The most common isolated pathogen was Pseudomonas aeruginosa (17%), and polymicrobial infections were detected in 18 patients (32%). Among the isolated bacteria, 36 (44.4%) were MDR. The complete resolution, defined as the disappearance of symptoms, eradication of the causative microorganism, and decrease in CRP levels, was achieved in 39% of cases. During treatment, we observed electrolyte imbalances, in particular a decrease in serum potassium (0.6 mEq/L [0.3–1.1]), calcium (0.7 mEq/L [0.3–1.1]) and magnesium levels (0.3 mg/dL [0.20–0.48]), and an increase in serum sodium levels (4 mEq/dL [2–7]). Changes in potassium and sodium levels were more pronounced in patients with prior kidney dysfunction and heart failure, respectively, and in patients receiving fosfomycin diluted with saline compared with 5% glucose solution (p = 0.04). Conclusions: Fosfomycin is effective in treating complicated infections in comorbid patients when combined with other antimicrobials. During treatment, major electrolyte imbalances occur that require careful monitoring and correction, especially in patients with prior kidney disease. Full article

Periodontitis is a highly prevalent, irreversible inflammatory disease characterized by the destruction of tooth-supporting tissues, eventually leading to tooth loss. Conventional treatment involves the mechanical removal of the subgingival biofilm, which is a major cause of gingival inflammation. However, the inaccessibility of deep-seated polymicrobial biofilms limits its effectiveness. Despite the adjunct use of systemic antimicrobials, their low site-specific bioavailability and systemic side effects remain concerns. Local drug administration offers a targeted alternative. However, the dynamic oral environment, which is characterized by continuous salivary and gingival crevicular fluid flow, poses challenges in maintaining therapeutic drug levels. Drug delivery systems (DDSs) provide technical solutions to overcome these limitations. With advancements in materials science and nanotechnology, diverse local DDS (LDDS) formulations tailored for periodontal applications have been developed. While traditionally focused on infection control, the application of LDDSs has expanded beyond antimicrobial therapy. Increasing attention has been paid to LDDS-based regenerative strategies, which aim to overcome the limitations of conventional regenerative therapies. This review aims to provide a comprehensive overview of the current and emerging DDS strategies in periodontal therapy, focusing on their applications in infection management and bone regeneration and discussing their limitations and prospects for clinical translation. Full article

Background: Intra-abdominal infections (IAIs) caused by Stenotrophomonas maltophilia have rarely been reported. This study aimed to describe the clinical characteristics and risk factors for mortality among patients with S. maltophilia IAIs. Methods: A retrospective study was conducted on inpatients with IAIs caused by S. maltophilia at Tri Service General Hospital from 2004 to 2017. Clinical and microbiologic data of the included cases were reviewed via medical charts and microbiology databases. Multivariable logistic regression analyses were performed to identify risk factors for in-hospital death. Results: In total, 110 patients were diagnosed with S. maltophilia IAIs. Malignancy (56.3%) and liver cirrhosis (35.3%) were the most commonly identified underlying diseases. The major causes of S. maltophilia IAIs were biliary tract infection (42.7%), recent abdominal surgery (35.4%), and spontaneous bacterial peritonitis (20.0%). Polymicrobial infections were observed in 84 (76.4%) patients. In addition to S. maltophilia, co-cultured bacteria (n = 140) included Enterobacterales, representing 19.3% (27/140) of the total isolates, and non-fermentative aerobes, comprising 29.3% (41/140). In addition, anaerobic bacteria and fungi accounted for 9.2% (13/140) and 10% (14/140), respectively. The overall mortality rate was 40.9%. Multivariable logistic regression analysis revealed that high Sequential Organ Failure Assessment scores and malignancies were independent risk factors for mortality, while the immediate administration of appropriate antibiotics targeting S. maltophilia was a protective factor (p < 0.05). Conclusions: Patients with an underlying malignancy or liver cirrhosis were at risk for IAIs caused by S. maltophilia. The prompt initiation of effective antibiotics against S. maltophilia is critical for achieving favorable outcomes. Full article

Multiplex Polymerase Chain Reaction (PCR) has significantly impacted the field of infectious disease diagnostics, offering rapid and precise identification of bacterial and fungal pathogens. Unlike traditional culture methods, which may take days to yield results, multiplex PCR provides diagnostic insights within hours, enabling faster, targeted antimicrobial therapy and reducing the delay in treating critical infections like sepsis. The technique’s high sensitivity and broad pathogen coverage make it ideal for both single and polymicrobial infections, improving outcomes across respiratory, bloodstream, and bacterial/fungal infections. However, multiplex PCR is not without challenges; initial high costs and the need for specialized training can limit its adoption, especially in low-resource settings. This review discusses the clinical advantages and limitations of multiplex PCR, highlighting its influence on diagnostic accuracy, antimicrobial stewardship, and the global fight against antimicrobial resistance (AMR). Furthermore, recent innovations in multiplex PCR, such as digital PCR and portable devices, are explored as potential tools for expanding access to rapid diagnostics worldwide. Full article

Background: Hidradenitis suppurativa (HS) is a chronic, disabling, and disfiguring inflammatory disease with a complex, incompletely elucidated pathogenesis. The role of skin dysbiosis in the development and progression of HS has not yet been clarified. Methods: We performed an observational, prospective culture-based study that included 40 HS patients and analyzed the bacterial load and diversity in HS skin lesions, their correlation with disease severity, and several host and environmental factors. Additionally, we investigated the prevalence of antibiotic resistance and determined the resistance profile of bacterial strains isolated from chronic HS lesions. Results: An impressive number and diversity of bacterial strains were isolated from both superficial and deep HS lesions. 201 aerobic and anaerobic bacterial strains were isolated, polymicrobial growth being detected in the majority of samples. The most frequently isolated bacteria were Staphylococcus epidermidis, Staphylococcus aureus, Staphylococcus lugdunensis, Peptoniphilus spp., and Enterococcus faecalis in superficial lesions and Staphylococcus epidermidis, Staphylococcus aureus, and Corynebacterium tuberculostearicum in deep lesions. A significantly higher bacterial density and diversity was found in male patients, regardless of the affected area and in patients with severe HS. The proportion of bacterial strains resistant to antibiotics was lower in our study (8.95%) compared to the previously reported data. Conclusions: Our findings indicate dysbiosis as a key player in the initiation and maintenance of the inflammatory process in HS. Further large-scale, prospective studies are required to comprehensively characterize the microbiological landscape of HS and shed light on its contribution in the pathogenesis of the disease. Full article

Background/Objectives: With the increasing use of dental implants in edentulous patients and the high prevalence of peri-implantitis, understanding its microbial and risk factors is crucial. This study investigated Romanian patients from two private dental clinics in Cluj-Napoca, Romania, diagnosed with peri-implantitis, focusing on identifying the predominant bacterial species at affected sites compared with healthy implant sites. Additionally, we examined the impact of factors such as smoking, gender, age, and prosthetic restoration type on disease prevalence. Methods: This cross-sectional study, conducted between January 2023 and December 2024, included randomly selected patients who met the predefined inclusion and exclusion criteria. We enrolled 22 patients and 50 implants in the study. Data collected from medical records, clinical evaluations, and microbiological assessments were subsequently entered into a computerized database. Clinical data were analyzed using Social Science Statistics software(Jeremy Staangroom 2018). Bacterial samples were assessed, incubated, and subsequently identified using the Vitek 2 Compact System (BioMérieux, Marcy—l’ Étoile, France). Results: Peri-implantitis incidence was found to be independent of gender, more prevalent in the mandible, and equally affected smokers and non-smokers. The disease involves a complex polymicrobial infection, with pathogenic bacteria triggering the condition and opportunistic bacteria sustaining it. Conclusions: Peri-implantitis is a complex polymicrobial infection that arises from the interaction of strict pathogenic bacteria and opportunistic bacteria. Peri-implantitis results from intricate interactions of local, systemic, and microbial factors. Identifying its causes is essential for developing effective treatments, with future research emphasizing the role of opportunistic bacteria in disease progression. Full article

The escalating global prevalence of fungal and bacterial co-infections underscores the significant and multifaceted impact of ubiquitous microorganisms on both environmental equilibria and human well-being. The human microbiome, a complex ecosystem of bacterial communities, harbors opportunistic pathogens capable of inducing superinfections or concurrent infections with Candida spp. The intricate interplay, exemplified by the interaction between Candida albicans and diverse bacteria, necessitates rigorous investigation to elucidate mechanisms by which this polymicrobial behavior potentiates fungal virulence, particularly in immunocompromised individuals. Our study aims to comprehensively examine the ramifications of these interactions, with a specific focus on their influence on fungal virulence and the consequent exacerbation of disease severity. Achieving a comprehensive understanding of these complex relationships is paramount for informing effective clinical management strategies for infectious diseases, and the accurate identification of fungal–bacterial co-infections holds substantial implications for optimizing clinical treatment paradigms, especially in vulnerable immunocompromised hosts. Full article

Actinomycosis is a chronic suppurative granulomatous disease caused by Actinomyces spp. Although cutaneous actinomycosis is rare, dermatologists must consider it due to its potential coexistence with other pathogens, often as part of polymicrobial infections. We present a rare case of primary axillary cutaneous actinomycosis in a young woman, likely triggered by cosmetic axillary hair removal and home shaving practices. Histological examination revealed characteristics of actinomycosis, including sulfur granules and Gram-positive filamentous structures. Bacterial cultures failed to isolate Actinomyces, but identified Staphylococcus epidermidis, S. aureus (MRSA), and Corynebacterium simulans, suggesting a polymicrobial infection contributing to the inflammatory response. Molecular analysis of DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue yielded a 675 bp PCR product using Actinomyces-specific primers. BLAST analysis confirmed the species as A. gerencseriae, establishing the diagnosis of actinomycosis. However, a 1000 bp PCR product obtained using universal 16S rDNA primers could not be sequenced successfully, likely due to the presence of multiple bacterial species. Notably, Actinomyces was detected only through molecular methods, while bacterial cultures identified the aforementioned bacteria. This discrepancy between FFPE-PCR results and bacterial culture findings demonstrates a key challenge in the microbiological diagnosis of polymicrobial infections. This case highlights the importance of integrating histopathological, microbiological, and molecular techniques for accurate pathogen identification in polymicrobial infections. The failure to detect Actinomyces in bacterial cultures, despite its presence in FFPE-PCR, suggests that conventional culture methods alone may be insufficient for diagnosing such infections. Extended culture durations, selective anaerobic culture techniques, and molecular diagnostic methods are essential for a comprehensive evaluation. Recognizing Actinomyces as more than a contaminant is important for timely diagnosis and effective treatment. Increased awareness of its potential involvement in polymicrobial infection should improve clinical outcomes. Full article

In contemporary dentistry, laser-based interventions have become one of the mainstays of care for patients with oral biofilm diseases, such as candidiasis, periodontal disease and peri-implantitis. The purpose of this study was to evaluate the effectiveness of Er:YAG laser (LightWalker, Ljubljana, Fotona, Slovenia) irradiation at varying irradiance levels (T1: 11.3 W/cm² and T2: 120.54 W/cm²) on microbial viability in single- and dual-species biofilm models, focusing on Candida albicans, Candida glabrata and Streptococcus mutans, to address challenges in managing complex oral biofilms in clinically relevant settings. The results showed substantial microbial reduction, with C. albicans being the most susceptible microorganism (93–99.9%), while C. glabrata exhibited marked resistance at higher irradiance levels. Interestingly, S. mutans demonstrated varying reductions based on the biofilm composition, highlighting the influence of microbial interactions. This study concluded that the Er:YAG laser effectively reduced biofilm viability, with its efficacy depending on the microbial composition and irradiance settings. These findings highlight the need for tailored erbium laser parameters to optimize clinical outcomes, underscoring the need for individualized polymicrobial biofilm management, particularly in periodontal and peri-implant therapies. Full article